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b/inc/abkuerzungen.tex @@ -9,6 +9,7 @@ \acro{BSA}{Bovines Serumalbumin} \acro{CBB}[CBB-G250]{Coomassie-Brilliant-Blau G-250} \acro{CD}{Circulardichroismus} + \acro{C. symbiosum}[\textit{C. symbiosum}]{\textit{Chlostridium symbiosum}} \acro{CV}{Säulenvolumen, engl. \textit{column volume}} \acro{dCTP}{Desoxycytidintriphosphat} \acro{ddH2O}[\ce{ddH2O}]{Doppelt destilliertes Wasser} @@ -18,6 +19,7 @@ \acro{EDTA}{Ethylendiamintetraessigsäure} \acro{E. coli}[\textit{E. coli}]{\textit{Escherichia coli}} \acro{F. trinervia}[\textit{F. trinervia}]{\textit{Flaveria trinervia}} + \acro{F. brownii}[\textit{F. brownii}]{\textit{Flaveria brownii}} %\acro{HCl}[\ce{HCl}]{Salzsäure} \acro{HRP}{Meerrettich-Peroxidase, engl. \textit{horseradish peroxidase}} \acro{IDA}{Iminodiessigsäure} @@ -32,21 +34,22 @@ %\acro{NaHCO3}[\ce{NaHCO3}]{Natriumhydrogencarbonat} \acro{NaN3}[\ce{NaN3}]{Natriumazid} \acro{OD}{Optische Dichte} - \acro{p. a.}{\textit{pro analysi} (lat.)} + \acro{p. a.}{\textit{pro analysi}~(lat.)} \acro{PAGE}{Polyacrylamidgelelektrophorese} \acro{PCR}{Polymerase-Kettenreaktion} \acro{PEP}{Phosphoenolpyruvat} \acro{PEPCase}{Phosphoenolpyruvat-Carboxylase} \acro{PMSF}{Phenylmethylsulfonylfluorid} \acro{PPDK}{Pyruvat-Phosphat Dikinase} - \acro{rcf}{\textit{relative centrifugal force} (engl.)} + \acro{rcf}{\textit{relative centrifugal force}~(engl.)} \acro{SDS}{Natriumdodecylsulfat} \acro{SLIC}{Sequenz und Ligase unabhängige Klonierung} - \acro{SOPMA}{\textit{Self-optimized prediction method} (engl.)} + \acro{SOPMA}{\textit{Self-optimized prediction method}~(engl.)} \acro{TAE}{Tris-Acetat-EDTA} - \acro{TBS}{\textit{Tris-buffered saline} (engl.)} - \acro{TBT}{\textit{Tris-buffered Tween} (engl.)} + \acro{TBS}{\textit{Tris-buffered saline}~(engl.)} + \acro{TBT}{\textit{Tris-buffered Tween}~(engl.)} \acro{TEMED}{Tetramethylethylendiamin} + \acro{TEV}{\textit{Tobacco etch virus}~(engl.)} \acro{Tris}{Tris(hydroxymethyl)-aminomethan} \acro{UV}{Ultraviolett} \end{acronym} \ No newline at end of file diff --git a/inc/anhang.tex b/inc/anhang.tex index 8f174f3..903f67f 100644 --- a/inc/anhang.tex +++ b/inc/anhang.tex @@ -1,17 +1,59 @@ \appendix -\chapter{Nuklein- und Aminosäuresequenzen} -\begin{texshade}{./misc/align_seq_ref.aln} +\chapter{Anhang} +\section{Nuklein- und Aminosäuresequenzen} +\microtypesetup{protrusion=false} + +\begin{texshade}{./misc/seq_ref_aln.fa} \setsize{names}{scriptsize} \setsize{residues}{scriptsize} +\setsize{features}{tiny} + +\setsize{names}{scriptsize} +\setfamily{names}{sf} + +\shadingcolors{grays} \showruler{1}{top} \hidenumbering \hideconsensus +\feature{bottom}{2}{71..71}{restriction}{Nde I} +\feature{bottom}{2}{2712..2712}{restriction}{BamH I} \showcaption{Sequenzalignment der \acs{PPDK}-kodierenden Sequenz im Vektor pETEV-16b-ppdk und der Referenzsequenz} \shortcaption{Sequenzalignment pETEV-16b-ppdk} \end{texshade} -\chapter{Anhang} +\clearpage + +\begin{texshade}{./misc/ma_as_aln.fa} +\shadingmode{similar} +\threshold[80]{50} + +\nameseq{1}{F. trinervia} +\nameseq{2}{F. brownii} +\nameseq{3}{Zea mays} +\nameseq{4}{C. symbiosum} + +\setsize{names}{scriptsize} +\setfamily{names}{sf} +\setsize{residues}{scriptsize} +\setsize{numbers}{scriptsize} +\setsize{features}{tiny} +\setfamily{legend}{sf} +\setsize{legend}{scriptsize} +\setsize{featurestyles}{scriptsize} +\showruler{1}{top} +\hidenumbering +\defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}} +\showconsensus[ColdHot]{bottom} +\nameconsensus{conservation} +% \showlegend +\showcaption{Multiples Alignment der Aminosäuresequenzen der \acs{PPDK}s aus \acs{F. trinervia}, \acs{F. brownii}, \textit{Zea mays} und +\acs{C. symbiosum}. Sequenzidentitäten sind farbkodiert dargestellt: \SI{100}{\percent} Identität (violett), \SI{75}{\percent} (blau) und +\SI{50}{\percent} (rosa).} +\shortcaption{Multiples Alignment der Primärstrukturen verschiedener PPDKs} +\end{texshade} + +\microtypesetup{protrusion=true} \chapter{Erklärung} Hiermit versichere ich, dass ich die vorliegende Masterarbeit selbstständig verfasst und keine anderen, als die angegebenen Quellen und diff --git a/inc/ergebnisse.tex b/inc/ergebnisse.tex index 0307e95..123d5fd 100644 --- a/inc/ergebnisse.tex +++ b/inc/ergebnisse.tex @@ -1 +1,64 @@ -\chapter{Ergebnisse} +\chapter{Ergebnisse} +\label{sec:ergebnisse} +% +\section{Klonierung} +\label{sec:erg_klonierung} +% +Sie \acs{SLIC}-Klonierung erfolgte wie in \ref{sec:slic} beschrieben. Die mittels \acs{PCR} synthetisierten \textit{Inserts} +(vgl.~\ref{sec:inserts_slic}), sowie der linearisierte Vektor (vgl.~\ref{sec:restriktionsverdau_dna}) wurden auf ein zur Reinigung auf +Agarosegel aufgetragen (vgl. \ref{sec:agarose_gelelektrophorese}). Es ergab sich das in Abbildung \ref{abb:agarosegel_vektor_insert} gezeigte Auftrennungsmuster. +% +\begin{figure}[htb] + \centering + \begin{subfigure}[b]{0.4\textwidth} + \centering + \includegraphics[keepaspectratio=true]{./img/ergebnisse/agarose_gele/vektor_linear_text.png} + % vektor_linear_text.png: 615x551 pixel, 300dpi, 5.21x4.67 cm, bb=0 0 148 132 + \caption{} + \label{abb:linearisierter_vektor} + \end{subfigure} + % + ~ + % + \begin{subfigure}[b]{0.4\textwidth} + \centering + \includegraphics[keepaspectratio=true]{./img/ergebnisse/agarose_gele/insert_pcr_text.png} + % insert_pcr_text.png: 474x551 pixel, 300dpi, 4.01x4.67 cm, bb=0 0 114 132 + \caption{} + \label{abb:} +\end{subfigure} + \caption[Agarosegel zur Reinigung von Vektor und dem Insert]{Exemplarischer Ausschnitt aus dem Agarosegel zur Reinigung von + linearisiertem Vektor (a) und dem Insert (b) zur SLIC-Klonierung. + Aufgetragen wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard und + je \SI{20}{\micro\liter} Probe. Die erwarteten Größen sind \SI{5720}{\bp} (Vektor) + und \SI{2691}{\bp} (Insert).} + \label{abb:agarosegel_vektor_insert} +\end{figure} + +Sowohl Vektor als auch Insert lagen innerhalb der erwarteten Größenordnung (\SI{5720}{\bp} bzw. \SI{2691}{\bp}) auf, so dass beide wie in \ref{sec:slic} +beschrieben in den Ligationsansatz gegeben wurden. Zur Amplifikation des Vektors wurden dann \acs{E. coli} Zellen des Stamms XL1-Blue mit diesem transformiert +(vgl. \ref{sec:transformation}) und auf Agarplatten angezogen. Mit einer Kolonie-PCR (vgl. \ref{sec:kolonie_pcr}) wurde überprüft, ob der untersuchte Klon +das korrekte Insert trägt. Das enstsprechende Gelbild ist in Abbildung \ref{abb:kolonie_pcr} dargestellt. +% +\begin{figure}[htb] + \centering + \includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/agarose_gele/colony_pcr.png} + % colony_pcr.png: 1586x1474 pixel, 300dpi, 13.43x12.48 cm, bb=0 0 381 354 + \caption[Agarosegel nach Kolonie-PCR]{Agarosegel nach Kolonie-PCR. Es wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard und je \SI{20}{\micro\liter} Probe aufgetragen. + Untersucht wurden 24 Klone, von denen fünf (10, 13, 22, 23 und 24) ein Plasmid mit der korrekten Größe tragen.} + \label{abb:kolonie_pcr} +\end{figure} + +Von untersuchten 24 Klonen wiesen fünf ein Plasmid auf, das der erwarteten Größe von \SI{8351}{\bp} (Vektor~+~Insert) entspricht. Die fünf positiven Klone +wurden in \SI{5}{\milli\liter} Kulturrörchen über Nacht angezogen und die Plasmid-DNA mit dem QIAprep Spin Miniprep Kit nach Herstellerangaben extrahiert. +Proben der isolierten Plasmid-DNA wurden zur Sequenzierung eingeschickt (StarSEQ GmbH, Mainz). Es konnte gezeigt werden, dass das aus Klon \#22 isolierte +Plasmid im für die \acs{PPDK} kodierenden Bereich keine Mutation trägt. Eine Plasmidkarte von pETEV-16b-ppdk ist in Abbildung \ref{abb:plasmidkarte} +aufgeführt. +% +\begin{figure}[htb] + \centering + \includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/pETEV-16b-ppdk.pdf} + % pETEV-16b-ppdk.pdf: 611x480 pixel, 72dpi, 21.55x16.93 cm, bb=0 0 611 480 + \caption{Plasmidkarte von pETEV-16b-ppdk} + \label{abb:plasmidkarte} +\end{figure} diff --git a/inc/material.tex b/inc/material.tex index 60feca6..3d1c3b6 100644 --- a/inc/material.tex +++ b/inc/material.tex @@ -132,8 +132,8 @@ \toprule \textbf{Bezeichnung} & \textbf{Hersteller} & \textbf{Erkennungssequenz (5'~--~3')}\\ \midrule - \textit{BamH}I & New England Biolabs, Frankfurt & CA/TATG\\ - \textit{Nde}I & New England Biolabs, Frankfurt & G/GATCC\\ + \textit{Nde}I & New England Biolabs, Frankfurt & CA/TATG\\ + \textit{BamH}I & New England Biolabs, Frankfurt & G/GATCC\\ \bottomrule \end{tabularx} @@ -168,8 +168,10 @@ \subsection{Plasmide} \label{sec:plasmide} - - +Das tatsächlich eingesetzte Plasmid trägt die Bezeichnung pETEV-16b und ist ein Derivat des pET-16b-Vektors, +das zusätzlich zwischen der für den Hexa-Histidin-Tag kodierenden Sequenz und dem Zielgen eine für die Schnittstelle +der \acs{TEV}-Protease kodierende Sequenz beinhaltet. +% \begin{samepage} \begin{tabularx}{\textwidth}{p{0.25\textwidth}p{0.3\textwidth}X} \toprule @@ -461,6 +463,7 @@ zwanzig Zyklen die Schmelztemperatur des zum Zielvektor homologen Primerbereichs \end{table} \subsubsection{Kolonie-\acs{PCR}} +\label{sec:kolonie_pcr} Zur Überprüfung des Klonierungserfolges wurden zufällig ausgewählte Kolonien mittels einer Kolonie-PCR untersucht. Hierzu wurden je Kolonie \SI{5}{\micro\liter} \acs{ddH2O} in einem \acs{PCR}-Gefäß vorgelegt. Mit einem sterilen Zahnstocher wurde eine Kolonie gepickt, in das vorgelegte Wasser getaucht @@ -791,7 +794,7 @@ Die \ac{CD}-Spektroskopie kann für die Analyse von Proteinsekundärstrukturen e \SIrange{160}{250}{\nano\meter} aufgenommen. Man macht sich dabei zu Nutze, dass in diesem Bereich die n~\textrightarrow~\textpi$^*$ bzw. \textpi~\textrightarrow~\textpi$^*$-Übergänge der Peptidbindung liegen. Durch ihre Chiralität reagiert das \ac{CD}-Spektrum eines Peptids sehr empfindlich auf Änderungen der Sekundärstruktur \citep{Greenfield2007}. Die Messungen erfolgten in CD-Puffer bei einer Proteinkonzentration -von \SI{0,1}{\milli\gram\per\milli\liter}. Von den Rohdaten wurde das Pufferspektrum abgezogen und unter Berücksichtigung von Konzentration und +von \SI{0,2}{\milli\gram\per\milli\liter}. Von den Rohdaten wurde das Pufferspektrum abgezogen und unter Berücksichtigung von Konzentration und Molekulargewicht in molaren \ac{CD} (\textDelta\textepsilon) umgerechnet. \subsection{Aktivitätsassay} @@ -839,6 +842,16 @@ $\epsilon_{340} = \SI{6,3e3}{\per\Molar\per\centi\meter}$ \citep{McComb1976} und \subsection{Analyse von \ac{CD}-Spektren} \label{sec:analyse_cd_spektren} +Die Analyse der aufgenommenen CD-Spektrem (siehe \ref{sec:cd_spektroskopie}) erfolgte mit dem Programmpaket \textit{CDPro} \citep{Sreerama2000}, sowie +dem Programm \textit{K2D3} \citep{Louis-Jeune2011}. Die Analyse erfolgte jeweils in einem Wellenlängenbereich von \SIrange{190}{240}{\nano\meter}. +Die berechneten Sekundärstrukturanteile wurden dann mit mit einer \textit{ab initio} Vorhersage, welche mit \acs{SOPMA} \citep{Geourjon1995a} +berechnet wurde verglichen. Zusätzlich wurden die Sekundärstrukturanteile aus der bereits bekannten \acs{PPDK}-Struktur aus \textit{Zea mays} +herangezogen. + +\subsection{Alignment von Nuklein- und Aminosäuresequenzen} +\label{sec:alignment} +Alignments von Nuklein- und Aminosäuren wurden mit dem Programm \textit{T-Coffee} \citep{Notredame2000,Wallace2006,Moretti2007,DiTommaso2011} erstellt. Das Programm \textit{Bowtie 2} +\citep{Langmead2012} kam zum Einsatz, um \textit{Reads} aus der Sequenzierung an die Referenzsequenz zu alignieren. \subsection{Erstellung von Homologiemodellen} \label{sec:erstellung_homologiemodell} diff --git a/library.bib b/library.bib index 4b40819..0b8e299 100644 --- a/library.bib +++ b/library.bib @@ -1,834 +1,67 @@ Automatically generated by Mendeley 1.6 Any changes to this file will be lost if it is regenerated by Mendeley. -@article{Laskowski1996, -abstract = {The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.}, -author = {Laskowski, RomanA. and Rullmann, J.AntoonC. and MacArthur, MalcolmW. and Kaptein, Robert and Thornton, JanetM.}, -doi = {10.1007/BF00228148}, -issn = {0925-2738}, -journal = {Journal of Biomolecular NMR}, -keywords = {Amino Acid Sequence,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: genetics,Evaluation Studies as Topic,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,Models,Molecular,Molecular Sequence Data,Molecular Structure,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,Quality Control,Reproducibility of Results,Secondary,Software,Solutions}, -month = dec, -number = {4}, -pages = {477--86}, -pmid = {9008363}, -title = {{AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/9008363 http://www.springerlink.com/index/10.1007/BF00228148}, -volume = {8}, -year = {1996} -} -@article{Evans1980, -author = {Evans, Claudia T and Goss, Neil H and Wood, Harland G}, -doi = {10.1021/bi00566a023}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Bacteroides,Bacteroides: enzymology,Binding Sites,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Pyruvate}, -month = dec, -number = {25}, -pages = {5809--14}, -pmid = {6257293}, -title = {{Pyruvate phosphate dikinase: affinity labeling of the adenosine 5'-triphosphate--adenosine 5'-monophosphate site.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023}, -volume = {19}, -year = {1980} -} -@article{Krystek1993, -abstract = {An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60\% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)}, -author = {Krystek, S and Stouch, T and Novotny, J}, -doi = {10.1006/jmbi.1993.1619}, -file = {:home/alex/Dokumente/Mendeley Desktop/Krystek, Stouch, Novotny/Journal of molecular biology/Krystek, Stouch, Novotny - 1993 - Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.pdf:pdf}, -issn = {0022-2836}, -journal = {Journal of molecular biology}, -keywords = {Amino Acid Sequence,Animals,Calorimetry,Chymotrypsin,Chymotrypsin: chemistry,Crystallography,Mathematics,Models,Molecular,Molecular Sequence Data,Ovomucin,Ovomucin: chemistry,Protein Conformation,Serine Endopeptidases,Serine Endopeptidases: chemistry,Serine Endopeptidases: metabolism,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: chemistry,Serine Proteinase Inhibitors: metabolism,Thermodynamics,Turkeys,X-Ray,X-Ray: methods}, -month = dec, -number = {3}, -pages = {661--79}, -pmid = {8254666}, -title = {{Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/8254666}, -volume = {234}, -year = {1993} -} -@article{Riener2002, -author = {Riener, Christian and Kada, Gerald and Gruber, Hermann}, -doi = {10.1007/s00216-002-1347-2}, -file = {:home/alex/Dokumente/Mendeley Desktop/Riener, Kada, Gruber/Analytical and Bioanalytical Chemistry/Riener, Kada, Gruber - 2002 - Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032-dithiodipyridine.pdf:pdf}, -issn = {1618-2642}, -journal = {Analytical and Bioanalytical Chemistry}, -month = jul, -number = {4-5}, -pages = {266--276}, -title = {{Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032;-dithiodipyridine}}, -url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00216-002-1347-2}, -volume = {373}, -year = {2002} -} -@article{Kendrick2008, -author = {Kendrick, M and Chang, C}, -doi = {10.1016/j.pbi.2008.06.011}, -file = {:home/alex/Dokumente/Mendeley Desktop/Kendrick, Chang/Current Opinion in Plant Biology/Kendrick, Chang - 2008 - Ethylene signaling new levels of complexity and regulation.pdf:pdf}, -issn = {13695266}, -journal = {Current Opinion in Plant Biology}, -keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -month = oct, -number = {5}, -pages = {479--485}, -title = {{Ethylene signaling: new levels of complexity and regulation}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S1369526608001143}, -volume = {11}, -year = {2008} -} -@book{Lottspeich2006a, -address = {M\"{u}nchen ;;Heidelberg}, -author = {Lottspeich, Friedrich}, -edition = {2. Aufl.}, -isbn = {9783827415202}, -keywords = {Folder - Biochemie}, -mendeley-tags = {Folder - Biochemie}, -publisher = {Spektrum Akademischer Verlag}, -title = {{Bioanalytik}}, -year = {2006} -} -@article{Chastain1997, -abstract = {A key regulatory enzyme of the C4-photosynthetic pathway is stromal pyruvate,orthophosphate dikinase (PPDK, EC 2.7.9.1). As a pivotal enzyme in the C4 pathway, it undergoes diurnal light-dark regulation of activity which is mediated by a single bifunctional regulatory protein (RP). RP specifically inactivates PPDK in the dark by an ADP-dependent phosphorylation of an active-site Thr residue (Thr-456 in maize). Conversely, RP activates inactive PPDK in the light by phosphorolytic dephosphorylation of this target Thr-P residue. We have employed a His-tagged maize recombinant C4 PPDK for directed mutagenesis of this active-site regulatory Thr. Three such mutants (T456V, T456S, T456D) were analyzed with respect to overall catalysis and regulation by exogenous maize RP. Substitution with Val and Ser at this position does not affect overall catalysis, whereas Asp abolishes enzyme activity. With respect to regulation by RP, it was found that Ser can effectively substitute for the wild-type Thr residue in that mutant enzyme is phosphorylated and inactivated by RP. The T456V mutant, however, could not be phosphorylated and was, thus, resistant to ADP-dependent inactivation by RP.}, -author = {Chastain, C J and Lee, M E and Moorman, M A and Shameekumar, P and Chollet, R}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/FEBS letters/Chastain et al. - 1997 - Site-directed mutagenesis of maize recombinant C4-pyruvate,orthophosphate dikinase at the phosphorylatable target threonine residue.pdf:pdf}, -issn = {0014-5793}, -journal = {FEBS letters}, -keywords = {Adenosine Diphosphate,Adenosine Diphosphate: pharmacology,Aspartic Acid,Aspartic Acid: genetics,Aspartic Acid: physiology,Histidine,Histidine: genetics,Mutagenesis,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Phosphorylation,Pyruvate,Serine,Serine: genetics,Serine: physiology,Site-Directed,Threonine,Threonine: physiology,Valine,Valine: genetics,Valine: physiology,Zea mays,Zea mays: enzymology,Zea mays: genetics}, -month = aug, -number = {1}, -pages = {169--73}, -pmid = {9287137}, -title = {{Site-directed mutagenesis of maize recombinant C4-pyruvate,orthophosphate dikinase at the phosphorylatable target threonine residue.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/9287137}, -volume = {413}, -year = {1997} -} -@book{Arber2009, -address = {Vatican City}, -author = {Arber, Werner and {Pontificia Accademia delle scienze.}}, -file = {:home/alex/Dokumente/Mendeley Desktop/Arber, Pontificia Accademia delle scienze/Unknown/Arber, Pontificia Accademia delle scienze. - 2009 - The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008.pdf:pdf}, -isbn = {9788877610973}, -publisher = {Ex Aedibus Academicis in Civitate Vaticana}, -title = {{The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008}}, -year = {2009} -} -@article{Koshland1966, -author = {Koshland, D E and Nemethy, G. and Filmer, D}, -doi = {10.1021/bi00865a047}, -file = {:home/alex/Dokumente/Mendeley Desktop/Koshland, Nemethy, Filmer/Biochemistry/Koshland, Nemethy, Filmer - 1966 - Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Chemistry,Computers,Hemoglobins,Kinetics,Models,Oxygen,Physical,Physicochemical Phenomena,Proteins,Theoretical}, -month = jan, -number = {1}, -pages = {365--385}, -pmid = {5938952}, -title = {{Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/5938952 http://pubs.acs.org/cgi-bin/doilookup/?10.1021/bi00865a047}, -volume = {5}, -year = {1966} -} -@article{Cornilescu2008, -author = {Cornilescu, Gabriel and Ulijasz, Andrew T. and Cornilescu, Claudia C. and Markley, John L. and Vierstra, Richard D.}, -doi = {10.1016/j.jmb.2008.08.034}, -file = {:home/alex/Dokumente/Mendeley Desktop/Cornilescu et al/Journal of Molecular Biology/Cornilescu et al. - 2008 - Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State.science:science}, -issn = {00222836}, -journal = {Journal of Molecular Biology}, -month = nov, -pages = {403--413}, -title = {{Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608010279}, -volume = {383}, -year = {2008} -} -@article{Pocalyko1990, -abstract = {In this paper we report the amino acid sequence of pyruvate phosphate dikinase (PPDK) from Bacteroides symbiosus as determined from the nucleotide sequence of the PPDK gene. Comparison of the B. symbiosus PPDK amino acid sequence with that of the maize PPDK [Matsuoka, M., Ozeki, Y., Yamamoto, N., Hirano, H., Kamo-Murakami, Y., \& Tanaka, Y. (1988) J. Biol. Chem. 263, 11080] revealed long stretches of homologous sequence (greater than 70\% identity), which contributed to an overall sequence identity of 53\%. The circular dichrosim spectra, hydropathy profiles, and calculated secondary structural elements of the two dikinases suggest that they may have very similar tertiary structures as well. A comparison made between the amino acid sequence of the maize and B. symbiosus dikinase with other known protein sequences revealed homology, concentrated in three stretches of sequences, to a mechanistically related enzyme, enzyme I of the Escherichia coli PEP: sugar phosphotransferase system [Saffen, D. W., Presper, K. A., Doering, T. L., Roseman, S. (1987) J. Biol. Chem. 262, 16241]. It is proposed that (i) these three stretches of sequence constitute the site for PEP binding and catalysis and a possible site for the regulation of enzymatic activity and (ii) the conserved sequences exist in a third mechanistically related enzyme, PEP synthase.}, -author = {Pocalyko, David J and Carroll, Lawrence J and Martin, Brian M and Babbitt, Patricia C and Dunaway-Mariano, Debra}, -doi = {10.1021/bi00500a006}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Amino Acid Sequence,Bacterial,Bacterial: genetics,Bacteroides,Bacteroides: enzymology,Base Sequence,Binding Sites,Catalysis,Circular Dichroism,Cloning,DNA,DNA Restriction Enzymes,Escherichia coli,Escherichia coli: genetics,Molecular,Molecular Sequence Data,Nucleic Acid,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: genetics,Peptide Fragments,Peptide Fragments: chemistry,Plants,Plants: enzymology,Plasmids,Protein Conformation,Pyruvate,Sequence Homology,Zea mays,purification}, -mendeley-tags = {purification}, -month = dec, -number = {48}, -pages = {10757--65}, -pmid = {2176881}, -title = {{Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/2176881 http://pubs.acs.org/doi/abs/10.1021/bi00500a006}, -volume = {29}, -year = {1990} -} -@article{Rivas2011, -author = {Rivas, Mario and Becerra, Arturo and Peret\'{o}, Juli and Bada, Jeffrey L. and Lazcano, Antonio}, -doi = {10.1007/s11084-011-9238-1}, -file = {:home/alex/Dokumente/Mendeley Desktop/Rivas et al/Origins of Life and Evolution of Biospheres/Rivas et al. - 2011 - Metalloproteins and the Pyrite-based Origin of Life A Critical Assessment.pdf:pdf}, -issn = {0169-6149}, -journal = {Origins of Life and Evolution of Biospheres}, -month = mar, -number = {4}, -pages = {347--356}, -shorttitle = {Metalloproteins and the Pyrite-based Origin of Lif}, -title = {{Metalloproteins and the Pyrite-based Origin of Life: A Critical Assessment}}, -url = {http://www.springerlink.com/index/10.1007/s11084-011-9238-1}, -volume = {41}, -year = {2011} -} -@article{Rader2011, -abstract = {Allosteric proteins demonstrate the phenomenon of a ligand binding to a protein at a regulatory or effector site and thereby changing the chemical affinity of the catalytic site. As such, allostery is extremely important biologically as a regulatory mechanism for molecular concentrations in many cellular processes. One particularly interesting feature of allostery is that often the catalytic and effector sites are separated by a large distance. Structural comparisons of allosteric proteins resolved in both inactive and active states indicate that a variety of structural rearrangement and changes in motions may contribute to general allosteric behavior. In general it is expected that the coupling of catalytic and regulatory sites is responsible for allosteric behavior. We utilize a novel examination of allostery using rigidity analysis of the underlying graph of the protein structures. Our results indicate a general global change in rigidity associated with allosteric transitions where the R state is more rigid than the T state. A set of allosteric proteins with heterotropic interactions is used to test the hypothesis that catalytic and effector sites are structurally coupled. Observation of a rigid path connecting the effector and catalytic sites in 68.75\% of the structures points to rigidity as a means by which the distal sites communicate with each other and so contribute to allosteric regulation. Thus structural rigidity is shown to be a fundamental underlying property that promotes cooperativity and non-locality seen in allostery.}, -author = {Rader, a J and Brown, Stephen M}, -doi = {10.1039/c0mb00054j}, -file = {:home/alex/Dokumente/Mendeley Desktop/Rader, Brown/Molecular bioSystems/Rader, Brown - 2011 - Correlating allostery with rigidity.pdf:pdf}, -issn = {1742-2051}, -journal = {Molecular bioSystems}, -keywords = {Allosteric Site,Catalytic Domain,Models,Molecular,Molecular Structure}, -month = feb, -number = {2}, -pages = {464--71}, -pmid = {21060909}, -title = {{Correlating allostery with rigidity.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/21060909}, -volume = {7}, -year = {2011} -} -@article{Bradford1976, -author = {Bradford, M M}, -file = {:home/alex/Dokumente/Mendeley Desktop/Bradford/Analytical biochemistry/Bradford - 1976 - A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.pdf:pdf}, -issn = {0003-2697}, -journal = {Analytical biochemistry}, -keywords = {Binding Sites,Colorimetry,Methods,Microchemistry,Protein Binding,Proteins,Proteins: analysis,Rosaniline Dyes,Time Factors}, -month = may, -pages = {248--54}, -pmid = {942051}, -title = {{A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/942051}, -volume = {72}, -year = {1976} -} -@article{Chiarabelli2009, -author = {Chiarabelli, Cristiano and Stano, Pasquale and Luisi, Pier Luigi}, -doi = {10.1016/j.copbio.2009.08.004}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chiarabelli, Stano, Luisi/Current Opinion in Biotechnology/Chiarabelli, Stano, Luisi - 2009 - Chemical approaches to synthetic biology.pdf:pdf}, -issn = {09581669}, -journal = {Current Opinion in Biotechnology}, -month = aug, -number = {4}, -pages = {492--497}, -title = {{Chemical approaches to synthetic biology}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0958166909000974}, -volume = {20}, -year = {2009} -} -@article{Iwakura2006, -abstract = {We developed a strategy for finding out the adapted variants of enzymes, and we applied it to an enzyme, dihydrofolate reductase (DHFR), in terms of its catalytic activity so that we successfully obtained several hyperactive cysteine- and methionine-free variants of DHFR in which all five methionyl and two cysteinyl residues were replaced by other amino acid residues. Among them, a variant (M1A/M16N/M20L/M42Y/C85A/M92F/C152S), named as ANLYF, has an approximately seven times higher k(cat) value than wild type DHFR. Enzyme kinetics and crystal structures of the variant were investigated for elucidating the mechanism of the hyperactivity. Steady-state and transient binding kinetics of the variant indicated that the kinetic scheme of the catalytic cycle of ANLYF was essentially the same as that of wild type, showing that the hyperactivity was brought about by an increase of the dissociation rate constants of tetrahydrofolate from the enzyme-NADPH-tetrahydrofolate ternary complex. The crystal structure of the variant, solved and refined to an R factor of 0.205 at 1.9-angstroms resolution, indicated that an increased structural flexibility of the variant and an increased size of the N-(p-aminobenzoyl)-L-glutamate binding cleft induced the increase of the dissociation constant. This was consistent with a large compressibility (volume fluctuation) of the variant. A comparison of folding kinetics between wild type and the variant showed that the folding of these two enzymes was similar to each other, suggesting that the activity enhancement of the enzyme can be attained without drastic changes of the folding mechanism.}, -author = {Iwakura, Masahiro and Maki, Kosuke and Takahashi, Hisashi and Takenawa, Tatsuyuki and Yokota, Akiko and Katayanagi, Katsuo and Kamiyama, Tadashi and Gekko, Kunihiko}, -doi = {10.1074/jbc.M508823200}, -file = {:home/alex/Dokumente/Mendeley Desktop/Iwakura et al/The Journal of biological chemistry/Iwakura et al. - 2006 - Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.pdf:pdf}, -issn = {0021-9258}, -journal = {The Journal of biological chemistry}, -keywords = {Binding Sites,Cysteine,Cysteine: chemistry,Directed Molecular Evolution,Escherichia coli,Escherichia coli: enzymology,Kinetics,Methionine,Methionine: chemistry,Models, Molecular,Mutation,Protein Binding,Protein Conformation,Protein Engineering,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Tetrahydrofolate Dehydrogenase: genetics,Tetrahydrofolate Dehydrogenase: metabolism}, -month = may, -number = {19}, -pages = {13234--46}, -pmid = {16510443}, -title = {{Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/16510443}, -volume = {281}, -year = {2006} -} -@article{Miroux1996, -author = {Miroux, B. and Walker, J. E}, -file = {:home/alex/Dokumente/Mendeley Desktop/Miroux, Walker/Journal of molecular biology/Miroux, Walker - 1996 - Over-production of proteins in Escherichia coli mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels.pdf:pdf}, -journal = {Journal of molecular biology}, -number = {3}, -pages = {289--298}, -shorttitle = {Over-production of proteins in Escherichia coli}, -title = {{Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels}}, -volume = {260}, -year = {1996} -} -@article{Wiedenheft2009, -author = {Wiedenheft, Blake and Zhou, Kaihong and Jinek, Martin and Coyle, Scott M. and Ma, Wendy and Doudna, Jennifer A.}, -doi = {10.1016/j.str.2009.03.019}, -file = {:home/alex/Dokumente/Mendeley Desktop/Wiedenheft et al/Structure/Wiedenheft et al. - 2009 - Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense.pdf:pdf}, -issn = {09692126}, -journal = {Structure}, -keywords = {Folder - In-silico-structure}, -mendeley-tags = {Folder - In-silico-structure}, -month = jun, -number = {6}, -pages = {904--912}, -title = {{Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212609001920}, -volume = {17}, -year = {2009} -} -@article{Daily2008, -abstract = {Allosteric proteins bind an effector molecule at one site resulting in a functional change at a second site. We hypothesize that networks of contacts altered, formed, or broken are a significant contributor to allosteric communication in proteins. In this work, we identify which interactions change significantly between the residue-residue contact networks of two allosteric structures, and then organize these changes into graphs. We perform the analysis on 15 pairs of allosteric structures with effector and substrate each present in at least one of the two structures. Most proteins exhibit large, dense regions of contact rearrangement, and the graphs form connected paths between allosteric effector and substrate sites in five of these proteins. In the remaining 10 proteins, large-scale conformational changes such as rigid-body motions are likely required in addition to contact rearrangement networks to account for substrate-effector communication. On average, clusters which contain at least one substrate or effector molecule comprise 20\% of the protein. These allosteric graphs are small worlds; that is, they typically have mean shortest path lengths comparable to those of corresponding random graphs and average clustering coefficients enhanced relative to those of random graphs. The networks capture 60-80\% of known allostery-perturbing mutants in three proteins, and the metrics degree and closeness are statistically good discriminators of mutant residues from nonmutant residues within the networks in two of these three proteins. For two proteins, coevolving clusters of residues which have been hypothesized to be allosterically important differ from the regions with the most contact rearrangement. Residues and contacts which modulate normal mode fluctuations also often participate in the contact rearrangement networks. In summary, residue-residue contact rearrangement networks provide useful representations of the portions of allosteric pathways resulting from coupled local motions.}, -author = {Daily, Michael D. and Upadhyaya, Tarak J. and Gray, Jeffrey J.}, -doi = {10.1002/prot.21800}, -file = {:home/alex/Dokumente/Mendeley Desktop/Daily, Upadhyaya, Gray/Proteins/Daily, Upadhyaya, Gray - 2008 - Contact rearrangements form coupled networks from local motions in allosteric proteins.pdf:pdf}, -issn = {1097-0134}, -journal = {Proteins}, -keywords = {Allosteric Regulation,Allosteric Site,Chemical,Folder - Allostery - Theory,Mechanism,Metabolic Networks and Pathways,Models,Motion,Proteins,Proteins: chemistry}, -mendeley-tags = {Folder - Allostery - Theory,Mechanism}, -month = may, -number = {1}, -pages = {455--66}, -pmid = {17957766}, -title = {{Contact rearrangements form coupled networks from local motions in allosteric proteins.}}, -url = {http://doi.wiley.com/10.1002/prot.21800 http://www.ncbi.nlm.nih.gov/pubmed/17957766}, -volume = {71}, -year = {2008} -} -@article{Kang2002, -abstract = {Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches. Several improvements of the original Coomassie protocol(1) have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20\% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution(2), and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol(3). Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol(4). The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins. Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group.}, -author = {Kang, D and Gho, YS}, -doi = {10.5012/bkcs.2002.23.11.1511}, -file = {:home/alex/Dokumente/Mendeley Desktop/Kang, Gho/Bulletin of the Korean Chemical Society/Kang, Gho - 2002 - Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis.pdf:pdf}, -issn = {0253-2964}, -journal = {Bulletin of the Korean Chemical Society}, -keywords = {Acrylic Resins,Acrylic Resins: chemistry,Colloids,Colloids: chemistry,Electrophoresis,Gel,Indicators and Reagents,Indicators and Reagents: chemistry,Proteins,Proteins: analysis,Proteins: chemistry,Rosaniline Dyes,Rosaniline Dyes: chemistry,Sensitivity and Specificity,Staining and Labeling,Staining and Labeling: methods,Two-Dimensional,Two-Dimensional: methods}, -month = nov, -number = {11}, -pages = {1511--1512}, -title = {{Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis}}, -url = {http://koreascience.or.kr/journal/view.jsp?issn=0253-2964\&vol=23\&no=11\&sp=1511}, -volume = {23}, -year = {2002} -} -@article{Fulle2009, -abstract = {A sophisticated interplay between the static properties of the ribosomal exit tunnel and its functional role in cotranslational processes is revealed by constraint counting on topological network representations of large ribosomal subunits from four different organisms. As for the global flexibility characteristics of the subunit, the results demonstrate a conserved stable structural environment of the tunnel. The findings render unlikely that deformations of the tunnel move peptides down the tunnel in an active manner. Furthermore, the stable environment rules out that the tunnel can adapt widely so as to allow tertiary folding of nascent chains. Nevertheless, there are local zones of flexible nucleotides within the tunnel, between the peptidyl transferase center and the tunnel constriction, and at the tunnel exit. These flexible zones strikingly agree with previously identified folding zones. As for cotranslational elongation regulation, flexible residues in the beta-hairpin of the ribosomal L22 protein were verified, as suggested previously based on structural results. These results support the hypothesis that L22 can undergo conformational changes that regulate the tunnel voyage of nascent polypeptides. Furthermore, rRNA elements, for which conformational changes have been observed upon interaction of the tunnel wall with a nascent SecM peptide, are less strongly coupled to the subunit core. Sequences of coupled rigid clusters are identified between the tunnel and some of these elements, suggesting signal transmission by a domino-like mechanical coupling. Finally, differences in the flexibility of the glycosidic bonds of bases that form antibiotics-binding crevices within the peptidyl transferase center and the tunnel region are revealed for ribosomal structures from different kingdoms. In order to explain antibiotics selectivity, action, and resistance, according to these results, differences in the degrees of freedom of the binding regions may need to be considered.}, -author = {Fulle, Simone and Gohlke, Holger}, -doi = {10.1016/j.jmb.2009.01.037}, -file = {:home/alex/Dokumente/Mendeley Desktop/Fulle, Gohlke/Journal of molecular biology/Fulle, Gohlke - 2009 - Statics of the ribosomal exit tunnel implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.pdf:pdf}, -issn = {1089-8638}, -journal = {Journal of molecular biology}, -keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: metabolism,Haloarcula marismortui,Haloarcula marismortui: metabolism,Models, Molecular,Peptide Chain Elongation, Translational,Peptides,Peptides: chemistry,Peptides: metabolism,Peptidyl Transferases,Peptidyl Transferases: metabolism,Pliability,Protein Folding,Protein Structure, Secondary,Protein Transport,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Signal Transduction}, -month = mar, -number = {2}, -pages = {502--17}, -pmid = {19356596}, -publisher = {Elsevier Ltd}, -title = {{Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/19356596}, -volume = {387}, -year = {2009} -} -@article{Pineda2004, -abstract = {Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.}, -author = {Pineda, Agustin O and Carrell, Christopher J and Bush, Leslie a and Prasad, Swati and Caccia, Sonia and Chen, Zhi-Wei and Mathews, F Scott and {Di Cera}, Enrico}, -doi = {10.1074/jbc.M401756200}, -file = {:home/alex/Dokumente/Mendeley Desktop/Pineda et al/The Journal of biological chemistry/Pineda et al. - 2004 - Molecular dissection of Na binding to thrombin.pdf:pdf}, -issn = {0021-9258}, -journal = {The Journal of biological chemistry}, -keywords = {Allosteric Site,Allosteric Site: genetics,Crystallography, X-Ray,Humans,Models, Molecular,Mutagenesis, Site-Directed,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Sodium,Sodium: metabolism,Static Electricity,Thermodynamics,Thrombin,Thrombin: chemistry,Thrombin: genetics,Thrombin: metabolism}, -month = jul, -number = {30}, -pages = {31842--53}, -pmid = {15152000}, -title = {{Molecular dissection of Na+ binding to thrombin.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/15152000}, -volume = {279}, -year = {2004} -} -@book{Purves2006, -address = {M\"{u}nchen; Heidelberg}, -author = {Purves, William K and Sadava, David and Orians, Gordon H and Heller, H. Craig}, -edition = {7}, -isbn = {9783827420077}, -keywords = {Folder - Allgemein}, -mendeley-tags = {Folder - Allgemein}, -month = aug, -publisher = {Spektrum Akademischer Verlag}, -title = {{Biologie}}, -year = {2006} -} -@article{Knecht1983, -abstract = {The complete amino acid sequence of a proteinase inhibitor, eglin c (Mr 8100), has been determined with less than 150 micrograms of the protein using the following microtechniques: (a) amino acid analysis with a low-nanogram amount of protein hydrolysate using dimethylaminoazobenzene sulfonyl chloride, (b) peptide isolation at the picomole level using the dimethylaminoazobenzene isothiocyanate (DABITC) precolumn derivatization method, and (c) automatic Edman degradation. One amino acid residue has been corrected for the previously reported sequence. The Contribution of each technique to the microsequencing is discussed. In addition, a new high-performance liquid chromatography system that gives a complete baseline separation of all phenylthiohydantoin-amino acids is described.}, -author = {Knecht, R and Seem\"{u}ller, U and Liersch, M and Fritz, H and Braun, D G and Chang, J Y}, -file = {:home/alex/Dokumente/Mendeley Desktop/Knecht et al/Analytical biochemistry/Knecht et al. - 1983 - Sequence determination of eglin C using combined microtechniques of amino acid. - 1983 - sequence determination of eglin c using combined microtechniques of amino acid analysis , peptide isolation , and automatic edman degradation: - 1983 - sequence determination of eglin c using combined microtechniques of amino acid analysis , peptide isolation , and automatic edman degradation}, -issn = {0003-2697}, -journal = {Analytical biochemistry}, -keywords = {Amino Acid Sequence,Amino Acids,Amino Acids: analysis,Chromatography, High Pressure Liquid,Microchemistry,Peptide Fragments,Peptide Fragments: isolation \& purification,Protease Inhibitors,Proteins,Serpins}, -month = may, -number = {1}, -pages = {65--71}, -pmid = {6869810}, -title = {{Sequence determination of eglin C using combined microtechniques of amino acid analysis, peptide isolation, and automatic Edman degradation.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/6869810}, -volume = {130}, -year = {1983} -} -@article{Boyer2008, -abstract = {Long-range effects, such as allostery, have evolved in proteins as a means of regulating function via communication between distal sites. An NMR-based perturbation mapping approach was used to more completely probe the dynamic response of the core mutation V54A in the protein eglin c by monitoring changes in picosecond to nanosecond aromatic side-chain dynamics and H/D exchange stabilities. Previous side-chain dynamics studies on this mutant were limited to methyl-bearing residues, most of which were found to rigidify on the picosecond to nanosecond time scale in the form of a contiguous "network". Here, high precision (13)C relaxation data from 13 aromatic side chains were acquired by applying canonical relaxation experiments to a newly developed carbon labeling scheme [Teilum et al. (2006) J. Am. Chem. Soc. 128, 2506-2507]. The fitting of model-free parameters yielded S (2) variability which is intermediate with respect to backbone and methyl-bearing side-chain variability and tau e values that are approximately 1 ns. Inclusion of the aromatic dynamic response results in an expanded network of dynamically coupled residues, with some aromatics showing increases in flexibility, which partially offsets the rigidification in methyl side chains. Using amide hydrogen exchange, dynamic propagation on a slower time scale was probed in response to the V54A perturbation. Surprisingly, regional stabilization (slowed exchange) 10-12 A from the site of mutation was observed despite a global destabilization of 1.5 kcal x mol (-1). Furthermore, this unlikely pocket of stabilized residues colocalizes with increases in aromatic flexibility on the faster time scale. Because the converse is also true (destabilized residues colocalize with rigidification on the fast time scale), a plausible entropy-driven mechanism is discussed for relating colocalization of opposing dynamic trends on vastly different time scales.}, -author = {Boyer, Joshua a and Lee, Andrew L}, -doi = {10.1021/bi702330t}, -file = {:home/alex/Dokumente/Mendeley Desktop/Boyer, Lee/Biochemistry/Boyer, Lee - 2008 - Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Amino Acids,Aromatic,Aromatic: chemistry,Carbon Isotopes,Hydrogen,Hydrogen: metabolism,Kinetics,Magnetic Resonance Spectroscopy,Models,Molecular,Movement,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: genetics,Mutant Proteins: metabolism,Mutation,Protein Conformation,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: metabolism,Thermodynamics,Time Factors}, -month = apr, -number = {17}, -pages = {4876--86}, -pmid = {18393447}, -title = {{Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3062916\&tool=pmcentrez\&rendertype=abstract}, -volume = {47}, -year = {2008} -} -@article{Chastain2002, -abstract = {Pyruvate,orthophosphate (Pi) dikinase (PPDK) is best recognized as a chloroplastic C(4) cycle enzyme. As one of the key regulatory foci for controlling flux through this photosynthetic pathway, it is strictly and reversibly regulated by light. This light/dark modulation is mediated by reversible phosphorylation of a conserved threonine residue in the active-site domain by the PPDK regulatory protein (RP), a bifunctional protein kinase/phosphatase. PPDK is also present in C(3) plants, although it has no known photosynthetic function. Nevertheless, in this report we show that C(3) PPDK in leaves of several angiosperms and in isolated intact spinach (Spinacia oleracea) chloroplasts undergoes light-/dark-induced changes in phosphorylation state in a manner similar to C(4) dikinase. In addition, the kinetics of this process closely resemble the reversible C(4) process, with light-induced dephosphorylation occurring rapidly (< or =15 min) and dark-induced phosphorylation occurring much more slowly (> or =30-60 min). In intact spinach chloroplasts, light-induced dephosphorylation of C(3) PPDK was shown to be dependent on exogenous Pi and photosystem II activity but independent of electron transfer from photosystem I. These in organello results implicate a role for stromal pools of Pi and adenylates in regulating the reversible phosphorylation of C(3)-PPDK. Last, we used an in vitro RP assay to directly demonstrate ADP-dependent PPDK phosphorylation in desalted leaf extracts of the C(3) plants Vicia faba and rice (Oryza sativa). We conclude that an RP-like activity mediates the light/dark modulation of PPDK phosphorylation state in C(3) leaves and chloroplasts and likely represents the ancestral isoform of this unusual and key C(4) pathway regulatory "converter" enzyme.}, -author = {Chastain, Chris J and Fries, Jason P and Vogel, Julie A and Randklev, Christa L and Vossen, Adam P and Dittmer, Sharon K and Watkins, Erin E and Fiedler, Lucas J and Wacker, Sarah A and Meinhover, Katherine C and Sarath, Gautam and Chollet, Raymond}, -doi = {10.1104/pp.010806}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Plant physiology/Chastain et al. - 2002 - Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-dark-induced reversible phosphorylation.pdf:pdf}, -issn = {0032-0889}, -journal = {Plant physiology}, -keywords = {Adenosine Diphosphate,Adenosine Diphosphate: metabolism,Adenosine Monophosphate,Adenosine Monophosphate: metabolism,Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Angiosperms,Angiosperms: classification,Angiosperms: enzymology,Biological,Chloroplasts,Chloroplasts: enzymology,Darkness,Fabaceae,Fabaceae: enzymology,Light,Models,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Oryza sativa,Oryza sativa: enzymology,Phosphates,Phosphates: metabolism,Phosphoenolpyruvate,Phosphoenolpyruvate: metabolism,Phosphorylation,Photosynthetic Reaction Center Complex Proteins,Photosynthetic Reaction Center Complex Proteins: m,Photosystem I Protein Complex,Photosystem II Protein Complex,Plant Leaves,Plant Leaves: enzymology,Pyruvate,Pyruvic Acid,Pyruvic Acid: metabolism,Spinacia oleracea,Spinacia oleracea: enzymology,Zea mays,Zea mays: enzymology}, -month = apr, -number = {4}, -pages = {1368--78}, -pmid = {11950985}, -title = {{Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-/dark-induced reversible phosphorylation.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=154264\&tool=pmcentrez\&rendertype=abstract}, -volume = {128}, -year = {2002} -} -@article{Crick1970, -author = {Crick, Francis}, -doi = {10.1038/227561a0}, -file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Nature/Crick - 1970 - Central Dogma of Molecular Biology.pdf:pdf}, -issn = {0028-0836}, -journal = {Nature}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = aug, -number = {5258}, -pages = {561--563}, -title = {{Central Dogma of Molecular Biology}}, -url = {http://www.nature.com/doifinder/10.1038/227561a0}, -volume = {227}, -year = {1970} -} -@article{Doyle2005, -abstract = {Plants using the C(4) photosynthetic pathway are highly represented among the world's worst weeds, with only 4 C(4) species being agriculturally productive (maize, sorghum, millet, and sugar cane). With the C(4) acid cycle operating as a biochemical appendage of C(3) photosynthesis, the additional enzymes involved in C(4) photosynthesis represent an attractive target for the development of weed-specific herbicides. The rate-limiting enzyme of this metabolic pathway is pyruvate orthophosphate dikinase (PPDK). PPDK, coupled with phosphoenolpyruvate carboxylase and nicotinamide adenine dinucleotide-malate dehydrogenase, was used to develop a microplate-based assay to detect inhibitors of enzymes of the C(4) acid cycle. The resulting assay had a Z' factor of 0.61, making it a high-quality assay able to reliably identify active test samples. Organic extracts of 6679 marine macroscopic organisms were tested within the assay, and 343 were identified that inhibited the 3 enzyme-coupled reaction. A high confirmation rate was achieved, with 95\% of these hit extracts proving active again upon retesting. Sequential addition of phosphoenolpyruvate and oxaloacetate to the assay facilitated identification of 83 extracts that specifically inhibited PPDK.}, -author = {Doyle, Jason R and Burnell, James N and Haines, Dianne S and Llewellyn, Lyndon E and Motti, Cherie a and Tapiolas, Dianne M}, -doi = {10.1177/1087057104269978}, -file = {:home/alex/Dokumente/Mendeley Desktop/Doyle et al/Journal of biomolecular screening/Doyle et al. - 2005 - A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.pdf:pdf}, -issn = {1087-0571}, -journal = {Journal of biomolecular screening}, -keywords = {Dimethyl Sulfoxide,Dimethyl Sulfoxide: pharmacology,Drug Evaluation, Preclinical,Drug Evaluation, Preclinical: methods,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Enzyme Inhibitors: pharmacology,Herbicides,Herbicides: chemistry,Herbicides: pharmacology,Malate Dehydrogenase,Malate Dehydrogenase: antagonists \& inhibitors,Malate Dehydrogenase: metabolism,Molecular Structure,Oxalic Acid,Oxalic Acid: pharmacology,Phosphoenolpyruvate Carboxylase,Phosphoenolpyruvate Carboxylase: antagonists \& inh,Phosphoenolpyruvate Carboxylase: metabolism,Plant Extracts,Plant Extracts: metabolism,Plants,Plants: drug effects,Plants: enzymology,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: antagonists \& i,Pyruvate, Orthophosphate Dikinase: metabolism,Species Specificity,Time Factors}, -month = feb, -number = {1}, -pages = {67--75}, -pmid = {15695345}, -title = {{A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/15695345}, -volume = {10}, -year = {2005} -} -@article{MONOD1965, -author = {MONOD, J and WYMAN, J and CHANGEUX, J P}, -issn = {0022-2836}, -journal = {Journal of molecular biology}, -keywords = {Chemistry,Enzymes,Hemoglobins,Kinetics,Models,Physical,Physicochemical Phenomena,Proteins,Research,Theoretical,Ultracentrifugation}, -month = may, -pages = {88--118}, -pmid = {14343300}, -title = {{ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/14343300}, -volume = {12}, -year = {1965} -} -@article{Schrader1985, -abstract = {The objective of this study was to determine the biochemical basis for genetic variability in pyruvate,Pi dikinase (PPDK) activity among inbred lines of maize (Zea mays L.). Although in vitro PPDK activity varied more than 5-fold among eight maize inbreds, immunochemical determinations of the proportion of leaf soluble protein as PPDK revealed no significant differences among the inbreds. Genetic differences in the stability of PPDK activity in crude homogenates over 5 hours were not evident, but PPDK from some inbreds could not be activated in vitro. In vitro PPDK activation in crude homogenates could be restored by addition of casein (1\% w/v) to homogenization media, and to a lesser extent, by gentle homogenization in a mortar. The major effect of casein appeared to be on processes other than proteolysis, as casein exerted its effects during tissue homogenization, rather than later. During homogenization, PPDK did not lose its ability to undergo in vitro activation; instead, it was instability of the regulatory protein responsible for PPDK activation that was the cause of the lack of PPDK activation in homogenates prepared without casein.}, -author = {Baer, G R and Schrader, Larry E}, -file = {:home/alex/Dokumente/Mendeley Desktop/Baer, Schrader/Plant physiology/Baer, Schrader - 1985 - Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.pdf:pdf}, -issn = {0032-0889}, -journal = {Plant physiology}, -month = mar, -number = {3}, -pages = {608--11}, -pmid = {16664106}, -title = {{Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1064572\&tool=pmcentrez\&rendertype=abstract}, -volume = {77}, -year = {1985} -} -@article{Luisi2003, -author = {Luisi, P. L}, -file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Philosophical Transactions Mathematical, Physical and Engineering Sciences/Luisi - 2003 - Contingency and determinism.pdf:pdf}, -journal = {Philosophical Transactions: Mathematical, Physical and Engineering Sciences}, -pages = {1141--1147}, -title = {{Contingency and determinism}}, -year = {2003} -} -@article{McComb1976, -abstract = {The molar absorptivity of NADH at 340 nm has been determined by an indirect procedure in which high-purity glucose is phosphorylated by ATP in the presence of hexokinase, coupled to oxidation of the glucose-6-phosphate by NAD+ in the presence of glucose-6-phosphate dehydrogenase. The average value from 85 independent determinations is 6317 liter mol-1 cm-1 at 25 degrees C and pH 7.8. The overall uncertainty is -4.0 to +5.5 ppt (6292 to 6352 liter mol-1 cm-1), based on a standard error of the mean of 0.48 ppt and an estimate of systematic error of -2.6 to +4.1 ppt. Effects of pH, buffer, and temperature on the molar absorptivity are also reported.}, -author = {McComb, R B and Bond, L W and Burnett, R W and Keech, R C and Bowers, G N}, -file = {:home/alex/Dokumente/Mendeley Desktop/McComb et al/Clinical chemistry/McComb et al. - 1976 - Determination of the molar absorptivity of NADH.pdf:pdf}, -issn = {0009-9147}, -journal = {Clinical chemistry}, -keywords = {Absorption,Adenosine Triphosphate,Evaluation Studies as Topic,Glucose,Glucosephosphate Dehydrogenase,Hexokinase,Hydrogen-Ion Concentration,NAD,NAD: analysis,Osmolar Concentration,Oxidation-Reduction,Spectrophotometry,Temperature,Ultraviolet}, -month = mar, -number = {2}, -pages = {141--50}, -pmid = {2388}, -title = {{Determination of the molar absorptivity of NADH.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/2388}, -volume = {22}, -year = {1976} -} -@article{Muller2006, -author = {M\"{u}ller, U. F.}, -doi = {10.1007/s00018-006-6047-1}, -issn = {1420-682X}, -journal = {Cellular and Molecular Life Sciences}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = may, -number = {11}, -pages = {1278--1293}, -title = {{Re-creating an RNA world}}, -url = {http://www.springerlink.com/index/10.1007/s00018-006-6047-1}, -volume = {63}, -year = {2006} -} -@article{Crump2004a, -abstract = {LFA-1 (lymphocyte function-associated antigen-1) plays a role in intercellular adhesion and lymphocyte trafficking and activation and is an attractive anti-inflammatory drug target. The alpha-subunit of LFA-1, in common with several other integrins, has an N-terminally inserted domain (I-domain) of approximately 200 amino acids that plays a central role in regulating ligand binding to LFA-1. An additional region, termed the I-domain allosteric site (IDAS), has been identified exclusively within the LFA-1 I-domain and shown to regulate the function of this protein. The IDAS is occupied by small molecule LFA-1 inhibitors when cocrystallized or analyzed by (15)N-(1)H HSQC (heteronuclear single-quantum coherence) NMR (nuclear magnetic resonance) titration experiments. We report here a novel arylthio inhibitor that binds the I-domain with a K(d) of 18.3 nM as determined by isothermal titration calorimetry (ITC). This value is in close agreement with the IC(50) (10.9 nM) derived from a biochemical competition assay (DELFIA) that measures the level of inhibition of binding of whole LFA-1 to its ligand, ICAM-1. Having established the strong affinity of the arylthio inhibitor for the isolated I-domain, we have used a range of techniques to further characterize the binding, including ITC, NMR, and X-ray crystallography. We have first developed an effective ITC binding assay for use with low-solubility inhibitors that avoids the need for ELISA-based assays. In addition, we utilized a fast NMR-based assay for the generation of I-domain-inhibitor models. This is based around the collection of HCCH-TOCSY spectra of LFA-1 in the bound form and the identification of a subset of side chain methyl groups that give chemical shift changes upon binding of LFA-1 inhibitors. This subset was used in two-dimensional (13)C-(15)N and (15)N-filtered and -edited two-dimensional NMR experiments to identify a minimal set of intraligand and ligand-protein NOEs, respectively (nuclear Overhauser enhancements). Models from the NMR data were assessed by comparison to an X-ray crystallographic structure of the complex, confirming that the method correctly predicted the essential features of the bound ligand.}, -author = {Crump, Matthew P and Ceska, Thomas A and Spyracopoulos, Leo and Henry, Alistair and Archibald, Sarah C and Alexander, Rikki and Taylor, Richard J and Findlow, Stuart C and O'Connell, James and Robinson, Martyn K and Shock, Anthony}, -doi = {10.1021/bi035422a}, -file = {:home/alex/Dokumente/Mendeley Desktop/Crump et al/Biochemistry/Crump et al. - 2004 - Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Allosteric Site,Amides,Amides: chemistry,Binding,Biomolecular,Calorimetry,Cinnamates,Cinnamates: chemistry,Cinnamates: metabolism,Competitive,Crystallography,Drug Design,Humans,Ligands,Lymphocyte Function-Associated Antigen-1,Lymphocyte Function-Associated Antigen-1: chemistr,Lymphocyte Function-Associated Antigen-1: metaboli,Models,Molecular,Nuclear Magnetic Resonance,Protein Binding,Protein Structure,Protein Subunits,Protein Subunits: antagonists \& inhibitors,Protein Subunits: chemistry,Recombinant Proteins,Recombinant Proteins: antagonists \& inhibitors,Recombinant Proteins: chemistry,Tertiary,X-Ray}, -month = mar, -number = {9}, -pages = {2394--404}, -pmid = {14992576}, -title = {{Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/14992576}, -volume = {43}, -year = {2004} -} -@book{Atkins2006, -address = {Weinheim}, -author = {Atkins, Peter W and de Paula, Julio}, -edition = {4., vollst}, -isbn = {9783527315468}, -keywords = {Folder - Physikalische Chemie}, -mendeley-tags = {Folder - Physikalische Chemie}, -publisher = {Wiley-VCH}, -title = {{Physikalische Chemie}}, -year = {2006} -} -@book{Taiz2007, -address = {M\"{u}nchen; Heidelberg}, -author = {Taiz, Lincoln and Zeiger, Eduardo}, -edition = {4. ed.}, -isbn = {9783827418654}, -keywords = {Folder - Pflanzenphysiologie}, -mendeley-tags = {Folder - Pflanzenphysiologie}, -publisher = {Spektrum Akademischer Verlag}, -title = {{Plant physiology das Original mit \"{U}bersetzungshilfen}}, -year = {2007} -} -@article{Crick1968, -author = {Crick, F H}, -file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Journal of Molecular Biology/Crick - 1968 - The origin of the genetic code.pdf:pdf}, -issn = {0022-2836}, -journal = {Journal of Molecular Biology}, -keywords = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger}, -mendeley-tags = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger}, -month = dec, -number = {3}, -pages = {367--379}, -title = {{The origin of the genetic code}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/4887876 http://www.sciencedirect.com/science?\_ob=MImg\&\_imagekey=B6WK7-4DM29RS-BH-1\&\_cdi=6899\&\_user=2665780\&\_pii=0022283668903926\&\_origin=\&\_coverDate=12/28/1968\&\_sk=999619996\&view=c\&wchp=dGLzVlz-zSkzV\&md5=04e907452df700b018f50eae6799bb6a\&ie=/sdarticle.pdf}, -volume = {38}, -year = {1968} -} -@article{Li2007, -author = {Li, Mamie Z and Elledge, Stephen J}, -doi = {10.1038/nprot.2007.90}, -issn = {2043-0116}, -journal = {Protocol Exchange}, -keywords = {Folder - Biochemie}, -mendeley-tags = {Folder - Biochemie}, -month = feb, -title = {{SLIC sub-cloning using T4 DNA polymerase treated inserts without RecA}}, -url = {http://www.natureprotocols.com/2007/02/15/slic\_subcloning\_using\_t4\_dna\_p.php http://www.nature.com/protocolexchange/protocols/167}, -year = {2007} -} -@article{Geourjon1995, +@article{Geourjon1995a, abstract = {Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins. In this paper we report improvements brought about by predicting all the sequences of a set of aligned proteins belonging to the same family. This improved SOPM method (SOPMA) correctly predicts 69.5\% of amino acids for a three-state description of the secondary structure (alpha-helix, beta-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25\% identity) proteins. Joint prediction with SOPMA and a neural networks method (PHD) correctly predicts 82.2\% of residues for 74\% of co-predicted amino acids. Predictions are available by Email to deleage@ibcp.fr or on a Web page (http:@www.ibcp.fr/predict.html).}, -author = {Geourjon, C and Del\'{e}age, G}, +author = {Geourjon, C. and Del\'{e}age, G.}, +doi = {10.1093/bioinformatics/11.6.681}, issn = {0266-7061}, -journal = {Computer Applications in the Biosciences: CABIOS}, -keywords = {Databases- Factual,Folder - RTE1,Neural Networks (Computer),Protein Structure- Secondary,Proteins,Sequence Alignment,Sequence Homology- Amino Acid,Software}, -mendeley-tags = {Databases- Factual,Folder - RTE1,Neural Networks (Computer),Protein Structure- Secondary,Proteins,Sequence Alignment,Sequence Homology- Amino Acid,Software}, +journal = {Computer applications in the biosciences : CABIOS}, +keywords = {Amino Acid,Databases,Factual,Neural Networks (Computer),Protein Structure,Proteins,Proteins: chemistry,Secondary,Sequence Alignment,Sequence Alignment: methods,Sequence Alignment: statistics \& numerical data,Sequence Homology,Software}, month = dec, number = {6}, -pages = {681--684}, -title = {{SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/8808585}, +pages = {681--4}, +pmid = {8808585}, +title = {{SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments.}}, +url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/11.6.681 http://www.ncbi.nlm.nih.gov/pubmed/8808585}, volume = {11}, year = {1995} } -@article{Chapman1981, -abstract = {Requirements for activation of inactive pyruvate, inorganic phosphate (Pi) dikinase extracted from darkened maize leaves were examined. Incubation with Pi plus dithiothreitol resulted in a rapid recovery of activity comparable to that in illuminated leaves. However, contrary to previous findings, most of this activity (60–95\%) was recovered by adding Pi alone. There was no activation with dithiothreitol alone. Dependency on dithiothreitol, in addition to Pi was minimal at about pH 7.5 but was substantial at higher pH. Anaerobic conditions did not enhance Pi-dependent activation. Active enzyme, isolated from illuminated leaves, was inactivated by incubating with ADP and this occurred in the presence of dithiothreitol. ATP and AMP were not effective but ATP may be a corequirment for ADP-dependent inactivation. Enzyme inactivated by ADP required Pi for reactivation. We conclude that interconversion of dithiol and disulfide forms of the enzyme is not critical for the dark/light regulation of pyruvate, Pi dikinase. The primary mechanism apparently involves an ADP-induced transformation to an inactive form which undergoes a Pi-mediated reactivation.}, -author = {Chapman, K S R and Hatch, M D}, -doi = {10.1016/0003-9861(81)90166-1}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chapman, Hatch/Archives of Biochemistry and Biophysics/Chapman, Hatch - 1981 - Regulation of C4 photosynthesis Mechanism of activation and inactivation of extracted pyruvate, inorganic phosphate dikinase in relation to darklight regulation.pdf:pdf}, -issn = {00039861}, -journal = {Archives of Biochemistry and Biophysics}, -month = aug, -number = {1}, -pages = {82--89}, -title = {{Regulation of C4 photosynthesis: Mechanism of activation and inactivation of extracted pyruvate, inorganic phosphate dikinase in relation to dark/light regulation}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/0003986181901661}, -volume = {210}, -year = {1981} -} -@article{Michalkova2011, -author = {Michalkova, Andrea and Kholod, Yana and Kosenkov, Dmytro and Gorb, Leonid and Leszczynski, Jerzy}, -doi = {10.1016/j.gca.2011.01.015}, -issn = {00167037}, -journal = {Geochimica et Cosmochimica Acta}, -month = apr, -number = {7}, -pages = {1933--1941}, -shorttitle = {Viability of pyrite pulled metabolism in the ‘iron}, -title = {{Viability of pyrite pulled metabolism in the ‘iron-sulfur world’ theory: Quantum chemical assessment}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0016703711000238}, -volume = {75}, -year = {2011} -} -@article{Schagger2006, -author = {Sch\"{a}gger, Hermann}, -doi = {10.1038/nprot.2006.4}, -issn = {1754-2189}, -journal = {Nature Protocols}, -keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll}, -mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll}, -month = jun, -number = {1}, -pages = {16--22}, -title = {{Tricine–SDS-PAGE}}, -url = {http://www.nature.com/doifinder/10.1038/nprot.2006.4 http://www.nature.com/nprot/journal/v1/n1/pdf/nprot.2006.4.pdf}, -volume = {1}, -year = {2006} -} -@article{Lu2000, -abstract = {Eglin c from the leech Hirudo medicinalis is a potent protein inhibitor of many serine proteinases including chymotrypsin and subtilisins. Unlike most small protein inhibitors whose solvent-exposed enzyme-binding loop is stabilized primarily by disulfide bridges flanking the reactive-site peptide bond, eglin c possesses an enzyme-binding loop supported predominantly by extensive electrostatic/H-bonding interactions involving three Arg residues (Arg48, Arg51, and Arg53) projecting from the scaffold of the inhibitor. As an adjacent residue, the C-terminal Gly70 participates in these interactions via its alpha-carboxyl group interacting with the side chain of Arg51 and the main chain of Arg48. In addition, the amide NH group of Gly70 donates an H-bond to the carbonyl C=O groups of Arg48 and Arg51. To understand the structural and functional relevance of the electrostatic/H-bonding network, we chemically synthesized wild-type eglin c and three analogues in which Gly70 was either deleted or replaced by glycine amide (NH(2)CH(2)CONH(2)) or by alpha-hydroxylacetamide (HOCH(2)CONH(2)). NMR analysis indicated that the core structure of eglin c was maintained in the analogues, but that the binding loop was significantly perturbed. It was found that deletion or replacement of Gly70 destabilized eglin c by an average of 2.7 kcal/mol or 20 degrees C in melting temperature. As a result, these inhibitors become substrates for their target enzymes. Binding assays on these analogues with a catalytically incompetent subtilisin BPN' mutant indicated that loss or weakening of the interactions involving the carboxylate of Gly70 caused a decrease in binding by approximately 2 orders of magnitude. Notably, for all four synthetic inhibitors, the relative free energy changes (DeltaDeltaG) associated with protein destabilization are strongly correlated (slope = 0.94, r(2) = 0. 9996) with the DeltaDeltaG values derived from a decreased binding to the enzyme.}, -author = {Lu, Wei-Yue and Starovasnik, Melissa a and Dwyer, John J and Kossiakoff, Anthony a and Kent, Stephen B. H. and Lu, Wuyuan}, -doi = {10.1021/bi992292q}, -file = {:home/alex/Dokumente/Mendeley Desktop/Lu et al/Biochemistry/Lu et al. - 2000 - Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Amino Acid Sequence,Animals,Binding Sites,Biomolecular,Chymotrypsin,Chymotrypsin: antagonists \& inhibitors,Glycine,Glycine: chemistry,Glycine: metabolism,Kinetics,Leeches,Molecular Sequence Data,Nuclear Magnetic Resonance,Protein Denaturation,Proteins,Serpins,Serpins: chemical synthesis,Serpins: chemistry,Serpins: metabolism,Static Electricity,Structure-Activity Relationship,Subtilisins,Subtilisins: antagonists \& inhibitors}, -month = apr, -number = {13}, -pages = {3575--3584}, -pmid = {10736156}, -title = {{Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/10736156 http://pubs.acs.org/doi/abs/10.1021/bi992292q}, -volume = {39}, -year = {2000} -} -@article{Puius1997, -abstract = {The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2\% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1\% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.}, -author = {Puius, Y a and Zhao, Y and Sullivan, M and Lawrence, D S and Almo, S C and Zhang, Z Y}, -file = {:home/alex/Dokumente/Mendeley Desktop/Puius et al/Proceedings of the National Academy of Sciences of the United States of America/Puius et al. - 1997 - Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B a paradigm for inhibitor design.pdf:pdf}, -issn = {0027-8424}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Base Sequence,Binding Sites,Binding Sites: genetics,Cloning, Molecular,DNA Primers,DNA Primers: genetics,Drug Design,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Escherichia coli,Escherichia coli: genetics,Humans,Models, Molecular,Molecular Sequence Data,Mutagenesis, Site-Directed,Phosphotyrosine,Phosphotyrosine: metabolism,Polymerase Chain Reaction,Protein Conformation,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: antagonists \& inhib,Protein Tyrosine Phosphatases: chemistry,Protein Tyrosine Phosphatases: genetics,Substrate Specificity}, -month = dec, -number = {25}, -pages = {13420--5}, -pmid = {9391040}, -title = {{Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=28320\&tool=pmcentrez\&rendertype=abstract}, -volume = {94}, -year = {1997} -} -@article{Clarkson2006, -abstract = {Long-range intraprotein interactions give rise to many important protein behaviors. Understanding how energy is transduced through protein structures to either transmit a signal or elicit conformational changes is therefore a current challenge in structural biology. In an effort to understand such linkages, multiple V --> A mutations were made in the small globular protein eglin c. The physical responses, as mapped by NMR spin relaxation, residual dipolar couplings (RDCs), and scalar couplings, illustrate that the interior of this nonallosteric protein forms a dynamic network and that local perturbations are transmitted as dynamic and structural changes to distal sites as far as 16 A away. Two basic types of propagation responses were observed: contiguous pathways of enhanced (attenuated) dynamics with no change in structure; and dispersed (noncontiguous) changes in methyl rotation rates that appear to result from subtle deformation of backbone structure. In addition, energy transmission is found to be unidirectional. In one mutant, an allosteric conformational change of a side chain is seen in the context of a pathway of propagated changes in picosecond to nanosecond dynamics. The observation of so many long-range interactions in a small, rigid system lends experimental weight to the idea that all well-folded proteins inherently possess allosteric features [Gunasekaran et al. (2004) Proteins 57, 433-443], and that dynamics are a rich source of information for mapping and gaining mechanistic insight into communication pathways in individual proteins.}, -author = {Clarkson, Michael W and Gilmore, Steven A and Edgell, Marshall H and Lee, Andrew L}, -doi = {10.1021/bi060652l}, -file = {:home/alex/Dokumente/Mendeley Desktop/Clarkson et al/Biochemistry/Clarkson et al. - 2006 - Dynamic coupling and allosteric behavior in a nonallosteric protein.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Allosteric Regulation,Amino Acid Substitution,Biomolecular,Eglin c,Models,Molecular,Nuclear Magnetic Resonance,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Proteins: genetics,Signal Transduction}, -mendeley-tags = {Eglin c}, -month = jun, -number = {25}, -pages = {7693--9}, -pmid = {16784220}, -title = {{Dynamic coupling and allosteric behavior in a nonallosteric protein.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2453595\&tool=pmcentrez\&rendertype=abstract}, -volume = {45}, -year = {2006} -} -@article{Cui2008a, -abstract = {Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/Pauling-KNF descriptions, and point out that the "new view" of allostery, emphasizing "population shifts," is, in fact, an "old view." The presentation offers not only an up-to-date description of allostery from a theoretical/computational perspective, but also helps to resolve several outstanding issues concerning allostery.}, -author = {Cui, Qiang and Karplus, Martin}, -doi = {10.1110/ps.03259908}, -file = {:home/alex/Dokumente/Mendeley Desktop/Cui, Karplus/Protein science a publication of the Protein Society/Cui, Karplus - 2008 - Allostery and cooperativity revisited.pdf:pdf}, -issn = {1469-896X}, -journal = {Protein science : a publication of the Protein Society}, -keywords = {Allosteric Regulation,Allosteric Site,Animals,Dimerization,Folder - Allostery - Theory,Hemoglobins,Hemoglobins: chemistry,Humans,Mechanism,Models,Molecular,Protein Structure,Proteins,Proteins: chemistry,Quaternary,Tertiary}, -mendeley-tags = {Folder - Allostery - Theory,Mechanism}, -month = aug, -number = {8}, -pages = {1295--307}, -pmid = {18560010}, -title = {{Allostery and cooperativity revisited.}}, -url = {http://doi.wiley.com/10.1110/ps.03259908 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2492820\&tool=pmcentrez\&rendertype=abstract}, -volume = {17}, -year = {2008} -} -@article{Voet-van-Vormizeele2008, -author = {Voet-van-Vormizeele, Jan and Groth, Georg}, -file = {:home/alex/Dokumente/Mendeley Desktop/Voet-van-Vormizeele, Groth/Current Topics in Biochemical Research/Voet-van-Vormizeele, Groth - 2008 - Mutants, molecules and mechanisms - Decipering the ethylene signalling network.pdf:pdf}, -issn = {09724583}, -journal = {Current Topics in Biochemical Research}, -keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -number = {2}, -pages = {25--34}, -title = {{Mutants, molecules and mechanisms - Decipering the ethylene signalling network}}, -volume = {10}, -year = {2008} -} -@article{Pfleger2012, -author = {Pfleger, Christopher and Radestock, Sebastian and Schmidt, S. and Gohlke, Holger}, -title = {{Global and local indices for characterizing biomolecular flexibility and rigidity}}, -year = {2012} -} -@article{Chastain1996, -abstract = {The gene for C4-pyruvate,orthophosphate dikinase (PPDK) from maize (Zea mays) was cloned into an Escherichia coli expression vector and recombinant PPDK produced in E. coli cells. Recombinant enzyme was found to be expressed in high amounts (5.3 U purified enzyme-activityliter-1 of induced cells) as a predominantly soluble and active protein. Biochemical analysis of partially purified recombinant PPDK showed this enzyme to be equivalent to enzyme extracted from illuminated maize leaves with respect to (i) molecular mass, (ii) specific activity, (iii) substrate requirements, and (iv) phosphorylation/inactivation by its bifunctional regulatory protein.}, -author = {Chastain, Chris J. and Thompson, Brent J. and Chollet, Raymond}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chastain, Thompson, Chollet/Photosynthesis Research/Chastain, Thompson, Chollet - 1996 - Maize recombinant C4-pyruvate, orthophosphate dikinase expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein.pdf:pdf}, -journal = {Photosynthesis Research}, -keywords = {C4 photosynthesis,C4 plant,PPDK,enzyme,maize (Zea mays),orthophosphate dikinase,pyruvate,recombinant}, -pages = {83--89}, -title = {{Maize recombinant C4-pyruvate, orthophosphate dikinase: expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein}}, -url = {http://www.springerlink.com/index/N642332887GN2U55.pdf}, -volume = {49}, -year = {1996} -} -@article{Sponer2011, -author = {\v{S}poner, Judit E. and \v{S}poner, Jiř\'{\i} and Fuentes-Cabrera, Miguel}, -doi = {10.1002/chem.201002057}, -issn = {09476539}, -journal = {Chemistry - A European Journal}, -month = jan, +@article{Luisi2002, +author = {Luisi, P. L}, +file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Foundations of Chemistry/Luisi - 2002 - Emergence in chemistry Chemistry as the embodiment of emergence.pdf:pdf}, +journal = {Foundations of Chemistry}, number = {3}, -pages = {847--854}, -shorttitle = {Prebiotic Routes to Nucleosides}, -title = {{Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways}}, -url = {http://doi.wiley.com/10.1002/chem.201002057}, -volume = {17}, -year = {2011} +pages = {183--200}, +shorttitle = {Emergence in chemistry}, +title = {{Emergence in chemistry: Chemistry as the embodiment of emergence}}, +volume = {4}, +year = {2002} } -@article{Wachtershauser2006, -author = {Wachtershauser, G.}, -doi = {10.1098/rstb.2006.1904}, -file = {:home/alex/Dokumente/Mendeley Desktop/Wachtershauser/Philosophical Transactions of the Royal Society B Biological Sciences/Wachtershauser - 2006 - From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya.pdf:pdf}, -issn = {0962-8436}, -journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, -month = oct, -number = {1474}, -pages = {1787--1808}, -title = {{From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya}}, -url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2006.1904}, -volume = {361}, -year = {2006} +@article{Datta2008, +abstract = {Structural studies of caspase-1 reveal that the dimeric thiol protease can exist in two states: in an on-state, when the active site is occupied, or in an off-state, when the active site is empty or when the enzyme is bound by a synthetic allosteric ligand at the dimer interface approximately 15 A from the active site. A network of 21 hydrogen bonds from nine side chains connecting the active and allosteric sites change partners when going between the on-state and the off-state. Alanine-scanning mutagenesis of these nine side chains shows that only two of them-Arg286 and Glu390, which form a salt bridge-have major effects, causing 100- to 200-fold reductions in catalytic efficiency (k(cat)/K(m)). Two neighbors, Ser332 and Ser339, have minor effects, causing 4- to 7-fold reductions. A more detailed mutational analysis reveals that the enzyme is especially sensitive to substitutions of the salt bridge: even a homologous R286K substitution causes a 150-fold reduction in k(cat)/K(m). X-ray crystal structures of these variants suggest the importance of both the salt bridge interaction and the coordination of solvent water molecules near the allosteric binding pocket. Thus, only a small subset of side chains from the larger hydrogen bonding network is critical for activity. These form a contiguous set of interactions that run from one active site through the allosteric site at the dimer interface and onto the second active site. This subset constitutes a functional allosteric circuit or "hot wire" that promotes site-to-site coupling.}, +author = {Datta, Debajyoti and Scheer, Justin M and Romanowski, Michael J and Wells, James a}, +doi = {10.1016/j.jmb.2008.06.040}, +file = {:home/alex/Dokumente/Mendeley Desktop/Datta et al/Journal of molecular biology/Datta et al. - 2008 - An allosteric circuit in caspase-1.pdf:pdf}, +issn = {1089-8638}, +journal = {Journal of molecular biology}, +keywords = {Allosteric Regulation,Amino Acid Substitution,Arginine,Caspase 1,Caspase 1: chemistry,Caspase 1: metabolism,Conserved Sequence,Crystallography, X-Ray,DNA Mutational Analysis,Glutamic Acid,Humans,Hydrogen Bonding,Kinetics,Models, Molecular,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: metabolism,Protein Structure, Secondary}, +month = sep, +number = {5}, +pages = {1157--67}, +pmid = {18590738}, +title = {{An allosteric circuit in caspase-1.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2626611\&tool=pmcentrez\&rendertype=abstract}, +volume = {381}, +year = {2008} } -@article{Dong2004, -author = {Dong, X. and Stothard, P. and Forsythe, I. J. and Wishart, D. S.}, -doi = {10.1093/nar/gkh410}, -file = {:home/alex/Dokumente/Mendeley Desktop/Dong et al/Nucleic Acids Research/Dong et al. - 2004 - PlasMapper a web server for drawing and auto-annotating plasmid maps.pdf:pdf}, -issn = {0305-1048}, -journal = {Nucleic Acids Research}, -month = jul, -number = {Web Server}, -pages = {W660--W664}, -title = {{PlasMapper: a web server for drawing and auto-annotating plasmid maps}}, -url = {http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkh410}, -volume = {32}, -year = {2004} -} -@book{Jander2006, -address = {Stuttgart}, -author = {Jander, Gerhart and Schweda, Eberhard}, -edition = {16., \"{u}bera}, -isbn = {9783777613888}, -keywords = {Folder - Anorganische Chemie}, -mendeley-tags = {Folder - Anorganische Chemie}, -month = jan, -publisher = {Hirzel}, -title = {{Lehrbuch der analytischen und pr\"{a}parativen anorganischen Chemie mit 67 Tabellen}}, -year = {2006} -} -@misc{CenterforHistoryandNewMedia, -annote = { - Welcome to Zotero! - - - -View the Quick Start Guide to learn how to begin collecting, managing, citing, and sharing your research sources. -Thanks for installing Zotero.}, -author = {{Center for History and New Media}}, -title = {{Zotero Quick Start Guide}}, -url = {http://zotero.org/support/quick\_start\_guide} -} -@book{Bruckner2007, -address = {Berlin [u.a.]}, -author = {Br\"{u}ckner, Reinhard}, -edition = {3. Aufl., }, -isbn = {9783827415790}, -keywords = {Folder - Organische Chemie}, -mendeley-tags = {Folder - Organische Chemie}, -publisher = {Spektrum Akademischer Verlag}, -title = {{Reaktionsmechanismen : organische Reaktionen, Stereochemie, moderne Synthesemethoden}}, -year = {2007} -} -@article{Stone1988, -abstract = {Kinetic studies on the reaction catalyzed by dihydrofolate reductase from Escherichia coli have been undertaken with the aim of characterizing further the kinetic mechanism of the reaction. For this purpose, the kinetic properties of substrates were determined by measurement of (a) initial velocities over a wide range of substrate concentrations and (b) the stickiness of substrates in ternary enzyme complexes. Stickiness is defined as the rate at which a substrate reacts to give products relative to the rate at which that substrate dissociates. Stickiness was determined by varying the viscosity of reaction mixtures and the concentration of one substrate in the presence of a saturating concentration of the other substrate. The results indicate that NADPH is sticky in the enzyme-NADPH-dihydrofolate complex, while dihydrofolate is much less sticky in this complex. At higher concentrations, NADPH functions as an activator through the formation of an enzyme-NADPH-tetrahydrofolate from which tetrahydrofolate is released more rapidly than from an enzyme-tetrahydrofolate complex. Higher concentrations of dihydrofolate also cause enzyme activation, and it appears that this effect is due to the ability of dihydrofolate to displace tetrahydrofolate from a binary enzyme complex through the formation of a transitory enzyme-tetrahydrofolate-dihydrofolate complex. As NADPH and dihydrofolate function as activators and as NADPH behaves as a sticky substrate, the kinetic mechanism of the dihydrofolate reductase reaction with the natural substrates is steady-state random. By contrast with NADPH, reduced 3-acetylpyridine adenine dinucleotide phosphate exhibits only slight stickiness and does not function as an activator.(ABSTRACT TRUNCATED AT 250 WORDS)}, -author = {Stone, S R and Morrison, J F}, -file = {:home/alex/Dokumente/Mendeley Desktop/Stone, Morrison/Biochemistry/Stone, Morrison - 1988 - Dihydrofolate reductase from Escherichia coli the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Deuterium,Escherichia coli,Escherichia coli: enzymology,Folic Acid,Folic Acid: analogs \& derivatives,Folic Acid: metabolism,Hydrogen-Ion Concentration,Kinetics,NAD,NAD: analogs \& derivatives,NAD: metabolism,NADP,NADP: metabolism,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: metabolism,Viscosity}, -month = jul, -number = {15}, -pages = {5493--9}, -pmid = {3052577}, -title = {{Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/3052577}, -volume = {27}, -year = {1988} -} -@article{Steitz2003, -author = {Steitz, Thomas A and Moore, Peter B}, -doi = {10.1016/S0968-0004(03)00169-5}, -file = {:home/alex/Dokumente/Mendeley Desktop/Steitz, Moore/Trends in Biochemical Sciences/Steitz, Moore - 2003 - RNA, the first macromolecular catalyst the ribosome is a ribozyme.pdf:pdf}, -issn = {09680004}, -journal = {Trends in Biochemical Sciences}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, +@article{Wiesmann2004, +abstract = {Obesity and type II diabetes are closely linked metabolic syndromes that afflict >100 million people worldwide. Although protein tyrosine phosphatase 1B (PTP1B) has emerged as a promising target for the treatment of both syndromes, the discovery of pharmaceutically acceptable inhibitors that bind at the active site remains a substantial challenge. Here we describe the discovery of an allosteric site in PTP1B. Crystal structures of PTP1B in complex with allosteric inhibitors reveal a novel site located approximately 20 A from the catalytic site. We show that allosteric inhibitors prevent formation of the active form of the enzyme by blocking mobility of the catalytic loop, thereby exploiting a general mechanism used by tyrosine phosphatases. Notably, these inhibitors exhibit selectivity for PTP1B and enhance insulin signaling in cells. Allosteric inhibition is a promising strategy for targeting PTP1B and constitutes a mechanism that may be applicable to other tyrosine phosphatases.}, +author = {Wiesmann, Christian and Barr, Kenneth J and Kung, Jenny and Zhu, Jiang and Erlanson, Daniel a and Shen, Wang and Fahr, Bruce J and Zhong, Min and Taylor, Lisa and Randal, Mike and McDowell, Robert S and Hansen, Stig K}, +doi = {10.1038/nsmb803}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wiesmann et al/Nature structural \& molecular biology/Wiesmann et al. - 2004 - Allosteric inhibition of protein tyrosine phosphatase 1B.pdf:pdf}, +issn = {1545-9993}, +journal = {Nature structural \& molecular biology}, +keywords = {Allosteric Site,Animals,Binding,Binding Sites,CHO Cells,Catalysis,Catalytic Domain,Chemical,Cloning,Competitive,Cricetinae,Crystallography,DNA,DNA: chemistry,Dose-Response Relationship,Drug,Humans,Inhibitory Concentration 50,Kinetics,Ligands,Models,Molecular,Non-Receptor Type 1,Obesity,Phosphoric Monoester Hydrolases,Phosphoric Monoester Hydrolases: chemistry,Protein Binding,Protein Conformation,Protein Structure,Protein Tyrosine Phosphatase,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: chemistry,Tertiary,Time Factors,Transfection,Tyrosine,Tyrosine: chemistry,X-Ray,allostery,ptp1b}, +mendeley-tags = {allostery,ptp1b}, month = aug, number = {8}, -pages = {411--418}, -shorttitle = {RNA, the first macromolecular catalyst}, -title = {{RNA, the first macromolecular catalyst: the ribosome is a ribozyme}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403001695}, -volume = {28}, -year = {2003} +pages = {730--7}, +pmid = {15258570}, +title = {{Allosteric inhibition of protein tyrosine phosphatase 1B.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/15258570}, +volume = {11}, +year = {2004} } @article{Louis-Jeune2011, abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used to investigate the structure of proteins. Major secondary structure types, alpha-helices and beta-strands, produce distinctive CD spectra. Thus, by comparing the CD spectrum of a protein of interest to a reference set consisting of CD spectra of proteins of known structure, predictive methods can estimate the secondary structure of the protein. Currently available methods, including K2D2, use such experimental CD reference sets, which are very small in size when compared to the number of tertiary structures available in the Protein Data Bank (PDB). Conversely, given a PDB structure, it is possible to predict a theoretical CD spectrum from it. The methodological framework for this calculation was established long ago but only recently a convenient implementation called DichroCalc has been developed. In this study, we set to determine whether theoretically derived spectra could be used as reference set for accurate CD based predictions of secondary structure. We used DichroCalc to calculate the theoretical CD spectra of a nonredundant set of structures representing most proteins in the PDB, and applied a straightforward approach for predicting protein secondary structure content using these theoretical CD spectra as reference set. We show that this method improves the predictions, particularly for the wavelength interval between 200 and 240 nm and for beta-strand content. We have implemented this method, called K2D3, in a publicly accessible web server at http://www. ogic.ca/projects/k2d3. Proteins 2011. © 2011 Wiley Periodicals, Inc.}, @@ -854,92 +87,92 @@ title = {{Translation of in Vitro Inhibition by Marine Natural Products of the C volume = {53}, year = {2005} } -@article{Tsai2008a, -abstract = {Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For several years, it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free-energy change due to the change in entropy, entropy is mainly responsible for binding.}, -author = {Tsai, Chung-Jung and del Sol, Antonio and Nussinov, Ruth}, -doi = {10.1016/j.jmb.2008.02.034}, -file = {:home/alex/Dokumente/Mendeley Desktop/Tsai, del Sol, Nussinov/Journal of molecular biology/Tsai, del Sol, Nussinov - 2008 - Allostery absence of a change in shape does not imply that allostery is not at play.pdf:pdf}, -issn = {1089-8638}, -journal = {Journal of molecular biology}, -keywords = {Allosteric Regulation,Animals,Folder - Allostery - Theory,Humans,Mechanism,Models,Molecular,Protein Conformation,Signal Transduction,Thermodynamics}, -mendeley-tags = {Folder - Allostery - Theory,Mechanism}, -month = apr, -number = {1}, -pages = {1--11}, -pmid = {18353365}, -shorttitle = {Allostery}, -title = {{Allostery: absence of a change in shape does not imply that allostery is not at play.}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608002313 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2684958\&tool=pmcentrez\&rendertype=abstract}, -volume = {378}, -year = {2008} -} -@article{Changeux2011, -author = {Changeux, Jean-Pierre}, -doi = {10.1002/pro.658}, -issn = {09618368}, -journal = {Protein Science}, -keywords = {Folder - Allostery - Theory, Mechanism}, -mendeley-tags = {Folder - Allostery - Theory, Mechanism}, +@article{Sashital2006, +author = {Sashital, Dipali G. and Butcher, Samuel E.}, +doi = {10.1021/cb6002465}, +file = {:home/alex/Dokumente/Mendeley Desktop/Sashital, Butcher/ACS Chemical Biology/Sashital, Butcher - 2006 - Flipping Off the Riboswitch RNA Structures That Control Gene Expression.pdf:pdf}, +issn = {1554-8929}, +journal = {ACS Chemical Biology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, month = jul, -pages = {1119--1124}, -title = {50th anniversary of the word “allosteric”}, -url = {http://doi.wiley.com/10.1002/pro.658}, -volume = {20}, +number = {6}, +pages = {341--345}, +shorttitle = {Flipping Off the Riboswitch}, +title = {{Flipping Off the Riboswitch: RNA Structures That Control Gene Expression}}, +url = {http://pubs.acs.org/doi/abs/10.1021/cb6002465 http://pubs.acs.org/doi/pdf/10.1021/cb6002465}, +volume = {1}, +year = {2006} +} +@article{Goss1980, +abstract = {Pyruvate phosphate dikinase contains a pivotal histidyl residue which functions to mediate the transfer of phosphoryl moieties during the reaction catalyzed by the enzyme. The tryptic peptide which contains this essential histidyl residue has been isolated by a two-step procedure originally developed by Wang and co-workers [Wang, T., Jurasek, L., \& Bridger, W. A. (1972) Biochemistry 11, 2067]. This peptide has been sequenced by the manual dansyl-Edman procedure and is shown to be NH2-Gly-Gly-Met-Thr-Ser-His-Ala-Ala-Val-Val-Ala-Arg-CO2H. There is no readily interpretable homology between this peptide and other phosphorylated histidyl peptides previously isolated from other enzymes. By use of Chou \& Fasman [Chou, P. Y., \& Fasman, G. D. (1974) Biochemistry 13, 222], it is predicted that the sequence contains an alpha helix from the methionine residue through to the carboxyl terminal arginine residue.}, +author = {Goss, Neil H. and Evans, Claudia T. and Wood, Harland G.}, +doi = {10.1021/bi00566a022}, +file = {:home/alex/Dokumente/Mendeley Desktop/Goss, Evans, Wood/Biochemistry/Goss, Evans, Wood - 1980 - Pyruvate phosphate dikinase sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Pyruvate,purification}, +mendeley-tags = {purification}, +month = dec, +number = {25}, +pages = {5805--5809}, +pmid = {6257292}, +title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier}}, +url = {http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, +volume = {19}, +year = {1980} +} +@article{Clarkson2004, +abstract = {Long-range interactions are fundamental to protein behaviors such as cooperativity and allostery. In an attempt to understand the role protein flexibility plays in such interactions, the distribution of local fluctuations in a globular protein was monitored in response to localized, nonelectrostatic perturbations. Two valine-to-alanine mutations were introduced into the small serine protease inhibitor eglin c, and the (15)N and (2)H NMR spin relaxation properties of these variants were analyzed in terms of the Lipari-Szabo dynamics formalism and compared to those of the wild type. Significant changes in picosecond to nanosecond dynamics were observed in side chains located as much as 13 A from the point of mutation. Additionally, those residues experiencing altered dynamics appear to form contiguous surfaces within the protein. In the case of V54A, the large-to-small mutation results in a rigidification of connected residues, even though this mutation decreases the global stability. These findings suggest that dynamic perturbations arising from single mutations may propagate away from the perturbed site through networks of interacting side chains. That this is observed in eglin c, a classically nonallosteric protein, suggests that such behavior will be observed in many, if not all, globular proteins. Differences in behavior between the two mutants suggest that dynamic responses will be context-dependent.}, +author = {Clarkson, Michael W and Lee, Andrew L}, +doi = {10.1021/bi0494424}, +file = {:home/alex/Dokumente/Mendeley Desktop/Clarkson, Lee/Biochemistry/Clarkson, Lee - 2004 - Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Alanine,Alanine: genetics,Animals,Biomolecular,Biomolecular: methods,Chemical,Eglin c,Leeches,Models,Molecular,Mutagenesis,Nanotechnology,Nanotechnology: methods,Nuclear Magnetic Resonance,Phenylalanine,Phenylalanine: genetics,Point Mutation,Polymerase Chain Reaction,Protein Conformation,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: genetics,Proteins,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: chemistry,Serine Proteinase Inhibitors: genetics,Serpins,Serpins: chemistry,Serpins: genetics,Site-Directed,Thermodynamics,Tryptophan,Tryptophan: genetics,Valine,Valine: genetics}, +mendeley-tags = {Eglin c}, +month = oct, +number = {39}, +pages = {12448--58}, +pmid = {15449934}, +title = {{Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/15449934}, +volume = {43}, +year = {2004} +} +@article{Wallace2006, +abstract = {We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from http://www.tcoffee.org/.}, +author = {Wallace, Iain M and O'Sullivan, Orla and Higgins, Desmond G and Notredame, Cedric}, +doi = {10.1093/nar/gkl091}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wallace et al/Nucleic acids research/Wallace et al. - 2006 - M-Coffee combining multiple sequence alignment methods with T-Coffee.pdf:pdf}, +issn = {1362-4962}, +journal = {Nucleic acids research}, +keywords = {Algorithms,Reproducibility of Results,Sequence Alignment,Sequence Alignment: methods,Software}, +month = jan, +number = {6}, +pages = {1692--9}, +pmid = {16556910}, +title = {{M-Coffee: combining multiple sequence alignment methods with T-Coffee.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1410914\&tool=pmcentrez\&rendertype=abstract}, +volume = {34}, +year = {2006} +} +@article{Radestock2011, +abstract = {We probe the hypothesis of corresponding states, according to which homologues from mesophilic and thermophilic organisms are in corresponding states of similar rigidity and flexibility at their respective optimal temperatures. For this, the local distribution of flexible and rigid regions in 19 pairs of homologous proteins from meso- and thermophilic organisms is analyzed and related to activity characteristics of the enzymes by constraint network analysis (CNA). Two pairs of enzymes are considered in more detail: 3-isopropylmalate dehydrogenase and thermolysin-like protease. By comparing microscopic stability features of homologues with the help of stability maps, introduced for the first time, we show that adaptive mutations in enzymes from thermophilic organisms maintain the balance between overall rigidity, important for thermostability, and local flexibility, important for activity, at the appropriate working temperature. Thermophilic adaptation in general leads to an increase of structural rigidity but conserves the distribution of functionally important flexible regions between homologues. This finding provides direct evidence for the hypothesis of corresponding states. CNA thereby implicitly captures and unifies many different mechanisms that contribute to increased thermostability and to activity at high temperatures. This allows to qualitatively relate changes in the flexibility of active site regions, induced either by a temperature change or by the introduction of mutations, to experimentally observed losses of the enzyme function. As for applications, the results demonstrate that exploiting the principle of corresponding states not only allows for successful thermostability optimization but also for guiding experiments in order to improve enzyme activity in protein engineering.}, +author = {Radestock, S. and Gohlke, H.}, +doi = {10.1002/prot.22946}, +file = {:home/alex/Dokumente/Mendeley Desktop/Radestock, Gohlke/Proteins/Radestock, Gohlke - 2011 - Protein rigidity and thermophilic adaptation.pdf:pdf}, +issn = {1097-0134}, +journal = {Proteins}, +month = apr, +number = {4}, +pages = {1089--108}, +pmid = {21246632}, +title = {{Protein rigidity and thermophilic adaptation.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/21246632}, +volume = {79}, year = {2011} } -@article{Tsutsui1982, -author = {Tsutsui, K. and Mueller, G. C}, -file = {:home/alex/Dokumente/Mendeley Desktop/Tsutsui, Mueller/Analytical Biochemistry/Tsutsui, Mueller - 1982 - Affinity chromatography of heme-binding proteins an improved method for the synthesis of hemin-agarose.pdf:pdf}, -journal = {Analytical Biochemistry}, -keywords = {Folder - Methoden}, -mendeley-tags = {Folder - Methoden}, -number = {2}, -pages = {244--250}, -shorttitle = {Affinity chromatography of heme-binding proteins}, -title = {{Affinity chromatography of heme-binding proteins: an improved method for the synthesis of hemin-agarose}}, -volume = {121}, -year = {1982} -} -@article{Luisi2003a, -author = {Luisi, P. L}, -file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Naturwissenschaften/Luisi - 2003 - Autopoiesis a review and a reappraisal.pdf:pdf}, -journal = {Naturwissenschaften}, -number = {2}, -pages = {49--59}, -shorttitle = {Autopoiesis}, -title = {{Autopoiesis: a review and a reappraisal}}, -volume = {90}, -year = {2003} -} -@misc{TheMendeleySupportTeam2011c, -abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, -address = {London}, -author = {{The Mendeley Support Team}}, -booktitle = {Mendeley Desktop}, -file = {:home/alex/Dokumente/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley.pdf:pdf}, -keywords = {Mendeley,how-to,user manual}, -pages = {1--16}, -publisher = {Mendeley Ltd.}, -title = {{Getting Started with Mendeley}}, -url = {http://www.mendeley.com}, -year = {2011} -} -@article{Wiechelman1988, -author = {Wiechelman, K}, -doi = {10.1016/0003-2697(88)90383-1}, -file = {:home/alex/Dokumente/Mendeley Desktop/Wiechelman/Analytical Biochemistry/Wiechelman - 1988 - Investigation of the bicinchoninic acid protein assay Identification of the groups responsible for color formation.pdf:pdf}, -issn = {00032697}, -journal = {Analytical Biochemistry}, -keywords = {Folder - Methoden}, -mendeley-tags = {Folder - Methoden}, -month = nov, -number = {1}, -pages = {231--237}, -title = {{Investigation of the bicinchoninic acid protein assay: Identification of the groups responsible for color formation}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/0003269788903831}, -volume = {175}, -year = {1988} -} @article{Chastain2008, abstract = {Pyruvate, orthophosphate dikinase (PPDK) is a ubiquitous, low-abundance metabolic enzyme of undetermined function in C3 plants. Its activity in C3 chloroplasts is light-regulated via reversible phosphorylation of an active-site Thr residue by the PPDK regulatory protein (RP), a most unusual bifunctional protein kinase (PK)/protein phosphatase (PP). In this paper we document the molecular cloning and functional analysis of the two unique C3 RPs in Arabidopsis thaliana. The first of these, AtRP1, encodes a typical chloroplast-targeted, bifunctional C4-like RP. The second RP gene, AtRP2, encodes a monofunctional polypeptide that possesses in vitro RP-like PK activity but lacks PP activity, and is localized in the cytosol. Notably, the deduced primary structures of these two highly homologous polypeptides are devoid of any canonical subdomain structure that unifies all known eukaryotic and prokaryotic Ser/Thr PKs into one of three superfamilies, despite the direct demonstration that AtRP1 is functionally a member of this group. Instead, these C3 RPs and the related C4 plant homologues encode a conserved, centrally positioned, approximately 260-residue sequence currently described as the 'domain of unknown function 299' (DUF 299). We propose that vascular plant RPs form a unique protein kinase family now designated as the DUF 299 gene family.}, author = {Chastain, Chris J and Xu, Wenxin and Parsley, Kate and Sarath, Gautam and Hibberd, Julian M and Chollet, Raymond}, @@ -973,75 +206,29 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/2988448}, volume = {239}, year = {1985} } -@article{Zhuravleva2011a, -abstract = {The 70-kDa heat shock protein (Hsp70) chaperones perform a wide array of cellular functions that all derive from the ability of their N-terminal nucleotide-binding domains (NBDs) to allosterically regulate the substrate affinity of their C-terminal substrate-binding domains in a nucleotide-dependent mechanism. To explore the structural origins of Hsp70 allostery, we performed NMR analysis on the NBD of DnaK, the Escherichia coli Hsp70, in six different states (ligand-bound or apo) and in two constructs, one that retains the conserved and functionally crucial portion of the interdomain linker (residues ) and another that lacks the linker. Chemical-shift perturbation patterns identify residues at subdomain interfaces that constitute allosteric networks and enable the NBD to act as a nucleotide-modulated switch. Nucleotide binding results in changes in subdomain orientations and long-range perturbations along subdomain interfaces. In particular, our findings provide structural details for a key mechanism of Hsp70 allostery, by which information is conveyed from the nucleotide-binding site to the interdomain linker. In the presence of ATP, the linker binds to the edge of the IIA $\beta$-sheet, which structurally connects the linker and the nucleotide-binding site. Thus, a pathway of allosteric communication leads from the NBD nucleotide-binding site to the substrate-binding domain via the interdomain linker.}, -author = {Zhuravleva, Anastasia and Gierasch, Lila M}, -doi = {10.1073/pnas.1014448108}, -file = {:home/alex/Dokumente/Mendeley Desktop/Zhuravleva, Gierasch/Proceedings of the National Academy of Sciences of the United States of America/Zhuravleva, Gierasch - 2011 - Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.pdf:pdf}, -issn = {1091-6490}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Adenosine Triphosphate,Adenosine Triphosphate: chemistry,Adenosine Triphosphate: genetics,Adenosine Triphosphate: metabolism,Allosteric Regulation,Allosteric Regulation: physiology,Binding Sites,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Escherichia coli: chemistry,Escherichia coli: genetics,Escherichia coli: metabolism,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: chemistry,HSP70 Heat-Shock Proteins: genetics,HSP70 Heat-Shock Proteins: metabolism,Nuclear Magnetic Resonance, Biomolecular,Protein Binding,Signal Transduction,Signal Transduction: physiology,Structure-Activity Relationship}, -month = apr, -number = {17}, -pages = {6987--92}, -pmid = {21482798}, -title = {{Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084084\&tool=pmcentrez\&rendertype=abstract}, -volume = {108}, -year = {2011} -} -@article{Wilkins1999, -author = {Wilkins, M R and Gasteiger, E and Bairoch, A and Sanchez, J C and Williams, K L and Appel, R D and Hochstrasser, D F}, -file = {:home/alex/Dokumente/Mendeley Desktop/Wilkins et al/Methods in Molecular Biology (Clifton, N.J.)/Wilkins et al. - 1999 - Protein identification and analysis tools in the ExPASy server.pdf:pdf}, -issn = {1064-3745}, -journal = {Methods in Molecular Biology (Clifton, N.J.)}, -keywords = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software}, -mendeley-tags = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software}, -pages = {531--552}, -title = {{Protein identification and analysis tools in the ExPASy server}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/10027275}, -volume = {112}, -year = {1999} -} -@article{Greenfield2007, -author = {Greenfield, Norma J}, -doi = {10.1038/nprot.2006.202}, -issn = {1754-2189}, -journal = {Nature Protocols}, -month = jan, -number = {6}, -pages = {2876--2890}, -title = {{Using circular dichroism spectra to estimate protein secondary structure}}, -url = {http://www.nature.com/doifinder/10.1038/nprot.2006.202}, -volume = {1}, +@book{Berg2007a, +address = {M\"{u}nchen; Heidelberg}, +author = {Berg, Jeremy and Stryer, Lubert and Tymoczko, John L}, +edition = {6. Aufl.}, +isbn = {9783827418005}, +keywords = {Folder - Biochemie}, +mendeley-tags = {Folder - Biochemie}, +publisher = {Spektrum Akademischer Verlag}, +title = {{Biochemie}}, year = {2007} } -@article{Riener2002a, -author = {Riener, Christian and Kada, Gerald and Gruber, Hermann}, -doi = {10.1007/s00216-002-1347-2}, -file = {:home/alex/Dokumente/Mendeley Desktop/Riener, Kada, Gruber/Analytical and Bioanalytical Chemistry/Riener, Kada, Gruber - 2002 - Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032-dithiodipyridine.pdf:pdf}, -issn = {1618-2642}, -journal = {Analytical and Bioanalytical Chemistry}, -keywords = {Folder - Methoden}, -mendeley-tags = {Folder - Methoden}, -month = jul, -number = {4-5}, -pages = {266--276}, -title = {{Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4'-dithiodipyridine}}, -url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00216-002-1347-2}, -volume = {373}, -year = {2002} -} -@article{Luisi2002, -author = {Luisi, P. L}, -file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Foundations of Chemistry/Luisi - 2002 - Emergence in chemistry Chemistry as the embodiment of emergence.pdf:pdf}, -journal = {Foundations of Chemistry}, -number = {3}, -pages = {183--200}, -shorttitle = {Emergence in chemistry}, -title = {{Emergence in chemistry: Chemistry as the embodiment of emergence}}, -volume = {4}, -year = {2002} +@misc{TheMendeleySupportTeam2011b, +abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, +address = {London}, +author = {{The Mendeley Support Team}}, +booktitle = {Mendeley Desktop}, +file = {:home/alex/Dokumente/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley.pdf:pdf}, +keywords = {Mendeley,how-to,user manual}, +pages = {1--16}, +publisher = {Mendeley Ltd.}, +title = {{Getting Started with Mendeley}}, +url = {http://www.mendeley.com}, +year = {2011} } @article{Russell2010, author = {Russell, M. J. and Hall, A. J. and Martin, W.}, @@ -1050,91 +237,20 @@ journal = {Geobiology}, title = {{Serpentinization as a source of energy at the origin of life}}, year = {2010} } -@article{Wiesmann2004, -abstract = {Obesity and type II diabetes are closely linked metabolic syndromes that afflict >100 million people worldwide. Although protein tyrosine phosphatase 1B (PTP1B) has emerged as a promising target for the treatment of both syndromes, the discovery of pharmaceutically acceptable inhibitors that bind at the active site remains a substantial challenge. Here we describe the discovery of an allosteric site in PTP1B. Crystal structures of PTP1B in complex with allosteric inhibitors reveal a novel site located approximately 20 A from the catalytic site. We show that allosteric inhibitors prevent formation of the active form of the enzyme by blocking mobility of the catalytic loop, thereby exploiting a general mechanism used by tyrosine phosphatases. Notably, these inhibitors exhibit selectivity for PTP1B and enhance insulin signaling in cells. Allosteric inhibition is a promising strategy for targeting PTP1B and constitutes a mechanism that may be applicable to other tyrosine phosphatases.}, -author = {Wiesmann, Christian and Barr, Kenneth J and Kung, Jenny and Zhu, Jiang and Erlanson, Daniel a and Shen, Wang and Fahr, Bruce J and Zhong, Min and Taylor, Lisa and Randal, Mike and McDowell, Robert S and Hansen, Stig K}, -doi = {10.1038/nsmb803}, -file = {:home/alex/Dokumente/Mendeley Desktop/Wiesmann et al/Nature structural \& molecular biology/Wiesmann et al. - 2004 - Allosteric inhibition of protein tyrosine phosphatase 1B.pdf:pdf}, -issn = {1545-9993}, -journal = {Nature structural \& molecular biology}, -keywords = {Allosteric Site,Animals,Binding,Binding Sites,CHO Cells,Catalysis,Catalytic Domain,Chemical,Cloning,Competitive,Cricetinae,Crystallography,DNA,DNA: chemistry,Dose-Response Relationship,Drug,Humans,Inhibitory Concentration 50,Kinetics,Ligands,Models,Molecular,Non-Receptor Type 1,Obesity,Phosphoric Monoester Hydrolases,Phosphoric Monoester Hydrolases: chemistry,Protein Binding,Protein Conformation,Protein Structure,Protein Tyrosine Phosphatase,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: chemistry,Tertiary,Time Factors,Transfection,Tyrosine,Tyrosine: chemistry,X-Ray,allostery,ptp1b}, -mendeley-tags = {allostery,ptp1b}, -month = aug, -number = {8}, -pages = {730--7}, -pmid = {15258570}, -title = {{Allosteric inhibition of protein tyrosine phosphatase 1B.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/15258570}, -volume = {11}, -year = {2004} -} -@article{Goss1980, -abstract = {Pyruvate phosphate dikinase contains a pivotal histidyl residue which functions to mediate the transfer of phosphoryl moieties during the reaction catalyzed by the enzyme. The tryptic peptide which contains this essential histidyl residue has been isolated by a two-step procedure originally developed by Wang and co-workers [Wang, T., Jurasek, L., \& Bridger, W. A. (1972) Biochemistry 11, 2067]. This peptide has been sequenced by the manual dansyl-Edman procedure and is shown to be NH2-Gly-Gly-Met-Thr-Ser-His-Ala-Ala-Val-Val-Ala-Arg-CO2H. There is no readily interpretable homology between this peptide and other phosphorylated histidyl peptides previously isolated from other enzymes. By use of Chou \& Fasman [Chou, P. Y., \& Fasman, G. D. (1974) Biochemistry 13, 222], it is predicted that the sequence contains an alpha helix from the methionine residue through to the carboxyl terminal arginine residue.}, -author = {Goss, Neil H. and Evans, Claudia T. and Wood, Harland G.}, -doi = {10.1021/bi00566a022}, -file = {:home/alex/Dokumente/Mendeley Desktop/Goss, Evans, Wood/Biochemistry/Goss, Evans, Wood - 1980 - Pyruvate phosphate dikinase sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Pyruvate,purification}, -mendeley-tags = {purification}, -month = dec, -number = {25}, -pages = {5805--5809}, -pmid = {6257292}, -title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier}}, -url = {http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, -volume = {19}, -year = {1980} -} -@article{Sashital2006, -author = {Sashital, Dipali G. and Butcher, Samuel E.}, -doi = {10.1021/cb6002465}, -file = {:home/alex/Dokumente/Mendeley Desktop/Sashital, Butcher/ACS Chemical Biology/Sashital, Butcher - 2006 - Flipping Off the Riboswitch RNA Structures That Control Gene Expression.pdf:pdf}, -issn = {1554-8929}, -journal = {ACS Chemical Biology}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = jul, -number = {6}, -pages = {341--345}, -shorttitle = {Flipping Off the Riboswitch}, -title = {{Flipping Off the Riboswitch: RNA Structures That Control Gene Expression}}, -url = {http://pubs.acs.org/doi/abs/10.1021/cb6002465 http://pubs.acs.org/doi/pdf/10.1021/cb6002465}, -volume = {1}, -year = {2006} -} -@article{Clarkson2004, -abstract = {Long-range interactions are fundamental to protein behaviors such as cooperativity and allostery. In an attempt to understand the role protein flexibility plays in such interactions, the distribution of local fluctuations in a globular protein was monitored in response to localized, nonelectrostatic perturbations. Two valine-to-alanine mutations were introduced into the small serine protease inhibitor eglin c, and the (15)N and (2)H NMR spin relaxation properties of these variants were analyzed in terms of the Lipari-Szabo dynamics formalism and compared to those of the wild type. Significant changes in picosecond to nanosecond dynamics were observed in side chains located as much as 13 A from the point of mutation. Additionally, those residues experiencing altered dynamics appear to form contiguous surfaces within the protein. In the case of V54A, the large-to-small mutation results in a rigidification of connected residues, even though this mutation decreases the global stability. These findings suggest that dynamic perturbations arising from single mutations may propagate away from the perturbed site through networks of interacting side chains. That this is observed in eglin c, a classically nonallosteric protein, suggests that such behavior will be observed in many, if not all, globular proteins. Differences in behavior between the two mutants suggest that dynamic responses will be context-dependent.}, -author = {Clarkson, Michael W and Lee, Andrew L}, -doi = {10.1021/bi0494424}, -file = {:home/alex/Dokumente/Mendeley Desktop/Clarkson, Lee/Biochemistry/Clarkson, Lee - 2004 - Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Alanine,Alanine: genetics,Animals,Biomolecular,Biomolecular: methods,Chemical,Eglin c,Leeches,Models,Molecular,Mutagenesis,Nanotechnology,Nanotechnology: methods,Nuclear Magnetic Resonance,Phenylalanine,Phenylalanine: genetics,Point Mutation,Polymerase Chain Reaction,Protein Conformation,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: genetics,Proteins,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: chemistry,Serine Proteinase Inhibitors: genetics,Serpins,Serpins: chemistry,Serpins: genetics,Site-Directed,Thermodynamics,Tryptophan,Tryptophan: genetics,Valine,Valine: genetics}, -mendeley-tags = {Eglin c}, +@article{Craig2011, +abstract = {The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads ).}, +author = {Craig, Ian R and Pfleger, Christopher and Gohlke, Holger and Essex, Jonathan W and Spiegel, Katrin}, +doi = {10.1021/ci200168b}, +file = {:home/alex/Dokumente/Mendeley Desktop/Craig et al/Journal of chemical information and modeling/Craig et al. - 2011 - Pocket-space maps to identify novel binding-site conformations in proteins.pdf:pdf}, +issn = {1549-960X}, +journal = {Journal of chemical information and modeling}, month = oct, -number = {39}, -pages = {12448--58}, -pmid = {15449934}, -title = {{Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/15449934}, -volume = {43}, -year = {2004} -} -@article{Radestock2011, -abstract = {We probe the hypothesis of corresponding states, according to which homologues from mesophilic and thermophilic organisms are in corresponding states of similar rigidity and flexibility at their respective optimal temperatures. For this, the local distribution of flexible and rigid regions in 19 pairs of homologous proteins from meso- and thermophilic organisms is analyzed and related to activity characteristics of the enzymes by constraint network analysis (CNA). Two pairs of enzymes are considered in more detail: 3-isopropylmalate dehydrogenase and thermolysin-like protease. By comparing microscopic stability features of homologues with the help of stability maps, introduced for the first time, we show that adaptive mutations in enzymes from thermophilic organisms maintain the balance between overall rigidity, important for thermostability, and local flexibility, important for activity, at the appropriate working temperature. Thermophilic adaptation in general leads to an increase of structural rigidity but conserves the distribution of functionally important flexible regions between homologues. This finding provides direct evidence for the hypothesis of corresponding states. CNA thereby implicitly captures and unifies many different mechanisms that contribute to increased thermostability and to activity at high temperatures. This allows to qualitatively relate changes in the flexibility of active site regions, induced either by a temperature change or by the introduction of mutations, to experimentally observed losses of the enzyme function. As for applications, the results demonstrate that exploiting the principle of corresponding states not only allows for successful thermostability optimization but also for guiding experiments in order to improve enzyme activity in protein engineering.}, -author = {Radestock, S. and Gohlke, H.}, -doi = {10.1002/prot.22946}, -file = {:home/alex/Dokumente/Mendeley Desktop/Radestock, Gohlke/Proteins/Radestock, Gohlke - 2011 - Protein rigidity and thermophilic adaptation.pdf:pdf}, -issn = {1097-0134}, -journal = {Proteins}, -month = apr, -number = {4}, -pages = {1089--108}, -pmid = {21246632}, -title = {{Protein rigidity and thermophilic adaptation.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/21246632}, -volume = {79}, +number = {10}, +pages = {2666--79}, +pmid = {21910474}, +title = {{Pocket-space maps to identify novel binding-site conformations in proteins.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/21910474}, +volume = {51}, year = {2011} } @article{Cosenza2002, @@ -1164,62 +280,6 @@ title = {{On the origin of biochemistry at an alkaline hydrothermal vent}}, volume = {362}, year = {2007} } -@article{Martin2003a, -author = {Martin, W. and Russell, M. J.}, -doi = {10.1098/rstb.2002.1183}, -file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2003 - On the origins of cells a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.pdf:pdf}, -issn = {0962-8436}, -journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = jan, -number = {1429}, -pages = {59--85}, -shorttitle = {On the origins of cells}, -title = {{On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells}}, -url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183}, -volume = {358}, -year = {2003} -} -@book{Berg2007a, -address = {M\"{u}nchen; Heidelberg}, -author = {Berg, Jeremy and Stryer, Lubert and Tymoczko, John L}, -edition = {6. Aufl.}, -isbn = {9783827418005}, -keywords = {Folder - Biochemie}, -mendeley-tags = {Folder - Biochemie}, -publisher = {Spektrum Akademischer Verlag}, -title = {{Biochemie}}, -year = {2007} -} -@misc{TheMendeleySupportTeam2011b, -abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, -address = {London}, -author = {{The Mendeley Support Team}}, -booktitle = {Mendeley Desktop}, -file = {:home/alex/Dokumente/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley.pdf:pdf}, -keywords = {Mendeley,how-to,user manual}, -pages = {1--16}, -publisher = {Mendeley Ltd.}, -title = {{Getting Started with Mendeley}}, -url = {http://www.mendeley.com}, -year = {2011} -} -@article{Nakanishi2003, -author = {Nakanishi, Tsugumi and Ohki, Yasushi and Oda, Jun'ichi and Matsuoka, Makoto and Sakata, Kanzo and Kato, Hiroaki}, -doi = {10.1107/S0907444903026179}, -file = {:home/alex/Dokumente/Mendeley Desktop/Nakanishi et al/Acta Crystallographica Section D Biological Crystallography/Nakanishi et al. - 2003 - Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize.pdf:pdf}, -isbn = {0907444903}, -issn = {0907-4449}, -journal = {Acta Crystallographica Section D Biological Crystallography}, -month = dec, -number = {1}, -pages = {193--194}, -title = {{Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize}}, -url = {http://scripts.iucr.org/cgi-bin/paper?S0907444903026179}, -volume = {60}, -year = {2003} -} @article{Gilbert1986, author = {Gilbert, Walter}, doi = {10.1038/319618a0}, @@ -1237,6 +297,48 @@ url = {http://www.nature.com/doifinder/10.1038/319618a0}, volume = {319}, year = {1986} } +@article{Formaneck2006, +abstract = {A combination of thirty-two 10-ns-scale molecular dynamics simulations were used to explore the coupling between conformational transition and phosphorylation in the bacteria chemotaxis Y protein (CheY), as a simple but representative example of protein allostery. Results from these simulations support an activation mechanism in which the beta4-alpha4 loop, at least partially, gates the isomerization of Tyr106. The roles of phosphorylation and the conserved Thr87 are deemed indirect in that they stabilize the active configuration of the beta4-alpha4 loop. The indirect role of the activation event (phosphorylation) and/or conserved residues in stabilizing, rather than causing, specific conformational transition is likely a feature in many signaling systems. The current analysis of CheY also helps to make clear that neither the "old" (induced fit) nor the "new" (population shift) views for protein allostery are complete, because they emphasize the kinetic (mechanistic) and thermodynamic aspects of allosteric transitions, respectively. In this regard, an issue that warrants further analysis concerns the interplay of concerted collective motion and sequential local structural changes in modulating cooperativity between distant sites in biomolecules.}, +author = {Formaneck, Mark S and Ma, Liang and Cui, Qiang}, +doi = {10.1002/prot.20893}, +file = {:home/alex/Dokumente/Mendeley Desktop/Formaneck, Ma, Cui/Proteins/Formaneck, Ma, Cui - 2006 - Reconciling the old and new views of protein allostery a molecular simulation study of chemotaxis Y protein (CheY).pdf:pdf}, +issn = {1097-0134}, +journal = {Proteins}, +keywords = {Allosteric Regulation,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Chemotaxis,Computer Simulation,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: metabolism,Models,Molecular,Mutation,Mutation: genetics,Phosphorylation,Protein Binding,Protein Structure,Tertiary,Threonine,Threonine: genetics,Threonine: metabolism,Tyrosine,Tyrosine: metabolism}, +month = jun, +number = {4}, +pages = {846--67}, +pmid = {16475196}, +title = {{Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/16475196}, +volume = {63}, +year = {2006} +} +@article{Ellington2009, +author = {Ellington, A. D and Chen, X. and Robertson, M. and Syrett, A.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Ellington et al/The international journal of biochemistry \& cell biology/Ellington et al. - 2009 - Evolutionary origins and directed evolution of RNA.pdf:pdf}, +journal = {The international journal of biochemistry \& cell biology}, +number = {2}, +pages = {254--265}, +title = {{Evolutionary origins and directed evolution of RNA}}, +volume = {41}, +year = {2009} +} +@article{Nakanishi2003, +author = {Nakanishi, Tsugumi and Ohki, Yasushi and Oda, Jun'ichi and Matsuoka, Makoto and Sakata, Kanzo and Kato, Hiroaki}, +doi = {10.1107/S0907444903026179}, +file = {:home/alex/Dokumente/Mendeley Desktop/Nakanishi et al/Acta Crystallographica Section D Biological Crystallography/Nakanishi et al. - 2003 - Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize.pdf:pdf}, +isbn = {0907444903}, +issn = {0907-4449}, +journal = {Acta Crystallographica Section D Biological Crystallography}, +month = dec, +number = {1}, +pages = {193--194}, +title = {{Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize}}, +url = {http://scripts.iucr.org/cgi-bin/paper?S0907444903026179}, +volume = {60}, +year = {2003} +} @article{Cochrane2008, author = {Cochrane, J. C. and Strobel, S. A.}, doi = {10.1261/rna.908408}, @@ -1269,116 +371,18 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/1992167}, volume = {217}, year = {1991} } -@article{Popovych2006, -abstract = {Allosteric interactions are typically considered to proceed through a series of discrete changes in bonding interactions that alter the protein conformation. Here we show that allostery can be mediated exclusively by transmitted changes in protein motions. We have characterized the negatively cooperative binding of cAMP to the dimeric catabolite activator protein (CAP) at discrete conformational states. Binding of the first cAMP to one subunit of a CAP dimer has no effect on the conformation of the other subunit. The dynamics of the system, however, are modulated in a distinct way by the sequential ligand binding process, with the first cAMP partially enhancing and the second cAMP completely quenching protein motions. As a result, the second cAMP binding incurs a pronounced conformational entropic penalty that is entirely responsible for the observed cooperativity. The results provide strong support for the existence of purely dynamics-driven allostery.}, -author = {Popovych, Nataliya and Sun, Shangjin and Ebright, Richard H and Kalodimos, Charalampos G}, -doi = {10.1038/nsmb1132}, -issn = {1545-9993}, -journal = {Nature structural \& molecular biology}, -keywords = {Allosteric Regulation,Biological,Biomolecular,Cyclic AMP,Cyclic AMP Receptor Protein,Cyclic AMP Receptor Protein: chemistry,Cyclic AMP Receptor Protein: metabolism,Cyclic AMP: metabolism,Entropy,Escherichia coli,Escherichia coli: metabolism,Models,Nuclear Magnetic Resonance,Protein Binding,Protein Structure,Protein Subunits,Protein Subunits: chemistry,Secondary}, -month = sep, -number = {9}, -pages = {831--8}, -pmid = {16906160}, -title = {{Dynamically driven protein allostery.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2757644\&tool=pmcentrez\&rendertype=abstract}, -volume = {13}, -year = {2006} -} -@article{Chastain1997a, -abstract = {Pyruvate, orthophosphate dikinase (PPDK; E.C. 2.7.9.1) catalyzes the synthesis of the primary inorganic carbon acceptor, phosphoenolpyruvate in the C4 photosynthetic pathway and is reversibly regulated by light. PPDK regulatory protein (RP), a bifunctional serine/threonine kinase-phosphatase, catalyzes both the ADP-dependent inactivation and the Pi-dependent activation of PPDK. Attempts to clone the RP have to date proven unsuccessful. A bioinformatics approach was taken to identify the nucleotide and amino acid sequence of the protein. Based on previously established characteristics including molecular mass, known inter- and intracellular location, functionality, and low level of expression, available databases were interrogated to ultimately identify a single candidate gene. In this paper, we describe the nucleotide and deduced amino acid sequence of this gene and establish its identity as maize PPDK RP by in vitro analysis of its catalytic properties via the cloning and expression of the recombinant protein.}, -author = {Burnell, Jim N and Chastain, Chris J.}, -doi = {10.1016/j.bbrc.2006.04.150}, -file = {:home/alex/Dokumente/Mendeley Desktop/Burnell, Chastain/Biochemical and biophysical research communications/Burnell, Chastain - 2006 - Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.pdf:pdf}, -issn = {0006-291X}, -journal = {Biochemical and biophysical research communications}, -keywords = {Amino Acid Sequence,Base Sequence,Catalysis,Cloning,Computational Biology,Extracellular Space,Extracellular Space: metabolism,Gene Expression Regulation,Intracellular Space,Intracellular Space: metabolism,Molecular Sequence Data,Organism,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Plant,Plant Leaves,Plant Leaves: genetics,Plant Leaves: metabolism,Pyruvate,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Zea mays,Zea mays: genetics}, -month = jun, -number = {2}, -pages = {675--80}, -pmid = {16696949}, -publisher = {Federation of European Biochemical Societies}, -title = {{Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397008843 http://www.ncbi.nlm.nih.gov/pubmed/16696949}, -volume = {345}, -year = {2006} -} -@article{Deng2009a, -abstract = {We report the binding free energy calculation and its decomposition for the complexes of alpha-lytic protease and its protein inhibitors using molecular dynamics simulation. Standard mechanism serine protease inhibitors eglin C and OMTKY3 are known to have strong binding affinity for many serine proteases. Their binding loops have significant similarities, including a common P1 Leu as the main anchor in the binding interface. However, recent experiments demonstrate that the two inhibitors have vastly different affinity towards alpha-lytic protease (ALP), a bacterial serine protease. OMTKY3 inhibits the enzyme much more weakly (by approximately 10(6) times) than eglin C. Moreover, a variant of OMTKY3 with five mutations, OMTKY3M, has been shown to inhibit 10(4) times more strongly than the wild-type inhibitor. The underlying mechanisms for the unusually large difference in binding affinities and the effect of mutation are not well understood. Here we use molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to investigate quantitatively the binding specificity. The calculated absolute binding free energies correctly differentiate the thermodynamic stabilities of these protein complexes, but the magnitudes of the binding affinities are systematically overestimated. Analysis of the binding free energy components provides insights into the molecular mechanism of binding specificity. The large DeltaDeltaG(bind) between eglin C and wild type OMTKY3 towards ALP is mainly attributable to the stronger nonpolar interactions in the ALP-eglin C complex, arising from a higher degree of structural complementarity. Here the electrostatic interaction contributes to a lesser extent. The enhanced inhibition in the penta-mutant OMTKY3M over its wild type is entirely due to an overall improvement in the solvent-mediated electrostatic interactions in the ALP-OMTKY3M complex. The results suggest that for these protein-complexes and similar enzyme-inhibitor systems (1) the binding is driven by nonpolar interactions, opposed by overall electrostatic and solute entropy contributions; (2) binding specificity can be tuned by improving the complementarity in electrostatics between two associating proteins. Binding free energy decomposition into contributions from individual protein residues provides additional detailed information on the structural determinants and subtle conformational changes responsible for the binding specificity.}, -author = {Deng, Nan-Jie and Cieplak, Piotr}, -doi = {10.1039/b820961h}, -file = {:home/alex/Dokumente/Mendeley Desktop/Deng, Cieplak/Physical chemistry chemical physics PCCP/Deng, Cieplak - 2009 - Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins binding free energy from molecular dynamics simulation.pdf:pdf}, -issn = {1463-9076}, -journal = {Physical chemistry chemical physics : PCCP}, -keywords = {Binding Sites,Computer Simulation,Models, Molecular,Protease Inhibitors,Protease Inhibitors: chemistry,Quantum Theory,Substrate Specificity,Thermodynamics}, -month = jul, -number = {25}, -pages = {4968--81}, -pmid = {19562127}, -title = {{Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/19562127}, -volume = {11}, -year = {2009} -} -@article{Formaneck2006, -abstract = {A combination of thirty-two 10-ns-scale molecular dynamics simulations were used to explore the coupling between conformational transition and phosphorylation in the bacteria chemotaxis Y protein (CheY), as a simple but representative example of protein allostery. Results from these simulations support an activation mechanism in which the beta4-alpha4 loop, at least partially, gates the isomerization of Tyr106. The roles of phosphorylation and the conserved Thr87 are deemed indirect in that they stabilize the active configuration of the beta4-alpha4 loop. The indirect role of the activation event (phosphorylation) and/or conserved residues in stabilizing, rather than causing, specific conformational transition is likely a feature in many signaling systems. The current analysis of CheY also helps to make clear that neither the "old" (induced fit) nor the "new" (population shift) views for protein allostery are complete, because they emphasize the kinetic (mechanistic) and thermodynamic aspects of allosteric transitions, respectively. In this regard, an issue that warrants further analysis concerns the interplay of concerted collective motion and sequential local structural changes in modulating cooperativity between distant sites in biomolecules.}, -author = {Formaneck, Mark S and Ma, Liang and Cui, Qiang}, -doi = {10.1002/prot.20893}, -file = {:home/alex/Dokumente/Mendeley Desktop/Formaneck, Ma, Cui/Proteins/Formaneck, Ma, Cui - 2006 - Reconciling the old and new views of protein allostery a molecular simulation study of chemotaxis Y protein (CheY).pdf:pdf}, -issn = {1097-0134}, -journal = {Proteins}, -keywords = {Allosteric Regulation,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Chemotaxis,Computer Simulation,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: metabolism,Models,Molecular,Mutation,Mutation: genetics,Phosphorylation,Protein Binding,Protein Structure,Tertiary,Threonine,Threonine: genetics,Threonine: metabolism,Tyrosine,Tyrosine: metabolism}, -month = jun, -number = {4}, -pages = {846--67}, -pmid = {16475196}, -title = {{Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/16475196}, -volume = {63}, -year = {2006} -} -@article{Craig2011, -abstract = {The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads ).}, -author = {Craig, Ian R and Pfleger, Christopher and Gohlke, Holger and Essex, Jonathan W and Spiegel, Katrin}, -doi = {10.1021/ci200168b}, -file = {:home/alex/Dokumente/Mendeley Desktop/Craig et al/Journal of chemical information and modeling/Craig et al. - 2011 - Pocket-space maps to identify novel binding-site conformations in proteins.pdf:pdf}, -issn = {1549-960X}, -journal = {Journal of chemical information and modeling}, -month = oct, -number = {10}, -pages = {2666--79}, -pmid = {21910474}, -title = {{Pocket-space maps to identify novel binding-site conformations in proteins.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/21910474}, -volume = {51}, -year = {2011} -} -@article{Ellington2009, -author = {Ellington, A. D and Chen, X. and Robertson, M. and Syrett, A.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Ellington et al/The international journal of biochemistry \& cell biology/Ellington et al. - 2009 - Evolutionary origins and directed evolution of RNA.pdf:pdf}, -journal = {The international journal of biochemistry \& cell biology}, -number = {2}, -pages = {254--265}, -title = {{Evolutionary origins and directed evolution of RNA}}, -volume = {41}, -year = {2009} -} -@article{Petit2009, -abstract = {Structure-function relationships in proteins are predicated on the spatial proximity of noncovalently interacting groups of atoms. Thus, structural elements located away from a protein's active site are typically presumed to serve a stabilizing or scaffolding role for the larger structure. Here we report a functional role for a distal structural element in a PDZ domain, even though it is not required to maintain PDZ structure. The third PDZ domain from PSD-95/SAP90 (PDZ3) has an unusual additional third alpha helix (alpha3) that packs in contiguous fashion against the globular domain. Although alpha3 lies outside the active site and does not make direct contact with C-terminal peptide ligand, removal of alpha3 reduces ligand affinity by 21-fold. Further investigation revealed that the difference in binding free energies between the full-length and truncated constructs is predominantly entropic in nature and that without alpha3, picosecond-nanosecond side-chain dynamics are enhanced throughout the domain, as determined by (2)H methyl NMR relaxation. Thus, the distal modulation of binding function appears to occur via a delocalized conformational entropy mechanism. Without removal of alpha3 and characterization of side-chain dynamics, this dynamic allostery would have gone unnoticed. Moreover, what appeared at first to be an artificial modification of PDZ3 has been corroborated by experimentally verified phosphorylation of alpha3, revealing a tangible biological mechanism for this novel regulatory scheme. This hidden dynamic allostery raises the possibility of as-yet unidentified or untapped allosteric regulation in this PDZ domain and is a very clear example of function arising from dynamics rather than from structure.}, -author = {Petit, Chad M and Zhang, Jun and Sapienza, Paul J and Fuentes, Ernesto J and Lee, Andrew L}, -doi = {10.1073/pnas.0904492106}, -file = {:home/alex/Dokumente/Mendeley Desktop/Petit et al/Proceedings of the National Academy of Sciences of the United States of America/Petit et al. - 2009 - Hidden dynamic allostery in a PDZ domain.pdf:pdf}, -issn = {1091-6490}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Allosteric Regulation,Animals,Biomolecular,Intracellular Signaling Peptides and Proteins,Intracellular Signaling Peptides and Proteins: che,Intracellular Signaling Peptides and Proteins: met,Ligands,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: metabolism,Models,Molecular,Nuclear Magnetic Resonance,PDZ Domains,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: metabolism,Protein Binding,Protein Structure,Rats,Secondary,Thermodynamics}, -month = oct, -number = {43}, -pages = {18249--54}, -pmid = {19828436}, -title = {{Hidden dynamic allostery in a PDZ domain.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2775317\&tool=pmcentrez\&rendertype=abstract}, -volume = {106}, -year = {2009} +@article{Bleecker2000, +author = {Bleecker, A. B and Kende, H.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Bleecker, Kende/Annual Review of Cell and Developmental Biology/Bleecker, Kende - 2000 - ETHYLENE A Gaseous Signal Molecule in Plants.1:1}, +journal = {Annual Review of Cell and Developmental Biology}, +keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +number = {1}, +pages = {1--18}, +shorttitle = {ETHYLENE}, +title = {{ETHYLENE: A Gaseous Signal Molecule in Plants}}, +volume = {16}, +year = {2000} } @article{Sali1993, abstract = {We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.}, @@ -1397,33 +401,21 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/8254673}, volume = {234}, year = {1993} } -@article{Bleecker2000, -author = {Bleecker, A. B and Kende, H.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Bleecker, Kende/Annual Review of Cell and Developmental Biology/Bleecker, Kende - 2000 - ETHYLENE A Gaseous Signal Molecule in Plants.1:1}, -journal = {Annual Review of Cell and Developmental Biology}, -keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, -number = {1}, -pages = {1--18}, -shorttitle = {ETHYLENE}, -title = {{ETHYLENE: A Gaseous Signal Molecule in Plants}}, -volume = {16}, -year = {2000} -} -@article{Schreiner2011, -author = {Schreiner, Eduard and Nair, Nisanth N. and Wittekindt, Carsten and Marx, Dominik}, -doi = {10.1021/ja111503z}, -file = {:home/alex/Dokumente/Mendeley Desktop/Schreiner et al/Journal of the American Chemical Society/Schreiner et al. - 2011 - Peptide Synthesis in Aqueous Environments The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides.pdf:pdf}, -issn = {0002-7863}, -journal = {Journal of the American Chemical Society}, -month = jun, -number = {21}, -pages = {8216--8226}, -shorttitle = {Peptide Synthesis in Aqueous Environments}, -title = {{Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides}}, -url = {http://pubs.acs.org/doi/abs/10.1021/ja111503z}, -volume = {133}, -year = {2011} +@article{Popovych2006, +abstract = {Allosteric interactions are typically considered to proceed through a series of discrete changes in bonding interactions that alter the protein conformation. Here we show that allostery can be mediated exclusively by transmitted changes in protein motions. We have characterized the negatively cooperative binding of cAMP to the dimeric catabolite activator protein (CAP) at discrete conformational states. Binding of the first cAMP to one subunit of a CAP dimer has no effect on the conformation of the other subunit. The dynamics of the system, however, are modulated in a distinct way by the sequential ligand binding process, with the first cAMP partially enhancing and the second cAMP completely quenching protein motions. As a result, the second cAMP binding incurs a pronounced conformational entropic penalty that is entirely responsible for the observed cooperativity. The results provide strong support for the existence of purely dynamics-driven allostery.}, +author = {Popovych, Nataliya and Sun, Shangjin and Ebright, Richard H and Kalodimos, Charalampos G}, +doi = {10.1038/nsmb1132}, +issn = {1545-9993}, +journal = {Nature structural \& molecular biology}, +keywords = {Allosteric Regulation,Biological,Biomolecular,Cyclic AMP,Cyclic AMP Receptor Protein,Cyclic AMP Receptor Protein: chemistry,Cyclic AMP Receptor Protein: metabolism,Cyclic AMP: metabolism,Entropy,Escherichia coli,Escherichia coli: metabolism,Models,Nuclear Magnetic Resonance,Protein Binding,Protein Structure,Protein Subunits,Protein Subunits: chemistry,Secondary}, +month = sep, +number = {9}, +pages = {831--8}, +pmid = {16906160}, +title = {{Dynamically driven protein allostery.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2757644\&tool=pmcentrez\&rendertype=abstract}, +volume = {13}, +year = {2006} } @article{Goodey2008a, abstract = {Allosteric regulation of protein function is a mechanism by which an event in one place of a protein structure causes an effect at another site, much like the behavior of a telecommunications network in which a collection of transmitters, receivers and transceivers communicate with each other across long distances. For example, ligand binding or an amino acid mutation at an allosteric site can alter enzymatic activity or binding affinity in a distal region such as the active site or a second binding site. The mechanism of this site-to-site communication is of great interest, especially since allosteric effects must be considered in drug design and protein engineering. In this review, conformational mobility as the common route between allosteric regulation and catalysis is discussed. We summarize recent experimental data and the resulting insights into allostery within proteins, and we discuss the nature of future studies and the new applications that may result from increased understanding of this regulatory mechanism.}, @@ -1455,17 +447,38 @@ title = {{Involvement of RTE1 in conformational changes promoting ETR1 ethylene volume = {56}, year = {2008} } -@article{Rathi2012, -abstract = {We apply Constraint Network Analysis (CNA) to investigate the relationship between structural rigidity and thermostability of five citrate synthase (CS) structures over a temperature range from 37°C to 100°C. For the first time, we introduce an ensemble-based variant of CNA and model the temperature-dependence of hydrophobic interactions in the constraint network. A very good correlation between the predicted thermostabilities of CS and optimal growth temperatures of their source organisms (R(2)=0.88, p=0.017) is obtained, which validates that CNA is able to quantitatively discriminate between less and more thermostable proteins even within a series of orthologs. Structural weak spots on a less thermostable CS, predicted by CNA to be in the top 5\% with respect to the frequency of occurrence over an ensemble, have a higher mutation ratio in a more thermostable CS than other sequence positions. Furthermore, highly ranked weak spots that are also highly conserved with respect to the amino acid type found at that sequence position are nevertheless found to be mutated in the more stable CS. As for mechanisms at an atomic level that lead to a reinforcement of weak spots in more stable CS, we observe that the thermophilic CS achieve a higher thermostability by better hydrogen bonding networks whereas hyperthermophilic CS incorporate more hydrophobic contacts to reach the same goal. Overall, these findings suggest that CNA can be applied as a pre-filter in data-driven protein engineering to focus on residues that are highly likely to improve thermostability upon mutation.}, -author = {Rathi, Prakash C and Radestock, Sebastian and Gohlke, Holger}, -doi = {10.1016/j.jbiotec.2012.01.027}, -issn = {1873-4863}, -journal = {Journal of biotechnology}, -month = feb, -pmid = {22326626}, -title = {{Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/22326626}, -year = {2012} +@article{Schreiner2011, +author = {Schreiner, Eduard and Nair, Nisanth N. and Wittekindt, Carsten and Marx, Dominik}, +doi = {10.1021/ja111503z}, +file = {:home/alex/Dokumente/Mendeley Desktop/Schreiner et al/Journal of the American Chemical Society/Schreiner et al. - 2011 - Peptide Synthesis in Aqueous Environments The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides.pdf:pdf}, +issn = {0002-7863}, +journal = {Journal of the American Chemical Society}, +month = jun, +number = {21}, +pages = {8216--8226}, +shorttitle = {Peptide Synthesis in Aqueous Environments}, +title = {{Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides}}, +url = {http://pubs.acs.org/doi/abs/10.1021/ja111503z}, +volume = {133}, +year = {2011} +} +@article{Chastain1997a, +abstract = {Pyruvate, orthophosphate dikinase (PPDK; E.C. 2.7.9.1) catalyzes the synthesis of the primary inorganic carbon acceptor, phosphoenolpyruvate in the C4 photosynthetic pathway and is reversibly regulated by light. PPDK regulatory protein (RP), a bifunctional serine/threonine kinase-phosphatase, catalyzes both the ADP-dependent inactivation and the Pi-dependent activation of PPDK. Attempts to clone the RP have to date proven unsuccessful. A bioinformatics approach was taken to identify the nucleotide and amino acid sequence of the protein. Based on previously established characteristics including molecular mass, known inter- and intracellular location, functionality, and low level of expression, available databases were interrogated to ultimately identify a single candidate gene. In this paper, we describe the nucleotide and deduced amino acid sequence of this gene and establish its identity as maize PPDK RP by in vitro analysis of its catalytic properties via the cloning and expression of the recombinant protein.}, +author = {Burnell, Jim N and Chastain, Chris J.}, +doi = {10.1016/j.bbrc.2006.04.150}, +file = {:home/alex/Dokumente/Mendeley Desktop/Burnell, Chastain/Biochemical and biophysical research communications/Burnell, Chastain - 2006 - Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.pdf:pdf}, +issn = {0006-291X}, +journal = {Biochemical and biophysical research communications}, +keywords = {Amino Acid Sequence,Base Sequence,Catalysis,Cloning,Computational Biology,Extracellular Space,Extracellular Space: metabolism,Gene Expression Regulation,Intracellular Space,Intracellular Space: metabolism,Molecular Sequence Data,Organism,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Plant,Plant Leaves,Plant Leaves: genetics,Plant Leaves: metabolism,Pyruvate,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Zea mays,Zea mays: genetics}, +month = jun, +number = {2}, +pages = {675--80}, +pmid = {16696949}, +publisher = {Federation of European Biochemical Societies}, +title = {{Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397008843 http://www.ncbi.nlm.nih.gov/pubmed/16696949}, +volume = {345}, +year = {2006} } @article{Smith1985, author = {Smith, P and Krohn, R and Hermanson, G and Mallia, A and Gartner, F and Provenzano, M and Fujimoto, E and Goeke, N and Olson, B and Klenk, D}, @@ -1498,6 +511,23 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/6544679}, volume = {11}, year = {1984} } +@article{Deng2009a, +abstract = {We report the binding free energy calculation and its decomposition for the complexes of alpha-lytic protease and its protein inhibitors using molecular dynamics simulation. Standard mechanism serine protease inhibitors eglin C and OMTKY3 are known to have strong binding affinity for many serine proteases. Their binding loops have significant similarities, including a common P1 Leu as the main anchor in the binding interface. However, recent experiments demonstrate that the two inhibitors have vastly different affinity towards alpha-lytic protease (ALP), a bacterial serine protease. OMTKY3 inhibits the enzyme much more weakly (by approximately 10(6) times) than eglin C. Moreover, a variant of OMTKY3 with five mutations, OMTKY3M, has been shown to inhibit 10(4) times more strongly than the wild-type inhibitor. The underlying mechanisms for the unusually large difference in binding affinities and the effect of mutation are not well understood. Here we use molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to investigate quantitatively the binding specificity. The calculated absolute binding free energies correctly differentiate the thermodynamic stabilities of these protein complexes, but the magnitudes of the binding affinities are systematically overestimated. Analysis of the binding free energy components provides insights into the molecular mechanism of binding specificity. The large DeltaDeltaG(bind) between eglin C and wild type OMTKY3 towards ALP is mainly attributable to the stronger nonpolar interactions in the ALP-eglin C complex, arising from a higher degree of structural complementarity. Here the electrostatic interaction contributes to a lesser extent. The enhanced inhibition in the penta-mutant OMTKY3M over its wild type is entirely due to an overall improvement in the solvent-mediated electrostatic interactions in the ALP-OMTKY3M complex. The results suggest that for these protein-complexes and similar enzyme-inhibitor systems (1) the binding is driven by nonpolar interactions, opposed by overall electrostatic and solute entropy contributions; (2) binding specificity can be tuned by improving the complementarity in electrostatics between two associating proteins. Binding free energy decomposition into contributions from individual protein residues provides additional detailed information on the structural determinants and subtle conformational changes responsible for the binding specificity.}, +author = {Deng, Nan-Jie and Cieplak, Piotr}, +doi = {10.1039/b820961h}, +file = {:home/alex/Dokumente/Mendeley Desktop/Deng, Cieplak/Physical chemistry chemical physics PCCP/Deng, Cieplak - 2009 - Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins binding free energy from molecular dynamics simulation.pdf:pdf}, +issn = {1463-9076}, +journal = {Physical chemistry chemical physics : PCCP}, +keywords = {Binding Sites,Computer Simulation,Models, Molecular,Protease Inhibitors,Protease Inhibitors: chemistry,Quantum Theory,Substrate Specificity,Thermodynamics}, +month = jul, +number = {25}, +pages = {4968--81}, +pmid = {19562127}, +title = {{Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/19562127}, +volume = {11}, +year = {2009} +} @book{Wedler2004, address = {Weinheim}, author = {Wedler, Gerd}, @@ -1524,23 +554,6 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/16280617}, volume = {2}, year = {2005} } -@article{Nechushtai2011a, -abstract = {Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.}, -author = {Nechushtai, Rachel and Lammert, Heiko and Michaeli, Dorit and Eisenberg-Domovich, Yael and Zuris, John A and Luca, Maria A and Capraro, Dominique T and Fish, Alex and Shimshon, Odelia and Roy, Melinda and Schug, Alexander and Whitford, Paul C and Livnah, Oded and Onuchic, Jos\'{e} N and Jennings, Patricia A}, -doi = {10.1073/pnas.1019502108}, -file = {:home/alex/Dokumente/Mendeley Desktop/Nechushtai et al/Proceedings of the National Academy of Sciences of the United States of America/Nechushtai et al. - 2011 - Allostery in the ferredoxin protein motif does not involve a conformational switch.pdf:pdf}, -issn = {1091-6490}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Allosteric Regulation,Allosteric Regulation: physiology,Amino Acid Motifs,Ferredoxins,Ferredoxins: chemistry,Ferredoxins: genetics,Ferredoxins: metabolism,Humans,Iron,Iron: chemistry,Iron: metabolism,Models,Molecular,Mutation,Protein Folding,Protein Stability,Protein Structure,Sulfur,Sulfur: chemistry,Sulfur: metabolism,Tertiary}, -month = feb, -number = {6}, -pages = {2240--5}, -pmid = {21266547}, -title = {{Allostery in the ferredoxin protein motif does not involve a conformational switch.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=pmcentrez\&rendertype=abstract}, -volume = {108}, -year = {2011} -} @article{Li2007a, abstract = {We describe a new cloning method, sequence and ligation-independent cloning (SLIC), which allows the assembly of multiple DNA fragments in a single reaction using in vitro homologous recombination and single-strand annealing. SLIC mimics in vivo homologous recombination by relying on exonuclease-generated ssDNA overhangs in insert and vector fragments, and the assembly of these fragments by recombination in vitro. SLIC inserts can also be prepared by incomplete PCR (iPCR) or mixed PCR. SLIC allows efficient and reproducible assembly of recombinant DNA with as many as 5 and 10 fragments simultaneously. SLIC circumvents the sequence requirements of traditional methods and functions much more efficiently at very low DNA concentrations when combined with RecA to catalyze homologous recombination. This flexibility allows much greater versatility in the generation of recombinant DNA for the purposes of synthetic biology.}, author = {Li, Mamie Z and Elledge, Stephen J}, @@ -1565,17 +578,16 @@ title = {{AMBER 11}}, url = {http://www.ambermd.org}, year = {2010} } -@article{Burnell1990, -abstract = {Pyruvate,Pi dikinase (PPDK) was isolated and purified from the leaf tissue of a number of Flaveria species and the cold lability of the purified enzymes studied. The PPDK from F. brownii (a C3/C4 intermediate species) showed a high level of stability compared to other Flaveria species.}, -author = {Burnell, James N}, -file = {:home/alex/Dokumente/Mendeley Desktop/Burnell/Plant Cell Physiol/Burnell - 1990 - A Comparative Study of the Cold-Sensitivity of Pyruvate,Pi Dikinase in Flaveria Species.pdf:pdf}, -journal = {Plant Cell Physiol.}, -keywords = {1,7,9,c 4,c 4 plants,catalyses,cold lability,ec 2,flaveria,ic carbon acceptor in,pi dikinase,pj dikinase,ppdk,pyruvate,slack and hatch 1967,the primary inorgan-,the synthesis of phosphoenolpyruvate}, -number = {2}, -pages = {295--297}, -title = {{A Comparative Study of the Cold-Sensitivity of Pyruvate,Pi Dikinase in Flaveria Species}}, -volume = {31}, -year = {1990} +@article{Pizzarello2007, +author = {Pizzarello, S.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Pizzarello/Chemistry \& biodiversity/Pizzarello - 2007 - The chemistry that preceded life's origin A study guide from meteorites.pdf:pdf}, +journal = {Chemistry \& biodiversity}, +number = {4}, +pages = {680--693}, +shorttitle = {The chemistry that preceded life's origin}, +title = {{The chemistry that preceded life's origin: A study guide from meteorites}}, +volume = {4}, +year = {2007} } @article{Pascal2006, author = {Pascal, Robert and Boiteau, Laurent and Forterre, Patrick and Gargaud, Muriel and Lazcano, Antonio and Lopez-Garcia, Purificaci\'{o}n and Maurel, Marie-Christine and Moreira, David and Pereto, Juli and Prieur, Daniel and Reisse, Jacques}, @@ -1618,20 +630,17 @@ publisher = {Spektrum Akademischer Verlag}, title = {{Biochemie}}, year = {2007} } -@article{Fleishman2006, -author = {Fleishman, S and Bental, N}, -doi = {10.1016/j.sbi.2006.06.003}, -issn = {0959440X}, -journal = {Current Opinion in Structural Biology}, -keywords = {Folder - Biochemie,Paper}, -mendeley-tags = {Folder - Biochemie,Paper}, -month = aug, -number = {4}, -pages = {496--504}, -title = {{Progress in structure prediction of $\alpha$-helical membrane proteins}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X06001072}, -volume = {16}, -year = {2006} +@article{Rathi2012, +abstract = {We apply Constraint Network Analysis (CNA) to investigate the relationship between structural rigidity and thermostability of five citrate synthase (CS) structures over a temperature range from 37°C to 100°C. For the first time, we introduce an ensemble-based variant of CNA and model the temperature-dependence of hydrophobic interactions in the constraint network. A very good correlation between the predicted thermostabilities of CS and optimal growth temperatures of their source organisms (R(2)=0.88, p=0.017) is obtained, which validates that CNA is able to quantitatively discriminate between less and more thermostable proteins even within a series of orthologs. Structural weak spots on a less thermostable CS, predicted by CNA to be in the top 5\% with respect to the frequency of occurrence over an ensemble, have a higher mutation ratio in a more thermostable CS than other sequence positions. Furthermore, highly ranked weak spots that are also highly conserved with respect to the amino acid type found at that sequence position are nevertheless found to be mutated in the more stable CS. As for mechanisms at an atomic level that lead to a reinforcement of weak spots in more stable CS, we observe that the thermophilic CS achieve a higher thermostability by better hydrogen bonding networks whereas hyperthermophilic CS incorporate more hydrophobic contacts to reach the same goal. Overall, these findings suggest that CNA can be applied as a pre-filter in data-driven protein engineering to focus on residues that are highly likely to improve thermostability upon mutation.}, +author = {Rathi, Prakash C and Radestock, Sebastian and Gohlke, Holger}, +doi = {10.1016/j.jbiotec.2012.01.027}, +issn = {1873-4863}, +journal = {Journal of biotechnology}, +month = feb, +pmid = {22326626}, +title = {{Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/22326626}, +year = {2012} } @book{Madigan2009, address = {München [u.a.]}, @@ -1644,22 +653,6 @@ publisher = {Pearson Studium}, title = {{Brock - Mikrobiologie}}, year = {2009} } -@article{Babu2011, -author = {Babu, Mohan and Beloglazova, Natalia and Flick, Robert and Graham, Chris and Skarina, Tatiana and Nocek, Boguslaw and Gagarinova, Alla and Pogoutse, Oxana and Brown, Greg and Binkowski, Andrew and Phanse, Sadhna and Joachimiak, Andrzej and Koonin, Eugene V. and Savchenko, Alexei and Emili, Andrew and Greenblatt, Jack and Edwards, Aled M. and Yakunin, Alexander F.}, -doi = {10.1111/j.1365-2958.2010.07465.x}, -file = {:home/alex/Dokumente/Mendeley Desktop/Babu et al/Molecular Microbiology/Babu et al. - 2011 - A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.pdf:pdf}, -issn = {0950382X}, -journal = {Molecular Microbiology}, -keywords = {Folder - In-silico-structure}, -mendeley-tags = {Folder - In-silico-structure}, -month = jan, -number = {2}, -pages = {484--502}, -title = {{A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair}}, -url = {http://doi.wiley.com/10.1111/j.1365-2958.2010.07465.x}, -volume = {79}, -year = {2011} -} @book{Lakowicz2006, address = {Boston, MA}, editor = {Lakowicz, Joseph R.}, @@ -1669,23 +662,6 @@ title = {{Principles of Fluorescence Spectroscopy}}, url = {http://www.springerlink.com/index/10.1007/978-0-387-46312-4}, year = {2006} } -@article{Chen2007, -abstract = {Escherichia coli dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate. During the catalytic cycle, DHFR undergoes conformational transitions between the closed (CS) and occluded (OS) states that, respectively, describe whether the active site is closed or occluded by the Met20 loop. The CS-->OS and the reverse transition may be viewed as allosteric transitions. Using a sequence-based approach, we identify a network of residues that represents the allostery wiring diagram. Many of the residues in the allostery wiring diagram, which are dispersed throughout the adenosine-binding domain as well as the loop domain, are not conserved. Several of the residues in the network have been previously shown by NMR experiments, mutational studies, and molecular dynamics simulations to be linked to equilibration conformational fluctuations of DHFR. To further probe the nature of events that occur during conformational fluctuations, we use a self-organized polymer model to monitor the kinetics of the CS-->OS and the reverse transitions. During the CS-->OS transition, coordinated changes in a number of residues in the loop domain enable the Met20 loop to slide along the alpha-helix in the adenosine-binding domain. Sliding is triggered by pulling of the Met20 loop by the betaG-betaH loop and the pushing action of the betaG-betaH loop. The residues that facilitate the Met20 loop motion are part of the network of residues that transmit allosteric signals during the CS-->OS transition. Replacement of M16 and G121, whose C(alpha) atoms are about 4.3 A in the CS, by a disulfide cross-link impedes that CS-->OS transition. The order of events in the OS-->CS transition is not the reverse of the forward transition. The contact Glu18-Ser49 in the OS persists until the sliding of the Met20 loop is nearly complete. The ensemble of structures in the transition state in both the allosteric transitions is heterogeneous. The most probable transition-state structure resembles the OS (CS) in the CS-->OS (OS-->CS) transition, which is in accord with the Hammond postulate. Structures resembling the OS (CS) are present as minor ( approximately 1-3\%) components in equilibrated CS (OS) structures.}, -author = {Chen, Jie and Dima, Ruxandra I and Thirumalai, D}, -doi = {10.1016/j.jmb.2007.08.047}, -file = {:home/alex/Dokumente/Mendeley Desktop/Chen, Dima, Thirumalai/Journal of molecular biology/Chen, Dima, Thirumalai - 2007 - Allosteric communication in dihydrofolate reductase signaling network and pathways for closed to occluded transition and back.pdf:pdf}, -issn = {1089-8638}, -journal = {Journal of molecular biology}, -keywords = {Allosteric Regulation,Binding Sites,Catalysis,Computer Simulation,Escherichia coli,Escherichia coli: enzymology,Hydrogen Bonding,Kinetics,Models, Molecular,Mutagenesis, Site-Directed,Protein Binding,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Signal Transduction,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Tetrahydrofolate Dehydrogenase: metabolism}, -month = nov, -number = {1}, -pages = {250--66}, -pmid = {17916364}, -title = {{Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/17916364}, -volume = {374}, -year = {2007} -} @article{Orgel2008, author = {Orgel, Leslie E.}, doi = {10.1371/journal.pbio.0060018}, @@ -1719,18 +695,22 @@ url = {http://dx.plos.org/10.1371/journal.pcbi.1002168}, volume = {7}, year = {2011} } -@article{Laskowski1993, -author = {Laskowski, R. A. and MacArthur, M. W. and Moss, D. S. and Thornton, J. M.}, -doi = {10.1107/S0021889892009944}, -issn = {00218898}, -journal = {Journal of Applied Crystallography}, -month = apr, -number = {2}, -pages = {283--291}, -title = {{PROCHECK: a program to check the stereochemical quality of protein structures}}, -url = {http://scripts.iucr.org/cgi-bin/paper?S0021889892009944}, -volume = {26}, -year = {1993} +@article{Nechushtai2011a, +abstract = {Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.}, +author = {Nechushtai, Rachel and Lammert, Heiko and Michaeli, Dorit and Eisenberg-Domovich, Yael and Zuris, John A and Luca, Maria A and Capraro, Dominique T and Fish, Alex and Shimshon, Odelia and Roy, Melinda and Schug, Alexander and Whitford, Paul C and Livnah, Oded and Onuchic, Jos\'{e} N and Jennings, Patricia A}, +doi = {10.1073/pnas.1019502108}, +file = {:home/alex/Dokumente/Mendeley Desktop/Nechushtai et al/Proceedings of the National Academy of Sciences of the United States of America/Nechushtai et al. - 2011 - Allostery in the ferredoxin protein motif does not involve a conformational switch.pdf:pdf}, +issn = {1091-6490}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Allosteric Regulation,Allosteric Regulation: physiology,Amino Acid Motifs,Ferredoxins,Ferredoxins: chemistry,Ferredoxins: genetics,Ferredoxins: metabolism,Humans,Iron,Iron: chemistry,Iron: metabolism,Models,Molecular,Mutation,Protein Folding,Protein Stability,Protein Structure,Sulfur,Sulfur: chemistry,Sulfur: metabolism,Tertiary}, +month = feb, +number = {6}, +pages = {2240--5}, +pmid = {21266547}, +title = {{Allostery in the ferredoxin protein motif does not involve a conformational switch.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=pmcentrez\&rendertype=abstract}, +volume = {108}, +year = {2011} } @article{Lazcano2008, author = {Lazcano, A.}, @@ -1767,22 +747,6 @@ title = {{\"{U}ber einen in biologischer Beziehung wichtigen Einfluss, den die K volume = {16}, year = {1904} } -@article{Burnell1985, -abstract = {Pyruvate,Pi dikinase regulatory protein (PDRP) has been highly purified from maize leaves, and its role in catalyzing both ADP-mediated inactivation (due to phosphorylation of a threonine residue) and Pi-mediated activation (due to dephosphorylation by phosphorolysis) of pyruvate,Pi dikinase has been confirmed. These reactions account for the dark/light-mediated regulation of pyruvate,Pi dikinase observed in the leaves of C4 plants. During purification to apparent homogeneity the ratio of these two activities remained constant. The molecular weight of the native PDRP was about 180,000 at pH 8.3 and 90,000 at pH 7.5. Its monomeric molecular weight was 45,000. It was confirmed that inactive pyruvate,Pi dikinase free of a phosphate group on a catalytic histidine was the preferred substrate for activation. Michaelis constants for orthophosphate and the above form of active pyruvate,Pi dikinase were determined, as well as the mechanism of inhibition of the PDRP-catalyzed reaction by ATP, ADP, AMP, and PPi. For the inactivation reaction, Km values were 1.2 microM for the active pyruvate,Pi dikinase and 52 microM for ADP. CDP and GDP but not UDP could substitute for ADP. The inactivation reaction is inhibited by inactive pyruvate,Pi dikinase competitively with respect to both active pyruvate,Pi dikinase and ADP. Both the activation and inactivation reactions catalyzed by PDRP have a broad pH optimum between 7.8 and 8.3. The results are discussed in terms of the likely mechanism of dark/light regulation of pyruvate,Pi dikinase in vivo.}, -author = {Burnell, J N and Hatch, M D}, -file = {:home/alex/Dokumente/Mendeley Desktop/Burnell, Hatch/Archives of biochemistry and biophysics/Burnell, Hatch - 1985 - Regulation of C4 photosynthesis purification and properties of the protein catalyzing ADP-mediated inactivation and Pi-mediated activation of pyruvate,Pi dikinase(2).pdf:pdf}, -issn = {0003-9861}, -journal = {Archives of biochemistry and biophysics}, -keywords = {Adenosine Diphosphate,Adenosine Diphosphate: analogs \& derivatives,Adenosine Diphosphate: pharmacology,Adenosine Diphosphate: physiology,Adenosine Monophosphate,Adenosine Monophosphate: pharmacology,Catalysis,Chemical Phenomena,Chemistry,Enzyme Activation,Hydrogen-Ion Concentration,Kinetics,Molecular Weight,Orthophosphate Dikinase,Orthophosphate Dikinase: antagonists \& inhibitors,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Photosynthesis,Plant Proteins,Plant Proteins: antagonists \& inhibitors,Plant Proteins: isolation \& purification,Plant Proteins: physiology,Pyruvate,Substrate Specificity,Zea mays,Zea mays: metabolism}, -month = mar, -number = {2}, -pages = {490--503}, -pmid = {2983615}, -title = {{Regulation of C4 photosynthesis: purification and properties of the protein catalyzing ADP-mediated inactivation and Pi-mediated activation of pyruvate,Pi dikinase.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/2983615}, -volume = {237}, -year = {1985} -} @book{Lottspeich2006, address = {M\"{u}nchen ;;Heidelberg}, author = {Lottspeich, Friedrich}, @@ -1813,6 +777,18 @@ url = {http://xlink.rsc.org/?DOI=b819720b http://www.ncbi.nlm.nih.gov/pubmed/192 volume = {5}, year = {2009} } +@article{Burnell1990, +abstract = {Pyruvate,Pi dikinase (PPDK) was isolated and purified from the leaf tissue of a number of Flaveria species and the cold lability of the purified enzymes studied. The PPDK from F. brownii (a C3/C4 intermediate species) showed a high level of stability compared to other Flaveria species.}, +author = {Burnell, James N}, +file = {:home/alex/Dokumente/Mendeley Desktop/Burnell/Plant Cell Physiol/Burnell - 1990 - A Comparative Study of the Cold-Sensitivity of Pyruvate,Pi Dikinase in Flaveria Species.pdf:pdf}, +journal = {Plant Cell Physiol.}, +keywords = {1,7,9,c 4,c 4 plants,catalyses,cold lability,ec 2,flaveria,ic carbon acceptor in,pi dikinase,pj dikinase,ppdk,pyruvate,slack and hatch 1967,the primary inorgan-,the synthesis of phosphoenolpyruvate}, +number = {2}, +pages = {295--297}, +title = {{A Comparative Study of the Cold-Sensitivity of Pyruvate,Pi Dikinase in Flaveria Species}}, +volume = {31}, +year = {1990} +} @article{Orgel1968, author = {Orgel, L E}, file = {:home/alex/Dokumente/Mendeley Desktop/Orgel/Journal of Molecular Biology/Orgel - 1968 - Evolution of the genetic apparatus.pdf:pdf}, @@ -1888,37 +864,70 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/2831971 http://pubs.acs.org/doi/abs/10 volume = {27}, year = {1988} } -@article{Smith1994, -author = {Smith, Christopher M. and Sarath, Gautam and Chollet, Raymond}, -doi = {10.1007/BF00034779}, -file = {:home/alex/Dokumente/Mendeley Desktop/Smith, Sarath, Chollet/Photosynthesis Research/Smith, Sarath, Chollet - 1994 - A simple, single-tube radioisotopic assay for the phosphorylationinactivation activity of the pyruvate,orthophosphate dikinase regulatory protein.pdf:pdf}, -issn = {0166-8595}, -journal = {Photosynthesis Research}, -keywords = {c4 photosynthesis,orthophosphate dikinase regulatory,ppdk,protein,protein phosphorylation,pyruvate,radioisotopic assay}, -month = jun, -number = {3}, -pages = {295--301}, -title = {{A simple, single-tube radioisotopic assay for the phosphorylation/inactivation activity of the pyruvate,orthophosphate dikinase regulatory protein}}, -url = {http://www.springerlink.com/index/10.1007/BF00034779}, -volume = {40}, -year = {1994} -} -@article{Jacobs2001, -abstract = {Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that identifies all the rigid and flexible substructures in the protein, including overconstrained regions (with more crosslinking bonds than are needed to rigidify the region) and underconstrained or flexible regions, in which dihedral bond rotations can occur. The number of extra constraints or remaining degrees of bond-rotational freedom within a substructure quantifies its relative rigidity/flexibility and provides a flexibility index for each bond in the structure. This novel computational procedure, first used in the analysis of glassy materials, is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side-chains from analysis of a single, static three-dimensional structure. This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase.}, -author = {Jacobs, D J and Rader, A J and Kuhn, L A and Thorpe, M F}, -doi = {10.1002/prot.1081}, -file = {:home/alex/Dokumente/Mendeley Desktop/Jacobs et al/Proteins/Jacobs et al. - 2001 - Protein flexibility predictions using graph theory.pdf:pdf}, -issn = {0887-3585}, -journal = {Proteins}, -keywords = {Adenylate Kinase,Adenylate Kinase: chemistry,Algorithms,Computational Biology,Computational Biology: methods,Computer Simulation,HIV Protease,HIV Protease: chemistry,Hydrogen Bonding,Models,Molecular,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Software,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Thermodynamics}, +@article{Fleishman2006, +author = {Fleishman, S and Bental, N}, +doi = {10.1016/j.sbi.2006.06.003}, +issn = {0959440X}, +journal = {Current Opinion in Structural Biology}, +keywords = {Folder - Biochemie,Paper}, +mendeley-tags = {Folder - Biochemie,Paper}, month = aug, -number = {2}, -pages = {150--65}, -pmid = {11391777}, -title = {{Protein flexibility predictions using graph theory.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/11391777}, -volume = {44}, -year = {2001} +number = {4}, +pages = {496--504}, +title = {{Progress in structure prediction of $\alpha$-helical membrane proteins}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X06001072}, +volume = {16}, +year = {2006} +} +@article{Langmead2012, +abstract = {As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.}, +author = {Langmead, Ben and Salzberg, Steven L}, +doi = {10.1038/nmeth.1923}, +issn = {1548-7105}, +journal = {Nature methods}, +keywords = {Algorithms,Computational Biology,Computational Biology: methods,DNA,DNA: methods,Databases,Genetic,Genome,Human,Human: genetics,Humans,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis}, +month = apr, +number = {4}, +pages = {357--9}, +pmid = {22388286}, +title = {{Fast gapped-read alignment with Bowtie 2.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/22388286}, +volume = {9}, +year = {2012} +} +@article{Chen2007, +abstract = {Escherichia coli dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate. During the catalytic cycle, DHFR undergoes conformational transitions between the closed (CS) and occluded (OS) states that, respectively, describe whether the active site is closed or occluded by the Met20 loop. The CS-->OS and the reverse transition may be viewed as allosteric transitions. Using a sequence-based approach, we identify a network of residues that represents the allostery wiring diagram. Many of the residues in the allostery wiring diagram, which are dispersed throughout the adenosine-binding domain as well as the loop domain, are not conserved. Several of the residues in the network have been previously shown by NMR experiments, mutational studies, and molecular dynamics simulations to be linked to equilibration conformational fluctuations of DHFR. To further probe the nature of events that occur during conformational fluctuations, we use a self-organized polymer model to monitor the kinetics of the CS-->OS and the reverse transitions. During the CS-->OS transition, coordinated changes in a number of residues in the loop domain enable the Met20 loop to slide along the alpha-helix in the adenosine-binding domain. Sliding is triggered by pulling of the Met20 loop by the betaG-betaH loop and the pushing action of the betaG-betaH loop. The residues that facilitate the Met20 loop motion are part of the network of residues that transmit allosteric signals during the CS-->OS transition. Replacement of M16 and G121, whose C(alpha) atoms are about 4.3 A in the CS, by a disulfide cross-link impedes that CS-->OS transition. The order of events in the OS-->CS transition is not the reverse of the forward transition. The contact Glu18-Ser49 in the OS persists until the sliding of the Met20 loop is nearly complete. The ensemble of structures in the transition state in both the allosteric transitions is heterogeneous. The most probable transition-state structure resembles the OS (CS) in the CS-->OS (OS-->CS) transition, which is in accord with the Hammond postulate. Structures resembling the OS (CS) are present as minor ( approximately 1-3\%) components in equilibrated CS (OS) structures.}, +author = {Chen, Jie and Dima, Ruxandra I and Thirumalai, D}, +doi = {10.1016/j.jmb.2007.08.047}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chen, Dima, Thirumalai/Journal of molecular biology/Chen, Dima, Thirumalai - 2007 - Allosteric communication in dihydrofolate reductase signaling network and pathways for closed to occluded transition and back.pdf:pdf}, +issn = {1089-8638}, +journal = {Journal of molecular biology}, +keywords = {Allosteric Regulation,Binding Sites,Catalysis,Computer Simulation,Escherichia coli,Escherichia coli: enzymology,Hydrogen Bonding,Kinetics,Models, Molecular,Mutagenesis, Site-Directed,Protein Binding,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Signal Transduction,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Tetrahydrofolate Dehydrogenase: metabolism}, +month = nov, +number = {1}, +pages = {250--66}, +pmid = {17916364}, +title = {{Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/17916364}, +volume = {374}, +year = {2007} +} +@article{DiTommaso2011, +abstract = {This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.}, +author = {{Di Tommaso}, Paolo and Moretti, Sebastien and Xenarios, Ioannis and Orobitg, Miquel and Montanyola, Alberto and Chang, Jia-Ming and Taly, Jean-Fran\c{c}ois and Notredame, Cedric}, +doi = {10.1093/nar/gkr245}, +file = {:home/alex/Dokumente/Mendeley Desktop/Di Tommaso et al/Nucleic acids research/Di Tommaso et al. - 2011 - T-Coffee a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.pdf:pdf}, +issn = {1362-4962}, +journal = {Nucleic acids research}, +keywords = {Internet,Nucleic Acid Conformation,Protein Conformation,RNA,RNA: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, Protein,Sequence Analysis, RNA,Software}, +month = jul, +number = {Web Server issue}, +pages = {W13--7}, +pmid = {21558174}, +title = {{T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3125728\&tool=pmcentrez\&rendertype=abstract}, +volume = {39}, +year = {2011} } @article{Guckian2008, abstract = {A series of meta-substituted anilines were designed and synthesized to inhibit the interaction of LFA-1 with ICAM for the treatment of autoimmune disease. Design of these molecules was performed by utilizing a co-crystal structure for structure-based drug design. The resulting molecules were found to be potent and to possess favorable pharmaceutical properties.}, @@ -1937,6 +946,22 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/18778938}, volume = {18}, year = {2008} } +@article{Burnell1985, +abstract = {Pyruvate,Pi dikinase regulatory protein (PDRP) has been highly purified from maize leaves, and its role in catalyzing both ADP-mediated inactivation (due to phosphorylation of a threonine residue) and Pi-mediated activation (due to dephosphorylation by phosphorolysis) of pyruvate,Pi dikinase has been confirmed. These reactions account for the dark/light-mediated regulation of pyruvate,Pi dikinase observed in the leaves of C4 plants. During purification to apparent homogeneity the ratio of these two activities remained constant. The molecular weight of the native PDRP was about 180,000 at pH 8.3 and 90,000 at pH 7.5. Its monomeric molecular weight was 45,000. It was confirmed that inactive pyruvate,Pi dikinase free of a phosphate group on a catalytic histidine was the preferred substrate for activation. Michaelis constants for orthophosphate and the above form of active pyruvate,Pi dikinase were determined, as well as the mechanism of inhibition of the PDRP-catalyzed reaction by ATP, ADP, AMP, and PPi. For the inactivation reaction, Km values were 1.2 microM for the active pyruvate,Pi dikinase and 52 microM for ADP. CDP and GDP but not UDP could substitute for ADP. The inactivation reaction is inhibited by inactive pyruvate,Pi dikinase competitively with respect to both active pyruvate,Pi dikinase and ADP. Both the activation and inactivation reactions catalyzed by PDRP have a broad pH optimum between 7.8 and 8.3. The results are discussed in terms of the likely mechanism of dark/light regulation of pyruvate,Pi dikinase in vivo.}, +author = {Burnell, J N and Hatch, M D}, +file = {:home/alex/Dokumente/Mendeley Desktop/Burnell, Hatch/Archives of biochemistry and biophysics/Burnell, Hatch - 1985 - Regulation of C4 photosynthesis purification and properties of the protein catalyzing ADP-mediated inactivation and Pi-mediated activation of pyruvate,Pi dikinase(2).pdf:pdf}, +issn = {0003-9861}, +journal = {Archives of biochemistry and biophysics}, +keywords = {Adenosine Diphosphate,Adenosine Diphosphate: analogs \& derivatives,Adenosine Diphosphate: pharmacology,Adenosine Diphosphate: physiology,Adenosine Monophosphate,Adenosine Monophosphate: pharmacology,Catalysis,Chemical Phenomena,Chemistry,Enzyme Activation,Hydrogen-Ion Concentration,Kinetics,Molecular Weight,Orthophosphate Dikinase,Orthophosphate Dikinase: antagonists \& inhibitors,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Photosynthesis,Plant Proteins,Plant Proteins: antagonists \& inhibitors,Plant Proteins: isolation \& purification,Plant Proteins: physiology,Pyruvate,Substrate Specificity,Zea mays,Zea mays: metabolism}, +month = mar, +number = {2}, +pages = {490--503}, +pmid = {2983615}, +title = {{Regulation of C4 photosynthesis: purification and properties of the protein catalyzing ADP-mediated inactivation and Pi-mediated activation of pyruvate,Pi dikinase.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/2983615}, +volume = {237}, +year = {1985} +} @article{Nechushtai2011, abstract = {Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.}, author = {Nechushtai, Rachel and Lammert, Heiko and Michaeli, Dorit and Eisenberg-Domovich, Yael and Zuris, John A and Luca, Maria A and Capraro, Dominique T and Fish, Alex and Shimshon, Odelia and Roy, Melinda and Schug, Alexander and Whitford, Paul C and Livnah, Oded and Onuchic, Jos\'{e} N and Jennings, Patricia A}, @@ -1953,6 +978,21 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=p volume = {108}, year = {2011} } +@article{Smith1994, +author = {Smith, Christopher M. and Sarath, Gautam and Chollet, Raymond}, +doi = {10.1007/BF00034779}, +file = {:home/alex/Dokumente/Mendeley Desktop/Smith, Sarath, Chollet/Photosynthesis Research/Smith, Sarath, Chollet - 1994 - A simple, single-tube radioisotopic assay for the phosphorylationinactivation activity of the pyruvate,orthophosphate dikinase regulatory protein.pdf:pdf}, +issn = {0166-8595}, +journal = {Photosynthesis Research}, +keywords = {c4 photosynthesis,orthophosphate dikinase regulatory,ppdk,protein,protein phosphorylation,pyruvate,radioisotopic assay}, +month = jun, +number = {3}, +pages = {295--301}, +title = {{A simple, single-tube radioisotopic assay for the phosphorylation/inactivation activity of the pyruvate,orthophosphate dikinase regulatory protein}}, +url = {http://www.springerlink.com/index/10.1007/BF00034779}, +volume = {40}, +year = {1994} +} @misc{TheMendeleySupportTeam2011a, abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, address = {London}, @@ -1966,21 +1006,22 @@ title = {{Getting Started with Mendeley}}, url = {http://www.mendeley.com}, year = {2011} } -@article{Ernst2008, -author = {Ernst, R. and Kueppers, P. and Klein, C. M. and Schwarzmueller, T. and Kuchler, K. and Schmitt, L.}, -doi = {10.1073/pnas.0800191105}, -file = {:home/alex/Dokumente/Mendeley Desktop/Ernst et al/Proceedings of the National Academy of Sciences/Ernst et al. - 2008 - A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5.pdf:pdf}, -issn = {0027-8424}, -journal = {Proceedings of the National Academy of Sciences}, -keywords = {Folder - Biochemie}, -mendeley-tags = {Folder - Biochemie}, -month = mar, -number = {13}, -pages = {5069--5074}, -title = {{A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5}}, -url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0800191105}, -volume = {105}, -year = {2008} +@article{Jacobs2001, +abstract = {Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that identifies all the rigid and flexible substructures in the protein, including overconstrained regions (with more crosslinking bonds than are needed to rigidify the region) and underconstrained or flexible regions, in which dihedral bond rotations can occur. The number of extra constraints or remaining degrees of bond-rotational freedom within a substructure quantifies its relative rigidity/flexibility and provides a flexibility index for each bond in the structure. This novel computational procedure, first used in the analysis of glassy materials, is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side-chains from analysis of a single, static three-dimensional structure. This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase.}, +author = {Jacobs, D J and Rader, A J and Kuhn, L A and Thorpe, M F}, +doi = {10.1002/prot.1081}, +file = {:home/alex/Dokumente/Mendeley Desktop/Jacobs et al/Proteins/Jacobs et al. - 2001 - Protein flexibility predictions using graph theory.pdf:pdf}, +issn = {0887-3585}, +journal = {Proteins}, +keywords = {Adenylate Kinase,Adenylate Kinase: chemistry,Algorithms,Computational Biology,Computational Biology: methods,Computer Simulation,HIV Protease,HIV Protease: chemistry,Hydrogen Bonding,Models,Molecular,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Software,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Thermodynamics}, +month = aug, +number = {2}, +pages = {150--65}, +pmid = {11391777}, +title = {{Protein flexibility predictions using graph theory.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/11391777}, +volume = {44}, +year = {2001} } @article{Iwakura1995, abstract = {Amino acid sequences in proteins can contain residues which complicate biochemical, biophysical, or protein engineering studies but which are not essential for folding or activity. Their replacement with other naturally-occurring amino acids which are not subject to such complications but which maintain essential properties of the protein is a desirable goal. A simple strategy for testing various mutants for their suitability is described for a pair of cysteine residues in dihydrofolate reductase (DHFR) from Escherichia coli. Using a reconstructed gene which preserves the amino acid sequence and introduces a variety of unique restriction sites, the cysteines at positions 85 and 152 were replaced by site-directed and cassette mutagenesis. The enzymatic activity, stability, and folding mechanism of six double mutant DHFR proteins were examined with the purpose of identifying a suitable alternative to wild type DHFR. The Cys85-->Ala and Cys152-->Ser double mutant DHFR was found to retain the four channel folding mechanism and have activity and stability which are comparable to the wild type enzyme. The replacement of the cysteines improved the resistance of DHFR to the irreversible loss of activity at high temperature.}, @@ -1998,6 +1039,22 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/7629011}, volume = {117}, year = {1995} } +@article{Ernst2008, +author = {Ernst, R. and Kueppers, P. and Klein, C. M. and Schwarzmueller, T. and Kuchler, K. and Schmitt, L.}, +doi = {10.1073/pnas.0800191105}, +file = {:home/alex/Dokumente/Mendeley Desktop/Ernst et al/Proceedings of the National Academy of Sciences/Ernst et al. - 2008 - A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5.pdf:pdf}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences}, +keywords = {Folder - Biochemie}, +mendeley-tags = {Folder - Biochemie}, +month = mar, +number = {13}, +pages = {5069--5074}, +title = {{A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5}}, +url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0800191105}, +volume = {105}, +year = {2008} +} @book{Purves2006a, address = {M\"{u}nchen; Heidelberg}, author = {Purves, William K and Sadava, David and Orians, Gordon H and Heller, H. Craig}, @@ -2010,22 +1067,6 @@ publisher = {Spektrum Akademischer Verlag}, title = {{Biologie}}, year = {2006} } -@article{Rosche1990, -abstract = {We have isolated and characterized cDNA clones encoding the entire precursor for the leafspecific isoform of pyruvate, orthophosphate dikinase (PPDK) from the dicotyledonous C4 plant Flaveria trinervia. The deduced amino acid sequence reveals a high degree of similarity to the corresponding maize protein indicating a common evolutionary basis. However, no significant similarities are apparent upon comparison of the putative transit peptides. The implications of this divergence are discussed with respect to the evolution of PPDK genes.}, -author = {Rosche, Elke and Westhoff, Peter}, -file = {:home/alex/Dokumente/Mendeley Desktop/Rosche, Westhoff/FEBS letters/Rosche, Westhoff - 1990 - Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.pdf:pdf}, -issn = {0014-5793}, -journal = {FEBS letters}, -keywords = {Amino Acid Sequence,Base Sequence,Cloning,DNA,DNA: genetics,DNA: isolation \& purification,Molecular,Molecular Sequence Data,Nucleic Acid,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Plants,Plants: enzymology,Plants: genetics,Protein Conformation,Pyruvate,Restriction Mapping,Sequence Homology}, -month = oct, -number = {1-2}, -pages = {116--21}, -pmid = {2172023}, -title = {{Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/2172023}, -volume = {273}, -year = {1990} -} @misc{TheMendeleySupportTeam2011, abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, address = {London}, @@ -2050,21 +1091,16 @@ title = {{Glycerol Viscosity Tables}}, volume = {9}, year = {1932} } -@article{Balzi1994, -abstract = {The complete sequence of the pleiotropic drug resistance gene PDR5 from Saccharomyces cerevisiae is reported and analyzed. PDR5 encodes a 160-kDa protein with a predicted duplicated six membrane-span domain and a repeated putative ATP-binding domain. PDR5 shares this structural feature with the mammalian multidrug resistance pumps as well as the functional capacity of conferring resistance to various inhibitors upon amplification (Leppert, G., McDevitt, R., Falco, S. C., Van Dyk, T. K., Ficke, M. B., and Golin, J. (1990) Genetics 125, 13-20). The yeast PDR5 is thus a new member of the ABC (ATP-binding cassette) protein superfamily. Mutations in another yeast pleiotropic drug resistance gene, PDR1, encoding a putative transcription regulator (Balzi, E., Chen, W., Ulaszewski, S., Capieaux, E., and Goffeau, A. (1987) J. Biol. Chem. 262, 16871-16879), increase markedly the mRNA levels of the PDR5 and STE6 genes. The multidrug resistance mutations pdr1-3 and pdr1-6 also lead to considerable overexpression of the PDR5 plasma membrane protein.}, -author = {Balzi, E and Wang, M and Leterme, S and {Van Dyck}, L and Goffeau, A}, -file = {:home/alex/Dokumente/Mendeley Desktop/Balzi et al/The Journal of Biological Chemistry/Balzi et al. - 1994 - PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1.pdf:pdf}, -issn = {0021-9258}, -journal = {The Journal of Biological Chemistry}, -keywords = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic}, -mendeley-tags = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic}, -month = jan, -number = {3}, -pages = {2206--2214}, -title = {{PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/8294477}, -volume = {269}, -year = {1994} +@book{Mortimer2007, +address = {Stuttgart}, +author = {Mortimer, Charles}, +edition = {9., \"{u}berar}, +isbn = {9783134843095}, +keywords = {Folder - Anorganische Chemie}, +mendeley-tags = {Folder - Anorganische Chemie}, +publisher = {Thieme}, +title = {{Chemie das Basiswissen der Chemie}}, +year = {2007} } @inproceedings{Resnick2006, author = {Resnick, J. S and Wen, C. K and Shockey, J. A and Chang, C.}, @@ -2074,39 +1110,6 @@ mendeley-tags = {Folder - RTE1}, title = {{REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis}}, year = {2006} } -@article{Bystroff1990, -abstract = {The crystal structure of dihydrofolate reductase (EC 1.5.1.3) from Escherichia coli has been solved as the binary complex with NADP+ (the holoenzyme) and as the ternary complex with NADP+ and folate. The Bragg law resolutions of the structures are 2.4 and 2.5 A, respectively. The new crystal forms are nonisomorphous with each other and with the methotrexate binary complex reported earlier [Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., \& Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662]. In general, NADP+ and folate binding conform to predictions, but the nicotinamide moiety of NADP+ is disordered in the holoenzyme and ordered in the ternary complex. A mobile loop (residues 16-20) involved in binding the nicotinamide is also disordered in the holoenzyme. We report a detailed analysis of the binding interactions for both ligands, paying special attention to several apparently strained interactions that may favor the transition state for hydride transfer. Hypothetical models are presented for the binding of 7,8-dihydrofolate in the Michaelis complex and for the transition-state complex.}, -author = {Bystroff, Christopher and Oatley, Stuart J and Kraut, Joseph}, -doi = {10.1021/bi00465a018}, -file = {:home/alex/Dokumente/Mendeley Desktop/Bystroff, Oatley, Kraut/Biochemistry/Bystroff, Oatley, Kraut - 1990 - Crystal structures of Escherichia coli dihydrofolate reductase the NADP holoenzyme and the folate.NADP ternary complex. Substrate binding and a model for the transition state.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Catalysis,Chemical,Escherichia coli,Escherichia coli: enzymology,Folic Acid,Folic Acid: metabolism,Kinetics,Models,NADP,NADP: metabolism,Protein Conformation,Substrate Specificity,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: metabolism}, -month = apr, -number = {13}, -pages = {3263--77}, -pmid = {2185835}, -title = {{Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/2185835 http://pubs.acs.org/doi/abs/10.1021/bi00465a018}, -volume = {29}, -year = {1990} -} -@article{Herzberg1996, -abstract = {The crystal structure of pyruvate phosphate dikinase, a histidyl multiphosphotransfer enzyme that synthesizes adenosine triphosphate, reveals a three-domain molecule in which the phosphohistidine domain is flanked by the nucleotide and the phosphoenolpyruvate/pyruvate domains, with the two substrate binding sites approximately 45 angstroms apart. The modes of substrate binding have been deduced by analogy to D-Ala-D-Ala ligase and to pyruvate kinase. Coupling between the two remote active sites is facilitated by two conformational states of the phosphohistidine domain. While the crystal structure represents the state of interaction with the nucleotide, the second state is achieved by swiveling around two flexible peptide linkers. This dramatic conformational transition brings the phosphocarrier residue in close proximity to phosphoenolpyruvate/pyruvate. The swiveling-domain paradigm provides an effective mechanism for communication in complex multidomain/multiactive site proteins.}, -author = {Herzberg, O and Chen, C C and Kapadia, G and McGuire, M and Carroll, L J and Noh, S J and Dunaway-Mariano, D}, -file = {:home/alex/Dokumente/Mendeley Desktop/Herzberg et al/Proceedings of the National Academy of Sciences of the United States of America/Herzberg et al. - 1996 - Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.pdf:pdf}, -issn = {0027-8424}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Amino Acid Sequence,Binding Sites,Clostridium,Clostridium: enzymology,Crystallography,Escherichia coli,Macromolecular Substances,Models,Molecular,Molecular Sequence Data,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: metabolism,Protein Folding,Protein Structure,Pyruvate,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,Secondary,Software,Structural,X-Ray}, -month = apr, -number = {7}, -pages = {2652--7}, -pmid = {8610096}, -title = {{Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=39685\&tool=pmcentrez\&rendertype=abstract}, -volume = {93}, -year = {1996} -} @article{Fischer1999, author = {Fischer, H.}, file = {:home/alex/Dokumente/Mendeley Desktop/Fischer/Nobel lectures in chemistry, 1922-1941/Fischer - 1999 - On haemin and the relationships between haemin and chlorophyll.pdf:pdf}, @@ -2143,6 +1146,182 @@ title = {{Hydrothermal vents and the origin of life}}, volume = {6}, year = {2008} } +@article{Lawrence2009, +author = {Lawrence, Ann-Marie and Besir, H\"{u}seyin}, +doi = {10.3791/1350}, +issn = {1940-087X}, +journal = {Journal of Visualized Experiments}, +month = aug, +number = {30}, +title = {{Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid}}, +url = {http://www.jove.com/index/Details.stp?ID=1350}, +year = {2009} +} +@article{Leeuw2010, +author = {de Leeuw, Nora H. and Catlow, C. Richard A. and King, Helen E. and Putnis, Andrew and Muralidharan, Krishna and Deymier, Pierre and Stimpfl, Marilena and Drake, Michael J.}, +doi = {10.1039/c0cc02312d}, +file = {:home/alex/Dokumente/Mendeley Desktop/Leeuw et al/Chemical Communications/Leeuw et al. - 2010 - Where on Earth has our water come from.pdf:pdf}, +issn = {1359-7345}, +journal = {Chemical Communications}, +number = {47}, +pages = {8923}, +title = {{Where on Earth has our water come from?}}, +url = {http://xlink.rsc.org/?DOI=c0cc02312d}, +volume = {46}, +year = {2010} +} +@book{Malach2009, +author = {Malach, Anuschka}, +publisher = {Heinrich-Heine-Universit\"{a}t D\"{u}sseldorf}, +title = {{Expression und Reinigung von RTE1 aus Arabidopsis thaliana [Diplomarbeit, unver\"{o}ffentlicht]}}, +year = {2009} +} +@article{Rosche1990, +abstract = {We have isolated and characterized cDNA clones encoding the entire precursor for the leafspecific isoform of pyruvate, orthophosphate dikinase (PPDK) from the dicotyledonous C4 plant Flaveria trinervia. The deduced amino acid sequence reveals a high degree of similarity to the corresponding maize protein indicating a common evolutionary basis. However, no significant similarities are apparent upon comparison of the putative transit peptides. The implications of this divergence are discussed with respect to the evolution of PPDK genes.}, +author = {Rosche, Elke and Westhoff, Peter}, +file = {:home/alex/Dokumente/Mendeley Desktop/Rosche, Westhoff/FEBS letters/Rosche, Westhoff - 1990 - Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.pdf:pdf}, +issn = {0014-5793}, +journal = {FEBS letters}, +keywords = {Amino Acid Sequence,Base Sequence,Cloning,DNA,DNA: genetics,DNA: isolation \& purification,Molecular,Molecular Sequence Data,Nucleic Acid,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Plants,Plants: enzymology,Plants: genetics,Protein Conformation,Pyruvate,Restriction Mapping,Sequence Homology}, +month = oct, +number = {1-2}, +pages = {116--21}, +pmid = {2172023}, +title = {{Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/2172023}, +volume = {273}, +year = {1990} +} +@article{Galperin2009, +abstract = {The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).}, +author = {Galperin, Michael Y and Cochrane, Guy R}, +doi = {10.1093/nar/gkn942}, +file = {:home/alex/Dokumente/Mendeley Desktop/Galperin, Cochrane/Nucleic acids research/Galperin, Cochrane - 2009 - Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.pdf:pdf}, +issn = {1362-4962}, +journal = {Nucleic acids research}, +keywords = {Databases, Genetic,Databases, Genetic: standards,Databases, Genetic: statistics \& numerical data,Internet,Molecular Biology}, +month = jan, +number = {Database issue}, +pages = {D1--4}, +pmid = {19033364}, +title = {{Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/21487621}, +volume = {37}, +year = {2009} +} +@article{Balzi1994, +abstract = {The complete sequence of the pleiotropic drug resistance gene PDR5 from Saccharomyces cerevisiae is reported and analyzed. PDR5 encodes a 160-kDa protein with a predicted duplicated six membrane-span domain and a repeated putative ATP-binding domain. PDR5 shares this structural feature with the mammalian multidrug resistance pumps as well as the functional capacity of conferring resistance to various inhibitors upon amplification (Leppert, G., McDevitt, R., Falco, S. C., Van Dyk, T. K., Ficke, M. B., and Golin, J. (1990) Genetics 125, 13-20). The yeast PDR5 is thus a new member of the ABC (ATP-binding cassette) protein superfamily. Mutations in another yeast pleiotropic drug resistance gene, PDR1, encoding a putative transcription regulator (Balzi, E., Chen, W., Ulaszewski, S., Capieaux, E., and Goffeau, A. (1987) J. Biol. Chem. 262, 16871-16879), increase markedly the mRNA levels of the PDR5 and STE6 genes. The multidrug resistance mutations pdr1-3 and pdr1-6 also lead to considerable overexpression of the PDR5 plasma membrane protein.}, +author = {Balzi, E and Wang, M and Leterme, S and {Van Dyck}, L and Goffeau, A}, +file = {:home/alex/Dokumente/Mendeley Desktop/Balzi et al/The Journal of Biological Chemistry/Balzi et al. - 1994 - PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1.pdf:pdf}, +issn = {0021-9258}, +journal = {The Journal of Biological Chemistry}, +keywords = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic}, +mendeley-tags = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic}, +month = jan, +number = {3}, +pages = {2206--2214}, +title = {{PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/8294477}, +volume = {269}, +year = {1994} +} +@article{Bystroff1990, +abstract = {The crystal structure of dihydrofolate reductase (EC 1.5.1.3) from Escherichia coli has been solved as the binary complex with NADP+ (the holoenzyme) and as the ternary complex with NADP+ and folate. The Bragg law resolutions of the structures are 2.4 and 2.5 A, respectively. The new crystal forms are nonisomorphous with each other and with the methotrexate binary complex reported earlier [Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., \& Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662]. In general, NADP+ and folate binding conform to predictions, but the nicotinamide moiety of NADP+ is disordered in the holoenzyme and ordered in the ternary complex. A mobile loop (residues 16-20) involved in binding the nicotinamide is also disordered in the holoenzyme. We report a detailed analysis of the binding interactions for both ligands, paying special attention to several apparently strained interactions that may favor the transition state for hydride transfer. Hypothetical models are presented for the binding of 7,8-dihydrofolate in the Michaelis complex and for the transition-state complex.}, +author = {Bystroff, Christopher and Oatley, Stuart J and Kraut, Joseph}, +doi = {10.1021/bi00465a018}, +file = {:home/alex/Dokumente/Mendeley Desktop/Bystroff, Oatley, Kraut/Biochemistry/Bystroff, Oatley, Kraut - 1990 - Crystal structures of Escherichia coli dihydrofolate reductase the NADP holoenzyme and the folate.NADP ternary complex. Substrate binding and a model for the transition state.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Catalysis,Chemical,Escherichia coli,Escherichia coli: enzymology,Folic Acid,Folic Acid: metabolism,Kinetics,Models,NADP,NADP: metabolism,Protein Conformation,Substrate Specificity,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: metabolism}, +month = apr, +number = {13}, +pages = {3263--77}, +pmid = {2185835}, +title = {{Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/2185835 http://pubs.acs.org/doi/abs/10.1021/bi00465a018}, +volume = {29}, +year = {1990} +} +@article{Orgel2004, +author = {Orgel, Leslie E.}, +doi = {10.1080/10409230490460765}, +file = {:home/alex/Dokumente/Mendeley Desktop/Leslie E/Critical Reviews in Biochemistry and Molecular Biology/Leslie E. - 2004 - Prebiotic Chemistry and the Origin of the RNA World.pdf:pdf}, +issn = {1040-9238}, +journal = {Critical Reviews in Biochemistry and Molecular Biology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = jan, +number = {2}, +pages = {99--123}, +title = {{Prebiotic Chemistry and the Origin of the RNA World}}, +url = {http://informahealthcare.com/doi/abs/10.1080/10409230490460765}, +volume = {39}, +year = {2004} +} +@article{Yarus2010, +author = {Yarus, M.}, +doi = {10.1101/cshperspect.a003590}, +file = {:home/alex/Dokumente/Mendeley Desktop/Yarus/Cold Spring Harbor Perspectives in Biology/Yarus - 2010 - Getting Past the RNA World The Initial Darwinian Ancestor.pdf:pdf}, +issn = {1943-0264}, +journal = {Cold Spring Harbor Perspectives in Biology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = apr, +number = {4}, +pages = {a003590--a003590}, +shorttitle = {Getting Past the RNA World}, +title = {{Getting Past the RNA World: The Initial Darwinian Ancestor}}, +url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a003590}, +volume = {3}, +year = {2010} +} +@article{Martin2003, +author = {Martin, W. and Russell, M. J.}, +doi = {10.1098/rstb.2002.1183}, +file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2003 - On the origins of cells a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.pdf:pdf}, +issn = {0962-8436}, +journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, +month = jan, +number = {1429}, +pages = {59--85}, +shorttitle = {On the origins of cells}, +title = {{On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells}}, +url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183}, +volume = {358}, +year = {2003} +} +@article{Herzberg1996, +abstract = {The crystal structure of pyruvate phosphate dikinase, a histidyl multiphosphotransfer enzyme that synthesizes adenosine triphosphate, reveals a three-domain molecule in which the phosphohistidine domain is flanked by the nucleotide and the phosphoenolpyruvate/pyruvate domains, with the two substrate binding sites approximately 45 angstroms apart. The modes of substrate binding have been deduced by analogy to D-Ala-D-Ala ligase and to pyruvate kinase. Coupling between the two remote active sites is facilitated by two conformational states of the phosphohistidine domain. While the crystal structure represents the state of interaction with the nucleotide, the second state is achieved by swiveling around two flexible peptide linkers. This dramatic conformational transition brings the phosphocarrier residue in close proximity to phosphoenolpyruvate/pyruvate. The swiveling-domain paradigm provides an effective mechanism for communication in complex multidomain/multiactive site proteins.}, +author = {Herzberg, O and Chen, C C and Kapadia, G and McGuire, M and Carroll, L J and Noh, S J and Dunaway-Mariano, D}, +file = {:home/alex/Dokumente/Mendeley Desktop/Herzberg et al/Proceedings of the National Academy of Sciences of the United States of America/Herzberg et al. - 1996 - Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.pdf:pdf}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Amino Acid Sequence,Binding Sites,Clostridium,Clostridium: enzymology,Crystallography,Escherichia coli,Macromolecular Substances,Models,Molecular,Molecular Sequence Data,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: metabolism,Protein Folding,Protein Structure,Pyruvate,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,Secondary,Software,Structural,X-Ray}, +month = apr, +number = {7}, +pages = {2652--7}, +pmid = {8610096}, +title = {{Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=39685\&tool=pmcentrez\&rendertype=abstract}, +volume = {93}, +year = {1996} +} +@article{Lawrence2008, +abstract = {Enzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site. Inhibitor binding is predicted to draw the oligomeric equilibrium toward the low-activity hexamer. In silico docking enriched a selection from a small-molecule library for compounds predicted to bind to this allosteric site. In vitro testing of selected compounds identified one compound whose inhibition mechanism is species-specific conversion of PBGS octamers to hexamers. We propose that this strategy for inhibitor discovery can be applied to other proteins that use the morpheein model for allosteric regulation.}, +author = {Lawrence, Sarah H and Ramirez, Ursula D and Tang, Lei and Fazliyez, Farit and Kundrat, Lenka and Markham, George D and Jaffe, Eileen K}, +doi = {10.1016/j.chembiol.2008.04.012}, +issn = {1074-5521}, +journal = {Chemistry \& biology}, +keywords = {Allosteric Site,Amino Acid,Amino Acid Sequence,Animals,Dimerization,Drug Design,Magnetic Resonance Spectroscopy,Models,Molecular,Molecular Sequence Data,Molecular Structure,Sequence Homology}, +month = jun, +number = {6}, +pages = {586--96}, +pmid = {18559269}, +title = {{Shape shifting leads to small-molecule allosteric drug discovery.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703447\&tool=pmcentrez\&rendertype=abstract}, +volume = {15}, +year = {2008} +} @article{Schulte2004, author = {Schulte, M. D and Rogers, K. L}, file = {:home/alex/Dokumente/Mendeley Desktop/Schulte, Rogers/Geochimica et cosmochimica acta/Schulte, Rogers - 2004 - Thiols in hydrothermal solution standard partial molal properties and their role in the organic geochemistry of hydrothermal environments3.pdf:pdf}, @@ -2154,22 +1333,15 @@ title = {{Thiols in hydrothermal solution: standard partial molal properties and volume = {68}, year = {2004} } -@article{Datta2008, -abstract = {Structural studies of caspase-1 reveal that the dimeric thiol protease can exist in two states: in an on-state, when the active site is occupied, or in an off-state, when the active site is empty or when the enzyme is bound by a synthetic allosteric ligand at the dimer interface approximately 15 A from the active site. A network of 21 hydrogen bonds from nine side chains connecting the active and allosteric sites change partners when going between the on-state and the off-state. Alanine-scanning mutagenesis of these nine side chains shows that only two of them-Arg286 and Glu390, which form a salt bridge-have major effects, causing 100- to 200-fold reductions in catalytic efficiency (k(cat)/K(m)). Two neighbors, Ser332 and Ser339, have minor effects, causing 4- to 7-fold reductions. A more detailed mutational analysis reveals that the enzyme is especially sensitive to substitutions of the salt bridge: even a homologous R286K substitution causes a 150-fold reduction in k(cat)/K(m). X-ray crystal structures of these variants suggest the importance of both the salt bridge interaction and the coordination of solvent water molecules near the allosteric binding pocket. Thus, only a small subset of side chains from the larger hydrogen bonding network is critical for activity. These form a contiguous set of interactions that run from one active site through the allosteric site at the dimer interface and onto the second active site. This subset constitutes a functional allosteric circuit or "hot wire" that promotes site-to-site coupling.}, -author = {Datta, Debajyoti and Scheer, Justin M and Romanowski, Michael J and Wells, James a}, -doi = {10.1016/j.jmb.2008.06.040}, -file = {:home/alex/Dokumente/Mendeley Desktop/Datta et al/Journal of molecular biology/Datta et al. - 2008 - An allosteric circuit in caspase-1.pdf:pdf}, -issn = {1089-8638}, -journal = {Journal of molecular biology}, -keywords = {Allosteric Regulation,Amino Acid Substitution,Arginine,Caspase 1,Caspase 1: chemistry,Caspase 1: metabolism,Conserved Sequence,Crystallography, X-Ray,DNA Mutational Analysis,Glutamic Acid,Humans,Hydrogen Bonding,Kinetics,Models, Molecular,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: metabolism,Protein Structure, Secondary}, -month = sep, -number = {5}, -pages = {1157--67}, -pmid = {18590738}, -title = {{An allosteric circuit in caspase-1.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2626611\&tool=pmcentrez\&rendertype=abstract}, -volume = {381}, -year = {2008} +@article{Deveau2010, +author = {Deveau, H. and Garneau, J. E and Moineau, S.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Deveau, Garneau, Moineau/Annual review of microbiology/Deveau, Garneau, Moineau - 2010 - CRISPRCas System and Its Role in Phage-Bacteria Interactions.pdf:pdf}, +issn = {0066-4227}, +journal = {Annual review of microbiology}, +keywords = {Folder - In-silico-structure}, +mendeley-tags = {Folder - In-silico-structure}, +title = {{CRISPR/Cas System and Its Role in Phage-Bacteria Interactions}}, +year = {2010} } @article{Forterre2007, author = {Forterre, Patrick and Gribaldo, Simonetta}, @@ -2218,85 +1390,52 @@ url = {http://www.springerlink.com/content/rkt60781642pw447/}, volume = {24}, year = {1990} } -@article{Lawrence2009, -author = {Lawrence, Ann-Marie and Besir, H\"{u}seyin}, -doi = {10.3791/1350}, -issn = {1940-087X}, -journal = {Journal of Visualized Experiments}, -month = aug, -number = {30}, -title = {{Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid}}, -url = {http://www.jove.com/index/Details.stp?ID=1350}, -year = {2009} +@article{Vincent1985, +author = {Vincent, Styliani H. and Muller-Eberhard, Ursula}, +file = {:home/alex/Dokumente/Mendeley Desktop/Vincent, Muller-Eberhard/The Journal of Biological Chemistry/Vincent, Muller-Eberhard - 1985 - A Protein of the Z Class of Liver Cytosolic Proteins in the Rat That Preferentially Binds Heme.pdf:pdf}, +journal = {The Journal of Biological Chemistry}, +keywords = {Folder - Methoden}, +mendeley-tags = {Folder - Methoden}, +number = {27}, +pages = {14521--14528}, +title = {{A Protein of the Z Class of Liver Cytosolic Proteins in the Rat That Preferentially Binds Heme}}, +url = {http://www.jbc.org/content/260/27/14521.full.pdf+html?sid=e76840b8-53e3-41f7-b398-8005fb22d700}, +volume = {260}, +year = {1985} } -@article{Leeuw2010, -author = {de Leeuw, Nora H. and Catlow, C. Richard A. and King, Helen E. and Putnis, Andrew and Muralidharan, Krishna and Deymier, Pierre and Stimpfl, Marilena and Drake, Michael J.}, -doi = {10.1039/c0cc02312d}, -file = {:home/alex/Dokumente/Mendeley Desktop/Leeuw et al/Chemical Communications/Leeuw et al. - 2010 - Where on Earth has our water come from.pdf:pdf}, -issn = {1359-7345}, -journal = {Chemical Communications}, -number = {47}, -pages = {8923}, -title = {{Where on Earth has our water come from?}}, -url = {http://xlink.rsc.org/?DOI=c0cc02312d}, -volume = {46}, -year = {2010} -} -@book{Malach2009, -author = {Malach, Anuschka}, -publisher = {Heinrich-Heine-Universit\"{a}t D\"{u}sseldorf}, -title = {{Expression und Reinigung von RTE1 aus Arabidopsis thaliana [Diplomarbeit, unver\"{o}ffentlicht]}}, -year = {2009} -} -@article{Galperin2009, -abstract = {The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).}, -author = {Galperin, Michael Y and Cochrane, Guy R}, -doi = {10.1093/nar/gkn942}, -file = {:home/alex/Dokumente/Mendeley Desktop/Galperin, Cochrane/Nucleic acids research/Galperin, Cochrane - 2009 - Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.pdf:pdf}, -issn = {1362-4962}, -journal = {Nucleic acids research}, -keywords = {Databases, Genetic,Databases, Genetic: standards,Databases, Genetic: statistics \& numerical data,Internet,Molecular Biology}, -month = jan, -number = {Database issue}, -pages = {D1--4}, -pmid = {19033364}, -title = {{Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/21487621}, -volume = {37}, -year = {2009} -} -@article{Orgel2004, -author = {Orgel, Leslie E.}, -doi = {10.1080/10409230490460765}, -file = {:home/alex/Dokumente/Mendeley Desktop/Leslie E/Critical Reviews in Biochemistry and Molecular Biology/Leslie E. - 2004 - Prebiotic Chemistry and the Origin of the RNA World.pdf:pdf}, -issn = {1040-9238}, -journal = {Critical Reviews in Biochemistry and Molecular Biology}, +@incollection{Woese1967, +address = {New York}, +author = {Woese, C.}, keywords = {Folder - Vortrag RNA-Welt}, mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = jan, -number = {2}, -pages = {99--123}, -title = {{Prebiotic Chemistry and the Origin of the RNA World}}, -url = {http://informahealthcare.com/doi/abs/10.1080/10409230490460765}, -volume = {39}, -year = {2004} +pages = {179--195}, +publisher = {Harper and Row}, +title = {{The genetic code}}, +year = {1967} } -@article{Yarus2010, -author = {Yarus, M.}, -doi = {10.1101/cshperspect.a003590}, -file = {:home/alex/Dokumente/Mendeley Desktop/Yarus/Cold Spring Harbor Perspectives in Biology/Yarus - 2010 - Getting Past the RNA World The Initial Darwinian Ancestor.pdf:pdf}, -issn = {1943-0264}, -journal = {Cold Spring Harbor Perspectives in Biology}, +@book{Vollhardt2007, +address = {Weinheim}, +author = {Vollhardt, K and Schore, Neil E and Peter, K}, +edition = {4. Aufl., }, +isbn = {9783527313808}, +keywords = {Folder - Organische Chemie}, +mendeley-tags = {Folder - Organische Chemie}, +publisher = {Wiley-VCH}, +title = {{Organische Chemie}}, +year = {2007} +} +@book{Gesteland2006, +address = {Cold Spring Harbor N.Y.}, +author = {Gesteland, Raymond}, +edition = {3rd ed.}, +isbn = {9780879697396}, keywords = {Folder - Vortrag RNA-Welt}, +language = {English}, mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = apr, -number = {4}, -pages = {a003590--a003590}, -shorttitle = {Getting Past the RNA World}, -title = {{Getting Past the RNA World: The Initial Darwinian Ancestor}}, -url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a003590}, -volume = {3}, -year = {2010} +publisher = {Cold Spring Harbor Laboratory Press}, +shorttitle = {The RNA world}, +title = {{The RNA world : the nature of modern RNA suggests a prebiotic RNA world}}, +year = {2006} } @article{Gohlke2004, abstract = {Changes in flexibility upon protein-protein complex formation of H-Ras and the Ras-binding domain of C-Raf1 have been investigated using the molecular framework approach FIRST (Floppy Inclusion and Rigid Substructure Topology) and molecular dynamics simulations (MD) of in total approximately 35 ns length. In a computational time of about one second, FIRST identifies flexible and rigid regions in a single, static three-dimensional molecular framework, whose vertices represent protein atoms and whose edges represent covalent and non-covalent (hydrogen bond and hydrophobic) constraints and fixed bond angles within the protein. The two methods show a very good agreement with respect to the identification of changes in flexibility in both binding partners on a local scale. This implies that flexibility can be successfully predicted by identifying which bonds limit motion within a molecule and how they are coupled. In particular, as identified by MD, the beta-sheet in Raf shows considerably more pronounced orientational correlations in the bound state compared to the unbound state. Similarly, FIRST assigns the beta-sheet to the largest rigid cluster of the complex. Interestingly, FIRST allows us to identify that interactions across the interface (but not conformational changes upon complex formation) result in the observed rigidification. Since regions of the beta-sheet of Raf that do not interact directly with Ras become rigidified, this also demonstrates the long-range aspect to rigidity percolation. Possible implications of the change of flexibility of the Ras-binding domain of Raf on the activation of Raf upon complex formation are discussed. Finally, the sensitivity of FIRST results with respect to the representation of non-covalent interactions used as constraints is probed.}, @@ -2315,31 +1454,21 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/15211515}, volume = {56}, year = {2004} } -@article{Martin2003, -author = {Martin, W. and Russell, M. J.}, -doi = {10.1098/rstb.2002.1183}, -file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2003 - On the origins of cells a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.pdf:pdf}, -issn = {0962-8436}, -journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, -month = jan, -number = {1429}, -pages = {59--85}, -shorttitle = {On the origins of cells}, -title = {{On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells}}, -url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183}, -volume = {358}, -year = {2003} -} -@book{Mortimer2007, -address = {Stuttgart}, -author = {Mortimer, Charles}, -edition = {9., \"{u}berar}, -isbn = {9783134843095}, -keywords = {Folder - Anorganische Chemie}, -mendeley-tags = {Folder - Anorganische Chemie}, -publisher = {Thieme}, -title = {{Chemie das Basiswissen der Chemie}}, -year = {2007} +@article{Laemmli1970, +author = {Laemmli, U. K.}, +doi = {10.1038/227680a0}, +file = {:home/alex/Dokumente/Mendeley Desktop/Laemmli/Nature/Laemmli - 1970 - Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4.pdf:pdf}, +issn = {0028-0836}, +journal = {Nature}, +keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol}, +mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol}, +month = aug, +number = {5259}, +pages = {680--685}, +title = {{Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4}}, +url = {http://www.nature.com/doifinder/10.1038/227680a0}, +volume = {227}, +year = {1970} } @article{Yukl2010, author = {Yukl, Erik T. and Jepkorir, Grace and Alontaga, Aileen Y. and Pautsch, Lawrence and Rodriguez, Juan C. and Rivera, Mario and Moënne-Loccoz, Pierre}, @@ -2355,22 +1484,6 @@ url = {http://pubs.acs.org/doi/abs/10.1021/bi100692f}, volume = {49}, year = {2010} } -@article{Lawrence2008, -abstract = {Enzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site. Inhibitor binding is predicted to draw the oligomeric equilibrium toward the low-activity hexamer. In silico docking enriched a selection from a small-molecule library for compounds predicted to bind to this allosteric site. In vitro testing of selected compounds identified one compound whose inhibition mechanism is species-specific conversion of PBGS octamers to hexamers. We propose that this strategy for inhibitor discovery can be applied to other proteins that use the morpheein model for allosteric regulation.}, -author = {Lawrence, Sarah H and Ramirez, Ursula D and Tang, Lei and Fazliyez, Farit and Kundrat, Lenka and Markham, George D and Jaffe, Eileen K}, -doi = {10.1016/j.chembiol.2008.04.012}, -issn = {1074-5521}, -journal = {Chemistry \& biology}, -keywords = {Allosteric Site,Amino Acid,Amino Acid Sequence,Animals,Dimerization,Drug Design,Magnetic Resonance Spectroscopy,Models,Molecular,Molecular Sequence Data,Molecular Structure,Sequence Homology}, -month = jun, -number = {6}, -pages = {586--96}, -pmid = {18559269}, -title = {{Shape shifting leads to small-molecule allosteric drug discovery.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703447\&tool=pmcentrez\&rendertype=abstract}, -volume = {15}, -year = {2008} -} @article{Thieffry1998, author = {Thieffry, Denis and Sarkar, Sahotra}, doi = {10.1016/S0968-0004(98)01244-4}, @@ -2387,16 +1500,6 @@ url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000498012444}, volume = {23}, year = {1998} } -@article{Deveau2010, -author = {Deveau, H. and Garneau, J. E and Moineau, S.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Deveau, Garneau, Moineau/Annual review of microbiology/Deveau, Garneau, Moineau - 2010 - CRISPRCas System and Its Role in Phage-Bacteria Interactions.pdf:pdf}, -issn = {0066-4227}, -journal = {Annual review of microbiology}, -keywords = {Folder - In-silico-structure}, -mendeley-tags = {Folder - In-silico-structure}, -title = {{CRISPR/Cas System and Its Role in Phage-Bacteria Interactions}}, -year = {2010} -} @incollection{Rathi2011, address = {Weinheim}, author = {Rathi, Prakash C. and Pfleger, Christopher and Fulle, Simone and Klein, Doris L. and Gohlke, Holger}, @@ -2410,39 +1513,50 @@ publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA}, title = {{Statics of Biomacromolecules}}, year = {2011} } -@article{Vincent1985, -author = {Vincent, Styliani H. and Muller-Eberhard, Ursula}, -file = {:home/alex/Dokumente/Mendeley Desktop/Vincent, Muller-Eberhard/The Journal of Biological Chemistry/Vincent, Muller-Eberhard - 1985 - A Protein of the Z Class of Liver Cytosolic Proteins in the Rat That Preferentially Binds Heme.pdf:pdf}, -journal = {The Journal of Biological Chemistry}, +@article{Babu2011, +author = {Babu, Mohan and Beloglazova, Natalia and Flick, Robert and Graham, Chris and Skarina, Tatiana and Nocek, Boguslaw and Gagarinova, Alla and Pogoutse, Oxana and Brown, Greg and Binkowski, Andrew and Phanse, Sadhna and Joachimiak, Andrzej and Koonin, Eugene V. and Savchenko, Alexei and Emili, Andrew and Greenblatt, Jack and Edwards, Aled M. and Yakunin, Alexander F.}, +doi = {10.1111/j.1365-2958.2010.07465.x}, +file = {:home/alex/Dokumente/Mendeley Desktop/Babu et al/Molecular Microbiology/Babu et al. - 2011 - A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.pdf:pdf}, +issn = {0950382X}, +journal = {Molecular Microbiology}, +keywords = {Folder - In-silico-structure}, +mendeley-tags = {Folder - In-silico-structure}, +month = jan, +number = {2}, +pages = {484--502}, +title = {{A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair}}, +url = {http://doi.wiley.com/10.1111/j.1365-2958.2010.07465.x}, +volume = {79}, +year = {2011} +} +@article{Duncan1999, +author = {Duncan, T. and Osawa, Y. and Kutty, R. K and Kutty, G. and Wiggert, B.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Duncan et al/The Journal of Lipid Research/Duncan et al. - 1999 - Heme-binding by Drosophila retinoid-and fatty acid-binding glycoprotein (RFABG), a member of the proapolipophorin gene family.pdf:pdf}, +journal = {The Journal of Lipid Research}, keywords = {Folder - Methoden}, mendeley-tags = {Folder - Methoden}, -number = {27}, -pages = {14521--14528}, -title = {{A Protein of the Z Class of Liver Cytosolic Proteins in the Rat That Preferentially Binds Heme}}, -url = {http://www.jbc.org/content/260/27/14521.full.pdf+html?sid=e76840b8-53e3-41f7-b398-8005fb22d700}, -volume = {260}, -year = {1985} +number = {7}, +pages = {1222}, +title = {{Heme-binding by Drosophila retinoid-and fatty acid-binding glycoprotein (RFABG), a member of the proapolipophorin gene family}}, +volume = {40}, +year = {1999} } -@book{Riedel2007, -address = {Berlin; New York}, -author = {Riedel, Erwin}, -edition = {7. Aufl.}, -isbn = {9783110189032}, -keywords = {Folder - Anorganische Chemie}, -mendeley-tags = {Folder - Anorganische Chemie}, -publisher = {de Gruyter}, -title = {{Anorganische Chemie : mit DVD}}, -year = {2007} -} -@incollection{Woese1967, -address = {New York}, -author = {Woese, C.}, +@article{Martin2003a, +author = {Martin, W. and Russell, M. J.}, +doi = {10.1098/rstb.2002.1183}, +file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2003 - On the origins of cells a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.pdf:pdf}, +issn = {0962-8436}, +journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {Folder - Vortrag RNA-Welt}, mendeley-tags = {Folder - Vortrag RNA-Welt}, -pages = {179--195}, -publisher = {Harper and Row}, -title = {{The genetic code}}, -year = {1967} +month = jan, +number = {1429}, +pages = {59--85}, +shorttitle = {On the origins of cells}, +title = {{On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells}}, +url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183}, +volume = {358}, +year = {2003} } @incollection{Ashton1990, abstract = {The history of the resolution of C4 photosynthesis follows a pattern of demonstrating the operation of unique photosynthetic biochemistry by various means and then identifying the enzymes necessary to support that biochemistry. Critical to the developing understanding of this process was the recognition of two types of photosynthetic cells in C4 plants (mesophyll and bundle sheath) with quite different enzyme complements and distinct biochemical roles (see Fig. 3.1). As currently interpreted (see Edwards and Walker, 1983; Hatch, 1987) the reactions unique to the C4 pathway serve, in association with some remarkable modifications of leaf anatomy and ultrastructure, to concentrate CO2 in bundle sheath cells for utilisatiqn by the photosynthetic carbon reduction cycle carboxylase, ribulose L5-bisphosphate carboxylase-oxygenase (Rubisco). The Rubisco-mediated oxygenase reaction and associated photorespiration are thereby eliminated.}, @@ -2456,16 +1570,21 @@ publisher = {Academic Press}, title = {{The enzymes in C4 photosynthesis}}, year = {1990} } -@book{Vollhardt2007, -address = {Weinheim}, -author = {Vollhardt, K and Schore, Neil E and Peter, K}, -edition = {4. Aufl., }, -isbn = {9783527313808}, -keywords = {Folder - Organische Chemie}, -mendeley-tags = {Folder - Organische Chemie}, -publisher = {Wiley-VCH}, -title = {{Organische Chemie}}, -year = {2007} +@article{Horvath2010, +author = {Horvath, P. and Barrangou, R.}, +doi = {10.1126/science.1179555}, +file = {:home/alex/Dokumente/Mendeley Desktop/Horvath, Barrangou/Science/Horvath, Barrangou - 2010 - CRISPRCas, the Immune System of Bacteria and Archaea.pdf:pdf}, +issn = {0036-8075}, +journal = {Science}, +keywords = {Folder - In-silico-structure}, +mendeley-tags = {Folder - In-silico-structure}, +month = jan, +number = {5962}, +pages = {167--170}, +title = {{CRISPR/Cas, the Immune System of Bacteria and Archaea}}, +url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1179555}, +volume = {327}, +year = {2010} } @article{Chastain2011, abstract = {Pyruvate,orthophosphate dikinase (PPDK) plays a controlling role in the PEP-regeneration phase of the C(4) photosynthetic pathway. Earlier studies have fully documented its biochemical properties and its post-translational regulation by the PPDK regulatory protein (PDRP). However, the question of its evolution into the C(4) pathway has, until recently, received little attention. One assumption concerning this evolution is that changes in catalytic and regulatory properties of PPDK were necessary for the enzyme to fulfil its role in the C(4) pathway. In this study, the functional evolution of PPDK from its ancient origins in the Archaea to its ascension as a photosynthetic enzyme in modern C(4) angiosperms is reviewed. This analysis is accompanied by a comparative investigation into key catalytic and regulatory properties of a C(3) PPDK isoform from Arabidopsis and the C(4) PPDK isoform from Zea mays. From these analyses, it is proposed that PPDK first became functionally seated in C(3) plants as an ancillary glycolytic enzyme and that its transition into a C(4) pathway enzyme involved only minor changes in enzyme properties per se.}, @@ -2484,34 +1603,16 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/21414960}, volume = {62}, year = {2011} } -@book{Gesteland2006, -address = {Cold Spring Harbor N.Y.}, -author = {Gesteland, Raymond}, -edition = {3rd ed.}, -isbn = {9780879697396}, -keywords = {Folder - Vortrag RNA-Welt}, -language = {English}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -publisher = {Cold Spring Harbor Laboratory Press}, -shorttitle = {The RNA world}, -title = {{The RNA world : the nature of modern RNA suggests a prebiotic RNA world}}, -year = {2006} -} -@article{Laemmli1970, -author = {Laemmli, U. K.}, -doi = {10.1038/227680a0}, -file = {:home/alex/Dokumente/Mendeley Desktop/Laemmli/Nature/Laemmli - 1970 - Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4.pdf:pdf}, -issn = {0028-0836}, -journal = {Nature}, -keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol}, -mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol}, -month = aug, -number = {5259}, -pages = {680--685}, -title = {{Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4}}, -url = {http://www.nature.com/doifinder/10.1038/227680a0}, -volume = {227}, -year = {1970} +@article{Lane2010, +author = {Lane, N. and Allen, J. F and Martin, W.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Lane, Allen, Martin/BioEssays/Lane, Allen, Martin - 2010 - How did LUCA make a living Chemiosmosis in the origin of life.pdf:pdf}, +journal = {BioEssays}, +number = {4}, +pages = {271--280}, +shorttitle = {How did LUCA make a living?}, +title = {{How did LUCA make a living? Chemiosmosis in the origin of life}}, +volume = {32}, +year = {2010} } @article{Chastain2011a, abstract = {Pyruvate,orthophosphate dikinase (PPDK) plays a controlling role in the PEP-regeneration phase of the C(4) photosynthetic pathway. Earlier studies have fully documented its biochemical properties and its post-translational regulation by the PPDK regulatory protein (PDRP). However, the question of its evolution into the C(4) pathway has, until recently, received little attention. One assumption concerning this evolution is that changes in catalytic and regulatory properties of PPDK were necessary for the enzyme to fulfil its role in the C(4) pathway. In this study, the functional evolution of PPDK from its ancient origins in the Archaea to its ascension as a photosynthetic enzyme in modern C(4) angiosperms is reviewed. This analysis is accompanied by a comparative investigation into key catalytic and regulatory properties of a C(3) PPDK isoform from Arabidopsis and the C(4) PPDK isoform from Zea mays. From these analyses, it is proposed that PPDK first became functionally seated in C(3) plants as an ancillary glycolytic enzyme and that its transition into a C(4) pathway enzyme involved only minor changes in enzyme properties per se.}, @@ -2543,24 +1644,6 @@ title = {{Natural and unnatural ribozymes: Back to the primordial RNA world}}, volume = {160}, year = {2009} } -@article{Hauske2008a, -abstract = {Allostery is a basic principle of control of enzymatic activities based on the interaction of a protein or small molecule at a site distinct from an enzyme's active center. Allosteric modulators represent an alternative approach to the design and synthesis of small-molecule activators or inhibitors of proteases and are therefore of wide interest for medicinal chemistry. The structural bases of some proteinaceous and small-molecule allosteric protease regulators have already been elucidated, indicating a general mechanism that might be exploitable for future rational design of small-molecule effectors.}, -author = {Hauske, Patrick and Ottmann, Christian and Meltzer, Michael and Ehrmann, Michael and Kaiser, Markus}, -doi = {10.1002/cbic.200800528}, -file = {:home/alex/Dokumente/Mendeley Desktop/Hauske et al/Chembiochem a European journal of chemical biology/Hauske et al. - 2008 - Allosteric regulation of proteases.pdf:pdf}, -issn = {1439-7633}, -journal = {Chembiochem : a European journal of chemical biology}, -keywords = {Allosteric Regulation,Caspases,Caspases: antagonists \& inhibitors,Caspases: chemistry,Caspases: metabolism,Chemistry,Crystallography,Drug Design,Folder - Allostery - Theory,Mechanism,Models,Molecular,Peptide Hydrolases,Peptide Hydrolases: chemical synthesis,Peptide Hydrolases: chemistry,Peptide Hydrolases: metabolism,Pharmaceutical,Protein Conformation,Protein Structure,Serine Endopeptidases,Serine Endopeptidases: chemistry,Serine Endopeptidases: metabolism,Structure-Activity Relationship,Tertiary,X-Ray}, -mendeley-tags = {Folder - Allostery - Theory,Mechanism}, -month = dec, -number = {18}, -pages = {2920--8}, -pmid = {19021141}, -title = {{Allosteric regulation of proteases.}}, -url = {http://doi.wiley.com/10.1002/cbic.200800528 http://www.ncbi.nlm.nih.gov/pubmed/19021141}, -volume = {9}, -year = {2008} -} @article{Johnson1999, abstract = {We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3\% for alpha-helix, 2.6\% for 3(10)-helix, 4.2\% for beta-strand, 4.2\% for beta-turn, 2.7\% for poly(L-proline) II type 3(1)-helix, and 5.1\% for other structures when compared with the X-ray structure.}, author = {Johnson, W C}, @@ -2594,55 +1677,106 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/8254673}, volume = {234}, year = {1993} } -@article{Duncan1999, -author = {Duncan, T. and Osawa, Y. and Kutty, R. K and Kutty, G. and Wiggert, B.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Duncan et al/The Journal of Lipid Research/Duncan et al. - 1999 - Heme-binding by Drosophila retinoid-and fatty acid-binding glycoprotein (RFABG), a member of the proapolipophorin gene family.pdf:pdf}, -journal = {The Journal of Lipid Research}, -keywords = {Folder - Methoden}, -mendeley-tags = {Folder - Methoden}, -number = {7}, -pages = {1222}, -title = {{Heme-binding by Drosophila retinoid-and fatty acid-binding glycoprotein (RFABG), a member of the proapolipophorin gene family}}, -volume = {40}, -year = {1999} +@article{Scheer2006a, +abstract = {We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23\% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.}, +author = {Scheer, Justin M and Romanowski, Michael J and Wells, James A}, +doi = {10.1073/pnas.0602571103}, +file = {:home/alex/Dokumente/Mendeley Desktop/Scheer, Romanowski, Wells/Proceedings of the National Academy of Sciences of the United States of America/Scheer, Romanowski, Wells - 2006 - A common allosteric site and mechanism in caspases.pdf:pdf}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Allosteric Regulation,Amino Acid Sequence,Apoptosis,Apoptosis: physiology,Binding Sites,Caspases,Caspases: antagonists \& inhibitors,Caspases: chemistry,Caspases: genetics,Caspases: metabolism,Crystallography,Disulfides,Disulfides: chemistry,Humans,Inflammation,Inflammation: metabolism,Models,Molecular,Molecular Sequence Data,Molecular Structure,Protein Conformation,Sequence Alignment,Sulfhydryl Compounds,Sulfhydryl Compounds: chemistry,X-Ray}, +month = may, +number = {20}, +pages = {7595--600}, +pmid = {16682620}, +title = {{A common allosteric site and mechanism in caspases.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1458511\&tool=pmcentrez\&rendertype=abstract}, +volume = {103}, +year = {2006} } -@article{Horvath2010, -author = {Horvath, P. and Barrangou, R.}, -doi = {10.1126/science.1179555}, -file = {:home/alex/Dokumente/Mendeley Desktop/Horvath, Barrangou/Science/Horvath, Barrangou - 2010 - CRISPRCas, the Immune System of Bacteria and Archaea.pdf:pdf}, -issn = {0036-8075}, -journal = {Science}, -keywords = {Folder - In-silico-structure}, -mendeley-tags = {Folder - In-silico-structure}, +@book{Alberts2003, +address = {Weinheim [etc.]}, +author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter}, +edition = {4., Aufl.}, +isbn = {9783527304929}, +keywords = {Folder - Zellbiologie}, +mendeley-tags = {Folder - Zellbiologie}, +publisher = {Wiley-VCH}, +title = {{Molekularbiologie der Zelle}}, +year = {2003} +} +@incollection{Eftink1991, +address = {Hoboken, NJ, USA}, +author = {Eftink, Maurice R.}, +isbn = {9780470110560}, month = jan, -number = {5962}, -pages = {167--170}, -title = {{CRISPR/Cas, the Immune System of Bacteria and Archaea}}, -url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1179555}, -volume = {327}, -year = {2010} +pages = {127--205}, +publisher = {John Wiley \& Sons, Inc.}, +title = {{Fluorescence Techniques for Studying Protein Structure}}, +url = {http://doi.wiley.com/10.1002/9780470110560.ch3}, +volume = {35}, +year = {1991} } -@article{Lane2010, -author = {Lane, N. and Allen, J. F and Martin, W.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Lane, Allen, Martin/BioEssays/Lane, Allen, Martin - 2010 - How did LUCA make a living Chemiosmosis in the origin of life.pdf:pdf}, -journal = {BioEssays}, -number = {4}, -pages = {271--280}, -shorttitle = {How did LUCA make a living?}, -title = {{How did LUCA make a living? Chemiosmosis in the origin of life}}, -volume = {32}, -year = {2010} +@article{McGinness2003, +author = {McGinness, K. E and Joyce, G. F}, +file = {:home/alex/Dokumente/Mendeley Desktop/McGinness, Joyce/Chemistry \& biology/McGinness, Joyce - 2003 - In search of an RNA replicase ribozyme.pdf:pdf}, +journal = {Chemistry \& biology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +number = {1}, +pages = {5--14}, +title = {{In search of an RNA replicase ribozyme}}, +volume = {10}, +year = {2003} } -@article{Pizzarello2007, -author = {Pizzarello, S.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Pizzarello/Chemistry \& biodiversity/Pizzarello - 2007 - The chemistry that preceded life's origin A study guide from meteorites.pdf:pdf}, -journal = {Chemistry \& biodiversity}, -number = {4}, -pages = {680--693}, -shorttitle = {The chemistry that preceded life's origin}, -title = {{The chemistry that preceded life's origin: A study guide from meteorites}}, -volume = {4}, -year = {2007} +@article{Evans1980, +author = {Evans, Claudia T and Goss, Neil H and Wood, Harland G}, +doi = {10.1021/bi00566a023}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Bacteroides,Bacteroides: enzymology,Binding Sites,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Pyruvate}, +month = dec, +number = {25}, +pages = {5809--14}, +pmid = {6257293}, +title = {{Pyruvate phosphate dikinase: affinity labeling of the adenosine 5'-triphosphate--adenosine 5'-monophosphate site.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023}, +volume = {19}, +year = {1980} +} +@article{Thompson1994, +abstract = {The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.}, +author = {Thompson, Julie D and Higgins, Desmond G and Gibson, Toby J}, +doi = {10.1093/nar/22.22.4673}, +file = {:home/alex/Dokumente/Mendeley Desktop/Thompson, Higgins, Gibson/Nucleic Acids Research/Thompson, Higgins, Gibson - 1994 - CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.pdf:pdf}, +issn = {0305-1048}, +journal = {Nucleic Acids Research}, +keywords = {Algorithms,Amino Acid Sequence,Globins,Globins: genetics,Molecular Sequence Data,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,Secondary,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Software}, +month = nov, +number = {22}, +pages = {4673--4680}, +pmid = {7984417}, +title = {{CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308517\&tool=pmcentrez\&rendertype=abstract http://nar.oxfordjournals.org/cgi/doi/10.1093/nar/22.22.4673}, +volume = {22}, +year = {1994} +} +@article{Krystek1993, +abstract = {An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60\% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)}, +author = {Krystek, S and Stouch, T and Novotny, J}, +doi = {10.1006/jmbi.1993.1619}, +file = {:home/alex/Dokumente/Mendeley Desktop/Krystek, Stouch, Novotny/Journal of molecular biology/Krystek, Stouch, Novotny - 1993 - Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.pdf:pdf}, +issn = {0022-2836}, +journal = {Journal of molecular biology}, +keywords = {Amino Acid Sequence,Animals,Calorimetry,Chymotrypsin,Chymotrypsin: chemistry,Crystallography,Mathematics,Models,Molecular,Molecular Sequence Data,Ovomucin,Ovomucin: chemistry,Protein Conformation,Serine Endopeptidases,Serine Endopeptidases: chemistry,Serine Endopeptidases: metabolism,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: chemistry,Serine Proteinase Inhibitors: metabolism,Thermodynamics,Turkeys,X-Ray,X-Ray: methods}, +month = dec, +number = {3}, +pages = {661--79}, +pmid = {8254666}, +title = {{Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/8254666}, +volume = {234}, +year = {1993} } @article{Goss1980, abstract = {Pyruvate phosphate dikinase contains a pivotal histidyl residue which functions to mediate the transfer of phosphoryl moieties during the reaction catalyzed by the enzyme. The tryptic peptide which contains this essential histidyl residue has been isolated by a two-step procedure originally developed by Wang and co-workers [Wang, T., Jurasek, L., \& Bridger, W. A. (1972) Biochemistry 11, 2067]. This peptide has been sequenced by the manual dansyl-Edman procedure and is shown to be NH2-Gly-Gly-Met-Thr-Ser-His-Ala-Ala-Val-Val-Ala-Arg-CO2H. There is no readily interpretable homology between this peptide and other phosphorylated histidyl peptides previously isolated from other enzymes. By use of Chou \& Fasman [Chou, P. Y., \& Fasman, G. D. (1974) Biochemistry 13, 222], it is predicted that the sequence contains an alpha helix from the methionine residue through to the carboxyl terminal arginine residue.}, @@ -2661,6 +1795,22 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10 volume = {19}, year = {1980} } +@article{Kendrick2008, +author = {Kendrick, M and Chang, C}, +doi = {10.1016/j.pbi.2008.06.011}, +file = {:home/alex/Dokumente/Mendeley Desktop/Kendrick, Chang/Current Opinion in Plant Biology/Kendrick, Chang - 2008 - Ethylene signaling new levels of complexity and regulation.pdf:pdf}, +issn = {13695266}, +journal = {Current Opinion in Plant Biology}, +keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +month = oct, +number = {5}, +pages = {479--485}, +title = {{Ethylene signaling: new levels of complexity and regulation}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S1369526608001143}, +volume = {11}, +year = {2008} +} @article{Goss1980, abstract = {Pyruvate phosphate dikinase contains a pivotal histidyl residue which functions to mediate the transfer of phosphoryl moieties during the reaction catalyzed by the enzyme. The tryptic peptide which contains this essential histidyl residue has been isolated by a two-step procedure originally developed by Wang and co-workers [Wang, T., Jurasek, L., \& Bridger, W. A. (1972) Biochemistry 11, 2067]. This peptide has been sequenced by the manual dansyl-Edman procedure and is shown to be NH2-Gly-Gly-Met-Thr-Ser-His-Ala-Ala-Val-Val-Ala-Arg-CO2H. There is no readily interpretable homology between this peptide and other phosphorylated histidyl peptides previously isolated from other enzymes. By use of Chou \& Fasman [Chou, P. Y., \& Fasman, G. D. (1974) Biochemistry 13, 222], it is predicted that the sequence contains an alpha helix from the methionine residue through to the carboxyl terminal arginine residue.}, author = {Goss, Neil H. and Evans, Claudia T. and Wood, Harland G.}, @@ -2716,55 +1866,1069 @@ title = {{Development of an artificial cell, from self-organization to computati volume = {108}, year = {2011} } -@article{Scheer2006a, -abstract = {We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23\% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.}, -author = {Scheer, Justin M and Romanowski, Michael J and Wells, James A}, -doi = {10.1073/pnas.0602571103}, -file = {:home/alex/Dokumente/Mendeley Desktop/Scheer, Romanowski, Wells/Proceedings of the National Academy of Sciences of the United States of America/Scheer, Romanowski, Wells - 2006 - A common allosteric site and mechanism in caspases.pdf:pdf}, -issn = {0027-8424}, -journal = {Proceedings of the National Academy of Sciences of the United States of America}, -keywords = {Allosteric Regulation,Amino Acid Sequence,Apoptosis,Apoptosis: physiology,Binding Sites,Caspases,Caspases: antagonists \& inhibitors,Caspases: chemistry,Caspases: genetics,Caspases: metabolism,Crystallography,Disulfides,Disulfides: chemistry,Humans,Inflammation,Inflammation: metabolism,Models,Molecular,Molecular Sequence Data,Molecular Structure,Protein Conformation,Sequence Alignment,Sulfhydryl Compounds,Sulfhydryl Compounds: chemistry,X-Ray}, +@book{Riedel2007, +address = {Berlin; New York}, +author = {Riedel, Erwin}, +edition = {7. Aufl.}, +isbn = {9783110189032}, +keywords = {Folder - Anorganische Chemie}, +mendeley-tags = {Folder - Anorganische Chemie}, +publisher = {de Gruyter}, +title = {{Anorganische Chemie : mit DVD}}, +year = {2007} +} +@article{Moretti2007, +abstract = {The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.}, +author = {Moretti, Sebastien and Armougom, Fabrice and Wallace, Iain M and Higgins, Desmond G and Jongeneel, Cornelius V and Notredame, Cedric}, +doi = {10.1093/nar/gkm333}, +file = {:home/alex/Dokumente/Mendeley Desktop/Moretti et al/Nucleic acids research/Moretti et al. - 2007 - The M-Coffee web server a meta-method for computing multiple sequence alignments by combining alternative alignment methods.pdf:pdf}, +issn = {1362-4962}, +journal = {Nucleic acids research}, +keywords = {Algorithms,Amino Acid Sequence,Computational Biology,Computational Biology: methods,Computer Simulation,Information Storage and Retrieval,Internet,Molecular Sequence Data,Reproducibility of Results,Sequence Alignment,Sequence Alignment: methods,Sequence Homology, Amino Acid,Software,User-Computer Interface}, +month = jul, +number = {Web Server issue}, +pages = {W645--8}, +pmid = {17526519}, +title = {{The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933118\&tool=pmcentrez\&rendertype=abstract}, +volume = {35}, +year = {2007} +} +@book{Arber2009, +address = {Vatican City}, +author = {Arber, Werner and {Pontificia Accademia delle scienze.}}, +file = {:home/alex/Dokumente/Mendeley Desktop/Arber, Pontificia Accademia delle scienze/Unknown/Arber, Pontificia Accademia delle scienze. - 2009 - The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008.pdf:pdf}, +isbn = {9788877610973}, +publisher = {Ex Aedibus Academicis in Civitate Vaticana}, +title = {{The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008}}, +year = {2009} +} +@article{Koshland1966, +author = {Koshland, D E and Nemethy, G. and Filmer, D}, +doi = {10.1021/bi00865a047}, +file = {:home/alex/Dokumente/Mendeley Desktop/Koshland, Nemethy, Filmer/Biochemistry/Koshland, Nemethy, Filmer - 1966 - Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Chemistry,Computers,Hemoglobins,Kinetics,Models,Oxygen,Physical,Physicochemical Phenomena,Proteins,Theoretical}, +month = jan, +number = {1}, +pages = {365--385}, +pmid = {5938952}, +title = {{Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/5938952 http://pubs.acs.org/cgi-bin/doilookup/?10.1021/bi00865a047}, +volume = {5}, +year = {1966} +} +@article{Cornilescu2008, +author = {Cornilescu, Gabriel and Ulijasz, Andrew T. and Cornilescu, Claudia C. and Markley, John L. and Vierstra, Richard D.}, +doi = {10.1016/j.jmb.2008.08.034}, +file = {:home/alex/Dokumente/Mendeley Desktop/Cornilescu et al/Journal of Molecular Biology/Cornilescu et al. - 2008 - Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State.science:science}, +issn = {00222836}, +journal = {Journal of Molecular Biology}, +month = nov, +pages = {403--413}, +title = {{Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608010279}, +volume = {383}, +year = {2008} +} +@misc{TheMendeleySupportTeam2011c, +abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.}, +address = {London}, +author = {{The Mendeley Support Team}}, +booktitle = {Mendeley Desktop}, +file = {:home/alex/Dokumente/Mendeley Desktop/The Mendeley Support Team/Mendeley Desktop/The Mendeley Support Team - 2011 - Getting Started with Mendeley.pdf:pdf}, +keywords = {Mendeley,how-to,user manual}, +pages = {1--16}, +publisher = {Mendeley Ltd.}, +title = {{Getting Started with Mendeley}}, +url = {http://www.mendeley.com}, +year = {2011} +} +@article{Riener2002, +author = {Riener, Christian and Kada, Gerald and Gruber, Hermann}, +doi = {10.1007/s00216-002-1347-2}, +file = {:home/alex/Dokumente/Mendeley Desktop/Riener, Kada, Gruber/Analytical and Bioanalytical Chemistry/Riener, Kada, Gruber - 2002 - Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032-dithiodipyridine.pdf:pdf}, +issn = {1618-2642}, +journal = {Analytical and Bioanalytical Chemistry}, +month = jul, +number = {4-5}, +pages = {266--276}, +title = {{Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032;-dithiodipyridine}}, +url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00216-002-1347-2}, +volume = {373}, +year = {2002} +} +@article{Rader2011, +abstract = {Allosteric proteins demonstrate the phenomenon of a ligand binding to a protein at a regulatory or effector site and thereby changing the chemical affinity of the catalytic site. As such, allostery is extremely important biologically as a regulatory mechanism for molecular concentrations in many cellular processes. One particularly interesting feature of allostery is that often the catalytic and effector sites are separated by a large distance. Structural comparisons of allosteric proteins resolved in both inactive and active states indicate that a variety of structural rearrangement and changes in motions may contribute to general allosteric behavior. In general it is expected that the coupling of catalytic and regulatory sites is responsible for allosteric behavior. We utilize a novel examination of allostery using rigidity analysis of the underlying graph of the protein structures. Our results indicate a general global change in rigidity associated with allosteric transitions where the R state is more rigid than the T state. A set of allosteric proteins with heterotropic interactions is used to test the hypothesis that catalytic and effector sites are structurally coupled. Observation of a rigid path connecting the effector and catalytic sites in 68.75\% of the structures points to rigidity as a means by which the distal sites communicate with each other and so contribute to allosteric regulation. Thus structural rigidity is shown to be a fundamental underlying property that promotes cooperativity and non-locality seen in allostery.}, +author = {Rader, a J and Brown, Stephen M}, +doi = {10.1039/c0mb00054j}, +file = {:home/alex/Dokumente/Mendeley Desktop/Rader, Brown/Molecular bioSystems/Rader, Brown - 2011 - Correlating allostery with rigidity.pdf:pdf}, +issn = {1742-2051}, +journal = {Molecular bioSystems}, +keywords = {Allosteric Site,Catalytic Domain,Models,Molecular,Molecular Structure}, +month = feb, +number = {2}, +pages = {464--71}, +pmid = {21060909}, +title = {{Correlating allostery with rigidity.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/21060909}, +volume = {7}, +year = {2011} +} +@article{Pocalyko1990, +abstract = {In this paper we report the amino acid sequence of pyruvate phosphate dikinase (PPDK) from Bacteroides symbiosus as determined from the nucleotide sequence of the PPDK gene. Comparison of the B. symbiosus PPDK amino acid sequence with that of the maize PPDK [Matsuoka, M., Ozeki, Y., Yamamoto, N., Hirano, H., Kamo-Murakami, Y., \& Tanaka, Y. (1988) J. Biol. Chem. 263, 11080] revealed long stretches of homologous sequence (greater than 70\% identity), which contributed to an overall sequence identity of 53\%. The circular dichrosim spectra, hydropathy profiles, and calculated secondary structural elements of the two dikinases suggest that they may have very similar tertiary structures as well. A comparison made between the amino acid sequence of the maize and B. symbiosus dikinase with other known protein sequences revealed homology, concentrated in three stretches of sequences, to a mechanistically related enzyme, enzyme I of the Escherichia coli PEP: sugar phosphotransferase system [Saffen, D. W., Presper, K. A., Doering, T. L., Roseman, S. (1987) J. Biol. Chem. 262, 16241]. It is proposed that (i) these three stretches of sequence constitute the site for PEP binding and catalysis and a possible site for the regulation of enzymatic activity and (ii) the conserved sequences exist in a third mechanistically related enzyme, PEP synthase.}, +author = {Pocalyko, David J and Carroll, Lawrence J and Martin, Brian M and Babbitt, Patricia C and Dunaway-Mariano, Debra}, +doi = {10.1021/bi00500a006}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Amino Acid Sequence,Bacterial,Bacterial: genetics,Bacteroides,Bacteroides: enzymology,Base Sequence,Binding Sites,Catalysis,Circular Dichroism,Cloning,DNA,DNA Restriction Enzymes,Escherichia coli,Escherichia coli: genetics,Molecular,Molecular Sequence Data,Nucleic Acid,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: genetics,Peptide Fragments,Peptide Fragments: chemistry,Plants,Plants: enzymology,Plasmids,Protein Conformation,Pyruvate,Sequence Homology,Zea mays,purification}, +mendeley-tags = {purification}, +month = dec, +number = {48}, +pages = {10757--65}, +pmid = {2176881}, +title = {{Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/2176881 http://pubs.acs.org/doi/abs/10.1021/bi00500a006}, +volume = {29}, +year = {1990} +} +@article{Laskowski1993, +author = {Laskowski, R. A. and MacArthur, M. W. and Moss, D. S. and Thornton, J. M.}, +doi = {10.1107/S0021889892009944}, +issn = {00218898}, +journal = {Journal of Applied Crystallography}, +month = apr, +number = {2}, +pages = {283--291}, +title = {{PROCHECK: a program to check the stereochemical quality of protein structures}}, +url = {http://scripts.iucr.org/cgi-bin/paper?S0021889892009944}, +volume = {26}, +year = {1993} +} +@article{Laskowski1996, +abstract = {The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.}, +author = {Laskowski, RomanA. and Rullmann, J.AntoonC. and MacArthur, MalcolmW. and Kaptein, Robert and Thornton, JanetM.}, +doi = {10.1007/BF00228148}, +issn = {0925-2738}, +journal = {Journal of Biomolecular NMR}, +keywords = {Amino Acid Sequence,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: genetics,Evaluation Studies as Topic,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,Models,Molecular,Molecular Sequence Data,Molecular Structure,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,Quality Control,Reproducibility of Results,Secondary,Software,Solutions}, +month = dec, +number = {4}, +pages = {477--86}, +pmid = {9008363}, +title = {{AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/9008363 http://www.springerlink.com/index/10.1007/BF00228148}, +volume = {8}, +year = {1996} +} +@article{Chiarabelli2009, +author = {Chiarabelli, Cristiano and Stano, Pasquale and Luisi, Pier Luigi}, +doi = {10.1016/j.copbio.2009.08.004}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chiarabelli, Stano, Luisi/Current Opinion in Biotechnology/Chiarabelli, Stano, Luisi - 2009 - Chemical approaches to synthetic biology.pdf:pdf}, +issn = {09581669}, +journal = {Current Opinion in Biotechnology}, +month = aug, +number = {4}, +pages = {492--497}, +title = {{Chemical approaches to synthetic biology}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0958166909000974}, +volume = {20}, +year = {2009} +} +@article{Chastain1997, +abstract = {A key regulatory enzyme of the C4-photosynthetic pathway is stromal pyruvate,orthophosphate dikinase (PPDK, EC 2.7.9.1). As a pivotal enzyme in the C4 pathway, it undergoes diurnal light-dark regulation of activity which is mediated by a single bifunctional regulatory protein (RP). RP specifically inactivates PPDK in the dark by an ADP-dependent phosphorylation of an active-site Thr residue (Thr-456 in maize). Conversely, RP activates inactive PPDK in the light by phosphorolytic dephosphorylation of this target Thr-P residue. We have employed a His-tagged maize recombinant C4 PPDK for directed mutagenesis of this active-site regulatory Thr. Three such mutants (T456V, T456S, T456D) were analyzed with respect to overall catalysis and regulation by exogenous maize RP. Substitution with Val and Ser at this position does not affect overall catalysis, whereas Asp abolishes enzyme activity. With respect to regulation by RP, it was found that Ser can effectively substitute for the wild-type Thr residue in that mutant enzyme is phosphorylated and inactivated by RP. The T456V mutant, however, could not be phosphorylated and was, thus, resistant to ADP-dependent inactivation by RP.}, +author = {Chastain, C J and Lee, M E and Moorman, M A and Shameekumar, P and Chollet, R}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/FEBS letters/Chastain et al. - 1997 - Site-directed mutagenesis of maize recombinant C4-pyruvate,orthophosphate dikinase at the phosphorylatable target threonine residue.pdf:pdf}, +issn = {0014-5793}, +journal = {FEBS letters}, +keywords = {Adenosine Diphosphate,Adenosine Diphosphate: pharmacology,Aspartic Acid,Aspartic Acid: genetics,Aspartic Acid: physiology,Histidine,Histidine: genetics,Mutagenesis,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Phosphorylation,Pyruvate,Serine,Serine: genetics,Serine: physiology,Site-Directed,Threonine,Threonine: physiology,Valine,Valine: genetics,Valine: physiology,Zea mays,Zea mays: enzymology,Zea mays: genetics}, +month = aug, +number = {1}, +pages = {169--73}, +pmid = {9287137}, +title = {{Site-directed mutagenesis of maize recombinant C4-pyruvate,orthophosphate dikinase at the phosphorylatable target threonine residue.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/9287137}, +volume = {413}, +year = {1997} +} +@article{Iwakura2006, +abstract = {We developed a strategy for finding out the adapted variants of enzymes, and we applied it to an enzyme, dihydrofolate reductase (DHFR), in terms of its catalytic activity so that we successfully obtained several hyperactive cysteine- and methionine-free variants of DHFR in which all five methionyl and two cysteinyl residues were replaced by other amino acid residues. Among them, a variant (M1A/M16N/M20L/M42Y/C85A/M92F/C152S), named as ANLYF, has an approximately seven times higher k(cat) value than wild type DHFR. Enzyme kinetics and crystal structures of the variant were investigated for elucidating the mechanism of the hyperactivity. Steady-state and transient binding kinetics of the variant indicated that the kinetic scheme of the catalytic cycle of ANLYF was essentially the same as that of wild type, showing that the hyperactivity was brought about by an increase of the dissociation rate constants of tetrahydrofolate from the enzyme-NADPH-tetrahydrofolate ternary complex. The crystal structure of the variant, solved and refined to an R factor of 0.205 at 1.9-angstroms resolution, indicated that an increased structural flexibility of the variant and an increased size of the N-(p-aminobenzoyl)-L-glutamate binding cleft induced the increase of the dissociation constant. This was consistent with a large compressibility (volume fluctuation) of the variant. A comparison of folding kinetics between wild type and the variant showed that the folding of these two enzymes was similar to each other, suggesting that the activity enhancement of the enzyme can be attained without drastic changes of the folding mechanism.}, +author = {Iwakura, Masahiro and Maki, Kosuke and Takahashi, Hisashi and Takenawa, Tatsuyuki and Yokota, Akiko and Katayanagi, Katsuo and Kamiyama, Tadashi and Gekko, Kunihiko}, +doi = {10.1074/jbc.M508823200}, +file = {:home/alex/Dokumente/Mendeley Desktop/Iwakura et al/The Journal of biological chemistry/Iwakura et al. - 2006 - Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.pdf:pdf}, +issn = {0021-9258}, +journal = {The Journal of biological chemistry}, +keywords = {Binding Sites,Cysteine,Cysteine: chemistry,Directed Molecular Evolution,Escherichia coli,Escherichia coli: enzymology,Kinetics,Methionine,Methionine: chemistry,Models, Molecular,Mutation,Protein Binding,Protein Conformation,Protein Engineering,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Tetrahydrofolate Dehydrogenase: genetics,Tetrahydrofolate Dehydrogenase: metabolism}, month = may, -number = {20}, -pages = {7595--600}, -pmid = {16682620}, -title = {{A common allosteric site and mechanism in caspases.}}, -url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1458511\&tool=pmcentrez\&rendertype=abstract}, -volume = {103}, +number = {19}, +pages = {13234--46}, +pmid = {16510443}, +title = {{Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/16510443}, +volume = {281}, year = {2006} } -@book{Alberts2003, -address = {Weinheim [etc.]}, -author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter}, -edition = {4., Aufl.}, -isbn = {9783527304929}, -keywords = {Folder - Zellbiologie}, -mendeley-tags = {Folder - Zellbiologie}, -publisher = {Wiley-VCH}, -title = {{Molekularbiologie der Zelle}}, -year = {2003} +@article{Miroux1996, +author = {Miroux, B. and Walker, J. E}, +file = {:home/alex/Dokumente/Mendeley Desktop/Miroux, Walker/Journal of molecular biology/Miroux, Walker - 1996 - Over-production of proteins in Escherichia coli mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels.pdf:pdf}, +journal = {Journal of molecular biology}, +number = {3}, +pages = {289--298}, +shorttitle = {Over-production of proteins in Escherichia coli}, +title = {{Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels}}, +volume = {260}, +year = {1996} } -@incollection{Eftink1991, -address = {Hoboken, NJ, USA}, -author = {Eftink, Maurice R.}, -isbn = {9780470110560}, -month = jan, -pages = {127--205}, -publisher = {John Wiley \& Sons, Inc.}, -title = {{Fluorescence Techniques for Studying Protein Structure}}, -url = {http://doi.wiley.com/10.1002/9780470110560.ch3}, -volume = {35}, -year = {1991} +@article{Wiedenheft2009, +author = {Wiedenheft, Blake and Zhou, Kaihong and Jinek, Martin and Coyle, Scott M. and Ma, Wendy and Doudna, Jennifer A.}, +doi = {10.1016/j.str.2009.03.019}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wiedenheft et al/Structure/Wiedenheft et al. - 2009 - Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense.pdf:pdf}, +issn = {09692126}, +journal = {Structure}, +keywords = {Folder - In-silico-structure}, +mendeley-tags = {Folder - In-silico-structure}, +month = jun, +number = {6}, +pages = {904--912}, +title = {{Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212609001920}, +volume = {17}, +year = {2009} } -@article{McGinness2003, -author = {McGinness, K. E and Joyce, G. F}, -file = {:home/alex/Dokumente/Mendeley Desktop/McGinness, Joyce/Chemistry \& biology/McGinness, Joyce - 2003 - In search of an RNA replicase ribozyme.pdf:pdf}, -journal = {Chemistry \& biology}, +@article{Fulle2009, +abstract = {A sophisticated interplay between the static properties of the ribosomal exit tunnel and its functional role in cotranslational processes is revealed by constraint counting on topological network representations of large ribosomal subunits from four different organisms. As for the global flexibility characteristics of the subunit, the results demonstrate a conserved stable structural environment of the tunnel. The findings render unlikely that deformations of the tunnel move peptides down the tunnel in an active manner. Furthermore, the stable environment rules out that the tunnel can adapt widely so as to allow tertiary folding of nascent chains. Nevertheless, there are local zones of flexible nucleotides within the tunnel, between the peptidyl transferase center and the tunnel constriction, and at the tunnel exit. These flexible zones strikingly agree with previously identified folding zones. As for cotranslational elongation regulation, flexible residues in the beta-hairpin of the ribosomal L22 protein were verified, as suggested previously based on structural results. These results support the hypothesis that L22 can undergo conformational changes that regulate the tunnel voyage of nascent polypeptides. Furthermore, rRNA elements, for which conformational changes have been observed upon interaction of the tunnel wall with a nascent SecM peptide, are less strongly coupled to the subunit core. Sequences of coupled rigid clusters are identified between the tunnel and some of these elements, suggesting signal transmission by a domino-like mechanical coupling. Finally, differences in the flexibility of the glycosidic bonds of bases that form antibiotics-binding crevices within the peptidyl transferase center and the tunnel region are revealed for ribosomal structures from different kingdoms. In order to explain antibiotics selectivity, action, and resistance, according to these results, differences in the degrees of freedom of the binding regions may need to be considered.}, +author = {Fulle, Simone and Gohlke, Holger}, +doi = {10.1016/j.jmb.2009.01.037}, +file = {:home/alex/Dokumente/Mendeley Desktop/Fulle, Gohlke/Journal of molecular biology/Fulle, Gohlke - 2009 - Statics of the ribosomal exit tunnel implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.pdf:pdf}, +issn = {1089-8638}, +journal = {Journal of molecular biology}, +keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: metabolism,Haloarcula marismortui,Haloarcula marismortui: metabolism,Models, Molecular,Peptide Chain Elongation, Translational,Peptides,Peptides: chemistry,Peptides: metabolism,Peptidyl Transferases,Peptidyl Transferases: metabolism,Pliability,Protein Folding,Protein Structure, Secondary,Protein Transport,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Signal Transduction}, +month = mar, +number = {2}, +pages = {502--17}, +pmid = {19356596}, +publisher = {Elsevier Ltd}, +title = {{Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/19356596}, +volume = {387}, +year = {2009} +} +@book{Purves2006, +address = {M\"{u}nchen; Heidelberg}, +author = {Purves, William K and Sadava, David and Orians, Gordon H and Heller, H. Craig}, +edition = {7}, +isbn = {9783827420077}, +keywords = {Folder - Allgemein}, +mendeley-tags = {Folder - Allgemein}, +month = aug, +publisher = {Spektrum Akademischer Verlag}, +title = {{Biologie}}, +year = {2006} +} +@article{Rivas2011, +author = {Rivas, Mario and Becerra, Arturo and Peret\'{o}, Juli and Bada, Jeffrey L. and Lazcano, Antonio}, +doi = {10.1007/s11084-011-9238-1}, +file = {:home/alex/Dokumente/Mendeley Desktop/Rivas et al/Origins of Life and Evolution of Biospheres/Rivas et al. - 2011 - Metalloproteins and the Pyrite-based Origin of Life A Critical Assessment.pdf:pdf}, +issn = {0169-6149}, +journal = {Origins of Life and Evolution of Biospheres}, +month = mar, +number = {4}, +pages = {347--356}, +shorttitle = {Metalloproteins and the Pyrite-based Origin of Lif}, +title = {{Metalloproteins and the Pyrite-based Origin of Life: A Critical Assessment}}, +url = {http://www.springerlink.com/index/10.1007/s11084-011-9238-1}, +volume = {41}, +year = {2011} +} +@article{Larkin2007, +abstract = {SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/}, +author = {Larkin, M A and Blackshields, G and Brown, N P and Chenna, R and McGettigan, P A and McWilliam, H and Valentin, F and Wallace, I M and Wilm, A and Lopez, R and Thompson, J D and Gibson, T J and Higgins, D G}, +doi = {10.1093/bioinformatics/btm404}, +issn = {1367-4811}, +journal = {Bioinformatics (Oxford, England)}, +keywords = {Algorithms,Amino Acid Sequence,Cluster Analysis,Computer Graphics,Molecular Sequence Data,Programming Languages,Protein,Protein: methods,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,User-Computer Interface}, +month = nov, +number = {21}, +pages = {2947--8}, +pmid = {17846036}, +title = {{Clustal W and Clustal X version 2.0.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/17846036}, +volume = {23}, +year = {2007} +} +@article{Bradford1976, +author = {Bradford, M M}, +file = {:home/alex/Dokumente/Mendeley Desktop/Bradford/Analytical biochemistry/Bradford - 1976 - A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.pdf:pdf}, +issn = {0003-2697}, +journal = {Analytical biochemistry}, +keywords = {Binding Sites,Colorimetry,Methods,Microchemistry,Protein Binding,Proteins,Proteins: analysis,Rosaniline Dyes,Time Factors}, +month = may, +pages = {248--54}, +pmid = {942051}, +title = {{A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/942051}, +volume = {72}, +year = {1976} +} +@article{Boyer2008, +abstract = {Long-range effects, such as allostery, have evolved in proteins as a means of regulating function via communication between distal sites. An NMR-based perturbation mapping approach was used to more completely probe the dynamic response of the core mutation V54A in the protein eglin c by monitoring changes in picosecond to nanosecond aromatic side-chain dynamics and H/D exchange stabilities. Previous side-chain dynamics studies on this mutant were limited to methyl-bearing residues, most of which were found to rigidify on the picosecond to nanosecond time scale in the form of a contiguous "network". Here, high precision (13)C relaxation data from 13 aromatic side chains were acquired by applying canonical relaxation experiments to a newly developed carbon labeling scheme [Teilum et al. (2006) J. Am. Chem. Soc. 128, 2506-2507]. The fitting of model-free parameters yielded S (2) variability which is intermediate with respect to backbone and methyl-bearing side-chain variability and tau e values that are approximately 1 ns. Inclusion of the aromatic dynamic response results in an expanded network of dynamically coupled residues, with some aromatics showing increases in flexibility, which partially offsets the rigidification in methyl side chains. Using amide hydrogen exchange, dynamic propagation on a slower time scale was probed in response to the V54A perturbation. Surprisingly, regional stabilization (slowed exchange) 10-12 A from the site of mutation was observed despite a global destabilization of 1.5 kcal x mol (-1). Furthermore, this unlikely pocket of stabilized residues colocalizes with increases in aromatic flexibility on the faster time scale. Because the converse is also true (destabilized residues colocalize with rigidification on the fast time scale), a plausible entropy-driven mechanism is discussed for relating colocalization of opposing dynamic trends on vastly different time scales.}, +author = {Boyer, Joshua a and Lee, Andrew L}, +doi = {10.1021/bi702330t}, +file = {:home/alex/Dokumente/Mendeley Desktop/Boyer, Lee/Biochemistry/Boyer, Lee - 2008 - Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Amino Acids,Aromatic,Aromatic: chemistry,Carbon Isotopes,Hydrogen,Hydrogen: metabolism,Kinetics,Magnetic Resonance Spectroscopy,Models,Molecular,Movement,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: genetics,Mutant Proteins: metabolism,Mutation,Protein Conformation,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: metabolism,Thermodynamics,Time Factors}, +month = apr, +number = {17}, +pages = {4876--86}, +pmid = {18393447}, +title = {{Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3062916\&tool=pmcentrez\&rendertype=abstract}, +volume = {47}, +year = {2008} +} +@article{Crick1970, +author = {Crick, Francis}, +doi = {10.1038/227561a0}, +file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Nature/Crick - 1970 - Central Dogma of Molecular Biology.pdf:pdf}, +issn = {0028-0836}, +journal = {Nature}, keywords = {Folder - Vortrag RNA-Welt}, mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = aug, +number = {5258}, +pages = {561--563}, +title = {{Central Dogma of Molecular Biology}}, +url = {http://www.nature.com/doifinder/10.1038/227561a0}, +volume = {227}, +year = {1970} +} +@article{Daily2008, +abstract = {Allosteric proteins bind an effector molecule at one site resulting in a functional change at a second site. We hypothesize that networks of contacts altered, formed, or broken are a significant contributor to allosteric communication in proteins. In this work, we identify which interactions change significantly between the residue-residue contact networks of two allosteric structures, and then organize these changes into graphs. We perform the analysis on 15 pairs of allosteric structures with effector and substrate each present in at least one of the two structures. Most proteins exhibit large, dense regions of contact rearrangement, and the graphs form connected paths between allosteric effector and substrate sites in five of these proteins. In the remaining 10 proteins, large-scale conformational changes such as rigid-body motions are likely required in addition to contact rearrangement networks to account for substrate-effector communication. On average, clusters which contain at least one substrate or effector molecule comprise 20\% of the protein. These allosteric graphs are small worlds; that is, they typically have mean shortest path lengths comparable to those of corresponding random graphs and average clustering coefficients enhanced relative to those of random graphs. The networks capture 60-80\% of known allostery-perturbing mutants in three proteins, and the metrics degree and closeness are statistically good discriminators of mutant residues from nonmutant residues within the networks in two of these three proteins. For two proteins, coevolving clusters of residues which have been hypothesized to be allosterically important differ from the regions with the most contact rearrangement. Residues and contacts which modulate normal mode fluctuations also often participate in the contact rearrangement networks. In summary, residue-residue contact rearrangement networks provide useful representations of the portions of allosteric pathways resulting from coupled local motions.}, +author = {Daily, Michael D. and Upadhyaya, Tarak J. and Gray, Jeffrey J.}, +doi = {10.1002/prot.21800}, +file = {:home/alex/Dokumente/Mendeley Desktop/Daily, Upadhyaya, Gray/Proteins/Daily, Upadhyaya, Gray - 2008 - Contact rearrangements form coupled networks from local motions in allosteric proteins.pdf:pdf}, +issn = {1097-0134}, +journal = {Proteins}, +keywords = {Allosteric Regulation,Allosteric Site,Chemical,Folder - Allostery - Theory,Mechanism,Metabolic Networks and Pathways,Models,Motion,Proteins,Proteins: chemistry}, +mendeley-tags = {Folder - Allostery - Theory,Mechanism}, +month = may, number = {1}, -pages = {5--14}, -title = {{In search of an RNA replicase ribozyme}}, +pages = {455--66}, +pmid = {17957766}, +title = {{Contact rearrangements form coupled networks from local motions in allosteric proteins.}}, +url = {http://doi.wiley.com/10.1002/prot.21800 http://www.ncbi.nlm.nih.gov/pubmed/17957766}, +volume = {71}, +year = {2008} +} +@article{Kang2002, +abstract = {Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches. Several improvements of the original Coomassie protocol(1) have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20\% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution(2), and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol(3). Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol(4). The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins. Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group.}, +author = {Kang, D and Gho, YS}, +doi = {10.5012/bkcs.2002.23.11.1511}, +file = {:home/alex/Dokumente/Mendeley Desktop/Kang, Gho/Bulletin of the Korean Chemical Society/Kang, Gho - 2002 - Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis.pdf:pdf}, +issn = {0253-2964}, +journal = {Bulletin of the Korean Chemical Society}, +keywords = {Acrylic Resins,Acrylic Resins: chemistry,Colloids,Colloids: chemistry,Electrophoresis,Gel,Indicators and Reagents,Indicators and Reagents: chemistry,Proteins,Proteins: analysis,Proteins: chemistry,Rosaniline Dyes,Rosaniline Dyes: chemistry,Sensitivity and Specificity,Staining and Labeling,Staining and Labeling: methods,Two-Dimensional,Two-Dimensional: methods}, +month = nov, +number = {11}, +pages = {1511--1512}, +title = {{Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis}}, +url = {http://koreascience.or.kr/journal/view.jsp?issn=0253-2964\&vol=23\&no=11\&sp=1511}, +volume = {23}, +year = {2002} +} +@article{MONOD1965, +author = {MONOD, J and WYMAN, J and CHANGEUX, J P}, +issn = {0022-2836}, +journal = {Journal of molecular biology}, +keywords = {Chemistry,Enzymes,Hemoglobins,Kinetics,Models,Physical,Physicochemical Phenomena,Proteins,Research,Theoretical,Ultracentrifugation}, +month = may, +pages = {88--118}, +pmid = {14343300}, +title = {{ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/14343300}, +volume = {12}, +year = {1965} +} +@article{Pineda2004, +abstract = {Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.}, +author = {Pineda, Agustin O and Carrell, Christopher J and Bush, Leslie a and Prasad, Swati and Caccia, Sonia and Chen, Zhi-Wei and Mathews, F Scott and {Di Cera}, Enrico}, +doi = {10.1074/jbc.M401756200}, +file = {:home/alex/Dokumente/Mendeley Desktop/Pineda et al/The Journal of biological chemistry/Pineda et al. - 2004 - Molecular dissection of Na binding to thrombin.pdf:pdf}, +issn = {0021-9258}, +journal = {The Journal of biological chemistry}, +keywords = {Allosteric Site,Allosteric Site: genetics,Crystallography, X-Ray,Humans,Models, Molecular,Mutagenesis, Site-Directed,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Sodium,Sodium: metabolism,Static Electricity,Thermodynamics,Thrombin,Thrombin: chemistry,Thrombin: genetics,Thrombin: metabolism}, +month = jul, +number = {30}, +pages = {31842--53}, +pmid = {15152000}, +title = {{Molecular dissection of Na+ binding to thrombin.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/15152000}, +volume = {279}, +year = {2004} +} +@article{Muller2006, +author = {M\"{u}ller, U. F.}, +doi = {10.1007/s00018-006-6047-1}, +issn = {1420-682X}, +journal = {Cellular and Molecular Life Sciences}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = may, +number = {11}, +pages = {1278--1293}, +title = {{Re-creating an RNA world}}, +url = {http://www.springerlink.com/index/10.1007/s00018-006-6047-1}, +volume = {63}, +year = {2006} +} +@article{Crump2004a, +abstract = {LFA-1 (lymphocyte function-associated antigen-1) plays a role in intercellular adhesion and lymphocyte trafficking and activation and is an attractive anti-inflammatory drug target. The alpha-subunit of LFA-1, in common with several other integrins, has an N-terminally inserted domain (I-domain) of approximately 200 amino acids that plays a central role in regulating ligand binding to LFA-1. An additional region, termed the I-domain allosteric site (IDAS), has been identified exclusively within the LFA-1 I-domain and shown to regulate the function of this protein. The IDAS is occupied by small molecule LFA-1 inhibitors when cocrystallized or analyzed by (15)N-(1)H HSQC (heteronuclear single-quantum coherence) NMR (nuclear magnetic resonance) titration experiments. We report here a novel arylthio inhibitor that binds the I-domain with a K(d) of 18.3 nM as determined by isothermal titration calorimetry (ITC). This value is in close agreement with the IC(50) (10.9 nM) derived from a biochemical competition assay (DELFIA) that measures the level of inhibition of binding of whole LFA-1 to its ligand, ICAM-1. Having established the strong affinity of the arylthio inhibitor for the isolated I-domain, we have used a range of techniques to further characterize the binding, including ITC, NMR, and X-ray crystallography. We have first developed an effective ITC binding assay for use with low-solubility inhibitors that avoids the need for ELISA-based assays. In addition, we utilized a fast NMR-based assay for the generation of I-domain-inhibitor models. This is based around the collection of HCCH-TOCSY spectra of LFA-1 in the bound form and the identification of a subset of side chain methyl groups that give chemical shift changes upon binding of LFA-1 inhibitors. This subset was used in two-dimensional (13)C-(15)N and (15)N-filtered and -edited two-dimensional NMR experiments to identify a minimal set of intraligand and ligand-protein NOEs, respectively (nuclear Overhauser enhancements). Models from the NMR data were assessed by comparison to an X-ray crystallographic structure of the complex, confirming that the method correctly predicted the essential features of the bound ligand.}, +author = {Crump, Matthew P and Ceska, Thomas A and Spyracopoulos, Leo and Henry, Alistair and Archibald, Sarah C and Alexander, Rikki and Taylor, Richard J and Findlow, Stuart C and O'Connell, James and Robinson, Martyn K and Shock, Anthony}, +doi = {10.1021/bi035422a}, +file = {:home/alex/Dokumente/Mendeley Desktop/Crump et al/Biochemistry/Crump et al. - 2004 - Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Allosteric Site,Amides,Amides: chemistry,Binding,Biomolecular,Calorimetry,Cinnamates,Cinnamates: chemistry,Cinnamates: metabolism,Competitive,Crystallography,Drug Design,Humans,Ligands,Lymphocyte Function-Associated Antigen-1,Lymphocyte Function-Associated Antigen-1: chemistr,Lymphocyte Function-Associated Antigen-1: metaboli,Models,Molecular,Nuclear Magnetic Resonance,Protein Binding,Protein Structure,Protein Subunits,Protein Subunits: antagonists \& inhibitors,Protein Subunits: chemistry,Recombinant Proteins,Recombinant Proteins: antagonists \& inhibitors,Recombinant Proteins: chemistry,Tertiary,X-Ray}, +month = mar, +number = {9}, +pages = {2394--404}, +pmid = {14992576}, +title = {{Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/14992576}, +volume = {43}, +year = {2004} +} +@book{Lottspeich2006a, +address = {M\"{u}nchen ;;Heidelberg}, +author = {Lottspeich, Friedrich}, +edition = {2. Aufl.}, +isbn = {9783827415202}, +keywords = {Folder - Biochemie}, +mendeley-tags = {Folder - Biochemie}, +publisher = {Spektrum Akademischer Verlag}, +title = {{Bioanalytik}}, +year = {2006} +} +@article{Sreerama2000, +abstract = {We have expanded the reference set of proteins used in SELCON3 by including 11 additional proteins (selected from the reference sets of Yang and co-workers and Keiderling and co-workers). Depending on the wavelength range and whether or not denatured proteins are included in the reference set, five reference sets were constructed with the number of reference proteins varying from 29 to 48. The performance of three popular methods for estimating protein secondary structure fractions from CD spectra (implemented in software packages CONTIN, SELCON3, and CDSSTR) and a variant of CONTIN, CONTIN/LL, that incorporates the variable selection method in the locally linearized model in CONTIN, were examined using the five reference sets described here, and a 22-protein reference set. Secondary structure assignments from DSSP were used in the analysis. The performances of all three methods were comparable, in spite of the differences in the algorithms used in the three software packages. While CDSSTR performed the best with a smaller reference set and larger wavelength range, and CONTIN/LL performed the best with a larger reference set and smaller wavelength range, the performances for individual secondary structures were mixed. Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions. The three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper. CDPro software is available at the website: http://lamar.colostate.edu/ approximately sreeram/CDPro.}, +author = {Sreerama, N and Woody, R W}, +doi = {10.1006/abio.2000.4880}, +file = {:home/alex/Dokumente/Mendeley Desktop/Sreerama, Woody/Analytical biochemistry/Sreerama, Woody - 2000 - Estimation of protein secondary structure from circular dichroism spectra comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.pdf:pdf}, +issn = {0003-2697}, +journal = {Analytical biochemistry}, +keywords = {Circular Dichroism,Protein Structure, Secondary,Proteins,Proteins: chemistry,Reference Standards}, +month = dec, +number = {2}, +pages = {252--60}, +pmid = {11112271}, +title = {{Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/11112271}, +volume = {287}, +year = {2000} +} +@book{Atkins2006, +address = {Weinheim}, +author = {Atkins, Peter W and de Paula, Julio}, +edition = {4., vollst}, +isbn = {9783527315468}, +keywords = {Folder - Physikalische Chemie}, +mendeley-tags = {Folder - Physikalische Chemie}, +publisher = {Wiley-VCH}, +title = {{Physikalische Chemie}}, +year = {2006} +} +@book{Taiz2007, +address = {M\"{u}nchen; Heidelberg}, +author = {Taiz, Lincoln and Zeiger, Eduardo}, +edition = {4. ed.}, +isbn = {9783827418654}, +keywords = {Folder - Pflanzenphysiologie}, +mendeley-tags = {Folder - Pflanzenphysiologie}, +publisher = {Spektrum Akademischer Verlag}, +title = {{Plant physiology das Original mit \"{U}bersetzungshilfen}}, +year = {2007} +} +@article{Chastain2002, +abstract = {Pyruvate,orthophosphate (Pi) dikinase (PPDK) is best recognized as a chloroplastic C(4) cycle enzyme. As one of the key regulatory foci for controlling flux through this photosynthetic pathway, it is strictly and reversibly regulated by light. This light/dark modulation is mediated by reversible phosphorylation of a conserved threonine residue in the active-site domain by the PPDK regulatory protein (RP), a bifunctional protein kinase/phosphatase. PPDK is also present in C(3) plants, although it has no known photosynthetic function. Nevertheless, in this report we show that C(3) PPDK in leaves of several angiosperms and in isolated intact spinach (Spinacia oleracea) chloroplasts undergoes light-/dark-induced changes in phosphorylation state in a manner similar to C(4) dikinase. In addition, the kinetics of this process closely resemble the reversible C(4) process, with light-induced dephosphorylation occurring rapidly (< or =15 min) and dark-induced phosphorylation occurring much more slowly (> or =30-60 min). In intact spinach chloroplasts, light-induced dephosphorylation of C(3) PPDK was shown to be dependent on exogenous Pi and photosystem II activity but independent of electron transfer from photosystem I. These in organello results implicate a role for stromal pools of Pi and adenylates in regulating the reversible phosphorylation of C(3)-PPDK. Last, we used an in vitro RP assay to directly demonstrate ADP-dependent PPDK phosphorylation in desalted leaf extracts of the C(3) plants Vicia faba and rice (Oryza sativa). We conclude that an RP-like activity mediates the light/dark modulation of PPDK phosphorylation state in C(3) leaves and chloroplasts and likely represents the ancestral isoform of this unusual and key C(4) pathway regulatory "converter" enzyme.}, +author = {Chastain, Chris J and Fries, Jason P and Vogel, Julie A and Randklev, Christa L and Vossen, Adam P and Dittmer, Sharon K and Watkins, Erin E and Fiedler, Lucas J and Wacker, Sarah A and Meinhover, Katherine C and Sarath, Gautam and Chollet, Raymond}, +doi = {10.1104/pp.010806}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Plant physiology/Chastain et al. - 2002 - Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-dark-induced reversible phosphorylation.pdf:pdf}, +issn = {0032-0889}, +journal = {Plant physiology}, +keywords = {Adenosine Diphosphate,Adenosine Diphosphate: metabolism,Adenosine Monophosphate,Adenosine Monophosphate: metabolism,Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Angiosperms,Angiosperms: classification,Angiosperms: enzymology,Biological,Chloroplasts,Chloroplasts: enzymology,Darkness,Fabaceae,Fabaceae: enzymology,Light,Models,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Oryza sativa,Oryza sativa: enzymology,Phosphates,Phosphates: metabolism,Phosphoenolpyruvate,Phosphoenolpyruvate: metabolism,Phosphorylation,Photosynthetic Reaction Center Complex Proteins,Photosynthetic Reaction Center Complex Proteins: m,Photosystem I Protein Complex,Photosystem II Protein Complex,Plant Leaves,Plant Leaves: enzymology,Pyruvate,Pyruvic Acid,Pyruvic Acid: metabolism,Spinacia oleracea,Spinacia oleracea: enzymology,Zea mays,Zea mays: enzymology}, +month = apr, +number = {4}, +pages = {1368--78}, +pmid = {11950985}, +title = {{Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-/dark-induced reversible phosphorylation.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=154264\&tool=pmcentrez\&rendertype=abstract}, +volume = {128}, +year = {2002} +} +@article{Crick1968, +author = {Crick, F H}, +file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Journal of Molecular Biology/Crick - 1968 - The origin of the genetic code.pdf:pdf}, +issn = {0022-2836}, +journal = {Journal of Molecular Biology}, +keywords = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger}, +mendeley-tags = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger}, +month = dec, +number = {3}, +pages = {367--379}, +title = {{The origin of the genetic code}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/4887876 http://www.sciencedirect.com/science?\_ob=MImg\&\_imagekey=B6WK7-4DM29RS-BH-1\&\_cdi=6899\&\_user=2665780\&\_pii=0022283668903926\&\_origin=\&\_coverDate=12/28/1968\&\_sk=999619996\&view=c\&wchp=dGLzVlz-zSkzV\&md5=04e907452df700b018f50eae6799bb6a\&ie=/sdarticle.pdf}, +volume = {38}, +year = {1968} +} +@article{Li2007, +author = {Li, Mamie Z and Elledge, Stephen J}, +doi = {10.1038/nprot.2007.90}, +issn = {2043-0116}, +journal = {Protocol Exchange}, +keywords = {Folder - Biochemie}, +mendeley-tags = {Folder - Biochemie}, +month = feb, +title = {{SLIC sub-cloning using T4 DNA polymerase treated inserts without RecA}}, +url = {http://www.natureprotocols.com/2007/02/15/slic\_subcloning\_using\_t4\_dna\_p.php http://www.nature.com/protocolexchange/protocols/167}, +year = {2007} +} +@article{Geourjon1995, +abstract = {Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins. In this paper we report improvements brought about by predicting all the sequences of a set of aligned proteins belonging to the same family. This improved SOPM method (SOPMA) correctly predicts 69.5\% of amino acids for a three-state description of the secondary structure (alpha-helix, beta-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25\% identity) proteins. Joint prediction with SOPMA and a neural networks method (PHD) correctly predicts 82.2\% of residues for 74\% of co-predicted amino acids. Predictions are available by Email to deleage@ibcp.fr or on a Web page (http:@www.ibcp.fr/predict.html).}, +author = {Geourjon, C and Del\'{e}age, G}, +issn = {0266-7061}, +journal = {Computer Applications in the Biosciences: CABIOS}, +keywords = {Databases- Factual,Folder - RTE1,Neural Networks (Computer),Protein Structure- Secondary,Proteins,Sequence Alignment,Sequence Homology- Amino Acid,Software}, +mendeley-tags = {Databases- Factual,Folder - RTE1,Neural Networks (Computer),Protein Structure- Secondary,Proteins,Sequence Alignment,Sequence Homology- Amino Acid,Software}, +month = dec, +number = {6}, +pages = {681--684}, +title = {{SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/8808585}, +volume = {11}, +year = {1995} +} +@article{Doyle2005, +abstract = {Plants using the C(4) photosynthetic pathway are highly represented among the world's worst weeds, with only 4 C(4) species being agriculturally productive (maize, sorghum, millet, and sugar cane). With the C(4) acid cycle operating as a biochemical appendage of C(3) photosynthesis, the additional enzymes involved in C(4) photosynthesis represent an attractive target for the development of weed-specific herbicides. The rate-limiting enzyme of this metabolic pathway is pyruvate orthophosphate dikinase (PPDK). PPDK, coupled with phosphoenolpyruvate carboxylase and nicotinamide adenine dinucleotide-malate dehydrogenase, was used to develop a microplate-based assay to detect inhibitors of enzymes of the C(4) acid cycle. The resulting assay had a Z' factor of 0.61, making it a high-quality assay able to reliably identify active test samples. Organic extracts of 6679 marine macroscopic organisms were tested within the assay, and 343 were identified that inhibited the 3 enzyme-coupled reaction. A high confirmation rate was achieved, with 95\% of these hit extracts proving active again upon retesting. Sequential addition of phosphoenolpyruvate and oxaloacetate to the assay facilitated identification of 83 extracts that specifically inhibited PPDK.}, +author = {Doyle, Jason R and Burnell, James N and Haines, Dianne S and Llewellyn, Lyndon E and Motti, Cherie a and Tapiolas, Dianne M}, +doi = {10.1177/1087057104269978}, +file = {:home/alex/Dokumente/Mendeley Desktop/Doyle et al/Journal of biomolecular screening/Doyle et al. - 2005 - A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.pdf:pdf}, +issn = {1087-0571}, +journal = {Journal of biomolecular screening}, +keywords = {Dimethyl Sulfoxide,Dimethyl Sulfoxide: pharmacology,Drug Evaluation, Preclinical,Drug Evaluation, Preclinical: methods,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Enzyme Inhibitors: pharmacology,Herbicides,Herbicides: chemistry,Herbicides: pharmacology,Malate Dehydrogenase,Malate Dehydrogenase: antagonists \& inhibitors,Malate Dehydrogenase: metabolism,Molecular Structure,Oxalic Acid,Oxalic Acid: pharmacology,Phosphoenolpyruvate Carboxylase,Phosphoenolpyruvate Carboxylase: antagonists \& inh,Phosphoenolpyruvate Carboxylase: metabolism,Plant Extracts,Plant Extracts: metabolism,Plants,Plants: drug effects,Plants: enzymology,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: antagonists \& i,Pyruvate, Orthophosphate Dikinase: metabolism,Species Specificity,Time Factors}, +month = feb, +number = {1}, +pages = {67--75}, +pmid = {15695345}, +title = {{A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/15695345}, volume = {10}, +year = {2005} +} +@article{Sievers2011, +abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.}, +author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S\"{o}ding, Johannes and Thompson, Julie D and Higgins, Desmond G}, +doi = {10.1038/msb.2011.75}, +issn = {1744-4292}, +journal = {Molecular systems biology}, +keywords = {Algorithms,Amino Acid Sequence,Base Sequence,Data Mining,Data Mining: methods,Databases,Factual,Molecular Sequence Data,Protein,Protein: methods,Proteins,Proteins: analysis,Proteins: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,Systems Biology,Systems Biology: instrumentation,Systems Biology: methods}, +month = jan, +pages = {539}, +pmid = {21988835}, +title = {{Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/21988835}, +volume = {7}, +year = {2011} +} +@article{Michalkova2011, +author = {Michalkova, Andrea and Kholod, Yana and Kosenkov, Dmytro and Gorb, Leonid and Leszczynski, Jerzy}, +doi = {10.1016/j.gca.2011.01.015}, +issn = {00167037}, +journal = {Geochimica et Cosmochimica Acta}, +month = apr, +number = {7}, +pages = {1933--1941}, +shorttitle = {Viability of pyrite pulled metabolism in the ‘iron}, +title = {{Viability of pyrite pulled metabolism in the ‘iron-sulfur world’ theory: Quantum chemical assessment}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0016703711000238}, +volume = {75}, +year = {2011} +} +@article{Schagger2006, +author = {Sch\"{a}gger, Hermann}, +doi = {10.1038/nprot.2006.4}, +issn = {1754-2189}, +journal = {Nature Protocols}, +keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll}, +mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll}, +month = jun, +number = {1}, +pages = {16--22}, +title = {{Tricine–SDS-PAGE}}, +url = {http://www.nature.com/doifinder/10.1038/nprot.2006.4 http://www.nature.com/nprot/journal/v1/n1/pdf/nprot.2006.4.pdf}, +volume = {1}, +year = {2006} +} +@article{Lu2000, +abstract = {Eglin c from the leech Hirudo medicinalis is a potent protein inhibitor of many serine proteinases including chymotrypsin and subtilisins. Unlike most small protein inhibitors whose solvent-exposed enzyme-binding loop is stabilized primarily by disulfide bridges flanking the reactive-site peptide bond, eglin c possesses an enzyme-binding loop supported predominantly by extensive electrostatic/H-bonding interactions involving three Arg residues (Arg48, Arg51, and Arg53) projecting from the scaffold of the inhibitor. As an adjacent residue, the C-terminal Gly70 participates in these interactions via its alpha-carboxyl group interacting with the side chain of Arg51 and the main chain of Arg48. In addition, the amide NH group of Gly70 donates an H-bond to the carbonyl C=O groups of Arg48 and Arg51. To understand the structural and functional relevance of the electrostatic/H-bonding network, we chemically synthesized wild-type eglin c and three analogues in which Gly70 was either deleted or replaced by glycine amide (NH(2)CH(2)CONH(2)) or by alpha-hydroxylacetamide (HOCH(2)CONH(2)). NMR analysis indicated that the core structure of eglin c was maintained in the analogues, but that the binding loop was significantly perturbed. It was found that deletion or replacement of Gly70 destabilized eglin c by an average of 2.7 kcal/mol or 20 degrees C in melting temperature. As a result, these inhibitors become substrates for their target enzymes. Binding assays on these analogues with a catalytically incompetent subtilisin BPN' mutant indicated that loss or weakening of the interactions involving the carboxylate of Gly70 caused a decrease in binding by approximately 2 orders of magnitude. Notably, for all four synthetic inhibitors, the relative free energy changes (DeltaDeltaG) associated with protein destabilization are strongly correlated (slope = 0.94, r(2) = 0. 9996) with the DeltaDeltaG values derived from a decreased binding to the enzyme.}, +author = {Lu, Wei-Yue and Starovasnik, Melissa a and Dwyer, John J and Kossiakoff, Anthony a and Kent, Stephen B. H. and Lu, Wuyuan}, +doi = {10.1021/bi992292q}, +file = {:home/alex/Dokumente/Mendeley Desktop/Lu et al/Biochemistry/Lu et al. - 2000 - Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Amino Acid Sequence,Animals,Binding Sites,Biomolecular,Chymotrypsin,Chymotrypsin: antagonists \& inhibitors,Glycine,Glycine: chemistry,Glycine: metabolism,Kinetics,Leeches,Molecular Sequence Data,Nuclear Magnetic Resonance,Protein Denaturation,Proteins,Serpins,Serpins: chemical synthesis,Serpins: chemistry,Serpins: metabolism,Static Electricity,Structure-Activity Relationship,Subtilisins,Subtilisins: antagonists \& inhibitors}, +month = apr, +number = {13}, +pages = {3575--3584}, +pmid = {10736156}, +title = {{Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/10736156 http://pubs.acs.org/doi/abs/10.1021/bi992292q}, +volume = {39}, +year = {2000} +} +@article{Puius1997, +abstract = {The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2\% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1\% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.}, +author = {Puius, Y a and Zhao, Y and Sullivan, M and Lawrence, D S and Almo, S C and Zhang, Z Y}, +file = {:home/alex/Dokumente/Mendeley Desktop/Puius et al/Proceedings of the National Academy of Sciences of the United States of America/Puius et al. - 1997 - Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B a paradigm for inhibitor design.pdf:pdf}, +issn = {0027-8424}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Base Sequence,Binding Sites,Binding Sites: genetics,Cloning, Molecular,DNA Primers,DNA Primers: genetics,Drug Design,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Escherichia coli,Escherichia coli: genetics,Humans,Models, Molecular,Molecular Sequence Data,Mutagenesis, Site-Directed,Phosphotyrosine,Phosphotyrosine: metabolism,Polymerase Chain Reaction,Protein Conformation,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: antagonists \& inhib,Protein Tyrosine Phosphatases: chemistry,Protein Tyrosine Phosphatases: genetics,Substrate Specificity}, +month = dec, +number = {25}, +pages = {13420--5}, +pmid = {9391040}, +title = {{Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=28320\&tool=pmcentrez\&rendertype=abstract}, +volume = {94}, +year = {1997} +} +@article{Schrader1985, +abstract = {The objective of this study was to determine the biochemical basis for genetic variability in pyruvate,Pi dikinase (PPDK) activity among inbred lines of maize (Zea mays L.). Although in vitro PPDK activity varied more than 5-fold among eight maize inbreds, immunochemical determinations of the proportion of leaf soluble protein as PPDK revealed no significant differences among the inbreds. Genetic differences in the stability of PPDK activity in crude homogenates over 5 hours were not evident, but PPDK from some inbreds could not be activated in vitro. In vitro PPDK activation in crude homogenates could be restored by addition of casein (1\% w/v) to homogenization media, and to a lesser extent, by gentle homogenization in a mortar. The major effect of casein appeared to be on processes other than proteolysis, as casein exerted its effects during tissue homogenization, rather than later. During homogenization, PPDK did not lose its ability to undergo in vitro activation; instead, it was instability of the regulatory protein responsible for PPDK activation that was the cause of the lack of PPDK activation in homogenates prepared without casein.}, +author = {Baer, G R and Schrader, Larry E}, +file = {:home/alex/Dokumente/Mendeley Desktop/Baer, Schrader/Plant physiology/Baer, Schrader - 1985 - Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.pdf:pdf}, +issn = {0032-0889}, +journal = {Plant physiology}, +month = mar, +number = {3}, +pages = {608--11}, +pmid = {16664106}, +title = {{Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1064572\&tool=pmcentrez\&rendertype=abstract}, +volume = {77}, +year = {1985} +} +@article{Petit2009, +abstract = {Structure-function relationships in proteins are predicated on the spatial proximity of noncovalently interacting groups of atoms. Thus, structural elements located away from a protein's active site are typically presumed to serve a stabilizing or scaffolding role for the larger structure. Here we report a functional role for a distal structural element in a PDZ domain, even though it is not required to maintain PDZ structure. The third PDZ domain from PSD-95/SAP90 (PDZ3) has an unusual additional third alpha helix (alpha3) that packs in contiguous fashion against the globular domain. Although alpha3 lies outside the active site and does not make direct contact with C-terminal peptide ligand, removal of alpha3 reduces ligand affinity by 21-fold. Further investigation revealed that the difference in binding free energies between the full-length and truncated constructs is predominantly entropic in nature and that without alpha3, picosecond-nanosecond side-chain dynamics are enhanced throughout the domain, as determined by (2)H methyl NMR relaxation. Thus, the distal modulation of binding function appears to occur via a delocalized conformational entropy mechanism. Without removal of alpha3 and characterization of side-chain dynamics, this dynamic allostery would have gone unnoticed. Moreover, what appeared at first to be an artificial modification of PDZ3 has been corroborated by experimentally verified phosphorylation of alpha3, revealing a tangible biological mechanism for this novel regulatory scheme. This hidden dynamic allostery raises the possibility of as-yet unidentified or untapped allosteric regulation in this PDZ domain and is a very clear example of function arising from dynamics rather than from structure.}, +author = {Petit, Chad M and Zhang, Jun and Sapienza, Paul J and Fuentes, Ernesto J and Lee, Andrew L}, +doi = {10.1073/pnas.0904492106}, +file = {:home/alex/Dokumente/Mendeley Desktop/Petit et al/Proceedings of the National Academy of Sciences of the United States of America/Petit et al. - 2009 - Hidden dynamic allostery in a PDZ domain.pdf:pdf}, +issn = {1091-6490}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Allosteric Regulation,Animals,Biomolecular,Intracellular Signaling Peptides and Proteins,Intracellular Signaling Peptides and Proteins: che,Intracellular Signaling Peptides and Proteins: met,Ligands,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: metabolism,Models,Molecular,Nuclear Magnetic Resonance,PDZ Domains,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: metabolism,Protein Binding,Protein Structure,Rats,Secondary,Thermodynamics}, +month = oct, +number = {43}, +pages = {18249--54}, +pmid = {19828436}, +title = {{Hidden dynamic allostery in a PDZ domain.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2775317\&tool=pmcentrez\&rendertype=abstract}, +volume = {106}, +year = {2009} +} +@article{Clarkson2006, +abstract = {Long-range intraprotein interactions give rise to many important protein behaviors. Understanding how energy is transduced through protein structures to either transmit a signal or elicit conformational changes is therefore a current challenge in structural biology. In an effort to understand such linkages, multiple V --> A mutations were made in the small globular protein eglin c. The physical responses, as mapped by NMR spin relaxation, residual dipolar couplings (RDCs), and scalar couplings, illustrate that the interior of this nonallosteric protein forms a dynamic network and that local perturbations are transmitted as dynamic and structural changes to distal sites as far as 16 A away. Two basic types of propagation responses were observed: contiguous pathways of enhanced (attenuated) dynamics with no change in structure; and dispersed (noncontiguous) changes in methyl rotation rates that appear to result from subtle deformation of backbone structure. In addition, energy transmission is found to be unidirectional. In one mutant, an allosteric conformational change of a side chain is seen in the context of a pathway of propagated changes in picosecond to nanosecond dynamics. The observation of so many long-range interactions in a small, rigid system lends experimental weight to the idea that all well-folded proteins inherently possess allosteric features [Gunasekaran et al. (2004) Proteins 57, 433-443], and that dynamics are a rich source of information for mapping and gaining mechanistic insight into communication pathways in individual proteins.}, +author = {Clarkson, Michael W and Gilmore, Steven A and Edgell, Marshall H and Lee, Andrew L}, +doi = {10.1021/bi060652l}, +file = {:home/alex/Dokumente/Mendeley Desktop/Clarkson et al/Biochemistry/Clarkson et al. - 2006 - Dynamic coupling and allosteric behavior in a nonallosteric protein.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Allosteric Regulation,Amino Acid Substitution,Biomolecular,Eglin c,Models,Molecular,Nuclear Magnetic Resonance,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Proteins: genetics,Signal Transduction}, +mendeley-tags = {Eglin c}, +month = jun, +number = {25}, +pages = {7693--9}, +pmid = {16784220}, +title = {{Dynamic coupling and allosteric behavior in a nonallosteric protein.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2453595\&tool=pmcentrez\&rendertype=abstract}, +volume = {45}, +year = {2006} +} +@article{Cui2008a, +abstract = {Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/Pauling-KNF descriptions, and point out that the "new view" of allostery, emphasizing "population shifts," is, in fact, an "old view." The presentation offers not only an up-to-date description of allostery from a theoretical/computational perspective, but also helps to resolve several outstanding issues concerning allostery.}, +author = {Cui, Qiang and Karplus, Martin}, +doi = {10.1110/ps.03259908}, +file = {:home/alex/Dokumente/Mendeley Desktop/Cui, Karplus/Protein science a publication of the Protein Society/Cui, Karplus - 2008 - Allostery and cooperativity revisited.pdf:pdf}, +issn = {1469-896X}, +journal = {Protein science : a publication of the Protein Society}, +keywords = {Allosteric Regulation,Allosteric Site,Animals,Dimerization,Folder - Allostery - Theory,Hemoglobins,Hemoglobins: chemistry,Humans,Mechanism,Models,Molecular,Protein Structure,Proteins,Proteins: chemistry,Quaternary,Tertiary}, +mendeley-tags = {Folder - Allostery - Theory,Mechanism}, +month = aug, +number = {8}, +pages = {1295--307}, +pmid = {18560010}, +title = {{Allostery and cooperativity revisited.}}, +url = {http://doi.wiley.com/10.1110/ps.03259908 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2492820\&tool=pmcentrez\&rendertype=abstract}, +volume = {17}, +year = {2008} +} +@article{Voet-van-Vormizeele2008, +author = {Voet-van-Vormizeele, Jan and Groth, Georg}, +file = {:home/alex/Dokumente/Mendeley Desktop/Voet-van-Vormizeele, Groth/Current Topics in Biochemical Research/Voet-van-Vormizeele, Groth - 2008 - Mutants, molecules and mechanisms - Decipering the ethylene signalling network.pdf:pdf}, +issn = {09724583}, +journal = {Current Topics in Biochemical Research}, +keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper}, +number = {2}, +pages = {25--34}, +title = {{Mutants, molecules and mechanisms - Decipering the ethylene signalling network}}, +volume = {10}, +year = {2008} +} +@article{Pfleger2012, +author = {Pfleger, Christopher and Radestock, Sebastian and Schmidt, S. and Gohlke, Holger}, +title = {{Global and local indices for characterizing biomolecular flexibility and rigidity}}, +year = {2012} +} +@article{Luisi2003, +author = {Luisi, P. L}, +file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Philosophical Transactions Mathematical, Physical and Engineering Sciences/Luisi - 2003 - Contingency and determinism.pdf:pdf}, +journal = {Philosophical Transactions: Mathematical, Physical and Engineering Sciences}, +pages = {1141--1147}, +title = {{Contingency and determinism}}, year = {2003} } +@article{McComb1976, +abstract = {The molar absorptivity of NADH at 340 nm has been determined by an indirect procedure in which high-purity glucose is phosphorylated by ATP in the presence of hexokinase, coupled to oxidation of the glucose-6-phosphate by NAD+ in the presence of glucose-6-phosphate dehydrogenase. The average value from 85 independent determinations is 6317 liter mol-1 cm-1 at 25 degrees C and pH 7.8. The overall uncertainty is -4.0 to +5.5 ppt (6292 to 6352 liter mol-1 cm-1), based on a standard error of the mean of 0.48 ppt and an estimate of systematic error of -2.6 to +4.1 ppt. Effects of pH, buffer, and temperature on the molar absorptivity are also reported.}, +author = {McComb, R B and Bond, L W and Burnett, R W and Keech, R C and Bowers, G N}, +file = {:home/alex/Dokumente/Mendeley Desktop/McComb et al/Clinical chemistry/McComb et al. - 1976 - Determination of the molar absorptivity of NADH.pdf:pdf}, +issn = {0009-9147}, +journal = {Clinical chemistry}, +keywords = {Absorption,Adenosine Triphosphate,Evaluation Studies as Topic,Glucose,Glucosephosphate Dehydrogenase,Hexokinase,Hydrogen-Ion Concentration,NAD,NAD: analysis,Osmolar Concentration,Oxidation-Reduction,Spectrophotometry,Temperature,Ultraviolet}, +month = mar, +number = {2}, +pages = {141--50}, +pmid = {2388}, +title = {{Determination of the molar absorptivity of NADH.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/2388}, +volume = {22}, +year = {1976} +} +@article{Sponer2011, +author = {\v{S}poner, Judit E. and \v{S}poner, Jiř\'{\i} and Fuentes-Cabrera, Miguel}, +doi = {10.1002/chem.201002057}, +issn = {09476539}, +journal = {Chemistry - A European Journal}, +month = jan, +number = {3}, +pages = {847--854}, +shorttitle = {Prebiotic Routes to Nucleosides}, +title = {{Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways}}, +url = {http://doi.wiley.com/10.1002/chem.201002057}, +volume = {17}, +year = {2011} +} +@article{Wachtershauser2006, +author = {Wachtershauser, G.}, +doi = {10.1098/rstb.2006.1904}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wachtershauser/Philosophical Transactions of the Royal Society B Biological Sciences/Wachtershauser - 2006 - From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya.pdf:pdf}, +issn = {0962-8436}, +journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, +month = oct, +number = {1474}, +pages = {1787--1808}, +title = {{From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya}}, +url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2006.1904}, +volume = {361}, +year = {2006} +} +@article{Dong2004, +author = {Dong, X. and Stothard, P. and Forsythe, I. J. and Wishart, D. S.}, +doi = {10.1093/nar/gkh410}, +file = {:home/alex/Dokumente/Mendeley Desktop/Dong et al/Nucleic Acids Research/Dong et al. - 2004 - PlasMapper a web server for drawing and auto-annotating plasmid maps.pdf:pdf}, +issn = {0305-1048}, +journal = {Nucleic Acids Research}, +month = jul, +number = {Web Server}, +pages = {W660--W664}, +title = {{PlasMapper: a web server for drawing and auto-annotating plasmid maps}}, +url = {http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkh410}, +volume = {32}, +year = {2004} +} +@misc{CenterforHistoryandNewMedia, +annote = { + Welcome to Zotero! + + + +View the Quick Start Guide to learn how to begin collecting, managing, citing, and sharing your research sources. +Thanks for installing Zotero.}, +author = {{Center for History and New Media}}, +title = {{Zotero Quick Start Guide}}, +url = {http://zotero.org/support/quick\_start\_guide} +} +@book{Bruckner2007, +address = {Berlin [u.a.]}, +author = {Br\"{u}ckner, Reinhard}, +edition = {3. Aufl., }, +isbn = {9783827415790}, +keywords = {Folder - Organische Chemie}, +mendeley-tags = {Folder - Organische Chemie}, +publisher = {Spektrum Akademischer Verlag}, +title = {{Reaktionsmechanismen : organische Reaktionen, Stereochemie, moderne Synthesemethoden}}, +year = {2007} +} +@article{Chapman1981, +abstract = {Requirements for activation of inactive pyruvate, inorganic phosphate (Pi) dikinase extracted from darkened maize leaves were examined. Incubation with Pi plus dithiothreitol resulted in a rapid recovery of activity comparable to that in illuminated leaves. However, contrary to previous findings, most of this activity (60–95\%) was recovered by adding Pi alone. There was no activation with dithiothreitol alone. Dependency on dithiothreitol, in addition to Pi was minimal at about pH 7.5 but was substantial at higher pH. Anaerobic conditions did not enhance Pi-dependent activation. Active enzyme, isolated from illuminated leaves, was inactivated by incubating with ADP and this occurred in the presence of dithiothreitol. ATP and AMP were not effective but ATP may be a corequirment for ADP-dependent inactivation. Enzyme inactivated by ADP required Pi for reactivation. We conclude that interconversion of dithiol and disulfide forms of the enzyme is not critical for the dark/light regulation of pyruvate, Pi dikinase. The primary mechanism apparently involves an ADP-induced transformation to an inactive form which undergoes a Pi-mediated reactivation.}, +author = {Chapman, K S R and Hatch, M D}, +doi = {10.1016/0003-9861(81)90166-1}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chapman, Hatch/Archives of Biochemistry and Biophysics/Chapman, Hatch - 1981 - Regulation of C4 photosynthesis Mechanism of activation and inactivation of extracted pyruvate, inorganic phosphate dikinase in relation to darklight regulation.pdf:pdf}, +issn = {00039861}, +journal = {Archives of Biochemistry and Biophysics}, +month = aug, +number = {1}, +pages = {82--89}, +title = {{Regulation of C4 photosynthesis: Mechanism of activation and inactivation of extracted pyruvate, inorganic phosphate dikinase in relation to dark/light regulation}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/0003986181901661}, +volume = {210}, +year = {1981} +} +@article{Hauske2008a, +abstract = {Allostery is a basic principle of control of enzymatic activities based on the interaction of a protein or small molecule at a site distinct from an enzyme's active center. Allosteric modulators represent an alternative approach to the design and synthesis of small-molecule activators or inhibitors of proteases and are therefore of wide interest for medicinal chemistry. The structural bases of some proteinaceous and small-molecule allosteric protease regulators have already been elucidated, indicating a general mechanism that might be exploitable for future rational design of small-molecule effectors.}, +author = {Hauske, Patrick and Ottmann, Christian and Meltzer, Michael and Ehrmann, Michael and Kaiser, Markus}, +doi = {10.1002/cbic.200800528}, +file = {:home/alex/Dokumente/Mendeley Desktop/Hauske et al/Chembiochem a European journal of chemical biology/Hauske et al. - 2008 - Allosteric regulation of proteases.pdf:pdf}, +issn = {1439-7633}, +journal = {Chembiochem : a European journal of chemical biology}, +keywords = {Allosteric Regulation,Caspases,Caspases: antagonists \& inhibitors,Caspases: chemistry,Caspases: metabolism,Chemistry,Crystallography,Drug Design,Folder - Allostery - Theory,Mechanism,Models,Molecular,Peptide Hydrolases,Peptide Hydrolases: chemical synthesis,Peptide Hydrolases: chemistry,Peptide Hydrolases: metabolism,Pharmaceutical,Protein Conformation,Protein Structure,Serine Endopeptidases,Serine Endopeptidases: chemistry,Serine Endopeptidases: metabolism,Structure-Activity Relationship,Tertiary,X-Ray}, +mendeley-tags = {Folder - Allostery - Theory,Mechanism}, +month = dec, +number = {18}, +pages = {2920--8}, +pmid = {19021141}, +title = {{Allosteric regulation of proteases.}}, +url = {http://doi.wiley.com/10.1002/cbic.200800528 http://www.ncbi.nlm.nih.gov/pubmed/19021141}, +volume = {9}, +year = {2008} +} +@article{Steitz2003, +author = {Steitz, Thomas A and Moore, Peter B}, +doi = {10.1016/S0968-0004(03)00169-5}, +file = {:home/alex/Dokumente/Mendeley Desktop/Steitz, Moore/Trends in Biochemical Sciences/Steitz, Moore - 2003 - RNA, the first macromolecular catalyst the ribosome is a ribozyme.pdf:pdf}, +issn = {09680004}, +journal = {Trends in Biochemical Sciences}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = aug, +number = {8}, +pages = {411--418}, +shorttitle = {RNA, the first macromolecular catalyst}, +title = {{RNA, the first macromolecular catalyst: the ribosome is a ribozyme}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403001695}, +volume = {28}, +year = {2003} +} +@article{Stone1988, +abstract = {Kinetic studies on the reaction catalyzed by dihydrofolate reductase from Escherichia coli have been undertaken with the aim of characterizing further the kinetic mechanism of the reaction. For this purpose, the kinetic properties of substrates were determined by measurement of (a) initial velocities over a wide range of substrate concentrations and (b) the stickiness of substrates in ternary enzyme complexes. Stickiness is defined as the rate at which a substrate reacts to give products relative to the rate at which that substrate dissociates. Stickiness was determined by varying the viscosity of reaction mixtures and the concentration of one substrate in the presence of a saturating concentration of the other substrate. The results indicate that NADPH is sticky in the enzyme-NADPH-dihydrofolate complex, while dihydrofolate is much less sticky in this complex. At higher concentrations, NADPH functions as an activator through the formation of an enzyme-NADPH-tetrahydrofolate from which tetrahydrofolate is released more rapidly than from an enzyme-tetrahydrofolate complex. Higher concentrations of dihydrofolate also cause enzyme activation, and it appears that this effect is due to the ability of dihydrofolate to displace tetrahydrofolate from a binary enzyme complex through the formation of a transitory enzyme-tetrahydrofolate-dihydrofolate complex. As NADPH and dihydrofolate function as activators and as NADPH behaves as a sticky substrate, the kinetic mechanism of the dihydrofolate reductase reaction with the natural substrates is steady-state random. By contrast with NADPH, reduced 3-acetylpyridine adenine dinucleotide phosphate exhibits only slight stickiness and does not function as an activator.(ABSTRACT TRUNCATED AT 250 WORDS)}, +author = {Stone, S R and Morrison, J F}, +file = {:home/alex/Dokumente/Mendeley Desktop/Stone, Morrison/Biochemistry/Stone, Morrison - 1988 - Dihydrofolate reductase from Escherichia coli the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Deuterium,Escherichia coli,Escherichia coli: enzymology,Folic Acid,Folic Acid: analogs \& derivatives,Folic Acid: metabolism,Hydrogen-Ion Concentration,Kinetics,NAD,NAD: analogs \& derivatives,NAD: metabolism,NADP,NADP: metabolism,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: metabolism,Viscosity}, +month = jul, +number = {15}, +pages = {5493--9}, +pmid = {3052577}, +title = {{Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/3052577}, +volume = {27}, +year = {1988} +} +@article{Tsai2008a, +abstract = {Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For several years, it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free-energy change due to the change in entropy, entropy is mainly responsible for binding.}, +author = {Tsai, Chung-Jung and del Sol, Antonio and Nussinov, Ruth}, +doi = {10.1016/j.jmb.2008.02.034}, +file = {:home/alex/Dokumente/Mendeley Desktop/Tsai, del Sol, Nussinov/Journal of molecular biology/Tsai, del Sol, Nussinov - 2008 - Allostery absence of a change in shape does not imply that allostery is not at play.pdf:pdf}, +issn = {1089-8638}, +journal = {Journal of molecular biology}, +keywords = {Allosteric Regulation,Animals,Folder - Allostery - Theory,Humans,Mechanism,Models,Molecular,Protein Conformation,Signal Transduction,Thermodynamics}, +mendeley-tags = {Folder - Allostery - Theory,Mechanism}, +month = apr, +number = {1}, +pages = {1--11}, +pmid = {18353365}, +shorttitle = {Allostery}, +title = {{Allostery: absence of a change in shape does not imply that allostery is not at play.}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608002313 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2684958\&tool=pmcentrez\&rendertype=abstract}, +volume = {378}, +year = {2008} +} +@article{Changeux2011, +author = {Changeux, Jean-Pierre}, +doi = {10.1002/pro.658}, +issn = {09618368}, +journal = {Protein Science}, +keywords = {Folder - Allostery - Theory, Mechanism}, +mendeley-tags = {Folder - Allostery - Theory, Mechanism}, +month = jul, +pages = {1119--1124}, +title = {50th anniversary of the word “allosteric”}, +url = {http://doi.wiley.com/10.1002/pro.658}, +volume = {20}, +year = {2011} +} +@article{Knecht1983, +abstract = {The complete amino acid sequence of a proteinase inhibitor, eglin c (Mr 8100), has been determined with less than 150 micrograms of the protein using the following microtechniques: (a) amino acid analysis with a low-nanogram amount of protein hydrolysate using dimethylaminoazobenzene sulfonyl chloride, (b) peptide isolation at the picomole level using the dimethylaminoazobenzene isothiocyanate (DABITC) precolumn derivatization method, and (c) automatic Edman degradation. One amino acid residue has been corrected for the previously reported sequence. The Contribution of each technique to the microsequencing is discussed. In addition, a new high-performance liquid chromatography system that gives a complete baseline separation of all phenylthiohydantoin-amino acids is described.}, +author = {Knecht, R and Seem\"{u}ller, U and Liersch, M and Fritz, H and Braun, D G and Chang, J Y}, +file = {:home/alex/Dokumente/Mendeley Desktop/Knecht et al/Analytical biochemistry/Knecht et al. - 1983 - Sequence determination of eglin C using combined microtechniques of amino acid. - 1983 - sequence determination of eglin c using combined microtechniques of amino acid analysis , peptide isolation , and automatic edman degradation: - 1983 - sequence determination of eglin c using combined microtechniques of amino acid analysis , peptide isolation , and automatic edman degradation}, +issn = {0003-2697}, +journal = {Analytical biochemistry}, +keywords = {Amino Acid Sequence,Amino Acids,Amino Acids: analysis,Chromatography, High Pressure Liquid,Microchemistry,Peptide Fragments,Peptide Fragments: isolation \& purification,Protease Inhibitors,Proteins,Serpins}, +month = may, +number = {1}, +pages = {65--71}, +pmid = {6869810}, +title = {{Sequence determination of eglin C using combined microtechniques of amino acid analysis, peptide isolation, and automatic Edman degradation.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/6869810}, +volume = {130}, +year = {1983} +} +@article{Tsutsui1982, +author = {Tsutsui, K. and Mueller, G. C}, +file = {:home/alex/Dokumente/Mendeley Desktop/Tsutsui, Mueller/Analytical Biochemistry/Tsutsui, Mueller - 1982 - Affinity chromatography of heme-binding proteins an improved method for the synthesis of hemin-agarose.pdf:pdf}, +journal = {Analytical Biochemistry}, +keywords = {Folder - Methoden}, +mendeley-tags = {Folder - Methoden}, +number = {2}, +pages = {244--250}, +shorttitle = {Affinity chromatography of heme-binding proteins}, +title = {{Affinity chromatography of heme-binding proteins: an improved method for the synthesis of hemin-agarose}}, +volume = {121}, +year = {1982} +} +@article{Notredame2000, +abstract = {We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests.}, +author = {Notredame, C and Higgins, D G and Heringa, J}, +doi = {10.1006/jmbi.2000.4042}, +issn = {0022-2836}, +journal = {Journal of molecular biology}, +keywords = {Algorithms,Amino Acid,Amino Acid Motifs,Amino Acid Sequence,Animals,Computational Biology,Computational Biology: methods,Databases as Topic,Humans,Molecular Sequence Data,Protein-Serine-Threonine Kinases,Protein-Serine-Threonine Kinases: chemistry,Reproducibility of Results,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Sequence Homology,Software}, +month = sep, +number = {1}, +pages = {205--17}, +pmid = {10964570}, +title = {{T-Coffee: A novel method for fast and accurate multiple sequence alignment.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/10964570}, +volume = {302}, +year = {2000} +} +@article{Luisi2003a, +author = {Luisi, P. L}, +file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Naturwissenschaften/Luisi - 2003 - Autopoiesis a review and a reappraisal.pdf:pdf}, +journal = {Naturwissenschaften}, +number = {2}, +pages = {49--59}, +shorttitle = {Autopoiesis}, +title = {{Autopoiesis: a review and a reappraisal}}, +volume = {90}, +year = {2003} +} +@article{Chastain1996, +abstract = {The gene for C4-pyruvate,orthophosphate dikinase (PPDK) from maize (Zea mays) was cloned into an Escherichia coli expression vector and recombinant PPDK produced in E. coli cells. Recombinant enzyme was found to be expressed in high amounts (5.3 U purified enzyme-activityliter-1 of induced cells) as a predominantly soluble and active protein. Biochemical analysis of partially purified recombinant PPDK showed this enzyme to be equivalent to enzyme extracted from illuminated maize leaves with respect to (i) molecular mass, (ii) specific activity, (iii) substrate requirements, and (iv) phosphorylation/inactivation by its bifunctional regulatory protein.}, +author = {Chastain, Chris J. and Thompson, Brent J. and Chollet, Raymond}, +file = {:home/alex/Dokumente/Mendeley Desktop/Chastain, Thompson, Chollet/Photosynthesis Research/Chastain, Thompson, Chollet - 1996 - Maize recombinant C4-pyruvate, orthophosphate dikinase expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein.pdf:pdf}, +journal = {Photosynthesis Research}, +keywords = {C4 photosynthesis,C4 plant,PPDK,enzyme,maize (Zea mays),orthophosphate dikinase,pyruvate,recombinant}, +pages = {83--89}, +title = {{Maize recombinant C4-pyruvate, orthophosphate dikinase: expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein}}, +url = {http://www.springerlink.com/index/N642332887GN2U55.pdf}, +volume = {49}, +year = {1996} +} +@article{Wiechelman1988, +author = {Wiechelman, K}, +doi = {10.1016/0003-2697(88)90383-1}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wiechelman/Analytical Biochemistry/Wiechelman - 1988 - Investigation of the bicinchoninic acid protein assay Identification of the groups responsible for color formation.pdf:pdf}, +issn = {00032697}, +journal = {Analytical Biochemistry}, +keywords = {Folder - Methoden}, +mendeley-tags = {Folder - Methoden}, +month = nov, +number = {1}, +pages = {231--237}, +title = {{Investigation of the bicinchoninic acid protein assay: Identification of the groups responsible for color formation}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/0003269788903831}, +volume = {175}, +year = {1988} +} +@article{Zhuravleva2011a, +abstract = {The 70-kDa heat shock protein (Hsp70) chaperones perform a wide array of cellular functions that all derive from the ability of their N-terminal nucleotide-binding domains (NBDs) to allosterically regulate the substrate affinity of their C-terminal substrate-binding domains in a nucleotide-dependent mechanism. To explore the structural origins of Hsp70 allostery, we performed NMR analysis on the NBD of DnaK, the Escherichia coli Hsp70, in six different states (ligand-bound or apo) and in two constructs, one that retains the conserved and functionally crucial portion of the interdomain linker (residues ) and another that lacks the linker. Chemical-shift perturbation patterns identify residues at subdomain interfaces that constitute allosteric networks and enable the NBD to act as a nucleotide-modulated switch. Nucleotide binding results in changes in subdomain orientations and long-range perturbations along subdomain interfaces. In particular, our findings provide structural details for a key mechanism of Hsp70 allostery, by which information is conveyed from the nucleotide-binding site to the interdomain linker. In the presence of ATP, the linker binds to the edge of the IIA $\beta$-sheet, which structurally connects the linker and the nucleotide-binding site. Thus, a pathway of allosteric communication leads from the NBD nucleotide-binding site to the substrate-binding domain via the interdomain linker.}, +author = {Zhuravleva, Anastasia and Gierasch, Lila M}, +doi = {10.1073/pnas.1014448108}, +file = {:home/alex/Dokumente/Mendeley Desktop/Zhuravleva, Gierasch/Proceedings of the National Academy of Sciences of the United States of America/Zhuravleva, Gierasch - 2011 - Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.pdf:pdf}, +issn = {1091-6490}, +journal = {Proceedings of the National Academy of Sciences of the United States of America}, +keywords = {Adenosine Triphosphate,Adenosine Triphosphate: chemistry,Adenosine Triphosphate: genetics,Adenosine Triphosphate: metabolism,Allosteric Regulation,Allosteric Regulation: physiology,Binding Sites,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Escherichia coli: chemistry,Escherichia coli: genetics,Escherichia coli: metabolism,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: chemistry,HSP70 Heat-Shock Proteins: genetics,HSP70 Heat-Shock Proteins: metabolism,Nuclear Magnetic Resonance, Biomolecular,Protein Binding,Signal Transduction,Signal Transduction: physiology,Structure-Activity Relationship}, +month = apr, +number = {17}, +pages = {6987--92}, +pmid = {21482798}, +title = {{Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084084\&tool=pmcentrez\&rendertype=abstract}, +volume = {108}, +year = {2011} +} +@article{Wilkins1999, +author = {Wilkins, M R and Gasteiger, E and Bairoch, A and Sanchez, J C and Williams, K L and Appel, R D and Hochstrasser, D F}, +file = {:home/alex/Dokumente/Mendeley Desktop/Wilkins et al/Methods in Molecular Biology (Clifton, N.J.)/Wilkins et al. - 1999 - Protein identification and analysis tools in the ExPASy server.pdf:pdf}, +issn = {1064-3745}, +journal = {Methods in Molecular Biology (Clifton, N.J.)}, +keywords = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software}, +mendeley-tags = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software}, +pages = {531--552}, +title = {{Protein identification and analysis tools in the ExPASy server}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/10027275}, +volume = {112}, +year = {1999} +} +@article{Greenfield2007, +author = {Greenfield, Norma J}, +doi = {10.1038/nprot.2006.202}, +issn = {1754-2189}, +journal = {Nature Protocols}, +month = jan, +number = {6}, +pages = {2876--2890}, +title = {{Using circular dichroism spectra to estimate protein secondary structure}}, +url = {http://www.nature.com/doifinder/10.1038/nprot.2006.202}, +volume = {1}, +year = {2007} +} +@article{Riener2002a, +author = {Riener, Christian and Kada, Gerald and Gruber, Hermann}, +doi = {10.1007/s00216-002-1347-2}, +file = {:home/alex/Dokumente/Mendeley Desktop/Riener, Kada, Gruber/Analytical and Bioanalytical Chemistry/Riener, Kada, Gruber - 2002 - Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032-dithiodipyridine.pdf:pdf}, +issn = {1618-2642}, +journal = {Analytical and Bioanalytical Chemistry}, +keywords = {Folder - Methoden}, +mendeley-tags = {Folder - Methoden}, +month = jul, +number = {4-5}, +pages = {266--276}, +title = {{Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4'-dithiodipyridine}}, +url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00216-002-1347-2}, +volume = {373}, +year = {2002} +} +@book{Jander2006, +address = {Stuttgart}, +author = {Jander, Gerhart and Schweda, Eberhard}, +edition = {16., \"{u}bera}, +isbn = {9783777613888}, +keywords = {Folder - Anorganische Chemie}, +mendeley-tags = {Folder - Anorganische Chemie}, +month = jan, +publisher = {Hirzel}, +title = {{Lehrbuch der analytischen und pr\"{a}parativen anorganischen Chemie mit 67 Tabellen}}, +year = {2006} +} diff --git a/masterarbeit.kilepr b/masterarbeit.kilepr index bc5dc75..60b060b 100644 --- a/masterarbeit.kilepr +++ b/masterarbeit.kilepr @@ -4,7 +4,7 @@ img_extIsRegExp=false img_extensions=.eps .jpg .jpeg .png .pdf .ps .fig .gif kileprversion=2 kileversion=2.1.2 -lastDocument=inc/material.tex +lastDocument=inc/ergebnisse.tex masterDocument= name=Masterarbeit pkg_extIsRegExp=false @@ -126,15 +126,55 @@ mode= open=false order=-1 +[item:img/ergebnisse/agarose_gele/colony_pcr.png] +archive=true +column=6750318 +encoding= +highlight= +line=0 +mode= +open=false +order=-1 + +[item:img/ergebnisse/agarose_gele/insert_pcr_text.png] +archive=true +column=2687015 +encoding= +highlight= +line=0 +mode= +open=false +order=-1 + +[item:img/ergebnisse/agarose_gele/vektor_linear_text.png] +archive=true +column=2 +encoding= +highlight= +line=0 +mode= +open=false +order=-1 + +[item:img/ergebnisse/pETEV-16b-ppdk.pdf] +archive=true +column=0 +encoding= +highlight= +line=0 +mode= +open=false +order=-1 + [item:inc/abkuerzungen.tex] archive=true -column=32 +column=35 encoding=UTF-8 highlight=LaTeX -line=5 +line=36 mode=LaTeX open=true -order=2 +order=3 [item:inc/abstract.tex] archive=true @@ -143,18 +183,18 @@ encoding=UTF-8 highlight=LaTeX line=0 mode=LaTeX -open=true +open=false order=3 [item:inc/anhang.tex] archive=true -column=45 +column=74 encoding=UTF-8 highlight=LaTeX -line=10 +line=52 mode=LaTeX open=true -order=5 +order=4 [item:inc/diskussion.tex] archive=true @@ -178,20 +218,20 @@ order=5 [item:inc/ergebnisse.tex] archive=true -column=20 +column=112 encoding=UTF-8 highlight=LaTeX -line=0 +line=47 mode=LaTeX -open=false -order=6 +open=true +order=2 [item:inc/material.tex] archive=true -column=69 +column=2 encoding=UTF-8 highlight=LaTeX -line=852 +line=122 mode=LaTeX open=true order=1 @@ -203,7 +243,7 @@ encoding=UTF-8 highlight=LaTeX line=1 mode=LaTeX -open=true +open=false order=4 [item:library.bib] @@ -228,17 +268,17 @@ order=-1 [item:masterarbeit.tex] archive=true -column=32 +column=0 encoding=UTF-8 highlight=LaTeX -line=185 +line=181 mode=LaTeX open=true order=0 [view-settings,view=0,item:inc/abkuerzungen.tex] -CursorColumn=32 -CursorLine=5 +CursorColumn=35 +CursorLine=36 JumpList= ViMarks= @@ -249,8 +289,8 @@ JumpList= ViMarks= [view-settings,view=0,item:inc/anhang.tex] -CursorColumn=45 -CursorLine=10 +CursorColumn=74 +CursorLine=52 JumpList= ViMarks= @@ -267,14 +307,14 @@ JumpList= ViMarks= [view-settings,view=0,item:inc/ergebnisse.tex] -CursorColumn=20 -CursorLine=0 +CursorColumn=112 +CursorLine=47 JumpList= ViMarks= [view-settings,view=0,item:inc/material.tex] -CursorColumn=69 -CursorLine=852 +CursorColumn=2 +CursorLine=122 JumpList= ViMarks= @@ -291,7 +331,7 @@ JumpList= ViMarks= [view-settings,view=0,item:masterarbeit.tex] -CursorColumn=32 -CursorLine=185 +CursorColumn=0 +CursorLine=181 JumpList= ViMarks= diff --git a/masterarbeit.tex b/masterarbeit.tex index 179241d..1d812d3 100644 --- a/masterarbeit.tex +++ b/masterarbeit.tex @@ -109,9 +109,14 @@ \setmathfont[range={"2212}]{Linux Libertine O}% "02212 = - \setmathfont[range={"002C}]{Linux Libertine O}% "0002C = , \setmathfont[range={"002B}]{Linux Libertine O}% "0002B = + +\setmathfont[range={"25B2}]{Linux Libertine O} +\setmathfont[range={"25BC}]{Linux Libertine O} +\renewcommand{\blacktriangledown}{\libertineGlyph{uni25BC}} +\renewcommand{\blacktriangle}{\libertineGlyph{uni25B2}} \newcommand{\todo}[1]{\textbf{\textsc{\textcolor{red}{(TODO: #1)}}}} + %opening \titlehead{\centering \includegraphics[keepaspectratio=true,width=0.4\textwidth]{./img/HHU_Logo.eps}} \subject{Institut für Biochemische Pflanzenphysiologie} diff --git a/misc/align_seq_ref.aln b/misc/align_seq_ref.aln deleted file mode 100644 index 4fd9c1d..0000000 --- a/misc/align_seq_ref.aln +++ /dev/null @@ -1,194 +0,0 @@ -CLUSTAL 2.1 multiple sequence alignment - - -pETEV-16b-ppdk ATAATTTTGTTTAACTTTAAGAAGGAGATATACCATGGGCCATCATCATCATCATCATCA -FtPPDK-ref ------------------------------------------------------------ - - -pETEV-16b-ppdk TCATCATCACAGCAGCGGCCATGAAAACCTGTATTTTCAGGGACATATGACCGCTAAAAA -FtPPDK-ref -------------------------------------------CATATGACCGCTAAAAA - ***************** - -pETEV-16b-ppdk ACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATCGCTGCT -FtPPDK-ref ACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATCGCTGCT - ************************************************************ - -pETEV-16b-ppdk GGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGG -FtPPDK-ref GGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGG - ************************************************************ - -pETEV-16b-ppdk TCTGACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCC -FtPPDK-ref TCTGACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCC - ************************************************************ - -pETEV-16b-ppdk GGGCCTGTGGGATGAAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTC -FtPPDK-ref GGGCCTGTGGGATGAAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTC - ************************************************************ - -pETEV-16b-ppdk GCTGGGCGATCCGTCGAAACCGCTGCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCAT -FtPPDK-ref GCTGGGCGATCCGTCGAAACCGCTGCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCAT - ************************************************************ - -pETEV-16b-ppdk GCCGGGCATGATGGATACCGTTCTGAACCTGGGTCTGAATGACGAAGTGGTTGCAGGTCT -FtPPDK-ref GCCGGGCATGATGGATACCGTTCTGAACCTGGGTCTGAATGACGAAGTGGTTGCAGGTCT - ************************************************************ - -pETEV-16b-ppdk GGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTCGCTTTCTGGACATGTT -FtPPDK-ref GGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTCGCTTTCTGGACATGTT - ************************************************************ - -pETEV-16b-ppdk CGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACAGATGAA -FtPPDK-ref CGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACAGATGAA - ************************************************************ - -pETEV-16b-ppdk AGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGT -FtPPDK-ref AGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGT - ************************************************************ - -pETEV-16b-ppdk GGAAAAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAA -FtPPDK-ref GGAAAAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAA - ************************************************************ - -pETEV-16b-ppdk AAAACAGCTGGAACTGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAA -FtPPDK-ref AAAACAGCTGGAACTGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAA - ************************************************************ - -pETEV-16b-ppdk CAAATATCGCTCCATTAATCAGATCACCGGTCTGAAAGGCACGGCAGTGAATATTCAATC -FtPPDK-ref CAAATATCGCTCCATTAATCAGATCACCGGTCTGAAAGGCACGGCAGTGAATATTCAATC - ************************************************************ - -pETEV-16b-ppdk TATGGTTTTCGGTAACATGGGCAATACCAGTGGCACGGGTGTGCTGTTTACCCGTAACCC -FtPPDK-ref TATGGTTTTCGGTAACATGGGCAATACCAGTGGCACGGGTGTGCTGTTTACCCGTAACCC - ************************************************************ - -pETEV-16b-ppdk GAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATGCCCAGGGTGAAGATGT -FtPPDK-ref GAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATGCCCAGGGTGAAGATGT - ************************************************************ - -pETEV-16b-ppdk TGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCCGGAAGC -FtPPDK-ref TGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCCGGAAGC - ************************************************************ - -pETEV-16b-ppdk GTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGA -FtPPDK-ref GTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGA - ************************************************************ - -pETEV-16b-ppdk CATCGAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACG -FtPPDK-ref CATCGAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACG - ************************************************************ - -pETEV-16b-ppdk CACGGGCAAAGGTGCTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACAC -FtPPDK-ref CACGGGCAAAGGTGCTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACAC - ************************************************************ - -pETEV-16b-ppdk CCGTACGGCAATCAAACGCGTTGAAACCCAGCATCTGGATCAACTGCTGCACCCGCAGTT -FtPPDK-ref CCGTACGGCAATCAAACGCGTTGAAACCCAGCATCTGGATCAACTGCTGCACCCGCAGTT - ************************************************************ - -pETEV-16b-ppdk CGAAGACCCGTCAGCGTATAAATCGCATGTGGTTGCCACCGGTCTGCCGGCATCCCCGGG -FtPPDK-ref CGAAGACCCGTCAGCGTATAAATCGCATGTGGTTGCCACCGGTCTGCCGGCATCCCCGGG - ************************************************************ - -pETEV-16b-ppdk TGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAACGTGGCACGCTCAGGG -FtPPDK-ref TGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAACGTGGCACGCTCAGGG - ************************************************************ - -pETEV-16b-ppdk TAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTATGCATGC -FtPPDK-ref TAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTATGCATGC - ************************************************************ - -pETEV-16b-ppdk AGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCG -FtPPDK-ref AGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCG - ************************************************************ - -pETEV-16b-ppdk CGGCTGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAA -FtPPDK-ref CGGCTGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAA - ************************************************************ - -pETEV-16b-ppdk AATCTTCACCATCGGTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTAC -FtPPDK-ref AATCTTCACCATCGGTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTAC - ************************************************************ - -pETEV-16b-ppdk CACGGGCGAAGTTATTCTGGGTAAACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCT -FtPPDK-ref CACGGGCGAAGTTATTCTGGGTAAACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCT - ************************************************************ - -pETEV-16b-ppdk GGAAATCTTTATGAGTTGGGCTGACCAGGCGCGTCGCCTGAAAGTGATGGCTAACGCGGA -FtPPDK-ref GGAAATCTTTATGAGTTGGGCTGACCAGGCGCGTCGCCTGAAAGTGATGGCTAACGCGGA - ************************************************************ - -pETEV-16b-ppdk TACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGGGTATTGGTCTGTGCCG -FtPPDK-ref TACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGGGTATTGGTCTGTGCCG - ************************************************************ - -pETEV-16b-ppdk TACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAATGATCAT -FtPPDK-ref TACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAATGATCAT - ************************************************************ - -pETEV-16b-ppdk GGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAG -FtPPDK-ref GGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAG - ************************************************************ - -pETEV-16b-ppdk TGACTTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGA -FtPPDK-ref TGACTTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGA - ************************************************************ - -pETEV-16b-ppdk TCCGCCGCTGCATGAATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGC -FtPPDK-ref TCCGCCGCTGCATGAATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGC - ************************************************************ - -pETEV-16b-ppdk AGTCGATACGGGCATGAGCGCTGACGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGT -FtPPDK-ref AGTCGATACGGGCATGAGCGCTGACGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGT - ************************************************************ - -pETEV-16b-ppdk TAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTGGGTATTTCGTACCCGGAACTGACCGA -FtPPDK-ref TAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTGGGTATTTCGTACCCGGAACTGACCGA - ************************************************************ - -pETEV-16b-ppdk AATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCAACCAGGGTGTGACGGT -FtPPDK-ref AATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCAACCAGGGTGTGACGGT - ************************************************************ - -pETEV-16b-ppdk TATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCAAATTTC -FtPPDK-ref TATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCAAATTTC - ************************************************************ - -pETEV-16b-ppdk TGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAA -FtPPDK-ref TGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAA - ************************************************************ - -pETEV-16b-ppdk AGTGGGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGA -FtPPDK-ref AGTGGGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGA - ************************************************************ - -pETEV-16b-ppdk AGCCGATTTCTTTAGCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCG -FtPPDK-ref AGCCGATTTCTTTAGCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCG - ************************************************************ - -pETEV-16b-ppdk CGATGACGTGGGCAAATTTCTGCAAATTTACCTGGCCCAGGGTATCCTGCAACATGATCC -FtPPDK-ref CGATGACGTGGGCAAATTTCTGCAAATTTACCTGGCCCAGGGTATCCTGCAACATGATCC - ************************************************************ - -pETEV-16b-ppdk GTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAACTGATCAAAATGGCAACCGAAAAAGG -FtPPDK-ref GTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAACTGATCAAAATGGCAACCGAAAAAGG - ************************************************************ - -pETEV-16b-ppdk CCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAACACGGCGGTGAACCGAG -FtPPDK-ref CCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAACACGGCGGTGAACCGAG - ************************************************************ - -pETEV-16b-ppdk TTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTTTCGTGT -FtPPDK-ref TTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTTTCGTGT - ************************************************************ - -pETEV-16b-ppdk CCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAGGATCCGGCTGCTAA -FtPPDK-ref CCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAG-------------- - ********************************************** - -pETEV-16b-ppdk CAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTAGCATAACC -FtPPDK-ref ------------------------------------------------------------ - - -pETEV-16b-ppdk CCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTG -FtPPDK-ref ------------------------------------- - diff --git a/misc/ma_as.score_ascii b/misc/ma_as.score_ascii new file mode 100644 index 0000000..28b5cbf --- /dev/null +++ b/misc/ma_as.score_ascii @@ -0,0 +1,149 @@ +T-COFFEE, Version_9.03.r1318 (2012-07-12 19:05:45 - Revision 1318 - Build 366) +Cedric Notredame +CPU TIME:0 sec. +SCORE=99 +* + BAD AVG GOOD +* +F. : 99 +F._1 : 99 +Zea : 99 +C. : 98 +cons : 99 + +F. 1 976789999788889999999999999999999999999999999999 48 +F._1 1 976789999778889999999999999999999999999999999999 48 +Zea 1 976789999788889999999999999999999999999999999999 48 +C. 1 86-678999----78999999999999999999999999999999999 43 +cons 1 875689999677779999999999999999999999999999999999 48 + + +F. 49 999999999999999999999999999999999999999999999999 96 +F._1 49 999999999999999999999999999999999999999999999999 96 +Zea 49 999999999999999999999999999999999999999999999999 96 +C. 44 999999999999999999999999999999999999999999999999 91 +cons 49 999999999999999999999999999999999999999999999999 96 + + +F. 97 999999999999999999999999999999999-89999999999999 143 +F._1 97 999999999999999999999999999999999-89999999999999 143 +Zea 97 999999999999999999999999999999999-89999999999999 143 +C. 92 999999999999999999999999999999999379999999999999 139 +cons 97 999999999999999999999999999999999289999999999999 144 + + +F. 144 999999999999999999999999999999999999999999999999 191 +F._1 144 999999999999999999999999999999999999999999999999 191 +Zea 144 999999999999999999999999999999999999999999999999 191 +C. 140 999999999999999999999999999999999999999999999999 187 +cons 145 999999999999999999999999999999999999999999999999 192 + + +F. 192 998-89999999999999999999999999999999999999999999 238 +F._1 192 998-89999999999999999999999999999999999999999999 238 +Zea 192 998-89999999999999999999999999999999999999999999 238 +C. 188 998389999999999999999999999999999999999999999999 235 +cons 193 998289999999999999999999999999999999999999999999 240 + + +F. 239 999999999999999999999999999999999999999999999999 286 +F._1 239 999999999999999999999999999999999999999999999999 286 +Zea 239 999999999999999999999999999999999999999999999999 286 +C. 236 999999999999999999999999999999999999999999999999 283 +cons 241 999999999999999999999999999999999999999999999999 288 + + +F. 287 999999999999999999999999999999999999999999999999 334 +F._1 287 999999999999999999999999999999999999999999999999 334 +Zea 287 999999999999999999999999999999999999999999999999 334 +C. 284 999999999999999999999999999999999999999999999999 331 +cons 289 999999999999999999999999999999999999999999999999 336 + + +F. 335 999999999999999999999999999999999999999999999999 382 +F._1 335 999999999999999999999999999999999999999999999999 382 +Zea 335 999999999999999999999999999999999999999999999999 382 +C. 332 999999999999999999999999999999999999999999999999 379 +cons 337 999999999999999999999999999999999999999999999999 384 + + +F. 383 997777777-79999999999999999999999999999999999999 429 +F._1 383 997777777-79999999999999999999999999999999999999 429 +Zea 383 997777777-79999999999999999999999999999999999999 429 +C. 380 99-666666378999999999999999999999999999999999999 426 +cons 385 996677777278999999999999999999999999999999999999 432 + + +F. 430 999999999999999999999999999999999999999999999999 477 +F._1 430 999999999999999999999999999999999999999999999999 477 +Zea 430 999999999999999999999999999999999999999999999999 477 +C. 427 999999999999999999999999999999999999999999999999 474 +cons 433 999999999999999999999999999999999999999999999999 480 + + +F. 478 999999999999999999999999999999999999999999999999 525 +F._1 478 999999999999999999999999999999999999999999999999 525 +Zea 478 999999999999999999999999999999999999999999999999 525 +C. 475 999999999999999999999999999999999999999999999999 522 +cons 481 999999999999999999999999999999999999999999999999 528 + + +F. 526 999999999999999999999999999999999999999999999998 573 +F._1 526 999999999999999999999999999999999999999999999998 573 +Zea 526 999999999999999999999999999999999999999999999998 573 +C. 523 999999999999999999999999999999999999999999999987 570 +cons 529 999999999999999999999999999999999999999999999998 576 + + +F. 574 788999999999999999999999999999999999999999999999 621 +F._1 574 788999999999999999999999999999999999999999999999 621 +Zea 574 788999999999999999999999999999999999999999999999 621 +C. 571 -78889999999999999999999999999999999999999999999 617 +cons 577 688899999999999999999999999999999999999999999999 624 + + +F. 622 999999999999987766899999999999999999999999999999 669 +F._1 622 999999999999987766899999999999999999999999999999 669 +Zea 622 999999999999987766899999999999999999999999999999 669 +C. 618 9999999999998766--689999999999999999999999999999 663 +cons 625 999999999999977655799999999999999999999999999999 672 + + +F. 670 999999999999999999999999999887-89999999999999999 716 +F._1 670 999999999999999999999999999887-89999999999999999 716 +Zea 670 999999999999999999999999999887-89999999999999999 716 +C. 664 999999999999999999999999999876389999999999999999 711 +cons 673 999999999999999999999999999876289999999999999999 720 + + +F. 717 999999999999999999999999999999999999999999999999 764 +F._1 717 999999999999999999999999999999999999999999999999 764 +Zea 717 999999999999999999999999999999999999999999999999 764 +C. 712 999999999999999999999999999999999999999999999999 759 +cons 721 999999999999999999999999999999999999999999999999 768 + + +F. 765 999999999999999999999999999999999999999999999999 812 +F._1 765 999999999999999999999999999999999999999999999999 812 +Zea 765 999999999999999999999999999999999999999999999999 812 +C. 760 999999999999999999999999999999999999999999999999 807 +cons 769 999999999999999999999999999999999999999999999999 816 + + +F. 813 999999999999999999999999999999999999999999999999 860 +F._1 813 999999999999999999999999999999999999999999999999 860 +Zea 813 999999999999999999999999999999999999999999999999 860 +C. 808 999999999999999999999999999999999999999999999999 855 +cons 817 999999999999999999999999999999999999999999999999 864 + + +F. 861 999999999999999---8 876 +F._1 861 999999999999999---8 876 +Zea 861 999999999999999---8 876 +C. 856 9999999999999983747 874 +cons 865 9999999999999982228 883 + + + + + diff --git a/misc/ma_as_aln.fa b/misc/ma_as_aln.fa new file mode 100644 index 0000000..f7613fc --- /dev/null +++ b/misc/ma_as_aln.fa @@ -0,0 +1,76 @@ +>F. trinervia +TAKKRVFTFGKGRSEGNRDMKSLLGGKGANLAEMSSIGLSVPPGLTISTE +ACEEYQQNGKSLPPGLWDEISEGLDYVQKEMSASLGDPSKPLLLSVRSGA +AISMPGMMDTVLNLGLNDEVVAGLAGKSG-ARFAYDSYRRFLDMFGNVVM +GIPHSLFDEKLEQMKAEKGIHLDTDLTAADLKDLVEKYKNVYVEA-KGEK +FPTDPKKQLELAVNAVFDSWDSPRANKYRSINQITGLKGTAVNIQSMVFG +NMGNTSGTGVLFTRNPSTGEKKLYGEFLINAQGEDVVAGIRTPEDLGTME +TCMPEAYKELVENCEILERHYKDMMDIEFTVQENRLWMLQCRTGKRTGKG +AVRIAVDMVNEGLIDTRTAIKRVETQHLDQLLHPQFEDPSAYK-SHVVAT +GLPASPGAAVGQVCFSAEDAETWHAQGKSAILVRTETSPEDVGGMHAAAG +ILTARGGMTSHAAVVARGWGKCCVSGCADIRVNDDMKIFTIGDRVIKEGD +WLSLNGTTGEVILGKQLLAPPAMSNDLEIFMSWADQARRLKVMANADTPN +DALTARNNGAQGIGLCRTEHMFFASDERIKAVRKMIMAVTPEQRKVALDL +LLPYQRSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGDLEHIVNELAVDT +GMSADEIYSKIENLSEVNPMLGFRGCRLGISYPELTEMQVRAIFQAAVSM +TN-QGVTVIPEIMVPLVGTPQELRHQISVIRGVAANVFAEMGVTLEYKVG +TMIEIPRAALIAEEIGKEADFFSFGTNDLTQMTFGYSRDDVGKFLQIYLA +QGILQHDPFEVIDQKGVGQLIKMATEKGRAANPSLKVGICGEHGGEPSSV +AFFDGVGLDYVSCSPFRVPIARLAAAQVI---V +>F. brownii +TTKKRVFTFGKGNSEGNKDMKSLLGGKGANLAEMASIGLSVPPGLTISTE +ACEEYQQNGKKLPPGLWDEILEGLQYVQKEMSASLGDPSKALLLSVRSGA +AISMPGMMDTVLNLGLNDEVVDGLAAKSG-ARFAYDSYRRFLDMFGNVVM +GIPHSLFDEKLEQMKAEKGIHLDTDLTAADLKDLAEQYKNVYVEA-KGEK +FPTDPKKQLELAVNAVFDSWDSPRANKYRSINQITGLKGTAVNIQCMVFG +NMGNTSGTGVLFTRNPSTGEKKLYGEFLVNAQGEDVVAGIRTPEDLVTME +TCMPEAYRELVENCVILERHYKDMMDIEFTVQENRLWMLQCRTGKRTGKG +AVRIAVDMVNEGLIDTRTAIKRVETQHLDQLLHPQFENPSAYK-SHVVAT +GLPASPGAAVGQVVFSAEDAETWHAQGKSAILVRTETSPEDVGGMHAAAG +ILTARGGMTSHAAVVARGWGKCCVSGCADIRVNDDMKVFTIGDRVIKEGD +WLSLNGSTGEVILGKQLLAPPAMSNDLETFMSWADQARRLKVMANADTPN +DALTARNNGAQGIGLCRTEHMFFASDERIKAVRKMIMAVTPEQRKAALDL +LLPYQRSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGDLEHIVNELTADT +GMSKDEIYSRIEKLSEVNPMLGFRGCRLGISYPELTEMQVRAIFQAAVSM +NN-QGVTVIPEIMVPLVGTPQELRHQIGVIRGVAANVFAEMGLTLEYKVG +TMIEIPRAALIADEIAKEAEFFSFGTNDLTQMTFGYSRDDVGKFLPIYLS +QGILQHDPFEVLDQKGVGQLIKMATEKGRAANPNLKVGICGEHGGEPSSV +AFFDGVGLDYVSCSPFRVPIARLAAAQVV---V +>Zea mays +TTKKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTE +ACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGA +AVSMPGMMDTVLNLGLNDEVAAGLAAKSG-ERFAYDSFRRFLDMFGNVVM +DIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSA-KGEP +FPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAVNVQCMVFG +NMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMK +NLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKS +AVKIAVDMVNEGLVEPRSAIKMVEPGHLDQLLHPQFENPSAYK-DQVIAT +GLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVG +ILTERGGMTSHAAVVARWWGKCCVSGCSGIRVNDAEKLVTIGSHVLREGE +WLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPD +DALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDR +LLTYQRSDFEGIFRAMDGLPVTIRLLDHPSYEFLPEGNIEDIVSELCAET +GANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAM +TN-QGVQVFPEIMVPLVGTPQELGHQVTLIRQVAEKVFANVGKTIGYKVG +TMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVHLA +QGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGEHGGEPSSV +AFFAKAGLDFVSCSPFRVPIARLAAAQVL---V +>C. symbiosum +MA-KWVYKF----EEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTE +ACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGA +RASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVM +EVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEE +FPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFG +NKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLE +NDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPA +ALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTF-NPAALKAGEVIGS +ALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEG +ILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGD +YISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPE +DTLNAVKLGAEGIGLCRTEHMFFEAD-RIMKIRKMILSDSVEAREEALNE +LIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEE--QAELAKNM +GLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEV +KEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIG +TMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYK +AKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSV +EFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK diff --git a/misc/seq_ref_aln.fa b/misc/seq_ref_aln.fa new file mode 100644 index 0000000..ba05a17 --- /dev/null +++ b/misc/seq_ref_aln.fa @@ -0,0 +1,80 @@ +>pETEV-16b-ppdk +ATGGGCCATCATCATCATCATCATCATCATCATCACAGCAGCGGCCATGAAAACCTGTATTTTCAGGGAC +ATATGACCGCTAAAAAACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATC +GCTGCTGGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGGTCTG +ACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCCGGGCCTGTGGGATG +AAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTCGCTGGGCGATCCGTCGAAACCGCT +GCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCATGCCGGGCATGATGGATACCGTTCTGAACCTGGGT +CTGAATGACGAAGTGGTTGCAGGTCTGGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTC +GCTTTCTGGACATGTTCGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACA +GATGAAAGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGTGGAA +AAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAAAAAACAGCTGGAAC +TGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAACAAATATCGCTCCATTAATCAGAT +CACCGGTCTGAAAGGCACGGCAGTGAATATTCAATCTATGGTTTTCGGTAACATGGGCAATACCAGTGGC +ACGGGTGTGCTGTTTACCCGTAACCCGAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATG +CCCAGGGTGAAGATGTTGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCC +GGAAGCGTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGACATC +GAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACGCACGGGCAAAGGTG +CTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACACCCGTACGGCAATCAAACGCGTTGA +AACCCAGCATCTGGATCAACTGCTGCACCCGCAGTTCGAAGACCCGTCAGCGTATAAATCGCATGTGGTT +GCCACCGGTCTGCCGGCATCCCCGGGTGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAA +CGTGGCACGCTCAGGGTAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTAT +GCATGCAGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCGCGGC +TGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAAAATCTTCACCATCG +GTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTACCACGGGCGAAGTTATTCTGGGTAA +ACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCTGGAAATCTTTATGAGTTGGGCTGACCAGGCGCGT +CGCCTGAAAGTGATGGCTAACGCGGATACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGG +GTATTGGTCTGTGCCGTACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAAT +GATCATGGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAGTGAC +TTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGATCCGCCGCTGCATG +AATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGCAGTCGATACGGGCATGAGCGCTGA +CGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGTTAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTG +GGTATTTCGTACCCGGAACTGACCGAAATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCA +ACCAGGGTGTGACGGTTATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCA +AATTTCTGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAAAGTG +GGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGAAGCCGATTTCTTTA +GCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCGCGATGACGTGGGCAAATTTCTGCA +AATTTACCTGGCCCAGGGTATCCTGCAACATGATCCGTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAA +CTGATCAAAATGGCAACCGAAAAAGGCCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAAC +ACGGCGGTGAACCGAGTTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTT +TCGTGTCCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAGGATCC +>FtPPDK-ref +ATGGGCCATCATCATCATCATCATCATCATCATCACAGCAGCGGCCATGAAAACCTGTATTTTCAGGGAC +ATATGACCGCTAAAAAACGCGTGTTTACGTTCGGCAAAGGTCGCTCGGAAGGCAACCGTGACATGAAATC +GCTGCTGGGTGGCAAAGGTGCGAACCTGGCGGAAATGAGCTCTATTGGTCTGTCCGTGCCGCCGGGTCTG +ACCATCTCAACGGAAGCCTGCGAAGAATATCAGCAAAATGGTAAATCGCTGCCGCCGGGCCTGTGGGATG +AAATCAGCGAAGGTCTGGACTACGTTCAGAAAGAAATGTCAGCCTCGCTGGGCGATCCGTCGAAACCGCT +GCTGCTGAGCGTCCGTTCTGGTGCGGCCATTAGCATGCCGGGCATGATGGATACCGTTCTGAACCTGGGT +CTGAATGACGAAGTGGTTGCAGGTCTGGCCGGTAAATCGGGTGCTCGTTTCGCGTATGATAGCTACCGTC +GCTTTCTGGACATGTTCGGTAACGTCGTGATGGGCATCCCGCATAGCCTGTTTGATGAAAAACTGGAACA +GATGAAAGCCGAAAAAGGTATTCACCTGGATACCGACCTGACGGCAGCTGATCTGAAAGACCTGGTGGAA +AAATATAAAAACGTTTACGTCGAAGCGAAAGGCGAAAAATTCCCGACCGATCCGAAAAAACAGCTGGAAC +TGGCCGTCAATGCAGTGTTTGATAGTTGGGACTCCCCGCGTGCCAACAAATATCGCTCCATTAATCAGAT +CACCGGTCTGAAAGGCACGGCAGTGAATATTCAATCTATGGTTTTCGGTAACATGGGCAATACCAGTGGC +ACGGGTGTGCTGTTTACCCGTAACCCGAGCACGGGCGAGAAAAAACTGTACGGCGAATTCCTGATTAATG +CCCAGGGTGAAGATGTTGTCGCAGGCATCCGCACCCCGGAAGATCTGGGTACCATGGAAACGTGCATGCC +GGAAGCGTATAAAGAACTGGTGGAAAACTGTGAAATTCTGGAACGTCATTACAAAGATATGATGGACATC +GAATTCACCGTTCAGGAAAATCGCCTGTGGATGCTGCAATGTCGTACCGGTAAACGCACGGGCAAAGGTG +CTGTGCGTATTGCGGTTGATATGGTCAACGAAGGCCTGATTGACACCCGTACGGCAATCAAACGCGTTGA +AACCCAGCATCTGGATCAACTGCTGCACCCGCAGTTCGAAGACCCGTCAGCGTATAAATCGCATGTGGTT +GCCACCGGTCTGCCGGCATCCCCGGGTGCAGCAGTGGGCCAGGTTTGCTTTTCAGCTGAAGATGCGGAAA +CGTGGCACGCTCAGGGTAAATCCGCGATCCTGGTGCGCACCGAAACGTCACCGGAAGATGTTGGCGGTAT +GCATGCAGCTGCGGGCATTCTGACCGCACGTGGCGGTATGACGTCCCACGCAGCAGTCGTGGCTCGCGGC +TGGGGTAAATGCTGTGTCTCAGGTTGTGCGGATATCCGTGTGAACGATGACATGAAAATCTTCACCATCG +GTGATCGCGTGATCAAAGAAGGCGACTGGCTGAGCCTGAACGGTACCACGGGCGAAGTTATTCTGGGTAA +ACAGCTGCTGGCACCGCCGGCAATGTCTAATGATCTGGAAATCTTTATGAGTTGGGCTGACCAGGCGCGT +CGCCTGAAAGTGATGGCTAACGCGGATACCCCGAATGACGCCCTGACGGCACGTAACAATGGTGCACAGG +GTATTGGTCTGTGCCGTACCGAACACATGTTTTTCGCTTCTGATGAACGTATTAAAGCGGTCCGCAAAAT +GATCATGGCCGTGACGCCGGAACAGCGTAAAGTTGCTCTGGATCTGCTGCTGCCGTATCAACGTAGTGAC +TTTGAAGGTATTTTCCGCGCAATGGATGGCCTGCCGGTGACCATCCGTCTGCTGGATCCGCCGCTGCATG +AATTTCTGCCGGAAGGTGATCTGGAACACATTGTTAACGAACTGGCAGTCGATACGGGCATGAGCGCTGA +CGAAATCTACTCTAAAATCGAAAACCTGAGTGAAGTTAATCCGATGCTGGGTTTCCGTGGCTGTCGCCTG +GGTATTTCGTACCCGGAACTGACCGAAATGCAGGTTCGTGCCATCTTTCAAGCTGCGGTCAGCATGACCA +ACCAGGGTGTGACGGTTATTCCGGAAATCATGGTCCCGCTGGTTGGCACCCCGCAGGAACTGCGTCACCA +AATTTCTGTTATCCGCGGCGTCGCCGCAAATGTGTTTGCGGAAATGGGTGTCACCCTGGAATATAAAGTG +GGCACGATGATTGAAATCCCGCGTGCTGCGCTGATTGCGGAAGAAATCGGTAAAGAAGCCGATTTCTTTA +GCTTTGGCACCAACGACCTGACCCAGATGACGTTCGGTTATAGTCGCGATGACGTGGGCAAATTTCTGCA +AATTTACCTGGCCCAGGGTATCCTGCAACATGATCCGTTTGAAGTTATTGACCAGAAAGGCGTCGGTCAA +CTGATCAAAATGGCAACCGAAAAAGGCCGCGCCGCAAATCCGAGTCTGAAAGTGGGTATTTGCGGCGAAC +ACGGCGGTGAACCGAGTTCCGTGGCGTTTTTCGATGGCGTTGGTCTGGACTACGTTAGTTGTTCCCCGTT +TCGTGTCCCGATTGCCCGTCTGGCTGCCGCCCAAGTGATTGTTTAACTCGAGGATCC