diff --git a/inc/abkuerzungen.tex b/inc/abkuerzungen.tex index a0c4b95..5192c5a 100644 --- a/inc/abkuerzungen.tex +++ b/inc/abkuerzungen.tex @@ -5,7 +5,7 @@ \acro{AA/BAA}{Acrylamid/Bisacrylamid} \acro{APS}{Ammoniumperoxodisulfat} \acro{BSA}{Bovines Serumalbumin} - \acro{CBB}[CBB G-250]{Coomassie-Brilliant-Blau G-250} + \acro{CBB}[CBB-G250]{Coomassie-Brilliant-Blau G-250} \acro{CD}{Circulardichroismus} \acro{CV}{Säulenvolumen, engl. \textit{column volume}} \acro{dCTP}{Desoxycytidintriphosphat} @@ -20,16 +20,20 @@ \acro{IDA}{Iminodiessigsäure} \acro{IMAC}{Immobilisierte Metallionen Affinitätschromatographie} \acro{IPTG}{Isopropyl-\textbeta-D-thiogalactopyranosid} + \acro{NaN3}[\ce{NaN3}]{Natriumazid} \acro{OD}{Optische Dichte} \acro{p. a.}{\textit{pro analysi} (lat.)} \acro{PAGE}{Polyacrylamidgelelektrophorese} \acro{PCR}{Polymerase-Kettenreaktion} \acro{PMSF}{Phenylmethylsulfonylfluorid} \acro{PPDK}{Pyruvat-Phosphat Dikinase} + \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{TAE}{Tris-Acetat-EDTA} + \acro{TBS}{\textit{Tris-buffered saline} (engl.)} + \acro{TBT}{\textit{Tris-buffered Tween} (engl.)} \acro{TEMED}{Tetramethylethylendiamin} \acro{Tris}{Tris(hydroxymethyl)-aminomethan} \acro{UV}{Ultraviolett} diff --git a/inc/material.tex b/inc/material.tex index dc651c5..1f40305 100644 --- a/inc/material.tex +++ b/inc/material.tex @@ -42,7 +42,8 @@ Chromatographiepapier 3MM Chr & Whatman, Maidstone, UK\\ Entsalzungssäulen PD10/MidiTrap G-25 & GE Healthcare, Uppsala, SE\\ Falconröhrchen \SI{15}{\milli\liter} und \SI{50}{\milli\liter} & Orange Scientific,\newline Braine-l'Alleud, BE\\ - \acs{IMAC}-Säule HisTrap HP \SI{5}{\milli\liter} & GE-Healthcare, Freiburg\\ + Filter für Ultrazentrifugation "`Amicon Ultra"' & Millipore, Schwalbach\\ + \acs{IMAC}-Säule HisTrap HP \SI{5}{\milli\liter} & GE Healthcare, Uppsala, SE\\ Mikrotiterplatten & Hartenstein, Würzburg\\ Petrischalen & Hartenstein, Würzburg\\ Pipettenspitzen & Brand, Wertheim\\ @@ -120,7 +121,7 @@ \midrule illustra GFX PCR DNA and Gel Band\newline Purification kit & GE Healthcare, Uppsala, SE\\ QIAprep Spin Miniprep & Qiagen, Hilden\\ - Roti-Quant$^\text{\textregistered}$ (Bradford) & Carl Roth, Karlsruhe\\ + Roti$^\text{\textregistered}$-Quant (Bradford) & Carl Roth, Karlsruhe\\ \bottomrule \end{tabularx} @@ -198,10 +199,60 @@ \SI{100}{\milli\liter} \acs{EDTA} (\SI{0,5}{\Molar}, pH 8)\\ \SI{57,1}{\milli\liter} Essigsäure\\ \SI{242}{\gram} Tris\\ - \SI{1}[ad~]{\liter} \ce{ddH2O} + \SI{1}[ad~]{\liter} \acs{ddH2O} \end{description} \end{samepage} +\subsection{Puffer für die \acs{SDS}-\acs{PAGE}} +\label{sec:puffer_sds_page} +\begin{description} + \item[\ac{AA/BAA} (Rotiphorese$^\text{\textregistered}$ Gel 30)] \hfill \\ + \SI{30}{\percent} Acrylamid\\ + \SI{0,8}{\percent} Bisacrylamid + \item[Laufpuffer (10\texttimes)] \hfill \\ + \SI{0,25}{\Molar} \acs{Tris}\\ + \SI{1,92}{\Molar} Glycin\\ + \SI{0,5}{\percent} (w/v) \acs{SDS} + \item[Sammelgelpuffer, pH 6,7 (5\texttimes)] \hfill \\ + \SI{0,25}{\Molar} \acs{Tris}/\ce{H3PO4}\\ + \SI{0,5}{\percent} (w/v) \acs{SDS} + \item[Trenngelpuffer, pH 8,9 (2,5\texttimes)] \hfill \\ + \SI{1,875}{\Molar} \acs{Tris}/\ce{H3PO4}\\ + \SI{0,25}{\percent} (w/v) \acs{SDS} + \item[Probenpuffer (4\texttimes)] \hfill \\ + \SI{30}{\milli\Molar} Borsäure\\ + \SI{30}{\milli\Molar} \acs{Tris}\\ + \SI{0,7}{\milli\Molar} \acs{EDTA}\\ + \SI{5}{\milli\Molar} Magnesiumchlorid\\ + \SI{50}{\milli\Molar} \ac{DTT}\\ + \SI{6,7}{\percent} (w/v) \acs{SDS}\\ + \SI{16,7}{\percent} (w/v) Saccharose\\ + \SI{0,16}{\percent} (w/v) Bromphenolblau + \item[Färbelösung] \hfill \\ + \SI{0,1}{\percent}~(w/v) \acs{CBB}\\ + \SI{2}{\percent}~(w/v) Phosphorsäure\\ + \SI{5}{\percent}~(w/w) Aluminiumsulfat\\ + \SI{10}{\percent}~(v/v) Ethanol +\end{description} + +\subsection{Puffer und Lösungen für den Westernblot} +\label{sec:puffer_westernblot} +\begin{description} + \item[Transferpuffer]\hfill \\ + \SI{25}{\milli\Molar} Tris\\ + \SI{190}{\milli\Molar} Glycin\\ + \SI{10}{\percent} (v/v) Ethanol + \item[TBS pH 7,5 - 8,0] \hfill \\ + \SI{10}{\milli\Molar} Tris/\ce{HCl}\\ + \SI{150}{\milli\Molar} Natriumchlorid + \item[TBT pH 7,5 - 8,0] \hfill \\ + \SI{20}{\milli\Molar} Tris\\ + \SI{500}{\milli\Molar} Natriumchlorid\\ + \SI{0,05}{\percent} (v/v) Polysorbat 20 + \item[Caseinlösung pH 7,5 - 8,0] \hfill \\ + \SI{1}{\percent} (w/v) Casein in TBS\\ + \SI{2}{\milli\liter} \SI{2}{\Molar} \ce{NaOH} je \SI{500}{\milli\liter} +\end{description} \subsection{Puffer für den Zellaufschluss} \label{sec:puffer_zellauschluss} @@ -263,6 +314,14 @@ \end{description} \end{samepage} +\subsection{Puffer für die \acs{CD}-Spektroskopie} +\label{sec:puffer_cd_spektroskopie} + \begin{description} + \item[CD-Puffer] \hfill \\ + \SI{50}{\milli\Molar} Kaliumphosphat pH 7,9\\ + \SI{10}{\milli\Molar} Magnesiumsulfat + \end{description} + \end{singlespace} \section{Molekularbiologische Methoden} \label{sec:methoden} @@ -299,7 +358,7 @@ Der Verdau erfolgte in einem Ansatzvolumen von \SI{25}{\micro\liter} bei \SI{37} \SI{3}{\micro\liter} NEBuffer 4 (New England Biolabs, Frankfurt)\\ \SI{10}{\Unit} \textit{BamH}I \\ \SI{10}{\Unit} \textit{Nde}I\\ - ad \SI{25}{\micro\liter} \ce{ddH2O} + ad \SI{25}{\micro\liter} \acs{ddH2O} \end{description} \end{samepage} @@ -352,7 +411,7 @@ Ansatz durchgeführt. Als Primer kamen die in \ref{sec:synthetische_oligonukleot \SI{5}{\micro\liter} Pwo-Puffer "`complete"' \\ \SI{0,5}{\micro\liter} Pwo-Polymerase (\SI{1}{\Unit\per\micro\liter}, peqlab, Erlangen) \\ \SI{0,5}{\micro\liter} dNTPs (\SI{10}{\milli\Molar}) \\ - \SI{50}[ad~]{\micro\liter} \ce{ddH2O} + \SI{50}[ad~]{\micro\liter} \acs{ddH2O} \end{description} \end{samepage} Das verwendete Cyclerprogramm ist in Tabelle \ref{tab:slic_cycler} aufgeführt. Bei der Berechnung @@ -384,10 +443,10 @@ zwanzig Zyklen die Schmelztemperatur des zum Zielvektor homologen Primerbereichs \subsubsection{Kolonie-\acs{PCR}} Zur Überprüfung des Klonierungserfolges wurden zufällig ausgewählte Kolonien mittels einer Kolonie-PCR -untersucht. Hierzu wurden je Kolonie \SI{5}{\micro\liter} \ce{ddH2O} in einem \acs{PCR}-Gefäß +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 und anschließend zum Animpfen eines \SI{5}{\milli\liter} Kulturröhrchens mit \acs{2YT}-Medium verwendet. - +% \begin{description} \item[Kolonie-PCR-Ansatz] \hfill \\ \SI{1}{\micro\liter} T7-Pro-Primer (\SI{10}{\micro\Molar})\\ @@ -395,9 +454,9 @@ und anschließend zum Animpfen eines \SI{5}{\milli\liter} Kulturröhrchens mit \ \SI{2,5}{\micro\liter} 10x~Thermo-Pol-Puffer (New England Biolabs, Frankfurt)\\ \SI{0,5}{\Unit} Taq-Polymerase (\SI{5}{\Unit\per\micro\liter}, New England Biolabs, Frankfurt)\\ \SI{0,25}{\micro\liter} dNTPs (\SI{10}{\milli\Molar})\\ - \SI{25}[ad~]{\micro\liter} \ce{ddH2O} + \SI{25}[ad~]{\micro\liter} \acs{ddH2O} \end{description} - +% Die Kolonie-\acs{PCR} wurde dann gemäß des in Tabelle \ref{tab:kolonie_pcr_cycler} dargelegten Programms durchgeführt. \begin{table}[hbt] @@ -427,30 +486,30 @@ Der Zielvektor pET-16b wurde zunächst über die Restriktionsenzyme \textit{Nde} wurde anschließend über ein Agarosegel gereinigt und die \acs{DNA} aus dem Gel gelöst (vgl. \ref{sec:extraktion_dna_agarosegel}). Die für die \ac{PPDK} kodierende Sequenz wurde wie in \ref{sec:pcr} beschrieben amplifiziert und ebenfalls über ein Agarosegel gereinigt. Zur Generierung der 5'-Überhänge wurden \SI{1000}{\nano\gram} Vektor- bzw. Insert-\acs{DNA} in folgendem Ansatz gedaut: - +% \begin{description} \item[Ansatz für \ac{SLIC}-Dau (\SI{35}{\micro\liter})] \hfill \\ x~\si{\micro\liter} \acs{DNA}~≡~\SI{1000}{\nano\gram} \acs{DNA}\\ \SI{2}{\micro\liter} \acs{BSA} (\SI{1}{\milli\gram\per\milli\liter})\\ \SI{4}{\micro\liter} NEBuffer 2 (New England Biolabs, Frankfurt)\\ \SI{1}{\Unit} T4-\acs{DNA}-Polymerase (New England Biolabs, Frankfurt)\\ - ad \SI{35}{\micro\liter} \ce{ddH2O} + ad \SI{35}{\micro\liter} \acs{ddH2O} \end{description} - +% Ziel war ein Dau von etwa \SI{30}{\bp} Länge. Aus der Exonukleaseaktivität der T4-\acs{DNA}-Polymerase von \SI{10}{\bp\per\minute} bei \SI{22}{\celsius} ergab sich eine Inkubationsdauer von \SI{40}{\minute}. Die Reaktion wurde durch Zugabe von $\frac{1}{10}$ des Ansatzvolumens \SI{10}{\milli\Molar} \ac{dCTP} gestoppt. In das nachfolgende Annealing wurden \SI{150}{\nano\gram} Vektor-\acs{DNA}, sowie Insert-\acs{DNA} (\SI{2691}{\bp}) im zweifachen molaren Verhältnis eingesetzt: - +% \begin{description} \item[\acs{SLIC}-Annealing (\SI{10}{\micro\liter})] \hfill \\ x \si{\micro\liter} Vektor-\acs{DNA} ≡~\SI{150}{\nano\gram}\\ y \si{\micro\liter} Insert-\acs{DNA} ≡~\SI{141}{\nano\gram}\\ \SI{1}{\micro\liter} T4-Ligase Puffer (New England Biolabs, Frankfurt)\\ - ad \SI{10}{\micro\liter} \ce{ddH2O} + ad \SI{10}{\micro\liter} \acs{ddH2O} \end{description} - +% Der Ansatz wurde anschließend für \SI{1}{\hour} bei \SI{37}{\celsius} inkubiert. \SI{5}{\micro\liter} der Ansätze wurden für die Transformation von \acs{E. coli} XL1-Blue eingesetzt. @@ -533,7 +592,7 @@ Die wie in \ref{sec:zellaufschluss} beschrieben aufgeschlossenen Zellen wurden z zentrifugiert um Zelltrümmer und \textit{Inclusion-Bodies} zu entfernen. Der Überstand wurde anschließend für \SI{1}{\hour} bei \SI{100000}{\xg} und \SI{15}{\celsius} ulrazentrifugiert um lediglich lösliche Proteine im Überstand zu halten und Membranfragmente zu präzipitieren. -Die mit \ce{Ni2+} beladene Säule wurde zunächst mit \SI{5}{\CV} \ce{ddH20} und \SI{20}{\CV} Waschpuffer \emph{ohne} \acs{DTT} gewaschen, um schwach bindende +Die mit \ce{Ni2+} beladene Säule wurde zunächst mit \SI{5}{\CV} \acs{ddH2O} und \SI{20}{\CV} Waschpuffer \emph{ohne} \acs{DTT} gewaschen, um schwach bindende \ce{Ni2+} von der Säule zu eluieren und die Bildung von amorphem Nickel bei der nachfolgenden Benutzung der Puffer mit reduzierend wirksamen \acs{DTT} zu minimieren. @@ -543,12 +602,28 @@ mit einem Volumen von \SI{5}{\milli\liter} gesammelt und ggf. vereinigt. Zur Det Nach Abschluss der Reinigung wurde die Säule nach Herstellerangaben gereinigt und neu mit \ce{Ni2+} beladen. - -\subsection{Konzentrierung} +\subsection{Konzentrierung von Proteinlösungen} \label{sec:konzentrierung} +Proteinlösungen wurden durch zentrifugale Ultrafiltration bei \SI{20}{\celsius} und \SI{5000}{\xg} aufkonzentriert. Hierbei kamen Konzentratoren mit einer Ausschlussgröße +von \SI{30}{\kilo\dalton} zu Einsatz. -\subsection{Entsalzung} +\subsection{Entsalzung von Proteinlösungen} \label{sec:entsalzung} +Nach der Reinigung wurden Fraktionen, welche die \acs{PPDK} enthielten mittels Ultrafiltration (vgl. \ref{sec:konzentrierung}) auf ein Volumen +von etwa \SI{2,5}{\milli\liter} eingeengt. Zur Umpufferung des Konzentrats in Lagerungspuffer kam eine PD-10-Säule zum Einsatz. Es handelt sich +hierbei um eine Größenauschlusschromatographie-Säule, bei welcher die Proteinanteile der Lösung eine wesentlich geringere Retentionszeit aufweisen, +als die gelösten Salzionen und somit mit einem geringeren Volumen von der Säule eluieren. + +Die Säule wurde mit \SI{25}{\milli\liter} Lagerungspuffer äquilibriert und anschließend mit der konzentrierten Probe beladen. Anschließend wurde die +Differenz des Probenvolumens zu \SI{2,5}{\milli\liter} durch Lagerungspuffer ausgeglichen. Die Elution erfolgte mit \SI{3,5}{\milli\liter} +Lagerungspuffer. Die entsalzten Proben wurden erneut aufkonzentriert (vgl. \ref{sec:konzentrierung}). + +\subsection{Lagerung von PPDK-Konzentraten} +\label{sec:lagerung} +Die kurzfristige Lagerung (max \SI{24}{\hour}) entsalzter \acs{PPDK}-Konzentrate (vgl. \ref{sec:entsalzung}) erfolgte nach Zugabe von \SI{1}{\percent}iger +\ac{NaN3}-Lösung im Verhältnis 1:1000 bei Raumtemperatur. + +Langfristig wurden \acs{PPDK}-Lösungen nach Zugabe von \SI{20}{\percent}~(w/v) Glycerin bei \SI{-20}{\celsius} gelagert. \section{Analytische Methoden} \label{sec:analytische_methoden} @@ -556,17 +631,156 @@ Nach Abschluss der Reinigung wurde die Säule nach Herstellerangaben gereinigt u \subsection{Differentielle Zentrifugation} \label{sec:differentielle_zentrifugation} + Nach dem Zellaufschluss (vgl. \ref{sec:zellaufschluss}) wurde eine Probe von \SI{10}{\micro\liter} aus dem Homogenisat als Kontrolle entnommen. + Anschließend wurde das Homogenisat bei \SI{2000}{\xg} für \SI{15}{\minute} bei \SI{15}{\celsius} zentrifugiert. Das resultierende Pellet + wurde im gleichen Volumen Aufschlusspuffer unter Zusatz von \SI{0,1}{\percent} (w/v) \acs{SDS} bei Raumtemperatur und unter Rühren rückgelöst. + + Es wurden jeweils vom Überstand, als auch vom resuspendierten Pellet weitere Proben von \SI{10}{\micro\liter} Volumen entnommen. Diese + wurden mit \SI{25}{\micro\liter} \acs{SDS}-Probenpuffer und \SI{65}{\micro\liter} \acs{ddH2O} versetzt. Alle weiteren Zentrifugationsschritte + erfolgten hierzu analog und sind in Tabelle \ref{tab:differentielle_zentrifugation} aufgeführt. +% +\begin{table}[htb] + \centering + \caption{Zentrifugationsschritte der differentiellen Zentrifugation} + \begin{tabularx}{0.85\textwidth}{rcX} + \toprule + \textbf{\acs{rcf} [\si{\xg}]} & \textbf{Dauer [\si{\minute}]} & \textbf{Sediment}\\ + \midrule + 2000 & 15 & Nicht aufgeschlossene Zellen und Zelltrümmer\\ + 10000 & 30 & Aggregierte Proteine (\textit{Inclusion Bodies})\\ + 30000 & 30 & Große Membransysteme und assoziierte Proteine\\ + 100000 & 60 & Kleine Membransysteme und assoziierte Proteine\\ + \bottomrule + \end{tabularx} + \label{tab:differentielle_zentrifugation} +\end{table} + \subsection{Größenauschlusschromatographie} \label{sec:groessenausschluss} +Um die Dispersität der gereinigten \acs{PPDK} zu bestimmen, wurde ein entsalztes Konzentrat (vgl. \ref{sec:entsalzung}) nach der Reinigung mittels +\acs{IMAC} (vgl. \ref{sec:affinitaetschromatographie}) einer analytischen Größenausschlusschromatographie unterzogen. Hierbei dient die Säulenmatrix +als Molekularsieb. Höhermolekulare Anteile eluieren hierbei schneller von der Säule, als niedermolekulare Anteile, da letztere in die Poren des +Säulenmaterials eindringen können. + +In dieser Arbeit wurde eine Superdex 200 5/150 GL-Säule der Firma GE Healthcare (Uppsala, SE) mit einem Säulenvolumen von \SI{3}{\milli\liter} +eingesetzt. + +Die Säule wurde mit \SI{5}{\CV} Lagerungspuffer äquilibriert und anschließend mit \SI{50}{\micro\liter} Probe in Lagerungspuffer beladen. Die +Detektion erfolgte durch Absorptionsmessung bei \SI{280}{\nano\meter}. Eluiert wurde mit \SI{2}{\CV} Lagerungspuffer bei einer Flussrate von +\SI{0,2}{\milli\liter\per\minute}. \subsection{SDS-\acl{PAGE}} \label{sec:sds_page} +Die Proteinproben wurden auf Polyacrylamid-Gele aufgetragen und dort nach ihrer Masse aufgetrennt +\citep{Laemmli1970}. Durch die Zugabe von \ac{SDS} werden die Proteine denaturiert und mit einr negativen +Ladung maskiert, wodurch sie ein einheitliches Ladungs-Masse-Verhältnis aufweisen. Somit ist die Wanderungsgeschwindigkeit +im elektrischen Feld allein von der Proteinmasse abhängig. Vor dem Auftragen auf das Geld wurden alle Proben mit +4\texttimes-Probenpuffer versetzt. Expressionsproben wurden darüber hinaus für \SI{10}{\minute} auf \SI{95}{\celsius} erhitzt. +Im Falle der Expressionsproben errechnete sich das Auftragungsvolumen für große bzw. kleine Gele nach Gleichung \eqref{eq:page_gross} und \eqref{eq:page_klein}. +% +\begin{align} + \label{eq:page_gross} + V_\text{groß}~[\si{\micro\liter}] &= \frac{15}{OD_{600}}\\ + \label{eq:page_klein} + V_\text{klein}~[\si{\micro\liter}] &= \frac{15}{OD_{600}} \ \cdot 0,75 +\end{align} +% +Für die Elektrophorese wurden \SI{10}{\percent}ige Gele eingesetzt. Tabelle \ref{tab:pipettierschema_sds_page} zeigt exemplarisch eine +Pipettierschema für drei kleine Gele (\SI{9}{\centi\meter}~\texttimes~\SI{10}{\centi\meter}). +% +\begin{table}[htb] +\centering +\caption{Pipettierschema für SDS-Gele} +\begin{tabular}{lll} +\toprule + & \textbf{Trenngel} & \textbf{Sammelgel}\\ +\midrule +\acs{AA/BAA} 30 & \SI{10,9}{\milli\liter} & \SI{2}{\milli\liter}\\ +Trenn-/Sammelgelpuffer & \SI{9,2}{\milli\liter} & \SI{2,6}{\milli\liter}\\ +\acs{ddH2O} & \SI{3,6}{\milli\liter} & \SI{7,4}{\milli\liter}\\ +\acs{TEMED} & \SI{16,5}{\micro\liter} & \SI{12,3}{\micro\liter}\\ +\acs{APS} \SI{10}{\percent} (w/v) & \SI{112}{\micro\liter} & \SI{129}{\micro\liter}\\ +\bottomrule +\end{tabular} +\label{tab:pipettierschema_sds_page} +\end{table} +% +Um die Größenzuordnung der Proteinbanden zu gewährleisten, wurden die in \ref{sec:standards_proteine_nukleinsaeuren} genannten +Standards eingesetzt. Bei kleinen Gelen wurde nach dem Beladen für \SI{1}{\hour} eine Stromstärke von \SI{35}{\milli\ampere} je Gel angelegt. +Größe Gele liefen über Nacht bei \SI{50}{\milli\ampere}. + +\subsection{Kolloidale Coomassie-Färbung} +\label{sec:faerbung_coomassie} +Mit der kolloidalen Coomassie-Färbung nach \citet{Kang2002} lassen sich Proteine in Polyacrylamid-Gelen bis zu einer Nachweisgrenze von etwa \SI{1}{\nano\gram} +detektieren. Sie ist damit ähnlich sensitiv wie eine Silberfärbung. + +Die Gele wurden drei Mal für jeweils \SI{10}{\minute} in \acs{ddH2O} gewaschen und anschließend für mindestens \SI{2}{\hour} in der Färbelösung +inkubiert. Nach dieser Zeit sind etwa \SI{90}{\percent} der maximalen Farbintensität erreicht \citep{Kang2002}. Eine Entfärbung des Hintergrunds kann durch mehrfaches +Waschen mit \acs{ddH2O} erreicht werden. + +\subsection{Westernblot und immunologischer Nachweis von Proteinen} +\label{sec:westernblot} +Über einen Westernblot können Proteine aus einem SDS-Gel elektrophoretisch auf einen Membran übertragen und dort fixiert werden. +Über eine Immunfärbung kann anschließend eine Visualisierung der Proteine auf der Membran erfolgen. Im Rahmen dieser Arbeit kam das +Semi-Dry-Blotverfahren, sowie eine Nitrozellulosemembran mit einer Porengröße von \SI{0,2}{\micro\meter} zum Einsatz. + +Bei Gelen, welche für einen Westernblot vorgesehen waren, kam ein gefärbter Proteingrößenstandard zum Einsatz. Das Gel wurde für etwa +\SI{10}{\minute} in Transferpuffer inkubiert. Die benötigten Filterpapiere, sowie die Nitrozellulosemembran wurden ebenfalls kurz in +Transferpuffer getränkt. + +Auf die Anode der Blotapparatur wurden zunächst drei Lagen Filterpapier, gefolgt von der Blotmembran, dem Gel sowie drei weiteren Lagen +Filterpapier gegeben. Anschließend wurde die Apparatur geschlossen und für \SI{2}{\hour} eine Stromstärke von +\SI{1}{\milli\ampere\per\square\centi\meter} angelegt. + +Nach Abschluss des Blotvorgangs wurde die Membran entnommen und \SI{1}{\hour} in einer \SI{1}{\percent}igen Caseinlösung in \acs{TBS} auf einem +Rotationsschüttler inkubiert. Es schlossen sich zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute} an. + +Die Membran wurde dann zusammen mit einer \SI{1}{\percent}igen Caseinlösung in TBS, welche den Anti-His-\acs{HRP}-Antikörper im Verhältnis 1:10000 +enthielt, in Folie eingeschweißt und über Nacht bei \SI{4}{\celsius} auf einem Taumelschüttler inkubiert. Am nächsten Tag erfolgten +zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute}. Der gebundene Antikörper ließ sich über die gekoppelte +Meerrettich-Peroxidase (\acs{HRP}) mit Hilfe eines Chemilumineszenzreagenzes nachweisen. die \acs{HRP} oxidiert in Anwesenheit von +Wasserstoffperoxid das Substrat Luminol, wobei es zu einer Lichtemission kommt. + +Hierfür wurde die Membran in Folie eingeschlagen und mit dem Reagenz überschichtet. Für die Visualisierung wurde ein Lumineszenzdetektor +(LAS 4000 mini, Fujifilm) eingesetzt. + \subsection{Konzentrationsbestimmung von Proteinen} \label{sec:konzentrationsbestimmung_proteine} +Die Konzentration von Proteinen wurde nach \citet{Bradford1976} bestimmt. Hierzu wurde in einer Mikrotiterplatte \SI{50}{\micro\liter} einer +Verdünnung der zu vermessenden Proteinlösung mit \SI{200}{\micro\liter} Bradford-Reagenz aus dem Roti$^{\text{\textregistered}}$-Quant-Kit versetzt. +Die Probe wurde für \SI{5}{\minute} bei Raumtemperatur inkubiert und die Absorption bei \SI{595}{\nano\meter} gemessen. + +Die Berechnung der Proteinkonzentration erfolgte anhand einer mit bovinem Serumalbumin \acs{BSA} erstellten Kalibriergeraden. Alle Messungen erfolgten in Dreifachbestimmung. \subsection{\acl{CD}-Spektroskopie} \label{sec:cd_spektroskopie} +Bei der \ac{CD}-Spektroskopie wird die Wechselwirkung von optisch aktiven Substanzen mit zirkular polarisiertem Licht zu analytischen Zwecken +ausgenutzt. Eine links- und eine rechtszirkulare Lichwelle überlagern sich hierbei zu linear polarisiertem Licht. Optisch aktive Substanzen +weisen für die links- bzw. rechtszirkulare Komponente unterschiedliche Absorptionskoeffizienten \textepsilon$_\text{L}$ und \textepsilon$_\text{R}$ +auf, wobei letztlich ihre Differenz \textDelta\textepsilon~gemessen und als Elliptizität \texttheta~angegeben wird -- d sei die Schichtdicke und c +die Konzentration \citep{Greenfield2007}: +% + \begin{equation} + \theta (\lambda) = \Delta\varepsilon \cdot c \cdot d + \end{equation} +% +Die \ac{CD}-Spektroskopie kann für die Analyse von Proteinsekundärstrukturen eingesetzt werden. Hierbei werden Spektren im Bereich von +\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 +Molekulargewicht in molaren \ac{CD} (\textDelta\textepsilon) umgerechnet. + +\subsection{Aktivitätsassay} +\label{sec:aktivitaetsassay} + \section{Bioinformatische Methoden} \label{sec:bioinformatische_methoden} + +\subsection{Analyse von \ac{CD}-Spektren} +\label{sec:analyse_cd_spektren} + +\subsection{Erstellung von Homologiemodellen} +\label{sec:erstellung_homologiemodell} diff --git a/library.bib b/library.bib index f265091..bf73432 100644 --- a/library.bib +++ b/library.bib @@ -1,319 +1,6 @@ -Automatically generated by Mendeley 1.5.2 +Automatically generated by Mendeley 1.6 Any changes to this file will be lost if it is regenerated by Mendeley. -@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} -} -@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{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{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{Talini2009, -author = {Talini, G. and Gallori, E. and Maurel, M. C}, -file = {:home/alex/Dokumente/Mendeley Desktop/Talini, Gallori, Maurel/Research in microbiology/Talini, Gallori, Maurel - 2009 - Natural and unnatural ribozymes Back to the primordial RNA world.pdf:pdf}, -journal = {Research in microbiology}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -number = {7}, -pages = {457--465}, -shorttitle = {Natural and unnatural ribozymes}, -title = {{Natural and unnatural ribozymes: Back to the primordial RNA world}}, -volume = {160}, -year = {2009} -} -@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.}, -author = {Goss, Neil H. and Evans, Claudia T. and Wood, Harland G.}, -doi = {10.1021/bi00566a022}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Binding Sites,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Orthophosphate Dikinase: metabolism,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Phosphotransferases: metabolism,Pyruvate,purification}, -mendeley-tags = {purification}, -month = dec, -number = {25}, -pages = {5805--9}, -pmid = {6257293}, -title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023 http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, -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.}, -doi = {10.1021/bi00566a022}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Binding Sites,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Orthophosphate Dikinase: metabolism,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Phosphotransferases: metabolism,Pyruvate,purification}, -mendeley-tags = {purification}, -month = dec, -number = {25}, -pages = {5805--9}, -pmid = {6257293}, -title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023 http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, -volume = {19}, -year = {1980} -} -@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{Brimacombe2000, -author = {Brimacombe, R.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Brimacombe/Structure/Brimacombe - 2000 - The bacterial ribosome at atomic resolution.pdf:pdf}, -journal = {Structure}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -number = {10}, -pages = {R195--R200}, -title = {{The bacterial ribosome at atomic resolution}}, -volume = {8}, -year = {2000} -} -@article{Noireaux2011, -author = {Noireaux, V. and Maeda, Y. T and Libchaber, A.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Noireaux, Maeda, Libchaber/Proceedings of the National Academy of Sciences/Noireaux, Maeda, Libchaber - 2011 - Development of an artificial cell, from self-organization to computation and self-reproduction.pdf:pdf}, -journal = {Proceedings of the National Academy of Sciences}, -number = {9}, -pages = {3473}, -title = {{Development of an artificial cell, from self-organization to computation and self-reproduction}}, -volume = {108}, -year = {2011} -} -@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} -} -@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{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{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{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} -} -@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{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 = {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{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}, @@ -327,54 +14,78 @@ url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608010279}, volume = {383}, year = {2008} } -@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}, +@article{MONOD1965, +author = {MONOD, J and WYMAN, J and CHANGEUX, J P}, +issn = {0022-2836}, 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} +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{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}, +@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 = {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} +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{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{Martin2007, +author = {Martin, W. and Russell, M. J}, +file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2007 - On the origin of biochemistry at an alkaline hydrothermal vent.pdf:pdf}, +journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +number = {1486}, +pages = {1887}, +title = {{On the origin of biochemistry at an alkaline hydrothermal vent}}, +volume = {362}, +year = {2007} +} +@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{Dyballa2009, +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 = {Dyballa, Nadine and Metzger, Sabine}, +doi = {10.3791/1431}, +file = {:home/alex/Dokumente/Mendeley Desktop/Dyballa, Metzger/Journal of visualized experiments JoVE/Dyballa, Metzger - 2009 - Fast and sensitive colloidal coomassie G-250 staining for proteins in polyacrylamide gels.pdf:pdf}, +issn = {1940-087X}, +journal = {Journal of visualized experiments : JoVE}, +keywords = {Acrylic Resins,Acrylic Resins: chemistry,Colloids,Colloids: chemistry,Electrophoresis, Gel, Two-Dimensional,Electrophoresis, Gel, Two-Dimensional: methods,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}, +month = jan, +number = {30}, +pages = {2--5}, +pmid = {19684561}, +title = {{Fast and sensitive colloidal coomassie G-250 staining for proteins in polyacrylamide gels.}}, +url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3149902\&tool=pmcentrez\&rendertype=abstract}, +year = {2009} } @article{Miroux1996, author = {Miroux, B. and Walker, J. E}, @@ -387,22 +98,6 @@ title = {{Over-production of proteins in Escherichia coli: mutant hosts that all volume = {260}, year = {1996} } -@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{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}, @@ -419,161 +114,22 @@ url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212609001920}, volume = {17}, year = {2009} } -@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} -} -@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{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{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, +@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 = {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{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}, +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{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{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{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{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{Michalkova2011, author = {Michalkova, Andrea and Kholod, Yana and Kosenkov, Dmytro and Gorb, Leonid and Leszczynski, Jerzy}, doi = {10.1016/j.gca.2011.01.015}, @@ -605,22 +161,17 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/10736156 http://pubs.acs.org/doi/abs/1 volume = {39}, year = {2000} } -@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{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.}, @@ -638,20 +189,21 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=28320\&tool=pmc 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{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{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.}, @@ -676,14 +228,6 @@ author = {Pfleger, Christopher and Radestock, Sebastian and Schmidt, S. and Gohl 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{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}, @@ -702,33 +246,19 @@ url = {http://doi.wiley.com/10.1110/ps.03259908 http://www.pubmedcentral.nih.gov volume = {17}, year = {2008} } -@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} +@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{Sponer2011, author = {\v{S}poner, Judit E. and \v{S}poner, Jiř\'{\i} and Fuentes-Cabrera, Miguel}, @@ -758,30 +288,38 @@ url = {http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkh410}, volume = {32}, year = {2004} } -@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{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{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{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} } @misc{CenterforHistoryandNewMedia, annote = { @@ -795,20 +333,22 @@ author = {{Center for History and New Media}}, title = {{Zotero Quick Start Guide}}, url = {http://zotero.org/support/quick\_start\_guide} } -@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} } @book{Bruckner2007, address = {Berlin [u.a.]}, @@ -821,21 +361,6 @@ 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{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}, @@ -852,47 +377,28 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/3052577}, volume = {27}, year = {1988} } -@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{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{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{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{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{Luisi2003a, author = {Luisi, P. L}, @@ -905,17 +411,22 @@ 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{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} } @article{Wiechelman1988, author = {Wiechelman, K}, @@ -933,6 +444,17 @@ url = {http://linkinghub.elsevier.com/retrieve/pii/0003269788903831}, volume = {175}, year = {1988} } +@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} +} @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}, @@ -950,19 +472,16 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084084\&tool=p volume = {108}, 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} +@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{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}, @@ -990,6 +509,33 @@ url = {http://www.nature.com/doifinder/10.1038/nprot.2006.202}, volume = {1}, year = {2007} } +@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} +} +@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{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}, @@ -1001,6 +547,48 @@ title = {{Emergence in chemistry: Chemistry as the embodiment of emergence}}, volume = {4}, year = {2002} } +@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{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{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}, @@ -1019,34 +607,20 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/15258570}, volume = {11}, year = {2004} } -@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{Haines2005, -abstract = {Marine organism derived extracts, previously identified as containing compounds that inhibited the C4 acid cycle enzyme pyruvate Pi dikinase (PPDK), were assessed for their ability to exhibit an effect on the C4 plants Digitaria ciliaris and Echinochloa crus-galli. Oxygen electrode studies revealed that over half of these extracts inhibited C4 acid driven photosynthesis in leaf slices. Seventeen extracts had a deleterious effect on C4 plants in vivo within 24 h, whereas 36 caused an observable phytotoxic response in one or both of the C4 plants used for in vivo testing. None of the extracts inhibited PPDK metabolism of pyruvate via a directly competitive mechanism, instead hindering the enzyme by either mixed or uncompetitive means. This screening strategy, using a suite of assays, led to the isolation and identification of the herbicidal marine natural product ilimaquinone.}, -author = {Haines, Dianne S and Burnell, James N and Doyle, Jason R and Llewellyn, Lyndon E and Motti, Cherie A and Tapiolas, Dianne M}, -file = {:home/alex/Dokumente/Mendeley Desktop/Haines et al/Journal of Agricultural and Food Chemistry/Haines et al. - 2005 - Translation of in Vitro Inhibition by Marine Natural Products of the C4 Acid Cycle Enzyme Pyruvate Pi Dikinase to in Vivo C4 Plant Tissue Death.pdf:pdf}, -journal = {Journal of Agricultural and Food Chemistry}, -keywords = {C4 plant,Herbicide,PPDK,oxygen evolution}, -number = {12}, -pages = {3856--3862}, -title = {{Translation of in Vitro Inhibition by Marine Natural Products of the C4 Acid Cycle Enzyme Pyruvate Pi Dikinase to in Vivo C4 Plant Tissue Death}}, -volume = {53}, -year = {2005} +@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{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.}, @@ -1083,6 +657,139 @@ url = {http://pubs.acs.org/doi/abs/10.1021/cb6002465 http://pubs.acs.org/doi/pdf volume = {1}, 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{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{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{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} +} +@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{Russell2010, +author = {Russell, M. J. and Hall, A. J. and Martin, W.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Russell, Hall, Martin/Geobiology/Russell, Hall, Martin - 2010 - Serpentinization as a source of energy at the origin of life.pdf:pdf}, +journal = {Geobiology}, +title = {{Serpentinization as a source of energy at the origin of life}}, +year = {2010} +} +@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{Haines2005, +abstract = {Marine organism derived extracts, previously identified as containing compounds that inhibited the C4 acid cycle enzyme pyruvate Pi dikinase (PPDK), were assessed for their ability to exhibit an effect on the C4 plants Digitaria ciliaris and Echinochloa crus-galli. Oxygen electrode studies revealed that over half of these extracts inhibited C4 acid driven photosynthesis in leaf slices. Seventeen extracts had a deleterious effect on C4 plants in vivo within 24 h, whereas 36 caused an observable phytotoxic response in one or both of the C4 plants used for in vivo testing. None of the extracts inhibited PPDK metabolism of pyruvate via a directly competitive mechanism, instead hindering the enzyme by either mixed or uncompetitive means. This screening strategy, using a suite of assays, led to the isolation and identification of the herbicidal marine natural product ilimaquinone.}, +author = {Haines, Dianne S and Burnell, James N and Doyle, Jason R and Llewellyn, Lyndon E and Motti, Cherie A and Tapiolas, Dianne M}, +file = {:home/alex/Dokumente/Mendeley Desktop/Haines et al/Journal of Agricultural and Food Chemistry/Haines et al. - 2005 - Translation of in Vitro Inhibition by Marine Natural Products of the C4 Acid Cycle Enzyme Pyruvate Pi Dikinase to in Vivo C4 Plant Tissue Death.pdf:pdf}, +journal = {Journal of Agricultural and Food Chemistry}, +keywords = {C4 plant,Herbicide,PPDK,oxygen evolution}, +number = {12}, +pages = {3856--3862}, +title = {{Translation of in Vitro Inhibition by Marine Natural Products of the C4 Acid Cycle Enzyme Pyruvate Pi Dikinase to in Vivo C4 Plant Tissue Death}}, +volume = {53}, +year = {2005} +} +@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{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}, @@ -1102,20 +809,46 @@ url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608002313 http://www. volume = {378}, year = {2008} } -@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, +@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 = {1089--108}, -pmid = {21246632}, -title = {{Protein rigidity and thermophilic adaptation.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/21246632}, -volume = {79}, +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{Gilbert1986, +author = {Gilbert, Walter}, +doi = {10.1038/319618a0}, +file = {:home/alex/Dokumente/Mendeley Desktop/Gilbert/Nature/Gilbert - 1986 - Origin of life The RNA world.pdf:pdf}, +issn = {0028-0836}, +journal = {Nature}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = feb, +number = {6055}, +pages = {618--618}, +shorttitle = {Origin of life}, +title = {{Origin of life: The RNA world}}, +url = {http://www.nature.com/doifinder/10.1038/319618a0}, +volume = {319}, +year = {1986} +} +@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{Tsutsui1982, @@ -1131,17 +864,6 @@ title = {{Affinity chromatography of heme-binding proteins: an improved method f volume = {121}, year = {1982} } -@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{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}, @@ -1191,117 +913,6 @@ url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00 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} -} -@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{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{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{Cosenza2002, -author = {Cosenza, Lawrence W and Bringaud, Frederic and Baltz, Theo and Vellieux, Frederic M.D}, -doi = {10.1016/S0022-2836(02)00113-4}, -file = {:home/alex/Dokumente/Mendeley Desktop/Cosenza et al/Journal of Molecular Biology/Cosenza et al. - 2002 - The 3.0\AA Resolution Crystal Structure of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma brucei.pdf:pdf}, -issn = {00222836}, -journal = {Journal of Molecular Biology}, -keywords = {crystal structure,intermediate metabolism,parasitology,pyruvate phosphate dikinase,trypanosome}, -month = may, -number = {5}, -pages = {1417--1432}, -title = {{The 3.0\AA Resolution Crystal Structure of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma brucei}}, -url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602001134}, -volume = {318}, -year = {2002} -} -@article{Gilbert1986, -author = {Gilbert, Walter}, -doi = {10.1038/319618a0}, -file = {:home/alex/Dokumente/Mendeley Desktop/Gilbert/Nature/Gilbert - 1986 - Origin of life The RNA world.pdf:pdf}, -issn = {0028-0836}, -journal = {Nature}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = feb, -number = {6055}, -pages = {618--618}, -shorttitle = {Origin of life}, -title = {{Origin of life: The RNA world}}, -url = {http://www.nature.com/doifinder/10.1038/319618a0}, -volume = {319}, -year = {1986} -} -@article{Russell2010, -author = {Russell, M. J. and Hall, A. J. and Martin, W.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Russell, Hall, Martin/Geobiology/Russell, Hall, Martin - 2010 - Serpentinization as a source of energy at the origin of life.pdf:pdf}, -journal = {Geobiology}, -title = {{Serpentinization as a source of energy at the origin of life}}, -year = {2010} -} @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}, @@ -1346,48 +957,54 @@ 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{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{Martin2007, -author = {Martin, W. and Russell, M. J}, -file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2007 - On the origin of biochemistry at an alkaline hydrothermal vent.pdf:pdf}, -journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, +@article{Cosenza2002, +author = {Cosenza, Lawrence W and Bringaud, Frederic and Baltz, Theo and Vellieux, Frederic M.D}, +doi = {10.1016/S0022-2836(02)00113-4}, +file = {:home/alex/Dokumente/Mendeley Desktop/Cosenza et al/Journal of Molecular Biology/Cosenza et al. - 2002 - The 3.0\AA Resolution Crystal Structure of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma brucei.pdf:pdf}, +issn = {00222836}, +journal = {Journal of Molecular Biology}, +keywords = {crystal structure,intermediate metabolism,parasitology,pyruvate phosphate dikinase,trypanosome}, +month = may, +number = {5}, +pages = {1417--1432}, +title = {{The 3.0\AA Resolution Crystal Structure of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma brucei}}, +url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602001134}, +volume = {318}, +year = {2002} +} +@article{Cochrane2008, +author = {Cochrane, J. C. and Strobel, S. A.}, +doi = {10.1261/rna.908408}, +file = {:home/alex/Dokumente/Mendeley Desktop/Cochrane, Strobel/RNA/Cochrane, Strobel - 2008 - Riboswitch effectors as protein enzyme cofactors.pdf:pdf}, +issn = {1355-8382}, +journal = {RNA}, keywords = {Folder - Vortrag RNA-Welt}, mendeley-tags = {Folder - Vortrag RNA-Welt}, -number = {1486}, -pages = {1887}, -title = {{On the origin of biochemistry at an alkaline hydrothermal vent}}, -volume = {362}, -year = {2007} -} -@article{Heinz1991, -abstract = {The crystal structures of the complexes formed between subtilisin Novo and three inhibitors, eglin c, Arg45-eglin c and Lys53-eglin c have been determined using molecular replacement and difference Fourier techniques and refined at 2.4 A, 2.1 A, and 2.4 A resolution, respectively. The mutants Arg45-eglin c and Lys53-eglin c were constructed by site-directed mutagenesis in order to investigate the inhibitory specificity and stability of eglin c. Arg45-eglin became a potent trypsin inhibitor, in contrast to native eglin, which is an elastase inhibitor. This specificity change was rationalized by comparing the structures of Arg45-eglin and basic pancreatic trypsin inhibitor and their interactions with trypsin. The residue Arg53, which participates in a complex network of hydrogen bonds formed between the core and the binding loop of eglin c, was replaced with the shorter basic amino acid lysine in the mutant Lys53-eglin. Two hydrogen bonds with Thr44, located in the binding loop, can no longer be formed but are partially restored by a water molecule bound in the vicinity of Lys53. Eglin c in complexes with both subtilisin Novo and subtilisin Carlsberg was crystallized in two different space groups. Comparison of the complexes showed a rigid body rotation for the eglin c core of 11.5 degrees with respect to the enzyme, probably caused by different intermolecular contacts in both crystal forms.}, -author = {Heinz, D W and Priestle, J P and Rahuel, J and Wilson, K S and Gr\"{u}tter, M G}, -file = {:home/alex/Dokumente/Mendeley Desktop/Heinz et al/Journal of molecular biology/Heinz et al. - 1991 - Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.pdf:pdf}, -issn = {0022-2836}, -journal = {Journal of molecular biology}, -keywords = {Amino Acid Sequence,Binding Sites,Computer Graphics,Crystallography,DNA Mutational Analysis,Humans,Kinetics,Macromolecular Substances,Models, Molecular,Molecular Sequence Data,Motion,Pancreatic Elastase,Pancreatic Elastase: antagonists \& inhibitors,Protein Binding,Protein Conformation,Proteins,Recombinant Proteins,Recombinant Proteins: ultrastructure,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: pharmacology,Serpins,Structure-Activity Relationship,Subtilisins,Subtilisins: antagonists \& inhibitors,Subtilisins: ultrastructure,Trypsin Inhibitors}, -month = jan, -number = {2}, -pages = {353--71}, -pmid = {1992167}, -title = {{Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/1992167}, -volume = {217}, -year = {1991} +month = apr, +number = {6}, +pages = {993--1002}, +title = {{Riboswitch effectors as protein enzyme cofactors}}, +url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.908408}, +volume = {14}, +year = {2008} } @article{Bleecker2000, author = {Bleecker, A. B and Kende, H.}, @@ -1431,6 +1048,22 @@ title = {{Involvement of RTE1 in conformational changes promoting ETR1 ethylene volume = {56}, year = {2008} } +@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.}, author = {Goodey, Nina M and Benkovic, Stephen J}, @@ -1449,22 +1082,15 @@ url = {http://www.nature.com/doifinder/10.1038/nchembio.98 http://www.ncbi.nlm.n volume = {4}, year = {2008} } -@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}, +@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{Smith1985, @@ -1498,14 +1124,22 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/6544679}, volume = {11}, year = {1984} } -@book{Wedler2004, -address = {Weinheim}, -author = {Wedler, Gerd}, -edition = {5., vollst}, -isbn = {9783527310661}, -publisher = {Wiley-VCH}, -title = {{Lehrbuch der physikalischen Chemie}}, -year = {2004} +@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{Whiteley2005, abstract = {We outline the mathematical models, and the related counting algorithms, that are the basis for fast computations to predict biomolecular flexibility and rigidity. Within these mathematical models, we describe the snap-shot flexibility (instantaneous motions) of biomolecules, extracted from a single snap-shot of the molecule and the connection to larger finite motions. We illustrate the results and techniques with direct analysis of simple secondary structures. Understanding these basic ideas clarifies both the limits and the power of the algorithms, as well as the prospects for extensions and refinements of these algorithms.}, @@ -1524,17 +1158,6 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/16280617}, volume = {2}, year = {2005} } -@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{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}, @@ -1551,60 +1174,36 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/21910474}, volume = {51}, year = {2011} } -@misc{Case2010, -address = {San Francisco}, -author = {Case, D.A. and Darden, T.A. and Cheatham, T.E. and Simmerling, C.L. and Wang, J. and Duke, R.E. and Luo, R. and Walker, R.C. and Zhang, W. and Merz, K.M. and Roberts, B.P. and Wang, B. and Hayik, S. and Roitberg, A. and Seabra, G. and Kolossv\'{a}ry, I. and Wong, K.F. and Paesani, F. and Vanicek, J. and Liu, J. and Wu, X. and Brozell, S.R. and Steinbrecher, T. and Gohlke, H. and Cai, Q. and Ye, X. and Hsieh, M.-J. and Cui, G. and Roe, D.R. and Mathews, D.H. and Seetin, M.G. and Sagui, C. and Babin, V. and Luchko, T. and Gusarov, S. and Kovalenko, A. and Kollmann, P.A.}, -publisher = {University of California}, -title = {{AMBER 11}}, -url = {http://www.ambermd.org}, -year = {2010} +@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}, -file = {:home/alex/Dokumente/Mendeley Desktop/Cochrane, Strobel/RNA/Cochrane, Strobel - 2008 - Riboswitch effectors as protein enzyme cofactors.pdf:pdf}, -issn = {1355-8382}, -journal = {RNA}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = apr, -number = {6}, -pages = {993--1002}, -title = {{Riboswitch effectors as protein enzyme cofactors}}, -url = {http://www.rnajournal.org/cgi/doi/10.1261/rna.908408}, -volume = {14}, -year = {2008} -} -@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{Heinz1991, +abstract = {The crystal structures of the complexes formed between subtilisin Novo and three inhibitors, eglin c, Arg45-eglin c and Lys53-eglin c have been determined using molecular replacement and difference Fourier techniques and refined at 2.4 A, 2.1 A, and 2.4 A resolution, respectively. The mutants Arg45-eglin c and Lys53-eglin c were constructed by site-directed mutagenesis in order to investigate the inhibitory specificity and stability of eglin c. Arg45-eglin became a potent trypsin inhibitor, in contrast to native eglin, which is an elastase inhibitor. This specificity change was rationalized by comparing the structures of Arg45-eglin and basic pancreatic trypsin inhibitor and their interactions with trypsin. The residue Arg53, which participates in a complex network of hydrogen bonds formed between the core and the binding loop of eglin c, was replaced with the shorter basic amino acid lysine in the mutant Lys53-eglin. Two hydrogen bonds with Thr44, located in the binding loop, can no longer be formed but are partially restored by a water molecule bound in the vicinity of Lys53. Eglin c in complexes with both subtilisin Novo and subtilisin Carlsberg was crystallized in two different space groups. Comparison of the complexes showed a rigid body rotation for the eglin c core of 11.5 degrees with respect to the enzyme, probably caused by different intermolecular contacts in both crystal forms.}, +author = {Heinz, D W and Priestle, J P and Rahuel, J and Wilson, K S and Gr\"{u}tter, M G}, +file = {:home/alex/Dokumente/Mendeley Desktop/Heinz et al/Journal of molecular biology/Heinz et al. - 1991 - Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.pdf:pdf}, +issn = {0022-2836}, +journal = {Journal of molecular biology}, +keywords = {Amino Acid Sequence,Binding Sites,Computer Graphics,Crystallography,DNA Mutational Analysis,Humans,Kinetics,Macromolecular Substances,Models, Molecular,Molecular Sequence Data,Motion,Pancreatic Elastase,Pancreatic Elastase: antagonists \& inhibitors,Protein Binding,Protein Conformation,Proteins,Recombinant Proteins,Recombinant Proteins: ultrastructure,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: pharmacology,Serpins,Structure-Activity Relationship,Subtilisins,Subtilisins: antagonists \& inhibitors,Subtilisins: ultrastructure,Trypsin Inhibitors}, +month = jan, +number = {2}, +pages = {353--71}, +pmid = {1992167}, +title = {{Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/1992167}, +volume = {217}, +year = {1991} } @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}, @@ -1647,17 +1246,23 @@ publisher = {Spektrum Akademischer Verlag}, title = {{Biochemie}}, year = {2007} } -@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{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} } @book{Madigan2009, address = {München [u.a.]}, @@ -1670,23 +1275,6 @@ publisher = {Pearson Studium}, title = {{Brock - Mikrobiologie}}, year = {2009} } -@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{Lakowicz2006, address = {Boston, MA}, editor = {Lakowicz, Joseph R.}, @@ -1711,22 +1299,6 @@ url = {http://biology.plosjournals.org/perlserv/?request=get-document\&doi=10.13 volume = {6}, year = {2008} } -@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}, -doi = {10.1038/nmeth1010}, -issn = {1548-7091}, -journal = {Nature methods}, -keywords = {Cloning,DNA,Genetic,Genetic Engineering,Genetic Engineering: methods,Genetic: genetics,Molecular,Molecular: methods,Nucleic Acid,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Recombinant,Recombinant: genetics,Recombination,Sequence Homology}, -month = mar, -number = {3}, -pages = {251--6}, -pmid = {17293868}, -title = {{Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/17293868}, -volume = {4}, -year = {2007} -} @article{Lazcano2008, author = {Lazcano, A.}, file = {:home/alex/Dokumente/Mendeley Desktop/Lazcano/Chemistry \& Biodiversity/Lazcano - 2008 - What Is Life.pdf:pdf}, @@ -1770,18 +1342,6 @@ 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,Pj 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,Pj 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}, @@ -1807,6 +1367,21 @@ title = {{Evolution in an RNA World}}, volume = {74}, year = {2009} } +@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{Mellet1998, abstract = {Serpins are thought to inhibit proteinases by first forming a Michaelis-type complex that later converts into a stable inhibitory species. However, there is only circumstantial evidence for such a two-step reaction pathway. Here we directly observe the sequential appearance of two complexes by measuring the time-dependent change in fluorescence resonance energy transfer between fluorescein-elastase and rhodamine-alpha1-protease inhibitor. A moderately tight initial Michaelis-type complex EI1 (Ki = 0.38-0.52 microM) forms and dissociates rapidly (k1 = 1.5 x 10(6) M-1 s-1, k-1 = 0.58 s-1). EI1 then slowly converts into EI2 (k2 = 0.13 s-1), the fluorescence intensity of which is stable for at least 50 s. The two species differ by their donor-acceptor energy transfer efficiency (0. 41 and 0.26, respectively). EI2 might be the final product of the elastase + inhibitor association because its transfer efficiency is the same as that of a complex incubated for 30 min. The time-dependent change in fluorescence resonance energy transfer between fluorescein-elastase and rhodamine-eglin c, a canonical inhibitor, again allows the fast formation of a complex to be observed. However, this complex does not undergo any fluorescently detectable transformation.}, author = {Mellet, P}, @@ -1841,23 +1416,74 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/2831971 http://pubs.acs.org/doi/abs/10 volume = {27}, year = {1988} } -@article{DuBay2011a, -abstract = {Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 A in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.}, -author = {DuBay, Kateri H. and Bothma, Jacques P. and Geissler, Phillip L.}, -doi = {10.1371/journal.pcbi.1002168}, -editor = {Shakhnovich, Eugene I.}, -file = {:home/alex/Dokumente/Mendeley Desktop/DuBay, Bothma, Geissler/PLoS Computational Biology/DuBay, Bothma, Geissler - 2011 - Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone.pdf:pdf}, -issn = {1553-7358}, -journal = {PLoS Computational Biology}, -keywords = {2FE-2S FERREDOXIN,ADENYLATE KINASE,ANGSTROM RESOLUTION,CRYSTAL-STRUCTURE,Calmodulin,DYNAMICS,ENERGY LANDSCAPE,Eglin c,HYDROGEN-DEUTERIUM EXCHANGE,PLANT-TYPE FERREDOXINS,STRUCTURE-BASED MODELS,TERMINAL SRC KINASE}, -mendeley-tags = {Calmodulin,Eglin c}, -month = sep, -number = {9}, -pages = {e1002168}, -title = {{Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone}}, -url = {http://dx.plos.org/10.1371/journal.pcbi.1002168}, -volume = {7}, -year = {2011} +@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{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} +} +@book{Wedler2004, +address = {Weinheim}, +author = {Wedler, Gerd}, +edition = {5., vollst}, +isbn = {9783527310661}, +publisher = {Wiley-VCH}, +title = {{Lehrbuch der physikalischen Chemie}}, +year = {2004} +} +@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{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}, +doi = {10.1038/nmeth1010}, +issn = {1548-7091}, +journal = {Nature methods}, +keywords = {Cloning,DNA,Genetic,Genetic Engineering,Genetic Engineering: methods,Genetic: genetics,Molecular,Molecular: methods,Nucleic Acid,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Recombinant,Recombinant: genetics,Recombination,Sequence Homology}, +month = mar, +number = {3}, +pages = {251--6}, +pmid = {17293868}, +title = {{Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/17293868}, +volume = {4}, +year = {2007} } @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.}, @@ -1876,23 +1502,6 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=p volume = {108}, year = {2011} } -@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} -} @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.}, author = {Guckian, Kevin M and Lin, Edward Yin-Shiang and Silvian, Laura and Friedman, Jessica E and Chin, Donovan and Scott, Daniel M}, @@ -1910,43 +1519,43 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/18778938}, volume = {18}, year = {2008} } -@article{Bohr1904, -abstract = {Complexes of hemoglobin and carbon dioxide have been known for a long time;(2) however, so far all researchers have regarded the oxygen uptake of the blood and its carbon dioxide uptake as two independent processes. Bohr found instead in the cited discussion that even though the carbon dioxide-uptake in the presence of oxygen remains uninfluenced, the oxygen uptake of the blood is usually reduced if a certain amount of carbon dioxide is present. However, from a quantitative point of view, the results were only reproducible with a relatively large error which may be due to great variability of the hemoglobin molecule.}, -author = {Bohr, Christian and Hasselbalch, K and Krogh, August}, -journal = {Skand Arch Physiol}, -keywords = {allostery,hemoglobine,oxygen}, -mendeley-tags = {allostery}, -pages = {401--412}, -title = {{\"{U}ber einen in biologischer Beziehung wichtigen Einfluss, den die Kohlens\"{a}urespannung des Blutes auf dessen Sauerstoffbindung \"{u}bt}}, -volume = {16}, -year = {1904} +@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{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, +@misc{Case2010, +address = {San Francisco}, +author = {Case, D.A. and Darden, T.A. and Cheatham, T.E. and Simmerling, C.L. and Wang, J. and Duke, R.E. and Luo, R. and Walker, R.C. and Zhang, W. and Merz, K.M. and Roberts, B.P. and Wang, B. and Hayik, S. and Roitberg, A. and Seabra, G. and Kolossv\'{a}ry, I. and Wong, K.F. and Paesani, F. and Vanicek, J. and Liu, J. and Wu, X. and Brozell, S.R. and Steinbrecher, T. and Gohlke, H. and Cai, Q. and Ye, X. and Hsieh, M.-J. and Cui, G. and Roe, D.R. and Mathews, D.H. and Seetin, M.G. and Sagui, C. and Babin, V. and Luchko, T. and Gusarov, S. and Kovalenko, A. and Kollmann, P.A.}, +publisher = {University of California}, +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,Pj 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 = {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}, -edition = {2. Aufl.}, -isbn = {9783827415202}, -keywords = {Folder - Biochemie}, -mendeley-tags = {Folder - Biochemie}, -publisher = {Spektrum Akademischer Verlag}, -title = {{Bioanalytik}}, -year = {2006} +pages = {295--297}, +title = {{A Comparative Study of the Cold-Sensitivity of Pyruvate,Pj Dikinase in Flaveria Species}}, +volume = {31}, +year = {1990} } @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.}, @@ -1964,85 +1573,6 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=p volume = {108}, year = {2011} } -@article{Provencher1981, -author = {Provencher, Stephen W. and Gloeckner, Juergen}, -doi = {10.1021/bi00504a006}, -file = {:home/alex/Dokumente/Mendeley Desktop/Provencher, Gloeckner/Biochemistry/Provencher, Gloeckner - 1981 - Estimation of globular protein secondary structure from circular dichroism.pdf:pdf}, -issn = {0006-2960}, -journal = {Biochemistry}, -keywords = {Folder - RTE1}, -mendeley-tags = {Folder - RTE1}, -month = jan, -number = {1}, -pages = {33--37}, -title = {{Estimation of globular protein secondary structure from circular dichroism}}, -url = {http://pubs.acs.org/doi/abs/10.1021/bi00504a006}, -volume = {20}, -year = {1981} -} -@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{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{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{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} -} @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}, @@ -2056,22 +1586,23 @@ title = {{Getting Started with Mendeley}}, url = {http://www.mendeley.com}, year = {2011} } -@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{DuBay2011a, +abstract = {Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 A in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.}, +author = {DuBay, Kateri H. and Bothma, Jacques P. and Geissler, Phillip L.}, +doi = {10.1371/journal.pcbi.1002168}, +editor = {Shakhnovich, Eugene I.}, +file = {:home/alex/Dokumente/Mendeley Desktop/DuBay, Bothma, Geissler/PLoS Computational Biology/DuBay, Bothma, Geissler - 2011 - Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone.pdf:pdf}, +issn = {1553-7358}, +journal = {PLoS Computational Biology}, +keywords = {2FE-2S FERREDOXIN,ADENYLATE KINASE,ANGSTROM RESOLUTION,CRYSTAL-STRUCTURE,Calmodulin,DYNAMICS,ENERGY LANDSCAPE,Eglin c,HYDROGEN-DEUTERIUM EXCHANGE,PLANT-TYPE FERREDOXINS,STRUCTURE-BASED MODELS,TERMINAL SRC KINASE}, +mendeley-tags = {Calmodulin,Eglin c}, +month = sep, +number = {9}, +pages = {e1002168}, +title = {{Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone}}, +url = {http://dx.plos.org/10.1371/journal.pcbi.1002168}, +volume = {7}, +year = {2011} } @article{Ernst2008, author = {Ernst, R. and Kueppers, P. and Klein, C. M. and Schwarzmueller, T. and Kuchler, K. and Schmitt, L.}, @@ -2125,6 +1656,60 @@ title = {{Glycerol Viscosity Tables}}, volume = {9}, year = {1932} } +@article{Bohr1904, +abstract = {Complexes of hemoglobin and carbon dioxide have been known for a long time;(2) however, so far all researchers have regarded the oxygen uptake of the blood and its carbon dioxide uptake as two independent processes. Bohr found instead in the cited discussion that even though the carbon dioxide-uptake in the presence of oxygen remains uninfluenced, the oxygen uptake of the blood is usually reduced if a certain amount of carbon dioxide is present. However, from a quantitative point of view, the results were only reproducible with a relatively large error which may be due to great variability of the hemoglobin molecule.}, +author = {Bohr, Christian and Hasselbalch, K and Krogh, August}, +journal = {Skand Arch Physiol}, +keywords = {allostery,hemoglobine,oxygen}, +mendeley-tags = {allostery}, +pages = {401--412}, +title = {{\"{U}ber einen in biologischer Beziehung wichtigen Einfluss, den die Kohlens\"{a}urespannung des Blutes auf dessen Sauerstoffbindung \"{u}bt}}, +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}, +edition = {2. Aufl.}, +isbn = {9783827415202}, +keywords = {Folder - Biochemie}, +mendeley-tags = {Folder - Biochemie}, +publisher = {Spektrum Akademischer Verlag}, +title = {{Bioanalytik}}, +year = {2006} +} +@article{Provencher1981, +author = {Provencher, Stephen W. and Gloeckner, Juergen}, +doi = {10.1021/bi00504a006}, +file = {:home/alex/Dokumente/Mendeley Desktop/Provencher, Gloeckner/Biochemistry/Provencher, Gloeckner - 1981 - Estimation of globular protein secondary structure from circular dichroism.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Folder - RTE1}, +mendeley-tags = {Folder - RTE1}, +month = jan, +number = {1}, +pages = {33--37}, +title = {{Estimation of globular protein secondary structure from circular dichroism}}, +url = {http://pubs.acs.org/doi/abs/10.1021/bi00504a006}, +volume = {20}, +year = {1981} +} @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}, @@ -2149,6 +1734,38 @@ url = {http://www.sciencemag.org/cgi/doi/10.1126/science.8128219 http://www.ncbi volume = {263}, year = {1994} } +@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}, +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{Lawrence2009, author = {Lawrence, Ann-Marie and Besir, H\"{u}seyin}, doi = {10.3791/1350}, @@ -2160,22 +1777,6 @@ title = {{Staining of Proteins in Gels with Coomassie G-250 without Organic Solv url = {http://www.jove.com/index/Details.stp?ID=1350}, year = {2009} } -@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.}, -author = {Iwakura, M and Jones, B E and Luo, J and Matthews, C R}, -file = {:home/alex/Dokumente/Mendeley Desktop/Iwakura et al/Journal of biochemistry/Iwakura et al. - 1995 - A strategy for testing the suitability of cysteine replacements in dihydrofolate reductase from Escherichia coli.pdf:pdf}, -issn = {0021-924X}, -journal = {Journal of biochemistry}, -keywords = {Amino Acid Sequence,Bacterial,Base Sequence,Cystine,Cystine: chemistry,Enzyme Stability,Escherichia coli,Escherichia coli: enzymology,Escherichia coli: genetics,Genes,Hot Temperature,Insertional,Kinetics,Molecular Sequence Data,Mutagenesis,Protein Denaturation,Protein Folding,Site-Directed,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry}, -month = mar, -number = {3}, -pages = {480--8}, -pmid = {7629011}, -title = {{A strategy for testing the suitability of cysteine replacements in dihydrofolate reductase from Escherichia coli.}}, -url = {http://www.ncbi.nlm.nih.gov/pubmed/7629011}, -volume = {117}, -year = {1995} -} @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}, @@ -2195,22 +1796,6 @@ 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}, @@ -2228,29 +1813,22 @@ 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} -} -@inproceedings{Resnick2006, -author = {Resnick, J. S and Wen, C. K and Shockey, J. A and Chang, C.}, -file = {:home/alex/Dokumente/Mendeley Desktop/Resnick et al/Unknown/Resnick et al. - 2006 - REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis.pdf:pdf}, -keywords = {Folder - RTE1}, -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{Orgel2004, author = {Orgel, Leslie E.}, @@ -2283,17 +1861,21 @@ url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183}, volume = {358}, year = {2003} } -@article{Martin2008, -author = {Martin, W. and Baross, J. and Kelley, D. and Russell, M. J}, -file = {:home/alex/Dokumente/Mendeley Desktop/Martin et al/Nature Reviews Microbiology/Martin et al. - 2008 - Hydrothermal vents and the origin of life.pdf:pdf}, -journal = {Nature Reviews: Microbiology}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -number = {11}, -pages = {805--814}, -title = {{Hydrothermal vents and the origin of life}}, -volume = {6}, -year = {2008} +@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.}, @@ -2311,6 +1893,159 @@ url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703447\&tool=p volume = {15}, year = {2008} } +@article{Forterre2007, +author = {Forterre, Patrick and Gribaldo, Simonetta}, +doi = {10.2976/1.2759103}, +file = {:home/alex/Dokumente/Mendeley Desktop/Forterre, Gribaldo/HFSP Journal/Forterre, Gribaldo - 2007 - The origin of modern terrestrial life.pdf:pdf}, +issn = {1955-2068}, +journal = {HFSP Journal}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +month = sep, +number = {3}, +pages = {156--168}, +title = {{The origin of modern terrestrial life}}, +url = {http://tandfprod.literatumonline.com/doi/abs/10.2976/1.2759103}, +volume = {1}, +year = {2007} +} +@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{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.}, +author = {Iwakura, M and Jones, B E and Luo, J and Matthews, C R}, +file = {:home/alex/Dokumente/Mendeley Desktop/Iwakura et al/Journal of biochemistry/Iwakura et al. - 1995 - A strategy for testing the suitability of cysteine replacements in dihydrofolate reductase from Escherichia coli.pdf:pdf}, +issn = {0021-924X}, +journal = {Journal of biochemistry}, +keywords = {Amino Acid Sequence,Bacterial,Base Sequence,Cystine,Cystine: chemistry,Enzyme Stability,Escherichia coli,Escherichia coli: enzymology,Escherichia coli: genetics,Genes,Hot Temperature,Insertional,Kinetics,Molecular Sequence Data,Mutagenesis,Protein Denaturation,Protein Folding,Site-Directed,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry}, +month = mar, +number = {3}, +pages = {480--8}, +pmid = {7629011}, +title = {{A strategy for testing the suitability of cysteine replacements in dihydrofolate reductase from Escherichia coli.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/7629011}, +volume = {117}, +year = {1995} +} +@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} +} +@incollection{Woese1967, +address = {New York}, +author = {Woese, C.}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +pages = {179--195}, +publisher = {Harper and Row}, +title = {{The genetic code}}, +year = {1967} +} +@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} +} +@inproceedings{Resnick2006, +author = {Resnick, J. S and Wen, C. K and Shockey, J. A and Chang, C.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Resnick et al/Unknown/Resnick et al. - 2006 - REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis.pdf:pdf}, +keywords = {Folder - RTE1}, +mendeley-tags = {Folder - RTE1}, +title = {{REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis}}, +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} +} +@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{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} +} +@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}, +doi = {10.1021/bi100692f}, +file = {:home/alex/Dokumente/Mendeley Desktop/Yukl et al/Biochemistry/Yukl et al. - 2010 - Kinetic and Spectroscopic Studies of Hemin Acquisition in the Hemophore HasAp from Pseudomonas aeruginosa.pdf:pdf}, +issn = {0006-2960}, +journal = {Biochemistry}, +month = aug, +number = {31}, +pages = {6646--6654}, +title = {{Kinetic and Spectroscopic Studies of Hemin Acquisition in the Hemophore HasAp from Pseudomonas aeruginosa}}, +url = {http://pubs.acs.org/doi/abs/10.1021/bi100692f}, +volume = {49}, +year = {2010} +} @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}, @@ -2322,6 +2057,18 @@ title = {{Thiols in hydrothermal solution: standard partial molal properties and volume = {68}, year = {2004} } +@article{Martin2008, +author = {Martin, W. and Baross, J. and Kelley, D. and Russell, M. J}, +file = {:home/alex/Dokumente/Mendeley Desktop/Martin et al/Nature Reviews Microbiology/Martin et al. - 2008 - Hydrothermal vents and the origin of life.pdf:pdf}, +journal = {Nature Reviews: Microbiology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +number = {11}, +pages = {805--814}, +title = {{Hydrothermal vents and the origin of life}}, +volume = {6}, +year = {2008} +} @article{Motti2007, abstract = {A total of 2,245 extracts, derived from 449 marine fungi cultivated in five types of media, were screened against the C(4) plant enzyme pyruvate phosphate dikinase (PPDK), a potential herbicide target. Extracts from several fungal isolates selectively inhibited PPDK. Bioassay-guided fractionation of one isolate led to the isolation of the known compound unguinol, which inhibited PPDK with a 50\% inhibitory concentration of 42.3 +/- 0.8 muM. Further kinetic analysis revealed that unguinol was a mixed noncompetitive inhibitor of PPDK with respect to the substrates pyruvate and ATP and an uncompetitive inhibitor of PPDK with respect to phosphate. Unguinol had deleterious effects on a model C(4) plant but no effect on a model C(3) plant. These results indicate that unguinol inhibits PPDK via a novel mechanism of action which also translates to an herbicidal effect on whole plants.}, author = {Motti, Cherie a and Bourne, David G and Burnell, James N and Doyle, Jason R and Haines, Dianne S and Liptrot, Catherine H and Llewellyn, Lyndon E and Ludke, Shilo and Muirhead, Andrew and Tapiolas, Dianne M}, @@ -2353,45 +2100,28 @@ url = {http://www.springerlink.com/content/rkt60781642pw447/}, volume = {24}, year = {1990} } -@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{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} } -@incollection{Woese1967, -address = {New York}, -author = {Woese, C.}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -pages = {179--195}, -publisher = {Harper and Row}, -title = {{The genetic code}}, -year = {1967} -} -@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{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{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.}, @@ -2427,48 +2157,18 @@ url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a003590}, volume = {3}, year = {2010} } -@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} -} -@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{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, +@article{Talini2009, +author = {Talini, G. and Gallori, E. and Maurel, M. C}, +file = {:home/alex/Dokumente/Mendeley Desktop/Talini, Gallori, Maurel/Research in microbiology/Talini, Gallori, Maurel - 2009 - Natural and unnatural ribozymes Back to the primordial RNA world.pdf:pdf}, +journal = {Research in microbiology}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, 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} +pages = {457--465}, +shorttitle = {Natural and unnatural ribozymes}, +title = {{Natural and unnatural ribozymes: Back to the primordial RNA world}}, +volume = {160}, +year = {2009} } @article{Thieffry1998, author = {Thieffry, Denis and Sarkar, Sahotra}, @@ -2496,21 +2196,18 @@ 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}, -doi = {10.2976/1.2759103}, -file = {:home/alex/Dokumente/Mendeley Desktop/Forterre, Gribaldo/HFSP Journal/Forterre, Gribaldo - 2007 - The origin of modern terrestrial life.pdf:pdf}, -issn = {1955-2068}, -journal = {HFSP Journal}, -keywords = {Folder - Vortrag RNA-Welt}, -mendeley-tags = {Folder - Vortrag RNA-Welt}, -month = sep, -number = {3}, -pages = {156--168}, -title = {{The origin of modern terrestrial life}}, -url = {http://tandfprod.literatumonline.com/doi/abs/10.2976/1.2759103}, -volume = {1}, -year = {2007} +@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} } @incollection{Rathi2011, address = {Weinheim}, @@ -2525,17 +2222,34 @@ publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA}, title = {{Statics of Biomacromolecules}}, 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 = {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} +} +@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} } @book{Vollhardt2007, address = {Weinheim}, @@ -2548,6 +2262,21 @@ publisher = {Wiley-VCH}, title = {{Organische Chemie}}, 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{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.}, author = {Chastain, Chris J and Failing, Christopher J and Manandhar, Lumu and Zimmerman, Margaret a and Lakner, Mitchell M and Nguyen, Tony H T}, @@ -2565,17 +2294,6 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/21414960}, volume = {62}, year = {2011} } -@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} -} @book{Gesteland2006, address = {Cold Spring Harbor N.Y.}, author = {Gesteland, Raymond}, @@ -2606,17 +2324,345 @@ url = {http://www.ncbi.nlm.nih.gov/pubmed/21414960}, volume = {62}, year = {2011} } -@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}, -doi = {10.1021/bi100692f}, -file = {:home/alex/Dokumente/Mendeley Desktop/Yukl et al/Biochemistry/Yukl et al. - 2010 - Kinetic and Spectroscopic Studies of Hemin Acquisition in the Hemophore HasAp from Pseudomonas aeruginosa.pdf:pdf}, +@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{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{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{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}, -month = aug, -number = {31}, -pages = {6646--6654}, -title = {{Kinetic and Spectroscopic Studies of Hemin Acquisition in the Hemophore HasAp from Pseudomonas aeruginosa}}, -url = {http://pubs.acs.org/doi/abs/10.1021/bi100692f}, -volume = {49}, +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{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{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{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}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Binding Sites,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Orthophosphate Dikinase: metabolism,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Phosphotransferases: metabolism,Pyruvate,purification}, +mendeley-tags = {purification}, +month = dec, +number = {25}, +pages = {5805--9}, +pmid = {6257293}, +title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023 http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, +volume = {19}, +year = {1980} +} +@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{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}, +issn = {0006-2960}, +journal = {Biochemistry}, +keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Binding Sites,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Orthophosphate Dikinase: metabolism,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Phosphotransferases: metabolism,Pyruvate,purification}, +mendeley-tags = {purification}, +month = dec, +number = {25}, +pages = {5805--9}, +pmid = {6257293}, +title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.}}, +url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023 http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292}, +volume = {19}, +year = {1980} +} +@article{Brimacombe2000, +author = {Brimacombe, R.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Brimacombe/Structure/Brimacombe - 2000 - The bacterial ribosome at atomic resolution.pdf:pdf}, +journal = {Structure}, +keywords = {Folder - Vortrag RNA-Welt}, +mendeley-tags = {Folder - Vortrag RNA-Welt}, +number = {10}, +pages = {R195--R200}, +title = {{The bacterial ribosome at atomic resolution}}, +volume = {8}, +year = {2000} +} +@article{Noireaux2011, +author = {Noireaux, V. and Maeda, Y. T and Libchaber, A.}, +file = {:home/alex/Dokumente/Mendeley Desktop/Noireaux, Maeda, Libchaber/Proceedings of the National Academy of Sciences/Noireaux, Maeda, Libchaber - 2011 - Development of an artificial cell, from self-organization to computation and self-reproduction.pdf:pdf}, +journal = {Proceedings of the National Academy of Sciences}, +number = {9}, +pages = {3473}, +title = {{Development of an artificial cell, from self-organization to computation and self-reproduction}}, +volume = {108}, +year = {2011} +} +@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} +} +@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{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{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{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{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{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} +} +@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{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} +} diff --git a/masterarbeit.kilepr b/masterarbeit.kilepr index 8492130..5d496b0 100644 --- a/masterarbeit.kilepr +++ b/masterarbeit.kilepr @@ -96,6 +96,16 @@ Indentation Mode=normal Mode=LaTeX ReadWrite=true +[document-settings,item:library.bib] +Bookmarks= +Encoding=UTF-8 +FoldedColumns= +FoldedLines= +Highlighting=BibTeX +Indentation Mode=normal +Mode=BibTeX +ReadWrite=false + [document-settings,item:masterarbeit.tex] Bookmarks= Encoding=UTF-8 @@ -118,10 +128,10 @@ order=-1 [item:inc/abkuerzungen.tex] archive=true -column=29 +column=16 encoding=UTF-8 highlight=LaTeX -line=19 +line=7 mode=LaTeX open=true order=2 @@ -178,10 +188,10 @@ order=6 [item:inc/material.tex] archive=true -column=121 +column=18 encoding=UTF-8 highlight=LaTeX -line=540 +line=211 mode=LaTeX open=true order=1 @@ -196,6 +206,16 @@ mode=LaTeX open=true order=4 +[item:library.bib] +archive=true +column=9 +encoding=UTF-8 +highlight=BibTeX +line=1760 +mode=BibTeX +open=true +order=6 + [item:masterarbeit.kilepr] archive=true column=6684777 @@ -208,17 +228,17 @@ order=-1 [item:masterarbeit.tex] archive=true -column=57 +column=0 encoding=UTF-8 highlight=LaTeX -line=104 +line=185 mode=LaTeX open=true order=0 [view-settings,view=0,item:inc/abkuerzungen.tex] -CursorColumn=29 -CursorLine=19 +CursorColumn=16 +CursorLine=7 JumpList= ViMarks= @@ -253,8 +273,8 @@ JumpList= ViMarks= [view-settings,view=0,item:inc/material.tex] -CursorColumn=121 -CursorLine=540 +CursorColumn=18 +CursorLine=211 JumpList= ViMarks= @@ -264,8 +284,14 @@ CursorLine=1 JumpList= ViMarks= -[view-settings,view=0,item:masterarbeit.tex] -CursorColumn=57 -CursorLine=104 +[view-settings,view=0,item:library.bib] +CursorColumn=9 +CursorLine=1760 +JumpList= +ViMarks= + +[view-settings,view=0,item:masterarbeit.tex] +CursorColumn=0 +CursorLine=185 JumpList= ViMarks= diff --git a/masterarbeit.tex b/masterarbeit.tex index 6b345d7..e173ba6 100644 --- a/masterarbeit.tex +++ b/masterarbeit.tex @@ -102,7 +102,9 @@ \setmathfont[range={"2261}]{Linux Libertine O}% "02261 = \eqiv \setmathfont[range={"2213}]{Linux Libertine O}% "02213 = \pm \setmathfont[range={"2219}]{Linux Libertine O}% "02219 = \cdot -\setmathfont[range={"2212}]{Linux Libertine O}% "02212 = +\setmathfont[range={"2212}]{Linux Libertine O}% "02212 = - +\setmathfont[range={"002C}]{Linux Libertine O}% "0002C = , +\setmathfont[range={"002B}]{Linux Libertine O}% "0002B = + \newcommand{\todo}[1]{\textbf{\textsc{\textcolor{red}{(TODO: #1)}}}} @@ -181,5 +183,4 @@ \bibliography{./library} \include{./inc/anhang} - \end{document} \ No newline at end of file