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@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.},
author = {Gohlke, Holger and Kuhn, Leslie a and Case, David a},
doi = {10.1002/prot.20116},
file = {:home/alex/Dokumente/Mendeley Desktop/Gohlke, Kuhn, Case/Proteins/Gohlke, Kuhn, Case - 2004 - Change in protein flexibility upon complex formation analysis of Ras-Raf using molecular dynamics and a molecular framework approach.pdf:pdf},
issn = {1097-0134},
journal = {Proteins},
keywords = {Algorithms,Animals,Binding Sites,Computer Simulation,Humans,Macromolecular Substances,Models, Molecular,Motion,Pliability,Protein Binding,Protein Conformation,Protein Interaction Mapping,Protein Structure, Secondary,Protein Structure, Tertiary,Proto-Oncogene Proteins c-raf,Proto-Oncogene Proteins c-raf: chemistry,Proto-Oncogene Proteins c-raf: metabolism,Proto-Oncogene Proteins p21(ras),Proto-Oncogene Proteins p21(ras): chemistry,Proto-Oncogene Proteins p21(ras): metabolism,Rats,Software},
month = aug,
number = {2},
pages = {322--37},
pmid = {15211515},
title = {{Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15211515},
volume = {56},
year = {2004}
}
@article{Orgel2004,
author = {Orgel, Leslie E.},
doi = {10.1080/10409230490460765},
file = {:home/alex/Dokumente/Mendeley Desktop/Leslie E/Critical Reviews in Biochemistry and Molecular Biology/Leslie E. - 2004 - Prebiotic Chemistry and the Origin of the RNA World.pdf:pdf},
issn = {1040-9238},
journal = {Critical Reviews in Biochemistry and Molecular Biology},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = jan,
number = {2},
pages = {99--123},
title = {{Prebiotic Chemistry and the Origin of the RNA World}},
url = {http://informahealthcare.com/doi/abs/10.1080/10409230490460765},
volume = {39},
year = {2004}
}
@article{Yarus2010,
author = {Yarus, M.},
doi = {10.1101/cshperspect.a003590},
file = {:home/alex/Dokumente/Mendeley Desktop/Yarus/Cold Spring Harbor Perspectives in Biology/Yarus - 2010 - Getting Past the RNA World The Initial Darwinian Ancestor.pdf:pdf},
issn = {1943-0264},
journal = {Cold Spring Harbor Perspectives in Biology},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = apr,
number = {4},
pages = {a003590--a003590},
shorttitle = {Getting Past the RNA World},
title = {{Getting Past the RNA World: The Initial Darwinian Ancestor}},
url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a003590},
volume = {3},
year = {2010}
}
@article{Martin2003,
author = {Martin, W. and Russell, M. J.},
doi = {10.1098/rstb.2002.1183},
file = {:home/alex/Dokumente/Mendeley Desktop/Martin, Russell/Philosophical Transactions of the Royal Society B Biological Sciences/Martin, Russell - 2003 - On the origins of cells a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.pdf:pdf},
issn = {0962-8436},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
month = jan,
number = {1429},
pages = {59--85},
shorttitle = {On the origins of cells},
title = {{On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells}},
url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2002.1183},
volume = {358},
year = {2003}
}
@article{Notredame2000,
abstract = {We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests.},
author = {Notredame, C and Higgins, D G and Heringa, J},
doi = {10.1006/jmbi.2000.4042},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Algorithms,Amino Acid,Amino Acid Motifs,Amino Acid Sequence,Animals,Computational Biology,Computational Biology: methods,Databases as Topic,Humans,Molecular Sequence Data,Protein-Serine-Threonine Kinases,Protein-Serine-Threonine Kinases: chemistry,Reproducibility of Results,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Sequence Homology,Software},
month = sep,
number = {1},
pages = {205--17},
pmid = {10964570},
title = {{T-Coffee: A novel method for fast and accurate multiple sequence alignment.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10964570},
volume = {302},
year = {2000}
}
@article{Sreerama1993,
abstract = {A self-consistent procedure for estimating the secondary structure content from circular dichroism spectra of proteins is presented. In this method the spectrum of the protein to be analyzed is included in the basis set and an initial guess is made for the unknown structure as a first approximation. The resulting matrix equation is solved using the singular value decomposition algorithm and the initial guess is replaced by the solution. The process is repeated until self-consistency is attained. The best features of the variable selection and the locally linearized methods are incorporated in this procedure. We have applied this method to examine the inconsistencies in the CD data, to compare the predictions with different ranges and resolutions of the CD data, and to compare different assignments of secondary structures from X-ray structure analyses in the context of secondary structure predictions. The results are compared using the root mean square differences and correlation coefficients. The results obtained are as good as or better than the previous analyses. For most of the proteins considered the self-consistent solutions obtained with different initial guesses were similar. We find the Kabsch and Sander protein crystal structure analysis to be most suitable for our prediction method.},
author = {Sreerama, N and Woody, R W},
doi = {10.1006/abio.1993.1079},
file = {:home/alex/Dokumente/Mendeley Desktop/Sreerama, Woody/Analytical biochemistry/Sreerama, Woody - 1993 - A self-consistent method for the analysis of protein secondary structure from circular dichroism.pdf:pdf},
issn = {0003-2697},
journal = {Analytical biochemistry},
keywords = {Circular Dichroism,Protein Structure,Proteins,Proteins: analysis,Secondary,X-Ray Diffraction},
month = feb,
number = {1},
pages = {32--44},
pmid = {8465960},
title = {{A self-consistent method for the analysis of protein secondary structure from circular dichroism.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8465960},
volume = {209},
year = {1993}
}
@article{Hennen-Bierwagen2009,
abstract = {Starch biosynthetic enzymes from maize (Zea mays) and wheat (Triticum aestivum) amyloplasts exist in cell extracts in high molecular weight complexes; however, the nature of those assemblies remains to be defined. This study tested the interdependence of the maize enzymes starch synthase IIa (SSIIa), SSIII, starch branching enzyme IIb (SBEIIb), and SBEIIa for assembly into multisubunit complexes. Mutations that eliminated any one of those proteins also prevented the others from assembling into a high molecular mass form of approximately 670 kD, so that SSIII, SSIIa, SBEIIa, and SBEIIb most likely all exist together in the same complex. SSIIa, SBEIIb, and SBEIIa, but not SSIII, were also interdependent for assembly into a complex of approximately 300 kD. SSIII, SSIIa, SBEIIa, and SBEIIb copurified through successive chromatography steps, and SBEIIa, SBEIIb, and SSIIa coimmunoprecipitated with SSIII in a phosphorylation-dependent manner. SBEIIa and SBEIIb also were retained on an affinity column bearing a specific conserved fragment of SSIII located outside of the SS catalytic domain. Additional proteins that copurified with SSIII in multiple biochemical methods included the two known isoforms of pyruvate orthophosphate dikinase (PPDK), large and small subunits of ADP-glucose pyrophosphorylase, and the sucrose synthase isoform SUS-SH1. PPDK and SUS-SH1 required SSIII, SSIIa, SBEIIa, and SBEIIb for assembly into the 670-kD complex. These complexes may function in global regulation of carbon partitioning between metabolic pathways in developing seeds.},
author = {Hennen-Bierwagen, Tracie a and Lin, Qiaohui and Grimaud, Florent and Planchot, V\'{e}ronique and Keeling, Peter L and James, Martha G and Myers, Alan M},
doi = {10.1104/pp.109.135293},
file = {:home/alex/Dokumente/Mendeley Desktop/Hennen-Bierwagen et al/Plant physiology/Hennen-Bierwagen et al. - 2009 - Proteins from multiple metabolic pathways associate with starch biosynthetic enzymes in high molecular weight complexes a model for regulation of carbon allocation in maize amyloplasts.pdf:pdf},
issn = {0032-0889},
journal = {Plant physiology},
keywords = {1,4-alpha-Glucan Branching Enzyme,1,4-alpha-Glucan Branching Enzyme: chemistry,1,4-alpha-Glucan Branching Enzyme: metabolism,Amino Acid Sequence,Carbon,Carbon: metabolism,Chromatography, Affinity,Chromatography, Gel,Glucans,Glucans: metabolism,Glucosyltransferases,Glucosyltransferases: chemistry,Glucosyltransferases: metabolism,Immunoprecipitation,Mass Spectrometry,Metabolic Networks and Pathways,Models, Biological,Molecular Sequence Data,Molecular Weight,Multienzyme Complexes,Multienzyme Complexes: chemistry,Multienzyme Complexes: isolation \& purification,Plant Extracts,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: metabolism,Plastids,Plastids: enzymology,Protein Binding,Protein Structure, Tertiary,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: chemistry,Pyruvate, Orthophosphate Dikinase: metabolism,Starch,Starch Synthase,Starch Synthase: chemistry,Starch Synthase: metabolism,Starch: biosynthesis,Zea mays,Zea mays: enzymology},
month = mar,
number = {3},
pages = {1541--59},
pmid = {19168640},
title = {{Proteins from multiple metabolic pathways associate with starch biosynthetic enzymes in high molecular weight complexes: a model for regulation of carbon allocation in maize amyloplasts.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2649383\&tool=pmcentrez\&rendertype=abstract},
volume = {149},
year = {2009}
}
@article{Lawrence2008,
abstract = {Enzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site. Inhibitor binding is predicted to draw the oligomeric equilibrium toward the low-activity hexamer. In silico docking enriched a selection from a small-molecule library for compounds predicted to bind to this allosteric site. In vitro testing of selected compounds identified one compound whose inhibition mechanism is species-specific conversion of PBGS octamers to hexamers. We propose that this strategy for inhibitor discovery can be applied to other proteins that use the morpheein model for allosteric regulation.},
author = {Lawrence, Sarah H and Ramirez, Ursula D and Tang, Lei and Fazliyez, Farit and Kundrat, Lenka and Markham, George D and Jaffe, Eileen K},
doi = {10.1016/j.chembiol.2008.04.012},
issn = {1074-5521},
journal = {Chemistry \& biology},
keywords = {Allosteric Site,Amino Acid,Amino Acid Sequence,Animals,Dimerization,Drug Design,Magnetic Resonance Spectroscopy,Models,Molecular,Molecular Sequence Data,Molecular Structure,Sequence Homology},
month = jun,
number = {6},
pages = {586--96},
pmid = {18559269},
title = {{Shape shifting leads to small-molecule allosteric drug discovery.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703447\&tool=pmcentrez\&rendertype=abstract},
volume = {15},
year = {2008}
}
@article{Thieffry1998,
author = {Thieffry, Denis and Sarkar, Sahotra},
doi = {10.1016/S0968-0004(98)01244-4},
file = {:home/alex/Dokumente/Mendeley Desktop/Thieffry, Sarkar/Trends in Biochemical Sciences/Thieffry, Sarkar - 1998 - Forty years under the central dogma.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 = {312--316},
title = {{Forty years under the central dogma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000498012444},
volume = {23},
year = {1998}
}
@article{Deveau2010,
author = {Deveau, H. and Garneau, J. E and Moineau, S.},
file = {:home/alex/Dokumente/Mendeley Desktop/Deveau, Garneau, Moineau/Annual review of microbiology/Deveau, Garneau, Moineau - 2010 - CRISPRCas System and Its Role in Phage-Bacteria Interactions.pdf:pdf},
issn = {0066-4227},
journal = {Annual review of microbiology},
keywords = {Folder - In-silico-structure},
mendeley-tags = {Folder - In-silico-structure},
title = {{CRISPR/Cas System and Its Role in Phage-Bacteria Interactions}},
year = {2010}
}
@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{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}
}
@incollection{Rathi2011,
address = {Weinheim},
author = {Rathi, Prakash C. and Pfleger, Christopher and Fulle, Simone and Klein, Doris L. and Gohlke, Holger},
booktitle = {Modeling of Molecular Properties},
chapter = {18},
doi = {10.1002/9783527636402.ch18},
editor = {Comba, Peter},
isbn = {9783527330218},
keywords = {Constraint network analysis,coarse-graining,protein engineering,protein flexibility,rigidity analysis,thermostabilization},
publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA},
title = {{Statics of Biomacromolecules}},
year = {2011}
}
@article{Vincent1985,
author = {Vincent, Styliani H. and Muller-Eberhard, Ursula},
file = {:home/alex/Dokumente/Mendeley Desktop/Vincent, Muller-Eberhard/The Journal of Biological Chemistry/Vincent, Muller-Eberhard - 1985 - A Protein of the Z Class of Liver Cytosolic Proteins in the Rat That Preferentially Binds Heme.pdf:pdf},
journal = {The Journal of Biological Chemistry},
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}
}
@book{Raghavendra2011,
address = {Dordrecht},
author = {Raghavendra, Agepati S. and Sage, Rowan F.},
booktitle = {Advances in Photosynthesis and Respiration},
doi = {10.1007/978-90-481-9407-0},
editor = {Raghavendra, Agepati S. and Sage, Rowan F.},
isbn = {978-90-481-9406-3},
pages = {201},
publisher = {Springer Netherlands},
series = {Advances in Photosynthesis and Respiration},
title = {{C4 Photosynthesis and Related CO2 Concentrating Mechanisms}},
url = {http://www.springerlink.com/index/10.1007/978-90-481-9407-0},
volume = {32},
year = {2011}
}
@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{Louis-Jeune2011,
abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used to investigate the structure of proteins. Major secondary structure types, alpha-helices and beta-strands, produce distinctive CD spectra. Thus, by comparing the CD spectrum of a protein of interest to a reference set consisting of CD spectra of proteins of known structure, predictive methods can estimate the secondary structure of the protein. Currently available methods, including K2D2, use such experimental CD reference sets, which are very small in size when compared to the number of tertiary structures available in the Protein Data Bank (PDB). Conversely, given a PDB structure, it is possible to predict a theoretical CD spectrum from it. The methodological framework for this calculation was established long ago but only recently a convenient implementation called DichroCalc has been developed. In this study, we set to determine whether theoretically derived spectra could be used as reference set for accurate CD based predictions of secondary structure. We used DichroCalc to calculate the theoretical CD spectra of a nonredundant set of structures representing most proteins in the PDB, and applied a straightforward approach for predicting protein secondary structure content using these theoretical CD spectra as reference set. We show that this method improves the predictions, particularly for the wavelength interval between 200 and 240 nm and for beta-strand content. We have implemented this method, called K2D3, in a publicly accessible web server at http://www. ogic.ca/projects/k2d3. Proteins 2011. © 2011 Wiley Periodicals, Inc.},
author = {Louis-Jeune, Caroline and Andrade-Navarro, Miguel A and Perez-Iratxeta, Carol},
doi = {10.1002/prot.23188},
issn = {1097-0134},
journal = {Proteins},
month = sep,
pmid = {22095872},
title = {{Prediction of protein secondary structure from circular dichroism using theoretically derived spectra.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22095872},
year = {2011}
}
@article{Shirahashi1978,
abstract = {Cold lability of pyruvate, orthophosphate dikinase was investigated using a homogeneous, purified enzyme preparation from maize (Zea mays L. var. Golden Cross Bantam T51) leaves. Its stability was markedly reduced below about 10 C and the rate of cold inactivation followed first order kinetics at a concentration lower than about 0.1 milligram of enzyme per milliliter. Cold inactivation was little affected by pH in the range which gives good stability for the enzyme at warm temperatures and the enzyme activity was protected strongly by inclusion of substrates (pyruvate and phosphoenolpyruvate) and polyols such as sucrose, sorbitol, and glycerol. Loss of catalytic activity was accompanied by an apparent dissociation of a tetrameric form of the enzyme (9S form) into a new, more slowly sedimenting (5.1S) component. Inclusion of pyruvate at 4 mM in the cold-treated enzyme had no effect on the sedimentation value. A sharp change in activation energy of the dikinase-catalyzed reaction was observed near 12 C and its break point appears to be close to the generally accepted critical low temperature limit for the growth of maize plants.},
author = {Shirahashi, Kenji and Hayakawa, S and Sugiyama, T},
file = {:home/alex/Dokumente/Mendeley Desktop/Shirahashi, Hayakawa, Sugiyama/Plant physiology/Shirahashi, Hayakawa, Sugiyama - 1978 - Cold lability of pyruvate, orthophosphate dikinase in the maize leaf.pdf:pdf},
issn = {0032-0889},
journal = {Plant physiology},
month = nov,
number = {5},
pages = {826--30},
pmid = {16660615},
title = {{Cold lability of pyruvate, orthophosphate dikinase in the maize leaf.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1092230\&tool=pmcentrez\&rendertype=abstract},
volume = {62},
year = {1978}
}
@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}
}
@book{Vollhardt2007,
address = {Weinheim},
author = {Vollhardt, K and Schore, Neil E and Peter, K},
edition = {4. Aufl., },
isbn = {9783527313808},
keywords = {Folder - Organische Chemie},
mendeley-tags = {Folder - Organische Chemie},
publisher = {Wiley-VCH},
title = {{Organische Chemie}},
year = {2007}
}
@article{Sreerama2000,
abstract = {We have expanded the reference set of proteins used in SELCON3 by including 11 additional proteins (selected from the reference sets of Yang and co-workers and Keiderling and co-workers). Depending on the wavelength range and whether or not denatured proteins are included in the reference set, five reference sets were constructed with the number of reference proteins varying from 29 to 48. The performance of three popular methods for estimating protein secondary structure fractions from CD spectra (implemented in software packages CONTIN, SELCON3, and CDSSTR) and a variant of CONTIN, CONTIN/LL, that incorporates the variable selection method in the locally linearized model in CONTIN, were examined using the five reference sets described here, and a 22-protein reference set. Secondary structure assignments from DSSP were used in the analysis. The performances of all three methods were comparable, in spite of the differences in the algorithms used in the three software packages. While CDSSTR performed the best with a smaller reference set and larger wavelength range, and CONTIN/LL performed the best with a larger reference set and smaller wavelength range, the performances for individual secondary structures were mixed. Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions. The three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper. CDPro software is available at the website: http://lamar.colostate.edu/ approximately sreeram/CDPro.},
author = {Sreerama, N and Woody, R W},
doi = {10.1006/abio.2000.4880},
file = {:home/alex/Dokumente/Mendeley Desktop/Sreerama, Woody/Analytical biochemistry/Sreerama, Woody - 2000 - Estimation of protein secondary structure from circular dichroism spectra comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.pdf:pdf},
issn = {0003-2697},
journal = {Analytical biochemistry},
keywords = {Circular Dichroism,Protein Structure, Secondary,Proteins,Proteins: chemistry,Reference Standards},
month = dec,
number = {2},
pages = {252--60},
pmid = {11112271},
title = {{Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11112271},
volume = {287},
year = {2000}
}
@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},
doi = {10.1093/jxb/err058},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Journal of experimental botany/Chastain et al. - 2011 - Functional evolution of C(4) pyruvate, orthophosphate dikinase.pdf:pdf},
issn = {1460-2431},
journal = {Journal of experimental botany},
keywords = {c 3 plants,c 4 evolution,c 4 photosynthesis,c 4 plants,distribution of,evolutionary origin and phylogenetic,introduction and review,orthophosphate dikinase,pyruvate},
month = may,
number = {9},
pages = {3083--91},
pmid = {21414960},
title = {{Functional evolution of C(4) pyruvate, orthophosphate dikinase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21414960},
volume = {62},
year = {2011}
}
@book{Gesteland2006,
address = {Cold Spring Harbor  N.Y.},
author = {Gesteland, Raymond},
edition = {3rd ed.},
isbn = {9780879697396},
keywords = {Folder - Vortrag RNA-Welt},
language = {English},
mendeley-tags = {Folder - Vortrag RNA-Welt},
publisher = {Cold Spring Harbor Laboratory Press},
shorttitle = {The RNA world},
title = {{The RNA world : the nature of modern RNA suggests a prebiotic RNA world}},
year = {2006}
}
@article{Laemmli1970,
author = {Laemmli, U. K.},
doi = {10.1038/227680a0},
file = {:home/alex/Dokumente/Mendeley Desktop/Laemmli/Nature/Laemmli - 1970 - Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol},
mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Paper,protocol},
month = aug,
number = {5259},
pages = {680--685},
title = {{Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4}},
url = {http://www.nature.com/doifinder/10.1038/227680a0},
volume = {227},
year = {1970}
}
@article{Chastain2011a,
abstract = {Pyruvate,orthophosphate dikinase (PPDK) plays a controlling role in the PEP-regeneration phase of the C(4) photosynthetic pathway. Earlier studies have fully documented its biochemical properties and its post-translational regulation by the PPDK regulatory protein (PDRP). However, the question of its evolution into the C(4) pathway has, until recently, received little attention. One assumption concerning this evolution is that changes in catalytic and regulatory properties of PPDK were necessary for the enzyme to fulfil its role in the C(4) pathway. In this study, the functional evolution of PPDK from its ancient origins in the Archaea to its ascension as a photosynthetic enzyme in modern C(4) angiosperms is reviewed. This analysis is accompanied by a comparative investigation into key catalytic and regulatory properties of a C(3) PPDK isoform from Arabidopsis and the C(4) PPDK isoform from Zea mays. From these analyses, it is proposed that PPDK first became functionally seated in C(3) plants as an ancillary glycolytic enzyme and that its transition into a C(4) pathway enzyme involved only minor changes in enzyme properties per se.},
author = {Chastain, Chris J and Failing, Christopher J and Manandhar, Lumu and Zimmerman, Margaret a and Lakner, Mitchell M and Nguyen, Tony H T},
doi = {10.1093/jxb/err058},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Journal of experimental botany/Chastain et al. - 2011 - Functional evolution of C(4) pyruvate, orthophosphate dikinase(2).pdf:pdf},
issn = {1460-2431},
journal = {Journal of experimental botany},
keywords = {c 3 plants,c 4 evolution,c 4 photosynthesis,c 4 plants,distribution of,evolutionary origin and phylogenetic,introduction and review,orthophosphate dikinase,pyruvate},
month = may,
number = {9},
pages = {3083--91},
pmid = {21414960},
title = {{Functional evolution of C(4) pyruvate, orthophosphate dikinase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21414960},
volume = {62},
year = {2011}
}
@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{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{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{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{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{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{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{Nakanishi2005,
abstract = {Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.},
author = {Nakanishi, Tsugumi and Nakatsu, Toru and Matsuoka, Makoto and Sakata, Kanzo and Kato, Hiroaki},
doi = {10.1021/bi0484522},
file = {:home/alex/Dokumente/Mendeley Desktop/Nakanishi et al/Biochemistry/Nakanishi et al. - 2005 - Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion.pdf:pdf},
isbn = {8175753927},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acid Sequence,Binding Sites,Catalysis,Computer Simulation,Crystallization,Crystallography, X-Ray,Dimerization,Ligands,Models, Molecular,Molecular Sequence Data,Phosphoenolpyruvate,Phosphoenolpyruvate: chemistry,Phosphoenolpyruvate: metabolism,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: metabolism,Protein Conformation,Protein Structure, Tertiary,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: chemistry,Pyruvate, Orthophosphate Dikinase: metabolism,Substrate Specificity,Thermodynamics,Zea mays,Zea mays: enzymology},
month = feb,
number = {4},
pages = {1136--44},
pmid = {15667207},
title = {{Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15667207},
volume = {44},
year = {2005}
}
@article{Ikemura1981,
author = {Ikemura, Toshimichi},
doi = {10.1016/0022-2836(81)90003-6},
file = {:home/alex/Dokumente/Mendeley Desktop/Ikemura/Journal of molecular biology/Ikemura - 1981 - Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes a proposal for a synonymous codon choice that is optimal for the E. coli translational system.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Bacterial,Bacterial: analysis,Biological Evolution,Codon,Escherichia coli,Escherichia coli: genetics,Genes,Genetic,Messenger,Models,Protein Biosynthesis,RNA,Transfer,Transfer: analysis},
month = sep,
number = {3},
pages = {389--409},
pmid = {6175758},
title = {{Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6175758 http://linkinghub.elsevier.com/retrieve/pii/0022283681900036},
volume = {151},
year = {1981}
}
@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{Reeves1968,
author = {Reeves, R E},
file = {:home/alex/Dokumente/Mendeley Desktop/Reeves/The Journal of biological chemistry/Reeves - 1968 - A new enzyme with the glycolytic function of pyruvate kinase.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adenine Nucleotides,Chemical Precipitation,Chromatography,Diphosphates,Entamoeba histolytica,Entamoeba histolytica: enzymology,Gel,Glycolysis,Phosphotransferases,Pyruvate Kinase,Pyruvates,Ultrasonics},
month = jun,
number = {11},
pages = {3202--4},
pmid = {4297474},
title = {{A new enzyme with the glycolytic function of pyruvate kinase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/4297474},
volume = {243},
year = {1968}
}
@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{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}
}
@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{Harris,
abstract = {We studied the inhibition of mitochondrial malate dehydrogenase (mMDH) by the nucleotides cAMP, AMP, ADP, ATP. The experimental kinetic studies showed that the nucleotides were competitive inhibitors and that cAMP was probably the most potent inhibitor. To explain these observations, we used molecular modeling to determine the location, orientation, and relative binding energy of the nucleotides to mMDH. The order of the calculated binding energies, from lowest (most favorable) to highest, was cAMP, AMP, ADP, and ATP, which corresponded somewhat to the order of the experimentally determined inhibition constants.},
author = {Harris, Douglas G and Marx, Douglas P and Anderson, Jonathan M and McCune, Ronald W and Zimmerman, S Scott},
doi = {10.1081/NCN-120016483},
issn = {1525-7770},
journal = {Nucleosides, nucleotides \& nucleic acids},
keywords = {Adenosine Monophosphate,Adenosine Monophosphate: chemistry,Adenosine Monophosphate: metabolism,Binding Sites,Cyclic AMP,Cyclic AMP: chemistry,Cyclic AMP: metabolism,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Enzyme Inhibitors: metabolism,Enzyme Inhibitors: pharmacology,Kinetics,Malate Dehydrogenase,Malate Dehydrogenase: antagonists \& inhibitors,Malate Dehydrogenase: chemistry,Malate Dehydrogenase: metabolism,Models,Molecular,NAD,NAD: chemistry,NAD: metabolism,Nucleosides,Nucleosides: chemistry,Nucleosides: metabolism,Nucleosides: pharmacology,Nucleotides,Nucleotides: chemistry,Nucleotides: metabolism,Nucleotides: pharmacology,Protein Conformation},
number = {11-12},
pages = {813--23},
pmid = {12537023},
title = {{Kinetic and molecular modeling of nucleoside and nucleotide inhibition of malate dehydrogenase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12537023},
volume = {21},
year = {2002}
}
@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{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{Shen2006,
abstract = {Protein structures in the Protein Data Bank provide a wealth of data about the interactions that determine the native states of proteins. Using the probability theory, we derive an atomic distance-dependent statistical potential from a sample of native structures that does not depend on any adjustable parameters (Discrete Optimized Protein Energy, or DOPE). DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. The DOPE potential was extracted from a nonredundant set of 1472 crystallographic structures. We tested DOPE and five other scoring functions by the detection of the native state among six multiple target decoy sets, the correlation between the score and model error, and the identification of the most accurate non-native structure in the decoy set. For all decoy sets, DOPE is the best performing function in terms of all criteria, except for a tie in one criterion for one decoy set. To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo-electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER-8.},
author = {Shen, Min-Yi and Sali, Andrej},
doi = {10.1110/ps.062416606},
file = {:home/alex/Dokumente/Mendeley Desktop/Shen, Sali/Protein science a publication of the Protein Society/Shen, Sali - 2006 - Statistical potential for assessment and prediction of protein structures.pdf:pdf},
issn = {0961-8368},
journal = {Protein science : a publication of the Protein Society},
keywords = {Computational Biology,Computational Biology: methods,Crystallography,Data Interpretation,Models,Molecular,Protein Folding,Protein Structure,Secondary,Sensitivity and Specificity,Statistical,Theoretical,X-Ray},
month = nov,
number = {11},
pages = {2507--24},
pmid = {17075131},
title = {{Statistical potential for assessment and prediction of protein structures.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2242414\&tool=pmcentrez\&rendertype=abstract},
volume = {15},
year = {2006}
}
@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{Evans1980,
author = {Evans, Claudia T and Goss, Neil H and Wood, Harland G},
doi = {10.1021/bi00566a023},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Adenosine Monophosphate,Adenosine Triphosphate,Affinity Labels,Bacteroides,Bacteroides: enzymology,Binding Sites,Kinetics,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Pyruvate},
month = dec,
number = {25},
pages = {5809--14},
pmid = {6257293},
title = {{Pyruvate phosphate dikinase: affinity labeling of the adenosine 5'-triphosphate--adenosine 5'-monophosphate site.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6257293 http://pubs.acs.org/doi/abs/10.1021/bi00566a023},
volume = {19},
year = {1980}
}
@article{Krystek1993,
abstract = {An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60\% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)},
author = {Krystek, S and Stouch, T and Novotny, J},
doi = {10.1006/jmbi.1993.1619},
file = {:home/alex/Dokumente/Mendeley Desktop/Krystek, Stouch, Novotny/Journal of molecular biology/Krystek, Stouch, Novotny - 1993 - Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Amino Acid Sequence,Animals,Calorimetry,Chymotrypsin,Chymotrypsin: chemistry,Crystallography,Mathematics,Models,Molecular,Molecular Sequence Data,Ovomucin,Ovomucin: chemistry,Protein Conformation,Serine Endopeptidases,Serine Endopeptidases: chemistry,Serine Endopeptidases: metabolism,Serine Proteinase Inhibitors,Serine Proteinase Inhibitors: chemistry,Serine Proteinase Inhibitors: metabolism,Thermodynamics,Turkeys,X-Ray,X-Ray: methods},
month = dec,
number = {3},
pages = {661--79},
pmid = {8254666},
title = {{Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8254666},
volume = {234},
year = {1993}
}
@article{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{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{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{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}
}
@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{Ohta1997,
author = {Ohta, Shozo and Usami, Satoru and Ueki, Jun and Kumashiro, Takashi and Komari, Toshihiko and Burnell, Jim N},
doi = {10.1016/S0014-5793(97)00015-X},
file = {:home/alex/Dokumente/Mendeley Desktop/Ohta et al/FEBS Letters/Ohta et al. - 1997 - Identification of the amino acid residues responsible for cold tolerance in Flaveria brownii pyruvate,orthophosphate dikinase.pdf:pdf},
issn = {00145793},
journal = {FEBS Letters},
keywords = {C4 photosynthesis,c 4 photosynthesis,chilling,flaveria,orthophosphate dikinase,pyruvate,sensitivity of,those amino acid residues,which affect the cold},
month = feb,
number = {1},
pages = {5--9},
publisher = {Federation of European Biochemical Societies},
title = {{Identification of the amino acid residues responsible for cold tolerance in Flaveria brownii pyruvate,orthophosphate dikinase}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S001457939700015X},
volume = {403},
year = {1997}
}
@book{Arber2009,
address = {Vatican City},
author = {Arber, Werner and {Pontificia Accademia delle scienze.}},
file = {:home/alex/Dokumente/Mendeley Desktop/Arber, Pontificia Accademia delle scienze/Unknown/Arber, Pontificia Accademia delle scienze. - 2009 - The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008.pdf:pdf},
isbn = {9788877610973},
publisher = {Ex Aedibus Academicis in Civitate Vaticana},
title = {{The proceedings of the Plenary Session on scientific insights into the evolution of the universe and of life, 31 October-4 November 2008}},
year = {2009}
}
@article{Koshland1966,
author = {Koshland, D E and Nemethy, G. and Filmer, D},
doi = {10.1021/bi00865a047},
file = {:home/alex/Dokumente/Mendeley Desktop/Koshland, Nemethy, Filmer/Biochemistry/Koshland, Nemethy, Filmer - 1966 - Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Chemistry,Computers,Hemoglobins,Kinetics,Models,Oxygen,Physical,Physicochemical Phenomena,Proteins,Theoretical},
month = jan,
number = {1},
pages = {365--385},
pmid = {5938952},
title = {{Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/5938952 http://pubs.acs.org/cgi-bin/doilookup/?10.1021/bi00865a047},
volume = {5},
year = {1966}
}
@article{Cornilescu2008,
author = {Cornilescu, Gabriel and Ulijasz, Andrew T. and Cornilescu, Claudia C. and Markley, John L. and Vierstra, Richard D.},
doi = {10.1016/j.jmb.2008.08.034},
file = {:home/alex/Dokumente/Mendeley Desktop/Cornilescu et al/Journal of Molecular Biology/Cornilescu et al. - 2008 - Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State.science:science},
issn = {00222836},
journal = {Journal of Molecular Biology},
month = nov,
pages = {403--413},
title = {{Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608010279},
volume = {383},
year = {2008}
}
@article{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{Sharkey1989,
author = {Sharkey, T. D. and Seemann, J. R.},
doi = {10.1104/pp.89.4.1060},
file = {:home/alex/Dokumente/Mendeley Desktop/Sharkey, Seemann/PLANT PHYSIOLOGY/Sharkey, Seemann - 1989 - Mild Water Stress Effects on Carbon-Reduction-Cycle Intermediates, Ribulose Bisphosphate Carboxylase Activity, and Spatial Homogeneity of Photosynthesis in Intact Leaves.pdf:pdf},
issn = {0032-0889},
journal = {PLANT PHYSIOLOGY},
month = apr,
number = {4},
pages = {1060--1065},
title = {{Mild Water Stress Effects on Carbon-Reduction-Cycle Intermediates, Ribulose Bisphosphate Carboxylase Activity, and Spatial Homogeneity of Photosynthesis in Intact Leaves}},
url = {http://www.plantphysiol.org/cgi/doi/10.1104/pp.89.4.1060},
volume = {89},
year = {1989}
}
@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}
}
@article{Herzberg2002,
abstract = {Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands. The mode of binding resembles closely the previously proposed PEP substrate binding mode, inferred by the homology of the structure (but not sequence homology) to pyruvate kinase. Kinetic analysis of site-directed mutants, probing residues involved in inhibitor binding, showed that all mutations resulted in inactivation, confirming the key role that these residues play in catalysis. Comparison between the structure of the PPDK-phosphonopyruvate complex and the structures of two complexes of pyruvate kinase, one with Mg(2+)-bound phospholactate and the other with Mg(2+)-oxalate and ATP, revealed that the two enzymes share some key features that facilitate common modes of substrate binding. There are also important structural differences; most notably, the machinery for acid/base catalysis is different.},
author = {Herzberg, Osnat and Chen, Celia C H and Liu, Sijiu and Tempczyk, Aleksandra and Howard, Andrew and Wei, Min and Ye, Dongmei and Dunaway-Mariano, Debra},
doi = {10.1021/bi011799+},
file = {:home/alex/Dokumente/Mendeley Desktop/Herzberg et al/Biochemistry/Herzberg et al. - 2002 - Pyruvate Site of Pyruvate Phosphate Dikinase Crystal Structure of the Enzyme−Phosphonopyruvate Complex, and Mutant Analysis † , ‡.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acid Substitution,Apoenzymes,Apoenzymes: chemistry,Apoenzymes: metabolism,Binding Sites,Cloning,Clostridium,Clostridium: enzymology,Crystallography,Escherichia coli,Kinetics,Models,Molecular,Mutagenesis,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: metabolism,Protein Conformation,Protein Folding,Protein Structure,Pyruvate,Pyruvic Acid,Pyruvic Acid: metabolism,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,Secondary,Site-Directed,X-Ray},
month = jan,
number = {3},
pages = {780--787},
pmid = {11790099},
title = {{Pyruvate Site of Pyruvate Phosphate Dikinase: Crystal Structure of the Enzyme−Phosphonopyruvate Complex, and Mutant Analysis † , ‡}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11790099 http://pubs.acs.org/doi/abs/10.1021/bi011799\%2B},
volume = {41},
year = {2002}
}
@article{Iwakura2006,
abstract = {We developed a strategy for finding out the adapted variants of enzymes, and we applied it to an enzyme, dihydrofolate reductase (DHFR), in terms of its catalytic activity so that we successfully obtained several hyperactive cysteine- and methionine-free variants of DHFR in which all five methionyl and two cysteinyl residues were replaced by other amino acid residues. Among them, a variant (M1A/M16N/M20L/M42Y/C85A/M92F/C152S), named as ANLYF, has an approximately seven times higher k(cat) value than wild type DHFR. Enzyme kinetics and crystal structures of the variant were investigated for elucidating the mechanism of the hyperactivity. Steady-state and transient binding kinetics of the variant indicated that the kinetic scheme of the catalytic cycle of ANLYF was essentially the same as that of wild type, showing that the hyperactivity was brought about by an increase of the dissociation rate constants of tetrahydrofolate from the enzyme-NADPH-tetrahydrofolate ternary complex. The crystal structure of the variant, solved and refined to an R factor of 0.205 at 1.9-angstroms resolution, indicated that an increased structural flexibility of the variant and an increased size of the N-(p-aminobenzoyl)-L-glutamate binding cleft induced the increase of the dissociation constant. This was consistent with a large compressibility (volume fluctuation) of the variant. A comparison of folding kinetics between wild type and the variant showed that the folding of these two enzymes was similar to each other, suggesting that the activity enhancement of the enzyme can be attained without drastic changes of the folding mechanism.},
author = {Iwakura, Masahiro and Maki, Kosuke and Takahashi, Hisashi and Takenawa, Tatsuyuki and Yokota, Akiko and Katayanagi, Katsuo and Kamiyama, Tadashi and Gekko, Kunihiko},
doi = {10.1074/jbc.M508823200},
file = {:home/alex/Dokumente/Mendeley Desktop/Iwakura et al/The Journal of biological chemistry/Iwakura et al. - 2006 - Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Binding Sites,Cysteine,Cysteine: chemistry,Directed Molecular Evolution,Escherichia coli,Escherichia coli: enzymology,Kinetics,Methionine,Methionine: chemistry,Models, Molecular,Mutation,Protein Binding,Protein Conformation,Protein Engineering,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: chemistry,Tetrahydrofolate Dehydrogenase: genetics,Tetrahydrofolate Dehydrogenase: metabolism},
month = may,
number = {19},
pages = {13234--46},
pmid = {16510443},
title = {{Evolutional design of a hyperactive cysteine- and methionine-free mutant of Escherichia coli dihydrofolate reductase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16510443},
volume = {281},
year = {2006}
}
@article{Miroux1996,
author = {Miroux, B. and Walker, J. E},
file = {:home/alex/Dokumente/Mendeley Desktop/Miroux, Walker/Journal of molecular biology/Miroux, Walker - 1996 - Over-production of proteins in Escherichia coli mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels.pdf:pdf},
journal = {Journal of molecular biology},
number = {3},
pages = {289--298},
shorttitle = {Over-production of proteins in Escherichia coli},
title = {{Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels}},
volume = {260},
year = {1996}
}
@article{Lasker2012,
abstract = {Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.},
author = {Lasker, Keren and Vel\'{a}zquez-Muriel, Javier a and Webb, Benjamin M and Yang, Zheng and Ferrin, Thomas E and Sali, Andrej},
doi = {10.1007/978-1-61779-588-6\_15},
file = {:home/alex/Dokumente/Mendeley Desktop/Lasker et al/Methods in molecular biology (Clifton, N.J.)/Lasker et al. - 2012 - Macromolecular assembly structures by comparative modeling and electron microscopy.pdf:pdf},
issn = {1940-6029},
journal = {Methods in molecular biology (Clifton, N.J.)},
keywords = {Amino Acid Sequence,Chaperonin 60,Chaperonin 60: chemistry,Electron,Electron: methods,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli: chemistry,Macromolecular Substances,Macromolecular Substances: chemistry,Microscopy,Models,Molecular,Molecular Sequence Data,Protein Conformation,Proteins,Proteins: chemistry,Sequence Alignment,Sequence Alignment: methods},
month = jan,
pages = {331--50},
pmid = {22323229},
title = {{Macromolecular assembly structures by comparative modeling and electron microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22323229},
volume = {857},
year = {2012}
}
@article{Wiedenheft2009,
author = {Wiedenheft, Blake and Zhou, Kaihong and Jinek, Martin and Coyle, Scott M. and Ma, Wendy and Doudna, Jennifer A.},
doi = {10.1016/j.str.2009.03.019},
file = {:home/alex/Dokumente/Mendeley Desktop/Wiedenheft et al/Structure/Wiedenheft et al. - 2009 - Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense.pdf:pdf},
issn = {09692126},
journal = {Structure},
keywords = {Folder - In-silico-structure},
mendeley-tags = {Folder - In-silico-structure},
month = jun,
number = {6},
pages = {904--912},
title = {{Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0969212609001920},
volume = {17},
year = {2009}
}
@article{Chastain2006,
abstract = {Pyruvate, orthophosphate dikinase (PPDK; E.C.2.7.9.1) is most well known as a photosynthetic enzyme in C4 plants. The enzyme is also ubiquitous in C3 plant tissues, although a precise non-photosynthetic C3 function(s) is yet to be validated, owing largely to its low abundance in most C3 organs. The single C3 organ type where PPDK is in high abundance, and, therefore, where its function is most amenable to elucidation, are the developing seeds of graminaceous cereals. In this report, we suggest a non-photosynthetic function for C3 PPDK by characterizing its abundance and posttranslational regulation in developing Oryza sativa (rice) seeds. Using primarily an immunoblot-based approach, we show that PPDK is a massively expressed protein during the early syncitial-endosperm/-cellularization stage of seed development. As seed development progresses from this early stage, the enzyme undergoes a rapid, posttranslational down-regulation in activity and amount via regulatory threonyl-phosphorylation (PPDK inactivation) and protein degradation. Immunoblot analysis of separated seed tissue fractions (pericarp, embryo + aleurone, seed embryo) revealed that regulatory phosphorylation of PPDK occurs in the non-green seed embryo and green outer pericarp layer, but not in the endosperm + aleurone layer. The modestly abundant pool of inactive PPDK (phosphorylated + dephosphorylated) that was found to persist in mature rice seeds was shown to remain largely unchanged (inactive) upon seed germination, suggesting that PPDK in rice seeds function in developmental rather than in post-developmental processes. These and related observations lead us to postulate a putative function for the enzyme that aligns its PEP to pyruvate-forming reaction with biosynthetic processes that are specific to early cereal seed development.},
author = {Chastain, Chris J and Heck, Jarrod W and Colquhoun, Thomas a and Voge, Dylan G and Gu, Xing-You},
doi = {10.1007/s00425-006-0259-3},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Planta/Chastain et al. - 2006 - Posttranslational regulation of pyruvate, orthophosphate dikinase in developing rice (Oryza sativa) seeds.pdf:pdf},
issn = {0032-0935},
journal = {Planta},
keywords = {Angiosperms,Angiosperms: enzymology,Enzymologic,Gene Expression Regulation,Germination,Germination: physiology,Immunoblotting,Isoenzymes,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Oryza sativa,Oryza sativa: enzymology,Oryza sativa: genetics,Oryza sativa: growth \& development,Phosphorylation,Plant,Post-Translational,Protein Processing,Pyruvate,Seeds,Seeds: enzymology,Seeds: genetics,Seeds: growth \& development},
month = sep,
number = {4},
pages = {924--34},
pmid = {16596412},
title = {{Posttranslational regulation of pyruvate, orthophosphate dikinase in developing rice (Oryza sativa) seeds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16596412},
volume = {224},
year = {2006}
}
@article{Wallace2006,
abstract = {We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice of constituent methods and reasonably tolerant to duplicate MSAs. We also show that performances can be improved by carefully selecting the constituent methods. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase. We also show that on a case-by-case basis, M-Coffee is twice as likely to deliver the best alignment than any individual method. Given a collection of pre-computed MSAs, M-Coffee has similar CPU requirements to the original T-Coffee. M-Coffee is a freeware open-source package available from http://www.tcoffee.org/.},
author = {Wallace, Iain M and O'Sullivan, Orla and Higgins, Desmond G and Notredame, Cedric},
doi = {10.1093/nar/gkl091},
file = {:home/alex/Dokumente/Mendeley Desktop/Wallace et al/Nucleic acids research/Wallace et al. - 2006 - M-Coffee combining multiple sequence alignment methods with T-Coffee.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Algorithms,Reproducibility of Results,Sequence Alignment,Sequence Alignment: methods,Software},
month = jan,
number = {6},
pages = {1692--9},
pmid = {16556910},
title = {{M-Coffee: combining multiple sequence alignment methods with T-Coffee.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1410914\&tool=pmcentrez\&rendertype=abstract},
volume = {34},
year = {2006}
}
@article{Fulle2009,
abstract = {A sophisticated interplay between the static properties of the ribosomal exit tunnel and its functional role in cotranslational processes is revealed by constraint counting on topological network representations of large ribosomal subunits from four different organisms. As for the global flexibility characteristics of the subunit, the results demonstrate a conserved stable structural environment of the tunnel. The findings render unlikely that deformations of the tunnel move peptides down the tunnel in an active manner. Furthermore, the stable environment rules out that the tunnel can adapt widely so as to allow tertiary folding of nascent chains. Nevertheless, there are local zones of flexible nucleotides within the tunnel, between the peptidyl transferase center and the tunnel constriction, and at the tunnel exit. These flexible zones strikingly agree with previously identified folding zones. As for cotranslational elongation regulation, flexible residues in the beta-hairpin of the ribosomal L22 protein were verified, as suggested previously based on structural results. These results support the hypothesis that L22 can undergo conformational changes that regulate the tunnel voyage of nascent polypeptides. Furthermore, rRNA elements, for which conformational changes have been observed upon interaction of the tunnel wall with a nascent SecM peptide, are less strongly coupled to the subunit core. Sequences of coupled rigid clusters are identified between the tunnel and some of these elements, suggesting signal transmission by a domino-like mechanical coupling. Finally, differences in the flexibility of the glycosidic bonds of bases that form antibiotics-binding crevices within the peptidyl transferase center and the tunnel region are revealed for ribosomal structures from different kingdoms. In order to explain antibiotics selectivity, action, and resistance, according to these results, differences in the degrees of freedom of the binding regions may need to be considered.},
author = {Fulle, Simone and Gohlke, Holger},
doi = {10.1016/j.jmb.2009.01.037},
file = {:home/alex/Dokumente/Mendeley Desktop/Fulle, Gohlke/Journal of molecular biology/Fulle, Gohlke - 2009 - Statics of the ribosomal exit tunnel implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: metabolism,Haloarcula marismortui,Haloarcula marismortui: metabolism,Models, Molecular,Peptide Chain Elongation, Translational,Peptides,Peptides: chemistry,Peptides: metabolism,Peptidyl Transferases,Peptidyl Transferases: metabolism,Pliability,Protein Folding,Protein Structure, Secondary,Protein Transport,Ribosomal Proteins,Ribosomal Proteins: metabolism,Ribosomes,Ribosomes: chemistry,Signal Transduction},
month = mar,
number = {2},
pages = {502--17},
pmid = {19356596},
publisher = {Elsevier Ltd},
title = {{Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19356596},
volume = {387},
year = {2009}
}
@book{Purves2006,
address = {M\"{u}nchen; Heidelberg},
author = {Purves, William K and Sadava, David and Orians, Gordon H and Heller, H. Craig},
edition = {7},
isbn = {9783827420077},
keywords = {Folder - Allgemein},
mendeley-tags = {Folder - Allgemein},
month = aug,
publisher = {Spektrum Akademischer Verlag},
title = {{Biologie}},
year = {2006}
}
@article{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{Langmead2012,
abstract = {As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.},
author = {Langmead, Ben and Salzberg, Steven L},
doi = {10.1038/nmeth.1923},
issn = {1548-7105},
journal = {Nature methods},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,DNA,DNA: methods,Databases,Genetic,Genome,Human,Human: genetics,Humans,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis},
month = apr,
number = {4},
pages = {357--9},
pmid = {22388286},
title = {{Fast gapped-read alignment with Bowtie 2.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22388286},
volume = {9},
year = {2012}
}
@article{Wise1997,
abstract = {Haemophilus parasuis malate dehydrogenase ((S)-malate:NAD+ oxidoreductase; EC 1.1.1.37) isolated from cell sonicates was purified 584-fold to electrophoretic homogeneity with a 19\% recovery and a specific activity of 222 units/mg protein. SDS-polyacrylamide gel electrophoresis and molecular exclusion chromatography indicated the purified enzyme to be a dimer composed of 34,600 molecular weight subunits. Kinetic parameters for all four substrates in the forward and reverse reactions indicated a sequential mechanism for this enzymic process. Product and dead-end inhibition studies were consistent with an ordered bi-bi mechanism in which NAD is the first substrate bound to the enzyme and NADH the second product released. Protection against thermodenaturation of the enzyme by NAD and not by malate was supportive of this mechanism. A pronounced product inhibition by NADH (K(i) = 9.0 microM) was observed. Although NADP did not serve as a coenzyme, a number of analogs of NAD structurally altered in the nitrogen base moieties were observed to function as coenzymes in the oxidation of malate catalyzed by the purified malate dehydrogenase. Coenzyme-competitive inhibition of the malate dehydrogenase was observed with five adenosine derivatives and six structural analogs of NAD. Of the NAD analogs studied as inhibitors, 3-pyridylcarbinol adenine dinucleotide was the most effective (K(i) = 18 microM). Although inhibition of growth of H. parasuis by this analog was observed, it was less effective (K(i) = 136 microM) than the inhibition of the purified dehydrogenase.},
author = {Wise, D J and Anderson, C D and Anderson, B M},
doi = {10.1006/abbi.1997.0186},
issn = {0003-9861},
journal = {Archives of biochemistry and biophysics},
keywords = {Adenosine,Adenosine Diphosphate,Adenosine Diphosphate: analogs \& derivatives,Adenosine Diphosphate: pharmacology,Adenosine: analogs \& derivatives,Adenosine: pharmacology,Chromatography,Coenzymes,Coenzymes: metabolism,Coenzymes: pharmacology,Dimerization,Electrophoresis,Enzyme Inhibitors,Enzyme Inhibitors: pharmacology,Gel,Haemophilus,Haemophilus: enzymology,Haemophilus: growth \& development,Kinetics,Malate Dehydrogenase,Malate Dehydrogenase: antagonists \& inhibitors,Malate Dehydrogenase: isolation \& purification,Malate Dehydrogenase: metabolism,Malates,Malates: metabolism,Molecular Weight,NAD,NAD: analogs \& derivatives,NAD: pharmacology,Nicotinyl Alcohol,Nicotinyl Alcohol: analogs \& derivatives,Nicotinyl Alcohol: pharmacology,Polyacrylamide Gel,Protein Denaturation,Substrate Specificity,Temperature},
month = aug,
number = {1},
pages = {176--83},
pmid = {9244395},
title = {{Purification and kinetic characterization of Haemophilus parasuis malate dehydrogenase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9244395},
volume = {344},
year = {1997}
}
@article{Boyer2008,
abstract = {Long-range effects, such as allostery, have evolved in proteins as a means of regulating function via communication between distal sites. An NMR-based perturbation mapping approach was used to more completely probe the dynamic response of the core mutation V54A in the protein eglin c by monitoring changes in picosecond to nanosecond aromatic side-chain dynamics and H/D exchange stabilities. Previous side-chain dynamics studies on this mutant were limited to methyl-bearing residues, most of which were found to rigidify on the picosecond to nanosecond time scale in the form of a contiguous "network". Here, high precision (13)C relaxation data from 13 aromatic side chains were acquired by applying canonical relaxation experiments to a newly developed carbon labeling scheme [Teilum et al. (2006) J. Am. Chem. Soc. 128, 2506-2507]. The fitting of model-free parameters yielded S (2) variability which is intermediate with respect to backbone and methyl-bearing side-chain variability and tau e values that are approximately 1 ns. Inclusion of the aromatic dynamic response results in an expanded network of dynamically coupled residues, with some aromatics showing increases in flexibility, which partially offsets the rigidification in methyl side chains. Using amide hydrogen exchange, dynamic propagation on a slower time scale was probed in response to the V54A perturbation. Surprisingly, regional stabilization (slowed exchange) 10-12 A from the site of mutation was observed despite a global destabilization of 1.5 kcal x mol (-1). Furthermore, this unlikely pocket of stabilized residues colocalizes with increases in aromatic flexibility on the faster time scale. Because the converse is also true (destabilized residues colocalize with rigidification on the fast time scale), a plausible entropy-driven mechanism is discussed for relating colocalization of opposing dynamic trends on vastly different time scales.},
author = {Boyer, Joshua a and Lee, Andrew L},
doi = {10.1021/bi702330t},
file = {:home/alex/Dokumente/Mendeley Desktop/Boyer, Lee/Biochemistry/Boyer, Lee - 2008 - Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acids,Aromatic,Aromatic: chemistry,Carbon Isotopes,Hydrogen,Hydrogen: metabolism,Kinetics,Magnetic Resonance Spectroscopy,Models,Molecular,Movement,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: genetics,Mutant Proteins: metabolism,Mutation,Protein Conformation,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: metabolism,Thermodynamics,Time Factors},
month = apr,
number = {17},
pages = {4876--86},
pmid = {18393447},
title = {{Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3062916\&tool=pmcentrez\&rendertype=abstract},
volume = {47},
year = {2008}
}
@article{Chastain2002,
abstract = {Pyruvate,orthophosphate (Pi) dikinase (PPDK) is best recognized as a chloroplastic C(4) cycle enzyme. As one of the key regulatory foci for controlling flux through this photosynthetic pathway, it is strictly and reversibly regulated by light. This light/dark modulation is mediated by reversible phosphorylation of a conserved threonine residue in the active-site domain by the PPDK regulatory protein (RP), a bifunctional protein kinase/phosphatase. PPDK is also present in C(3) plants, although it has no known photosynthetic function. Nevertheless, in this report we show that C(3) PPDK in leaves of several angiosperms and in isolated intact spinach (Spinacia oleracea) chloroplasts undergoes light-/dark-induced changes in phosphorylation state in a manner similar to C(4) dikinase. In addition, the kinetics of this process closely resemble the reversible C(4) process, with light-induced dephosphorylation occurring rapidly (< or =15 min) and dark-induced phosphorylation occurring much more slowly (> or =30-60 min). In intact spinach chloroplasts, light-induced dephosphorylation of C(3) PPDK was shown to be dependent on exogenous Pi and photosystem II activity but independent of electron transfer from photosystem I. These in organello results implicate a role for stromal pools of Pi and adenylates in regulating the reversible phosphorylation of C(3)-PPDK. Last, we used an in vitro RP assay to directly demonstrate ADP-dependent PPDK phosphorylation in desalted leaf extracts of the C(3) plants Vicia faba and rice (Oryza sativa). We conclude that an RP-like activity mediates the light/dark modulation of PPDK phosphorylation state in C(3) leaves and chloroplasts and likely represents the ancestral isoform of this unusual and key C(4) pathway regulatory "converter" enzyme.},
author = {Chastain, Chris J and Fries, Jason P and Vogel, Julie A and Randklev, Christa L and Vossen, Adam P and Dittmer, Sharon K and Watkins, Erin E and Fiedler, Lucas J and Wacker, Sarah A and Meinhover, Katherine C and Sarath, Gautam and Chollet, Raymond},
doi = {10.1104/pp.010806},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/Plant physiology/Chastain et al. - 2002 - Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-dark-induced reversible phosphorylation.pdf:pdf},
issn = {0032-0889},
journal = {Plant physiology},
keywords = {Adenosine Diphosphate,Adenosine Diphosphate: metabolism,Adenosine Monophosphate,Adenosine Monophosphate: metabolism,Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Angiosperms,Angiosperms: classification,Angiosperms: enzymology,Biological,Chloroplasts,Chloroplasts: enzymology,Darkness,Fabaceae,Fabaceae: enzymology,Light,Models,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Oryza sativa,Oryza sativa: enzymology,Phosphates,Phosphates: metabolism,Phosphoenolpyruvate,Phosphoenolpyruvate: metabolism,Phosphorylation,Photosynthetic Reaction Center Complex Proteins,Photosynthetic Reaction Center Complex Proteins: m,Photosystem I Protein Complex,Photosystem II Protein Complex,Plant Leaves,Plant Leaves: enzymology,Pyruvate,Pyruvic Acid,Pyruvic Acid: metabolism,Spinacia oleracea,Spinacia oleracea: enzymology,Zea mays,Zea mays: enzymology},
month = apr,
number = {4},
pages = {1368--78},
pmid = {11950985},
title = {{Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-/dark-induced reversible phosphorylation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=154264\&tool=pmcentrez\&rendertype=abstract},
volume = {128},
year = {2002}
}
@article{DiTommaso2011,
abstract = {This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.},
author = {{Di Tommaso}, Paolo and Moretti, Sebastien and Xenarios, Ioannis and Orobitg, Miquel and Montanyola, Alberto and Chang, Jia-Ming and Taly, Jean-Fran\c{c}ois and Notredame, Cedric},
doi = {10.1093/nar/gkr245},
file = {:home/alex/Dokumente/Mendeley Desktop/Di Tommaso et al/Nucleic acids research/Di Tommaso et al. - 2011 - T-Coffee a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Internet,Nucleic Acid Conformation,Protein Conformation,RNA,RNA: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis, Protein,Sequence Analysis, RNA,Software},
month = jul,
number = {Web Server issue},
pages = {W13--7},
pmid = {21558174},
title = {{T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3125728\&tool=pmcentrez\&rendertype=abstract},
volume = {39},
year = {2011}
}
@article{Crick1970,
author = {Crick, Francis},
doi = {10.1038/227561a0},
file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Nature/Crick - 1970 - Central Dogma of Molecular Biology.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = aug,
number = {5258},
pages = {561--563},
title = {{Central Dogma of Molecular Biology}},
url = {http://www.nature.com/doifinder/10.1038/227561a0},
volume = {227},
year = {1970}
}
@article{Doyle2005,
abstract = {Plants using the C(4) photosynthetic pathway are highly represented among the world's worst weeds, with only 4 C(4) species being agriculturally productive (maize, sorghum, millet, and sugar cane). With the C(4) acid cycle operating as a biochemical appendage of C(3) photosynthesis, the additional enzymes involved in C(4) photosynthesis represent an attractive target for the development of weed-specific herbicides. The rate-limiting enzyme of this metabolic pathway is pyruvate orthophosphate dikinase (PPDK). PPDK, coupled with phosphoenolpyruvate carboxylase and nicotinamide adenine dinucleotide-malate dehydrogenase, was used to develop a microplate-based assay to detect inhibitors of enzymes of the C(4) acid cycle. The resulting assay had a Z' factor of 0.61, making it a high-quality assay able to reliably identify active test samples. Organic extracts of 6679 marine macroscopic organisms were tested within the assay, and 343 were identified that inhibited the 3 enzyme-coupled reaction. A high confirmation rate was achieved, with 95\% of these hit extracts proving active again upon retesting. Sequential addition of phosphoenolpyruvate and oxaloacetate to the assay facilitated identification of 83 extracts that specifically inhibited PPDK.},
author = {Doyle, Jason R and Burnell, James N and Haines, Dianne S and Llewellyn, Lyndon E and Motti, Cherie a and Tapiolas, Dianne M},
doi = {10.1177/1087057104269978},
file = {:home/alex/Dokumente/Mendeley Desktop/Doyle et al/Journal of biomolecular screening/Doyle et al. - 2005 - A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.pdf:pdf},
issn = {1087-0571},
journal = {Journal of biomolecular screening},
keywords = {Dimethyl Sulfoxide,Dimethyl Sulfoxide: pharmacology,Drug Evaluation, Preclinical,Drug Evaluation, Preclinical: methods,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Enzyme Inhibitors: pharmacology,Herbicides,Herbicides: chemistry,Herbicides: pharmacology,Malate Dehydrogenase,Malate Dehydrogenase: antagonists \& inhibitors,Malate Dehydrogenase: metabolism,Molecular Structure,Oxalic Acid,Oxalic Acid: pharmacology,Phosphoenolpyruvate Carboxylase,Phosphoenolpyruvate Carboxylase: antagonists \& inh,Phosphoenolpyruvate Carboxylase: metabolism,Plant Extracts,Plant Extracts: metabolism,Plants,Plants: drug effects,Plants: enzymology,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: antagonists \& i,Pyruvate, Orthophosphate Dikinase: metabolism,Species Specificity,Time Factors},
month = feb,
number = {1},
pages = {67--75},
pmid = {15695345},
title = {{A rapid screening method to detect specific inhibitors of pyruvate orthophosphate dikinase as leads for C4 plant-selective herbicides.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15695345},
volume = {10},
year = {2005}
}
@article{Burnell2006,
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(2).pdf:pdf},
issn = {0006-291X},
journal = {Biochemical and biophysical research communications},
keywords = {Amino Acid Sequence,Base Sequence,Catalysis,Cloning, Organism,Computational Biology,Extracellular Space,Extracellular Space: metabolism,Gene Expression Regulation, Plant,Intracellular Space,Intracellular Space: metabolism,Molecular Sequence Data,Plant Leaves,Plant Leaves: genetics,Plant Leaves: metabolism,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: genetics,Pyruvate, Orthophosphate Dikinase: metabolism,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Zea mays,Zea mays: genetics},
month = jun,
number = {2},
pages = {675--80},
pmid = {16696949},
title = {{Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16696949},
volume = {345},
year = {2006}
}
@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{MONOD1965,
author = {MONOD, J and WYMAN, J and CHANGEUX, J P},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Chemistry,Enzymes,Hemoglobins,Kinetics,Models,Physical,Physicochemical Phenomena,Proteins,Research,Theoretical,Ultracentrifugation},
month = may,
pages = {88--118},
pmid = {14343300},
title = {{ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14343300},
volume = {12},
year = {1965}
}
@article{Pineda2004,
abstract = {Na(+) binding near the primary specificity pocket of thrombin promotes the procoagulant, prothrombotic, and signaling functions of the enzyme. The effect is mediated allosterically by a communication between the Na(+) site and regions involved in substrate recognition. Using a panel of 78 Ala mutants of thrombin, we have mapped the allosteric core of residues that are energetically linked to Na(+) binding. These residues are Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the bound Na(+). Among these residues, Asp-189 shares with Asp-221 the important function of transducing Na(+) binding into enhanced catalytic activity. None of the residues of exosite I, exosite II, or the 60-loop plays a significant role in Na(+) binding and allosteric transduction. X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast) forms of thrombin, free or bound to the active site inhibitor H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes induced by Na(+) binding. The slow --> fast transition results in formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189 and Ser-195 for substrate binding, and a significant shift of the side chain of Glu-192 linked to a rearrangement of the network of water molecules that connect the bound Na(+) to Ser-195 in the active site. The changes in the water network and the allosteric core explain the thermodynamic signatures linked to Na(+) binding and the mechanism of thrombin activation by Na(+). The role of the water network uncovered in this study establishes a new paradigm for the allosteric regulation of thrombin and other Na(+)-activated enzymes involved in blood coagulation and the immune response.},
author = {Pineda, Agustin O and Carrell, Christopher J and Bush, Leslie a and Prasad, Swati and Caccia, Sonia and Chen, Zhi-Wei and Mathews, F Scott and {Di Cera}, Enrico},
doi = {10.1074/jbc.M401756200},
file = {:home/alex/Dokumente/Mendeley Desktop/Pineda et al/The Journal of biological chemistry/Pineda et al. - 2004 - Molecular dissection of Na binding to thrombin.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Allosteric Site,Allosteric Site: genetics,Crystallography, X-Ray,Humans,Models, Molecular,Mutagenesis, Site-Directed,Protein Conformation,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Sodium,Sodium: metabolism,Static Electricity,Thermodynamics,Thrombin,Thrombin: chemistry,Thrombin: genetics,Thrombin: metabolism},
month = jul,
number = {30},
pages = {31842--53},
pmid = {15152000},
title = {{Molecular dissection of Na+ binding to thrombin.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15152000},
volume = {279},
year = {2004}
}
@article{Moretti2007,
abstract = {The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.},
author = {Moretti, Sebastien and Armougom, Fabrice and Wallace, Iain M and Higgins, Desmond G and Jongeneel, Cornelius V and Notredame, Cedric},
doi = {10.1093/nar/gkm333},
file = {:home/alex/Dokumente/Mendeley Desktop/Moretti et al/Nucleic acids research/Moretti et al. - 2007 - The M-Coffee web server a meta-method for computing multiple sequence alignments by combining alternative alignment methods.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Algorithms,Amino Acid Sequence,Computational Biology,Computational Biology: methods,Computer Simulation,Information Storage and Retrieval,Internet,Molecular Sequence Data,Reproducibility of Results,Sequence Alignment,Sequence Alignment: methods,Sequence Homology, Amino Acid,Software,User-Computer Interface},
month = jul,
number = {Web Server issue},
pages = {W645--8},
pmid = {17526519},
title = {{The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933118\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Yankie1995,
abstract = {Pyruvate phosphate dikinase catalyzes the interconversion of adenosine 5'-triphosphate (ATP), orthophosphate (P(i)), and pyruvate with adenosine 5'-monophosphate (AMP), pyrophosphate (PP(i)), and phosphoenolpyruvate (PEP). The Arg 561 residue of Clostridium symbiosum PPDK is contained within a Gly-rich stretch of sequence spanning positions 553-563 (viz., GAEGIGLCRTE) located in the 35 kDa C-terminal domain of the enzyme. The possible role of this stretch of sequence as a phosphate binding loop participating in catalysis of the PEP/pyruvate partial reaction (viz., E+PEP<-->E-P+pyruvate, where E-P represents enzyme phosphorylated at the catalytic histidine) was deduced from the similarity of this sequence to other known phosphate binding loops and by its location in the 35 kDa PEP/pyruvate binding domain of PPDK. To test the proposed role of Arg 561, and hence, the signature sequence, in catalysis of the E+PEP<-->E-P+pyruvate partial reaction, the C. symbiosum PPDK site-directed mutants Arg 561-->Leu 561 and Arg 561-->Lys 561 were constructed and expressed in Escherichia coli JM101. Neither mutant catalyzed the full PPDK reaction, ATP+P(i)+pyruvate<-->AMP+PP(i)+PEP, but both catalyzed the E+ATP+P(i)<-->E-P+AMP+PP(i) partial reaction as efficiently as wild-type PPDK. Both mutants were shown to be unable to catalyze the PEP/pyruvate partial reaction. On the basis of these results it was proposed that Arg 561 and, possibly, the Gly-rich stretch of sequence spanning positions 553-563 are essential components of the active site of the PEP/pyruvate partial reaction.},
author = {Yankie, Linda and Xu, Yuan and Dunaway-Mariano, Debra},
doi = {10.1021/bi00007a012},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acid Sequence,Arginine,Arginine: chemistry,Binding Sites,Circular Dichroism,Clostridium,Clostridium: enzymology,Consensus Sequence,Cysteine,Cysteine: chemistry,Kinetics,Molecular Sequence Data,Mutagenesis,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: metabolism,Orthophosphate Dikinase: ultrastructure,Pyruvate,Recombinant Proteins,Sequence Alignment,Site-Directed,Structure-Activity Relationship},
month = feb,
number = {7},
pages = {2188--94},
pmid = {7857930},
title = {{Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 2. Site-directed mutagenesis of an essential arginine contained within an apparent P-loop.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7857930 http://pubs.acs.org/doi/abs/10.1021/bi00007a012},
volume = {34},
year = {1995}
}
@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{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{Muller2006,
author = {M\"{u}ller, U. F.},
doi = {10.1007/s00018-006-6047-1},
issn = {1420-682X},
journal = {Cellular and Molecular Life Sciences},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = may,
number = {11},
pages = {1278--1293},
title = {{Re-creating an RNA world}},
url = {http://www.springerlink.com/index/10.1007/s00018-006-6047-1},
volume = {63},
year = {2006}
}
@article{Crump2004a,
abstract = {LFA-1 (lymphocyte function-associated antigen-1) plays a role in intercellular adhesion and lymphocyte trafficking and activation and is an attractive anti-inflammatory drug target. The alpha-subunit of LFA-1, in common with several other integrins, has an N-terminally inserted domain (I-domain) of approximately 200 amino acids that plays a central role in regulating ligand binding to LFA-1. An additional region, termed the I-domain allosteric site (IDAS), has been identified exclusively within the LFA-1 I-domain and shown to regulate the function of this protein. The IDAS is occupied by small molecule LFA-1 inhibitors when cocrystallized or analyzed by (15)N-(1)H HSQC (heteronuclear single-quantum coherence) NMR (nuclear magnetic resonance) titration experiments. We report here a novel arylthio inhibitor that binds the I-domain with a K(d) of 18.3 nM as determined by isothermal titration calorimetry (ITC). This value is in close agreement with the IC(50) (10.9 nM) derived from a biochemical competition assay (DELFIA) that measures the level of inhibition of binding of whole LFA-1 to its ligand, ICAM-1. Having established the strong affinity of the arylthio inhibitor for the isolated I-domain, we have used a range of techniques to further characterize the binding, including ITC, NMR, and X-ray crystallography. We have first developed an effective ITC binding assay for use with low-solubility inhibitors that avoids the need for ELISA-based assays. In addition, we utilized a fast NMR-based assay for the generation of I-domain-inhibitor models. This is based around the collection of HCCH-TOCSY spectra of LFA-1 in the bound form and the identification of a subset of side chain methyl groups that give chemical shift changes upon binding of LFA-1 inhibitors. This subset was used in two-dimensional (13)C-(15)N and (15)N-filtered and -edited two-dimensional NMR experiments to identify a minimal set of intraligand and ligand-protein NOEs, respectively (nuclear Overhauser enhancements). Models from the NMR data were assessed by comparison to an X-ray crystallographic structure of the complex, confirming that the method correctly predicted the essential features of the bound ligand.},
author = {Crump, Matthew P and Ceska, Thomas A and Spyracopoulos, Leo and Henry, Alistair and Archibald, Sarah C and Alexander, Rikki and Taylor, Richard J and Findlow, Stuart C and O'Connell, James and Robinson, Martyn K and Shock, Anthony},
doi = {10.1021/bi035422a},
file = {:home/alex/Dokumente/Mendeley Desktop/Crump et al/Biochemistry/Crump et al. - 2004 - Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Allosteric Site,Amides,Amides: chemistry,Binding,Biomolecular,Calorimetry,Cinnamates,Cinnamates: chemistry,Cinnamates: metabolism,Competitive,Crystallography,Drug Design,Humans,Ligands,Lymphocyte Function-Associated Antigen-1,Lymphocyte Function-Associated Antigen-1: chemistr,Lymphocyte Function-Associated Antigen-1: metaboli,Models,Molecular,Nuclear Magnetic Resonance,Protein Binding,Protein Structure,Protein Subunits,Protein Subunits: antagonists \& inhibitors,Protein Subunits: chemistry,Recombinant Proteins,Recombinant Proteins: antagonists \& inhibitors,Recombinant Proteins: chemistry,Tertiary,X-Ray},
month = mar,
number = {9},
pages = {2394--404},
pmid = {14992576},
title = {{Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14992576},
volume = {43},
year = {2004}
}
@book{Atkins2006,
address = {Weinheim},
author = {Atkins, Peter W and de Paula, Julio},
edition = {4., vollst},
isbn = {9783527315468},
keywords = {Folder - Physikalische Chemie},
mendeley-tags = {Folder - Physikalische Chemie},
publisher = {Wiley-VCH},
title = {{Physikalische Chemie}},
year = {2006}
}
@book{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}
}
@book{Taiz2007,
address = {M\"{u}nchen; Heidelberg},
author = {Taiz, Lincoln and Zeiger, Eduardo},
edition = {4. ed.},
isbn = {9783827418654},
keywords = {Folder - Pflanzenphysiologie},
mendeley-tags = {Folder - Pflanzenphysiologie},
publisher = {Spektrum Akademischer Verlag},
title = {{Plant physiology das Original mit \"{U}bersetzungshilfen}},
year = {2007}
}
@article{Crick1968,
author = {Crick, F H},
file = {:home/alex/Dokumente/Mendeley Desktop/Crick/Journal of Molecular Biology/Crick - 1968 - The origin of the genetic code.pdf:pdf},
issn = {0022-2836},
journal = {Journal of Molecular Biology},
keywords = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger},
mendeley-tags = {Amino Acids,Biological Evolution,Escherichia coli,Folder - Vortrag RNA-Welt,Genetic Code,Nucleosides,Protein Biosynthesis,RNA- Messenger},
month = dec,
number = {3},
pages = {367--379},
title = {{The origin of the genetic code}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/4887876 http://www.sciencedirect.com/science?\_ob=MImg\&\_imagekey=B6WK7-4DM29RS-BH-1\&\_cdi=6899\&\_user=2665780\&\_pii=0022283668903926\&\_origin=\&\_coverDate=12/28/1968\&\_sk=999619996\&view=c\&wchp=dGLzVlz-zSkzV\&md5=04e907452df700b018f50eae6799bb6a\&ie=/sdarticle.pdf},
volume = {38},
year = {1968}
}
@article{Li2007,
author = {Li, Mamie Z and Elledge, Stephen J},
doi = {10.1038/nprot.2007.90},
issn = {2043-0116},
journal = {Protocol Exchange},
keywords = {Folder - Biochemie},
mendeley-tags = {Folder - Biochemie},
month = feb,
title = {{SLIC sub-cloning using T4 DNA polymerase treated inserts without RecA}},
url = {http://www.natureprotocols.com/2007/02/15/slic\_subcloning\_using\_t4\_dna\_p.php http://www.nature.com/protocolexchange/protocols/167},
year = {2007}
}
@article{Geourjon1995,
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{Michalkova2011,
author = {Michalkova, Andrea and Kholod, Yana and Kosenkov, Dmytro and Gorb, Leonid and Leszczynski, Jerzy},
doi = {10.1016/j.gca.2011.01.015},
issn = {00167037},
journal = {Geochimica et Cosmochimica Acta},
month = apr,
number = {7},
pages = {1933--1941},
shorttitle = {Viability of pyrite pulled metabolism in the ‘iron},
title = {{Viability of pyrite pulled metabolism in the ‘iron-sulfur world’ theory: Quantum chemical assessment}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0016703711000238},
volume = {75},
year = {2011}
}
@article{Laskowski1993a,
author = {Laskowski, R. A. and MacArthur, M. W. and Moss, D. S. and Thornton, J. M.},
doi = {10.1107/S0021889892009944},
issn = {00218898},
journal = {Journal of Applied Crystallography},
month = apr,
number = {2},
pages = {283--291},
title = {{PROCHECK: a program to check the stereochemical quality of protein structures}},
url = {http://scripts.iucr.org/cgi-bin/paper?S0021889892009944},
volume = {26},
year = {1993}
}
@article{Schagger2006,
author = {Sch\"{a}gger, Hermann},
doi = {10.1038/nprot.2006.4},
issn = {1754-2189},
journal = {Nature Protocols},
keywords = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll},
mendeley-tags = {Folder - Biochemie,Folder - Biochemie - Protokolle,Methode,Protokoll},
month = jun,
number = {1},
pages = {16--22},
title = {{Tricine–SDS-PAGE}},
url = {http://www.nature.com/doifinder/10.1038/nprot.2006.4 http://www.nature.com/nprot/journal/v1/n1/pdf/nprot.2006.4.pdf},
volume = {1},
year = {2006}
}
@article{Lu2000,
abstract = {Eglin c from the leech Hirudo medicinalis is a potent protein inhibitor of many serine proteinases including chymotrypsin and subtilisins. Unlike most small protein inhibitors whose solvent-exposed enzyme-binding loop is stabilized primarily by disulfide bridges flanking the reactive-site peptide bond, eglin c possesses an enzyme-binding loop supported predominantly by extensive electrostatic/H-bonding interactions involving three Arg residues (Arg48, Arg51, and Arg53) projecting from the scaffold of the inhibitor. As an adjacent residue, the C-terminal Gly70 participates in these interactions via its alpha-carboxyl group interacting with the side chain of Arg51 and the main chain of Arg48. In addition, the amide NH group of Gly70 donates an H-bond to the carbonyl C=O groups of Arg48 and Arg51. To understand the structural and functional relevance of the electrostatic/H-bonding network, we chemically synthesized wild-type eglin c and three analogues in which Gly70 was either deleted or replaced by glycine amide (NH(2)CH(2)CONH(2)) or by alpha-hydroxylacetamide (HOCH(2)CONH(2)). NMR analysis indicated that the core structure of eglin c was maintained in the analogues, but that the binding loop was significantly perturbed. It was found that deletion or replacement of Gly70 destabilized eglin c by an average of 2.7 kcal/mol or 20 degrees C in melting temperature. As a result, these inhibitors become substrates for their target enzymes. Binding assays on these analogues with a catalytically incompetent subtilisin BPN' mutant indicated that loss or weakening of the interactions involving the carboxylate of Gly70 caused a decrease in binding by approximately 2 orders of magnitude. Notably, for all four synthetic inhibitors, the relative free energy changes (DeltaDeltaG) associated with protein destabilization are strongly correlated (slope = 0.94, r(2) = 0. 9996) with the DeltaDeltaG values derived from a decreased binding to the enzyme.},
author = {Lu, Wei-Yue and Starovasnik, Melissa a and Dwyer, John J and Kossiakoff, Anthony a and Kent, Stephen B. H. and Lu, Wuyuan},
doi = {10.1021/bi992292q},
file = {:home/alex/Dokumente/Mendeley Desktop/Lu et al/Biochemistry/Lu et al. - 2000 - Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acid Sequence,Animals,Binding Sites,Biomolecular,Chymotrypsin,Chymotrypsin: antagonists \& inhibitors,Glycine,Glycine: chemistry,Glycine: metabolism,Kinetics,Leeches,Molecular Sequence Data,Nuclear Magnetic Resonance,Protein Denaturation,Proteins,Serpins,Serpins: chemical synthesis,Serpins: chemistry,Serpins: metabolism,Static Electricity,Structure-Activity Relationship,Subtilisins,Subtilisins: antagonists \& inhibitors},
month = apr,
number = {13},
pages = {3575--3584},
pmid = {10736156},
title = {{Deciphering the Role of the Electrostatic Interactions Involving Gly70 in Eglin C by Total Chemical Protein Synthesis}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10736156 http://pubs.acs.org/doi/abs/10.1021/bi992292q},
volume = {39},
year = {2000}
}
@article{Puius1997,
abstract = {The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2\% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1\% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.},
author = {Puius, Y a and Zhao, Y and Sullivan, M and Lawrence, D S and Almo, S C and Zhang, Z Y},
file = {:home/alex/Dokumente/Mendeley Desktop/Puius et al/Proceedings of the National Academy of Sciences of the United States of America/Puius et al. - 1997 - Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B a paradigm for inhibitor design.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Base Sequence,Binding Sites,Binding Sites: genetics,Cloning, Molecular,DNA Primers,DNA Primers: genetics,Drug Design,Enzyme Inhibitors,Enzyme Inhibitors: chemistry,Escherichia coli,Escherichia coli: genetics,Humans,Models, Molecular,Molecular Sequence Data,Mutagenesis, Site-Directed,Phosphotyrosine,Phosphotyrosine: metabolism,Polymerase Chain Reaction,Protein Conformation,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: antagonists \& inhib,Protein Tyrosine Phosphatases: chemistry,Protein Tyrosine Phosphatases: genetics,Substrate Specificity},
month = dec,
number = {25},
pages = {13420--5},
pmid = {9391040},
title = {{Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=28320\&tool=pmcentrez\&rendertype=abstract},
volume = {94},
year = {1997}
}
@article{Schrader1985,
abstract = {The objective of this study was to determine the biochemical basis for genetic variability in pyruvate,Pi dikinase (PPDK) activity among inbred lines of maize (Zea mays L.). Although in vitro PPDK activity varied more than 5-fold among eight maize inbreds, immunochemical determinations of the proportion of leaf soluble protein as PPDK revealed no significant differences among the inbreds. Genetic differences in the stability of PPDK activity in crude homogenates over 5 hours were not evident, but PPDK from some inbreds could not be activated in vitro. In vitro PPDK activation in crude homogenates could be restored by addition of casein (1\% w/v) to homogenization media, and to a lesser extent, by gentle homogenization in a mortar. The major effect of casein appeared to be on processes other than proteolysis, as casein exerted its effects during tissue homogenization, rather than later. During homogenization, PPDK did not lose its ability to undergo in vitro activation; instead, it was instability of the regulatory protein responsible for PPDK activation that was the cause of the lack of PPDK activation in homogenates prepared without casein.},
author = {Baer, G R and Schrader, Larry E},
file = {:home/alex/Dokumente/Mendeley Desktop/Baer, Schrader/Plant physiology/Baer, Schrader - 1985 - Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.pdf:pdf},
issn = {0032-0889},
journal = {Plant physiology},
month = mar,
number = {3},
pages = {608--11},
pmid = {16664106},
title = {{Stabilization of pyruvate, pi dikinase regulatory protein in maize leaf extracts.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1064572\&tool=pmcentrez\&rendertype=abstract},
volume = {77},
year = {1985}
}
@article{Clarkson2006,
abstract = {Long-range intraprotein interactions give rise to many important protein behaviors. Understanding how energy is transduced through protein structures to either transmit a signal or elicit conformational changes is therefore a current challenge in structural biology. In an effort to understand such linkages, multiple V --> A mutations were made in the small globular protein eglin c. The physical responses, as mapped by NMR spin relaxation, residual dipolar couplings (RDCs), and scalar couplings, illustrate that the interior of this nonallosteric protein forms a dynamic network and that local perturbations are transmitted as dynamic and structural changes to distal sites as far as 16 A away. Two basic types of propagation responses were observed: contiguous pathways of enhanced (attenuated) dynamics with no change in structure; and dispersed (noncontiguous) changes in methyl rotation rates that appear to result from subtle deformation of backbone structure. In addition, energy transmission is found to be unidirectional. In one mutant, an allosteric conformational change of a side chain is seen in the context of a pathway of propagated changes in picosecond to nanosecond dynamics. The observation of so many long-range interactions in a small, rigid system lends experimental weight to the idea that all well-folded proteins inherently possess allosteric features [Gunasekaran et al. (2004) Proteins 57, 433-443], and that dynamics are a rich source of information for mapping and gaining mechanistic insight into communication pathways in individual proteins.},
author = {Clarkson, Michael W and Gilmore, Steven A and Edgell, Marshall H and Lee, Andrew L},
doi = {10.1021/bi060652l},
file = {:home/alex/Dokumente/Mendeley Desktop/Clarkson et al/Biochemistry/Clarkson et al. - 2006 - Dynamic coupling and allosteric behavior in a nonallosteric protein.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Allosteric Regulation,Amino Acid Substitution,Biomolecular,Eglin c,Models,Molecular,Nuclear Magnetic Resonance,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Proteins: genetics,Signal Transduction},
mendeley-tags = {Eglin c},
month = jun,
number = {25},
pages = {7693--9},
pmid = {16784220},
title = {{Dynamic coupling and allosteric behavior in a nonallosteric protein.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2453595\&tool=pmcentrez\&rendertype=abstract},
volume = {45},
year = {2006}
}
@article{Cui2008a,
abstract = {Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/Pauling-KNF descriptions, and point out that the "new view" of allostery, emphasizing "population shifts," is, in fact, an "old view." The presentation offers not only an up-to-date description of allostery from a theoretical/computational perspective, but also helps to resolve several outstanding issues concerning allostery.},
author = {Cui, Qiang and Karplus, Martin},
doi = {10.1110/ps.03259908},
file = {:home/alex/Dokumente/Mendeley Desktop/Cui, Karplus/Protein science a publication of the Protein Society/Cui, Karplus - 2008 - Allostery and cooperativity revisited.pdf:pdf},
issn = {1469-896X},
journal = {Protein science : a publication of the Protein Society},
keywords = {Allosteric Regulation,Allosteric Site,Animals,Dimerization,Folder - Allostery - Theory,Hemoglobins,Hemoglobins: chemistry,Humans,Mechanism,Models,Molecular,Protein Structure,Proteins,Proteins: chemistry,Quaternary,Tertiary},
mendeley-tags = {Folder - Allostery - Theory,Mechanism},
month = aug,
number = {8},
pages = {1295--307},
pmid = {18560010},
title = {{Allostery and cooperativity revisited.}},
url = {http://doi.wiley.com/10.1110/ps.03259908 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2492820\&tool=pmcentrez\&rendertype=abstract},
volume = {17},
year = {2008}
}
@article{Voet-van-Vormizeele2008,
author = {Voet-van-Vormizeele, Jan and Groth, Georg},
file = {:home/alex/Dokumente/Mendeley Desktop/Voet-van-Vormizeele, Groth/Current Topics in Biochemical Research/Voet-van-Vormizeele, Groth - 2008 - Mutants, molecules and mechanisms - Decipering the ethylene signalling network.pdf:pdf},
issn = {09724583},
journal = {Current Topics in Biochemical Research},
keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper},
mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper},
number = {2},
pages = {25--34},
title = {{Mutants, molecules and mechanisms - Decipering the ethylene signalling network}},
volume = {10},
year = {2008}
}
@article{Pfleger2012,
author = {Pfleger, Christopher and Radestock, Sebastian and Schmidt, S. and Gohlke, Holger},
title = {{Global and local indices for characterizing biomolecular flexibility and rigidity}},
year = {2012}
}
@article{Chastain1996,
abstract = {The gene for C4-pyruvate,orthophosphate dikinase (PPDK) from maize (Zea mays) was cloned into an Escherichia coli expression vector and recombinant PPDK produced in E. coli cells. Recombinant enzyme was found to be expressed in high amounts (5.3 U purified enzyme-activityliter-1 of induced cells) as a predominantly soluble and active protein. Biochemical analysis of partially purified recombinant PPDK showed this enzyme to be equivalent to enzyme extracted from illuminated maize leaves with respect to (i) molecular mass, (ii) specific activity, (iii) substrate requirements, and (iv) phosphorylation/inactivation by its bifunctional regulatory protein.},
author = {Chastain, Chris J. and Thompson, Brent J. and Chollet, Raymond},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain, Thompson, Chollet/Photosynthesis Research/Chastain, Thompson, Chollet - 1996 - Maize recombinant C4-pyruvate, orthophosphate dikinase expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein.pdf:pdf},
journal = {Photosynthesis Research},
keywords = {C4 photosynthesis,C4 plant,PPDK,enzyme,maize (Zea mays),orthophosphate dikinase,pyruvate,recombinant},
pages = {83--89},
title = {{Maize recombinant C4-pyruvate, orthophosphate dikinase: expression in Escherichia coli, partial purification, and characterization of the phosphorylatable protein}},
url = {http://www.springerlink.com/index/N642332887GN2U55.pdf},
volume = {49},
year = {1996}
}
@article{Cortazzo2002,
abstract = {As an approach to investigate the molecular mechanism of in vivo protein folding and the role of translation kinetics on specific folding pathways, we made codon substitutions in the EgFABP1 (Echinococcus granulosus fatty acid binding protein1) gene that replaced five minor codons with their synonymous major ones. The altered region corresponds to a turn between two short alpha helices. One of the silent mutations of EgFABP1 markedly decreased the solubility of the protein when expressed in Escherichia coli. Expression of this protein also caused strong activation of a reporter gene designed to detect misfolded proteins, suggesting that the turn region seems to have special translation kinetic requirements that ensure proper folding of the protein. Our results highlight the importance of codon usage in the in vivo protein folding.},
author = {Cortazzo, Patricia and Cerve\~{n}ansky, Carlos and Mar\'{\i}n, M\'{o}nica and Reiss, Claude and Ehrlich, Ricardo and Deana, Atilio},
doi = {10.1016/S0006-291X(02)00226-7},
file = {:home/alex/Dokumente/Mendeley Desktop/Cortazzo et al/Biochemical and biophysical research communications/Cortazzo et al. - 2002 - Silent mutations affect in vivo protein folding in Escherichia coli.pdf:pdf},
issn = {0006-291X},
journal = {Biochemical and biophysical research communications},
keywords = {Amino Acid Substitution,Bacterial Proteins,Bacterial Proteins: genetics,Base Sequence,Carrier Proteins,Carrier Proteins: genetics,Codon,Escherichia coli,Escherichia coli: genetics,Fatty Acid-Binding Proteins,Fish Proteins,Models, Molecular,Mutation,Oligodeoxyribonucleotides,Peptide Fragments,Peptide Fragments: chemistry,Protein Folding,Protein Structure, Secondary},
month = apr,
number = {1},
pages = {537--41},
pmid = {12054634},
title = {{Silent mutations affect in vivo protein folding in Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12054634},
volume = {293},
year = {2002}
}
@article{Sponer2011,
author = {\v{S}poner, Judit E. and \v{S}poner, Jiř\'{\i} and Fuentes-Cabrera, Miguel},
doi = {10.1002/chem.201002057},
issn = {09476539},
journal = {Chemistry - A European Journal},
month = jan,
number = {3},
pages = {847--854},
shorttitle = {Prebiotic Routes to Nucleosides},
title = {{Prebiotic Routes to Nucleosides: A Quantum Chemical Insight into the Energetics of the Multistep Reaction Pathways}},
url = {http://doi.wiley.com/10.1002/chem.201002057},
volume = {17},
year = {2011}
}
@article{Wachtershauser2006,
author = {Wachtershauser, G.},
doi = {10.1098/rstb.2006.1904},
file = {:home/alex/Dokumente/Mendeley Desktop/Wachtershauser/Philosophical Transactions of the Royal Society B Biological Sciences/Wachtershauser - 2006 - From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya.pdf:pdf},
issn = {0962-8436},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
month = oct,
number = {1474},
pages = {1787--1808},
title = {{From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya}},
url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2006.1904},
volume = {361},
year = {2006}
}
@article{Dong2004,
author = {Dong, X. and Stothard, P. and Forsythe, I. J. and Wishart, D. S.},
doi = {10.1093/nar/gkh410},
file = {:home/alex/Dokumente/Mendeley Desktop/Dong et al/Nucleic Acids Research/Dong et al. - 2004 - PlasMapper a web server for drawing and auto-annotating plasmid maps.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
month = jul,
number = {Web Server},
pages = {W660--W664},
title = {{PlasMapper: a web server for drawing and auto-annotating plasmid maps}},
url = {http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkh410},
volume = {32},
year = {2004}
}
@misc{CenterforHistoryandNewMedia,
annote = {
        Welcome to Zotero!
        

        
View the Quick Start Guide to learn how to begin collecting, managing, citing, and sharing your research sources.
Thanks for installing Zotero.},
author = {{Center for History and New Media}},
title = {{Zotero Quick Start Guide}},
url = {http://zotero.org/support/quick\_start\_guide}
}
@book{Bruckner2007,
address = {Berlin [u.a.]},
author = {Br\"{u}ckner, Reinhard},
edition = {3. Aufl., },
isbn = {9783827415790},
keywords = {Folder - Organische Chemie},
mendeley-tags = {Folder - Organische Chemie},
publisher = {Spektrum Akademischer Verlag},
title = {{Reaktionsmechanismen : organische Reaktionen, Stereochemie, moderne Synthesemethoden}},
year = {2007}
}
@article{Steitz2003,
author = {Steitz, Thomas A and Moore, Peter B},
doi = {10.1016/S0968-0004(03)00169-5},
file = {:home/alex/Dokumente/Mendeley Desktop/Steitz, Moore/Trends in Biochemical Sciences/Steitz, Moore - 2003 - RNA, the first macromolecular catalyst the ribosome is a ribozyme.pdf:pdf},
issn = {09680004},
journal = {Trends in Biochemical Sciences},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = aug,
number = {8},
pages = {411--418},
shorttitle = {RNA, the first macromolecular catalyst},
title = {{RNA, the first macromolecular catalyst: the ribosome is a ribozyme}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0968000403001695},
volume = {28},
year = {2003}
}
@article{Stone1988,
abstract = {Kinetic studies on the reaction catalyzed by dihydrofolate reductase from Escherichia coli have been undertaken with the aim of characterizing further the kinetic mechanism of the reaction. For this purpose, the kinetic properties of substrates were determined by measurement of (a) initial velocities over a wide range of substrate concentrations and (b) the stickiness of substrates in ternary enzyme complexes. Stickiness is defined as the rate at which a substrate reacts to give products relative to the rate at which that substrate dissociates. Stickiness was determined by varying the viscosity of reaction mixtures and the concentration of one substrate in the presence of a saturating concentration of the other substrate. The results indicate that NADPH is sticky in the enzyme-NADPH-dihydrofolate complex, while dihydrofolate is much less sticky in this complex. At higher concentrations, NADPH functions as an activator through the formation of an enzyme-NADPH-tetrahydrofolate from which tetrahydrofolate is released more rapidly than from an enzyme-tetrahydrofolate complex. Higher concentrations of dihydrofolate also cause enzyme activation, and it appears that this effect is due to the ability of dihydrofolate to displace tetrahydrofolate from a binary enzyme complex through the formation of a transitory enzyme-tetrahydrofolate-dihydrofolate complex. As NADPH and dihydrofolate function as activators and as NADPH behaves as a sticky substrate, the kinetic mechanism of the dihydrofolate reductase reaction with the natural substrates is steady-state random. By contrast with NADPH, reduced 3-acetylpyridine adenine dinucleotide phosphate exhibits only slight stickiness and does not function as an activator.(ABSTRACT TRUNCATED AT 250 WORDS)},
author = {Stone, S R and Morrison, J F},
file = {:home/alex/Dokumente/Mendeley Desktop/Stone, Morrison/Biochemistry/Stone, Morrison - 1988 - Dihydrofolate reductase from Escherichia coli the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Deuterium,Escherichia coli,Escherichia coli: enzymology,Folic Acid,Folic Acid: analogs \& derivatives,Folic Acid: metabolism,Hydrogen-Ion Concentration,Kinetics,NAD,NAD: analogs \& derivatives,NAD: metabolism,NADP,NADP: metabolism,Tetrahydrofolate Dehydrogenase,Tetrahydrofolate Dehydrogenase: metabolism,Viscosity},
month = jul,
number = {15},
pages = {5493--9},
pmid = {3052577},
title = {{Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3052577},
volume = {27},
year = {1988}
}
@article{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{Tsai2008a,
abstract = {Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For several years, it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free-energy change due to the change in entropy, entropy is mainly responsible for binding.},
author = {Tsai, Chung-Jung and del Sol, Antonio and Nussinov, Ruth},
doi = {10.1016/j.jmb.2008.02.034},
file = {:home/alex/Dokumente/Mendeley Desktop/Tsai, del Sol, Nussinov/Journal of molecular biology/Tsai, del Sol, Nussinov - 2008 - Allostery absence of a change in shape does not imply that allostery is not at play.pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Allosteric Regulation,Animals,Folder - Allostery - Theory,Humans,Mechanism,Models,Molecular,Protein Conformation,Signal Transduction,Thermodynamics},
mendeley-tags = {Folder - Allostery - Theory,Mechanism},
month = apr,
number = {1},
pages = {1--11},
pmid = {18353365},
shorttitle = {Allostery},
title = {{Allostery: absence of a change in shape does not imply that allostery is not at play.}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283608002313 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2684958\&tool=pmcentrez\&rendertype=abstract},
volume = {378},
year = {2008}
}
@article{Changeux2011,
author = {Changeux, Jean-Pierre},
doi = {10.1002/pro.658},
issn = {09618368},
journal = {Protein Science},
keywords = {Folder - Allostery - Theory, Mechanism},
mendeley-tags = {Folder - Allostery - Theory, Mechanism},
month = jul,
pages = {1119--1124},
title = {50th anniversary of the word “allosteric”},
url = {http://doi.wiley.com/10.1002/pro.658},
volume = {20},
year = {2011}
}
@article{Tsutsui1982,
author = {Tsutsui, K. and Mueller, G. C},
file = {:home/alex/Dokumente/Mendeley Desktop/Tsutsui, Mueller/Analytical Biochemistry/Tsutsui, Mueller - 1982 - Affinity chromatography of heme-binding proteins an improved method for the synthesis of hemin-agarose.pdf:pdf},
journal = {Analytical Biochemistry},
keywords = {Folder - Methoden},
mendeley-tags = {Folder - Methoden},
number = {2},
pages = {244--250},
shorttitle = {Affinity chromatography of heme-binding proteins},
title = {{Affinity chromatography of heme-binding proteins: an improved method for the synthesis of hemin-agarose}},
volume = {121},
year = {1982}
}
@article{Luisi2003a,
author = {Luisi, P. L},
file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Naturwissenschaften/Luisi - 2003 - Autopoiesis a review and a reappraisal.pdf:pdf},
journal = {Naturwissenschaften},
number = {2},
pages = {49--59},
shorttitle = {Autopoiesis},
title = {{Autopoiesis: a review and a reappraisal}},
volume = {90},
year = {2003}
}
@article{Wiechelman1988,
author = {Wiechelman, K},
doi = {10.1016/0003-2697(88)90383-1},
file = {:home/alex/Dokumente/Mendeley Desktop/Wiechelman/Analytical Biochemistry/Wiechelman - 1988 - Investigation of the bicinchoninic acid protein assay Identification of the groups responsible for color formation.pdf:pdf},
issn = {00032697},
journal = {Analytical Biochemistry},
keywords = {Folder - Methoden},
mendeley-tags = {Folder - Methoden},
month = nov,
number = {1},
pages = {231--237},
title = {{Investigation of the bicinchoninic acid protein assay: Identification of the groups responsible for color formation}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0003269788903831},
volume = {175},
year = {1988}
}
@article{Chastain2008,
abstract = {Pyruvate, orthophosphate dikinase (PPDK) is a ubiquitous, low-abundance metabolic enzyme of undetermined function in C3 plants. Its activity in C3 chloroplasts is light-regulated via reversible phosphorylation of an active-site Thr residue by the PPDK regulatory protein (RP), a most unusual bifunctional protein kinase (PK)/protein phosphatase (PP). In this paper we document the molecular cloning and functional analysis of the two unique C3 RPs in Arabidopsis thaliana. The first of these, AtRP1, encodes a typical chloroplast-targeted, bifunctional C4-like RP. The second RP gene, AtRP2, encodes a monofunctional polypeptide that possesses in vitro RP-like PK activity but lacks PP activity, and is localized in the cytosol. Notably, the deduced primary structures of these two highly homologous polypeptides are devoid of any canonical subdomain structure that unifies all known eukaryotic and prokaryotic Ser/Thr PKs into one of three superfamilies, despite the direct demonstration that AtRP1 is functionally a member of this group. Instead, these C3 RPs and the related C4 plant homologues encode a conserved, centrally positioned, approximately 260-residue sequence currently described as the 'domain of unknown function 299' (DUF 299). We propose that vascular plant RPs form a unique protein kinase family now designated as the DUF 299 gene family.},
author = {Chastain, Chris J and Xu, Wenxin and Parsley, Kate and Sarath, Gautam and Hibberd, Julian M and Chollet, Raymond},
doi = {10.1111/j.1365-313X.2007.03366.x},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain et al/The Plant journal for cell and molecular biology/Chastain et al. - 2008 - The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented SerThr protein kinase primary structure.pdf:pdf},
issn = {1365-313X},
journal = {The Plant journal : for cell and molecular biology},
keywords = {Amino Acid Sequence,Arabidopsis,Arabidopsis Proteins,Arabidopsis Proteins: chemistry,Arabidopsis Proteins: genetics,Arabidopsis: enzymology,Arabidopsis: genetics,Cloning,Molecular,Molecular Sequence Data,Orthophosphate Dikinase,Orthophosphate Dikinase: chemistry,Orthophosphate Dikinase: genetics,Phylogeny,Protein-Serine-Threonine Kinases,Protein-Serine-Threonine Kinases: chemistry,Protein-Serine-Threonine Kinases: genetics,Pyruvate},
month = mar,
number = {5},
pages = {854--63},
pmid = {17996018},
title = {{The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17996018},
volume = {53},
year = {2008}
}
@article{Zhuravleva2011a,
abstract = {The 70-kDa heat shock protein (Hsp70) chaperones perform a wide array of cellular functions that all derive from the ability of their N-terminal nucleotide-binding domains (NBDs) to allosterically regulate the substrate affinity of their C-terminal substrate-binding domains in a nucleotide-dependent mechanism. To explore the structural origins of Hsp70 allostery, we performed NMR analysis on the NBD of DnaK, the Escherichia coli Hsp70, in six different states (ligand-bound or apo) and in two constructs, one that retains the conserved and functionally crucial portion of the interdomain linker (residues ) and another that lacks the linker. Chemical-shift perturbation patterns identify residues at subdomain interfaces that constitute allosteric networks and enable the NBD to act as a nucleotide-modulated switch. Nucleotide binding results in changes in subdomain orientations and long-range perturbations along subdomain interfaces. In particular, our findings provide structural details for a key mechanism of Hsp70 allostery, by which information is conveyed from the nucleotide-binding site to the interdomain linker. In the presence of ATP, the linker binds to the edge of the IIA $\beta$-sheet, which structurally connects the linker and the nucleotide-binding site. Thus, a pathway of allosteric communication leads from the NBD nucleotide-binding site to the substrate-binding domain via the interdomain linker.},
author = {Zhuravleva, Anastasia and Gierasch, Lila M},
doi = {10.1073/pnas.1014448108},
file = {:home/alex/Dokumente/Mendeley Desktop/Zhuravleva, Gierasch/Proceedings of the National Academy of Sciences of the United States of America/Zhuravleva, Gierasch - 2011 - Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Adenosine Triphosphate,Adenosine Triphosphate: chemistry,Adenosine Triphosphate: genetics,Adenosine Triphosphate: metabolism,Allosteric Regulation,Allosteric Regulation: physiology,Binding Sites,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Escherichia coli: chemistry,Escherichia coli: genetics,Escherichia coli: metabolism,HSP70 Heat-Shock Proteins,HSP70 Heat-Shock Proteins: chemistry,HSP70 Heat-Shock Proteins: genetics,HSP70 Heat-Shock Proteins: metabolism,Nuclear Magnetic Resonance, Biomolecular,Protein Binding,Signal Transduction,Signal Transduction: physiology,Structure-Activity Relationship},
month = apr,
number = {17},
pages = {6987--92},
pmid = {21482798},
title = {{Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084084\&tool=pmcentrez\&rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Wilkins1999,
author = {Wilkins, M R and Gasteiger, E and Bairoch, A and Sanchez, J C and Williams, K L and Appel, R D and Hochstrasser, D F},
file = {:home/alex/Dokumente/Mendeley Desktop/Wilkins et al/Methods in Molecular Biology (Clifton, N.J.)/Wilkins et al. - 1999 - Protein identification and analysis tools in the ExPASy server.pdf:pdf},
issn = {1064-3745},
journal = {Methods in Molecular Biology (Clifton, N.J.)},
keywords = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software},
mendeley-tags = {Electrophoresis- Gel- Two-Dimensional,Folder - In-silico-structure,Internet,Proteins,Software},
pages = {531--552},
title = {{Protein identification and analysis tools in the ExPASy server}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10027275},
volume = {112},
year = {1999}
}
@article{Greenfield2007,
author = {Greenfield, Norma J},
doi = {10.1038/nprot.2006.202},
issn = {1754-2189},
journal = {Nature Protocols},
month = jan,
number = {6},
pages = {2876--2890},
title = {{Using circular dichroism spectra to estimate protein secondary structure}},
url = {http://www.nature.com/doifinder/10.1038/nprot.2006.202},
volume = {1},
year = {2007}
}
@article{Riener2002a,
author = {Riener, Christian and Kada, Gerald and Gruber, Hermann},
doi = {10.1007/s00216-002-1347-2},
file = {:home/alex/Dokumente/Mendeley Desktop/Riener, Kada, Gruber/Analytical and Bioanalytical Chemistry/Riener, Kada, Gruber - 2002 - Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4\&\#x02032-dithiodipyridine.pdf:pdf},
issn = {1618-2642},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {Folder - Methoden},
mendeley-tags = {Folder - Methoden},
month = jul,
number = {4-5},
pages = {266--276},
title = {{Quick measurement of protein sulfhydryls with Ellman's reagent and with 4,4'-dithiodipyridine}},
url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/s00216-002-1347-2},
volume = {373},
year = {2002}
}
@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{Luisi2002,
author = {Luisi, P. L},
file = {:home/alex/Dokumente/Mendeley Desktop/Luisi/Foundations of Chemistry/Luisi - 2002 - Emergence in chemistry Chemistry as the embodiment of emergence.pdf:pdf},
journal = {Foundations of Chemistry},
number = {3},
pages = {183--200},
shorttitle = {Emergence in chemistry},
title = {{Emergence in chemistry: Chemistry as the embodiment of emergence}},
volume = {4},
year = {2002}
}
@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{Wiesmann2004,
abstract = {Obesity and type II diabetes are closely linked metabolic syndromes that afflict >100 million people worldwide. Although protein tyrosine phosphatase 1B (PTP1B) has emerged as a promising target for the treatment of both syndromes, the discovery of pharmaceutically acceptable inhibitors that bind at the active site remains a substantial challenge. Here we describe the discovery of an allosteric site in PTP1B. Crystal structures of PTP1B in complex with allosteric inhibitors reveal a novel site located approximately 20 A from the catalytic site. We show that allosteric inhibitors prevent formation of the active form of the enzyme by blocking mobility of the catalytic loop, thereby exploiting a general mechanism used by tyrosine phosphatases. Notably, these inhibitors exhibit selectivity for PTP1B and enhance insulin signaling in cells. Allosteric inhibition is a promising strategy for targeting PTP1B and constitutes a mechanism that may be applicable to other tyrosine phosphatases.},
author = {Wiesmann, Christian and Barr, Kenneth J and Kung, Jenny and Zhu, Jiang and Erlanson, Daniel a and Shen, Wang and Fahr, Bruce J and Zhong, Min and Taylor, Lisa and Randal, Mike and McDowell, Robert S and Hansen, Stig K},
doi = {10.1038/nsmb803},
file = {:home/alex/Dokumente/Mendeley Desktop/Wiesmann et al/Nature structural \& molecular biology/Wiesmann et al. - 2004 - Allosteric inhibition of protein tyrosine phosphatase 1B.pdf:pdf},
issn = {1545-9993},
journal = {Nature structural \& molecular biology},
keywords = {Allosteric Site,Animals,Binding,Binding Sites,CHO Cells,Catalysis,Catalytic Domain,Chemical,Cloning,Competitive,Cricetinae,Crystallography,DNA,DNA: chemistry,Dose-Response Relationship,Drug,Humans,Inhibitory Concentration 50,Kinetics,Ligands,Models,Molecular,Non-Receptor Type 1,Obesity,Phosphoric Monoester Hydrolases,Phosphoric Monoester Hydrolases: chemistry,Protein Binding,Protein Conformation,Protein Structure,Protein Tyrosine Phosphatase,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: chemistry,Tertiary,Time Factors,Transfection,Tyrosine,Tyrosine: chemistry,X-Ray,allostery,ptp1b},
mendeley-tags = {allostery,ptp1b},
month = aug,
number = {8},
pages = {730--7},
pmid = {15258570},
title = {{Allosteric inhibition of protein tyrosine phosphatase 1B.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15258570},
volume = {11},
year = {2004}
}
@article{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{Sashital2006,
author = {Sashital, Dipali G. and Butcher, Samuel E.},
doi = {10.1021/cb6002465},
file = {:home/alex/Dokumente/Mendeley Desktop/Sashital, Butcher/ACS Chemical Biology/Sashital, Butcher - 2006 - Flipping Off the Riboswitch RNA Structures That Control Gene Expression.pdf:pdf},
issn = {1554-8929},
journal = {ACS Chemical Biology},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
month = jul,
number = {6},
pages = {341--345},
shorttitle = {Flipping Off the Riboswitch},
title = {{Flipping Off the Riboswitch: RNA Structures That Control Gene Expression}},
url = {http://pubs.acs.org/doi/abs/10.1021/cb6002465 http://pubs.acs.org/doi/pdf/10.1021/cb6002465},
volume = {1},
year = {2006}
}
@article{Goss1980,
abstract = {Pyruvate phosphate dikinase contains a pivotal histidyl residue which functions to mediate the transfer of phosphoryl moieties during the reaction catalyzed by the enzyme. The tryptic peptide which contains this essential histidyl residue has been isolated by a two-step procedure originally developed by Wang and co-workers [Wang, T., Jurasek, L., \& Bridger, W. A. (1972) Biochemistry 11, 2067]. This peptide has been sequenced by the manual dansyl-Edman procedure and is shown to be NH2-Gly-Gly-Met-Thr-Ser-His-Ala-Ala-Val-Val-Ala-Arg-CO2H. There is no readily interpretable homology between this peptide and other phosphorylated histidyl peptides previously isolated from other enzymes. By use of Chou \& Fasman [Chou, P. Y., \& Fasman, G. D. (1974) Biochemistry 13, 222], it is predicted that the sequence contains an alpha helix from the methionine residue through to the carboxyl terminal arginine residue.},
author = {Goss, Neil H. and Evans, Claudia T. and Wood, Harland G.},
doi = {10.1021/bi00566a022},
file = {:home/alex/Dokumente/Mendeley Desktop/Goss, Evans, Wood/Biochemistry/Goss, Evans, Wood - 1980 - Pyruvate phosphate dikinase sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier.pdf:pdf},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Amino Acid Sequence,Bacteroides,Bacteroides: enzymology,Chemical Phenomena,Chemistry,Histidine,Histidine: analysis,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Peptide Fragments,Peptide Fragments: analysis,Phosphotransferases,Phosphotransferases: isolation \& purification,Pyruvate,purification},
mendeley-tags = {purification},
month = dec,
number = {25},
pages = {5805--5809},
pmid = {6257292},
title = {{Pyruvate phosphate dikinase: sequence of the histidyl peptide, the pyrophosphoryl and phosphoryl carrier}},
url = {http://pubs.acs.org/doi/abs/10.1021/bi00566a022 http://www.ncbi.nlm.nih.gov/pubmed/6257292},
volume = {19},
year = {1980}
}
@article{Slack1968,
abstract = {1. An enzyme was isolated from leaves of tropical grasses that catalyses the reversible conversion of pyruvate, ATP and orthophosphate into phosphopyruvate, AMP and pyrophosphate. A requirement for Mg(2+) could not be replaced by Mn(2+) or Ca(2+). 2. By replacing orthophosphate with [(32)P]orthophosphate or with arsenate, evidence was provided that the orthophosphate consumed appears in pyrophosphate. 3. Without Mg(2+) or 2-mercaptoethanol the enzyme was rapidly and irreversibly inactivated. EDTA only partially replaced the requirement for the thiol compound. The enzyme was considerably more unstable at 0 degrees or when frozen than at 22 degrees . Even with the best conditions devised the enzyme lost about 25\% of its activity every 3hr. 4. The activities of the enzyme in leaves of the tropical grasses sugar cane (Saccharum hybrid var. Pindar), maize (Zea mays) and sorghum (Sorghum vulgare) were comparable with their maximum photosynthesis rates. The enzyme was not detectable in leaf extracts from several other plants. 5. Its role in photosynthesis is discussed.},
author = {Hatch, M D and Slack, C R},
file = {:home/alex/Dokumente/Mendeley Desktop/Hatch, Slack/The Biochemical journal/Hatch, Slack - 1968 - A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C4 dicarboxylic acid pathway of photosynthesis.pdf:pdf},
issn = {0264-6021},
journal = {The Biochemical journal},
keywords = {Adenine Nucleotides,Adenosine Triphosphate,Arsenic,Calcium,Chemical Precipitation,Chromatography,Cold Temperature,Diphosphates,Drug Stability,Edetic Acid,Gel,Ligases,Ligases: isolation \& purification,Magnesium,Manganese,Mercaptoethanol,Phosphates,Phosphorus Isotopes,Phosphotransferases,Photosynthesis,Plants,Plants: enzymology,Poaceae,Poaceae: enzymology,Pyruvates,Sulfhydryl Compounds,Sunlight,Time Factors,Zea mays,Zea mays: enzymology},
month = jan,
number = {1},
pages = {141--6},
pmid = {4305612},
title = {{A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C4 dicarboxylic acid pathway of photosynthesis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1198479\&tool=pmcentrez\&rendertype=abstract},
volume = {106},
year = {1968}
}
@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{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{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{Okabayashi1984,
abstract = {Purification and characterization of mitochondrial malate dehydrogenase [EC 1.1.1.37] from unfertilized eggs of the sea urchin, Anthocidaris crassispina, are described. The purification method consisted of dextran sulfate fractionation, Blue Dextran Sepharose chromatography, Phenyl-Sepharose hydrophobic chromatography and DEAE-cellulose chromatography. The enzyme was purified 771-fold with a 7\% yield from the crude extract. The purified enzyme appeared homogeneous on polyacrylamide gel electrophoresis under both native and denatured conditions. After incubation at 45 degrees C for 50 min, the enzyme lost about 90\% of its activity. In the presence of NADH, however, the enzyme was protected against the heat denaturation. The native enzyme had a molecular weight of about 65,000 and probably consisted of two identical subunits. In the reduction of oxaloacetate with NADH, a broad optimum pH ranging from 8.2 to 9.4 was found with 50 mM Tris-HCl and glycine-NaOH buffers. Sodium phosphate buffer apparently activated the enzyme. The apparent Km values for oxaloacetate and NADH were 19 microM and 30 microM, respectively. The optimum pH for malate oxidation with NAD+ was 10.2 in 50 mM NaHCO3-Na2CO3 buffer. The apparent Km values for malate and NAD+ were 7.0 mM and 0.6 mM, respectively. Zinc ion, sulfite ion, p-chloromercuriphenylsulfonate and adenine nucleotides strongly inhibited the enzyme.},
author = {Okabayashi, K and Nakano, E},
issn = {0021-924X},
journal = {Journal of biochemistry},
keywords = {Animals,Female,Hydrogen-Ion Concentration,Kinetics,Macromolecular Substances,Malate Dehydrogenase,Malate Dehydrogenase: isolation \& purification,Malate Dehydrogenase: metabolism,Mitochondria,Mitochondria: enzymology,Molecular Weight,Ovum,Ovum: enzymology,Sea Urchins},
month = jun,
number = {6},
pages = {1625--32},
pmid = {6469942},
title = {{Purification and properties of mitochondrial malate dehydrogenase from unfertilized eggs of the sea urchin, Anthocidaris crassispina.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6469942},
volume = {95},
year = {1984}
}
@article{Jenkins1985,
abstract = {The properties and reaction mechanism of maize leaf pyruvate,Pi dikinase are described. Km values were determined for the forward reaction substrates, pyruvate, ATP, and Pi, at pH 7.4 and 8.0 and for reverse reaction substrates at pH 7.4. Enzyme activity was almost totally dependent on added monovalent cations in both directions. NH+4 was most effective, with Ka values of about 0.38 mM for the forward reaction and 2 mM for the reverse reaction. K+ also completely activated the enzyme in the forward direction (Ka = 8 mM) but only partially activated in the reverse direction. Na+ had little effect on either reaction. The pH optimum for the forward reaction was about 8.2; the reverse reaction optimum was about 6.9. Maximum activity for the reverse direction was about twice the maximum forward direction rate. From data on the requirements for the ATP-AMP exchange reaction, on the mechanism of inhibition of the forward reaction by PEP, AMP, and PPi, and from the kinetics of the interaction of varying certain substrate pairs, it was concluded that the maize leaf pyruvate,Pi dikinase reaction proceeded by the two-step Bi Bi Uni Uni mechanism. This differs from the mechanism of catalysis by the bacterial enzyme.},
author = {Jenkins, C L and Hatch, M D},
file = {:home/alex/Dokumente/Mendeley Desktop/Jenkins, Hatch/Archives of biochemistry and biophysics/Jenkins, Hatch - 1985 - Properties and reaction mechanism of C4 leaf pyruvate,Pi dikinase.pdf:pdf},
issn = {0003-9861},
journal = {Archives of biochemistry and biophysics},
keywords = {Adenosine Monophosphate,Adenosine Monophosphate: metabolism,Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Catalysis,Cations,Chloroplasts,Chloroplasts: enzymology,Darkness,Enzyme Activation,Kinetics,Light,Monovalent,Monovalent: pharmacology,Orthophosphate Dikinase,Orthophosphate Dikinase: metabolism,Phosphotransferases,Phosphotransferases: metabolism,Photochemistry,Pyruvate,Substrate Specificity,Zea mays,Zea mays: enzymology},
month = may,
number = {1},
pages = {53--62},
pmid = {2988448},
title = {{Properties and reaction mechanism of C4 leaf pyruvate,Pi dikinase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2988448},
volume = {239},
year = {1985}
}
@article{Hatch2002,
abstract = {This Minireview provides a brief account of the scene and interesting turn of events surrounding the discovery and resolution of the mechanism of C(4) photosynthesis, as well as the recognition of the process by the wider plant science community.},
author = {Hatch, Marshall D},
doi = {10.1023/A:1020471718805},
issn = {1573-5079},
journal = {Photosynthesis research},
month = jan,
number = {1-3},
pages = {251--6},
pmid = {16245128},
title = {{C(4) photosynthesis: discovery and resolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16245128},
volume = {73},
year = {2002}
}
@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{Matsuoka1995,
abstract = {Pyruvate, orthophosphate dikinase (PPDK; EC 2.7.9.1) is a key enzyme in photosynthesis in plants that exploit the C4 photosynthetic pathway for the fixation of CO2. This review focuses on the structure, regulation and evolution of the C4-type ppdk gene in the maize genome. The C4-ppdk gene in maize consists of 19 exons spanning about 12 kbp. The gene is transcribed from two different initiation sites under the control of two promoters to produce two mRNAs of different sizes. The larger one contains the exon 1 sequence that encodes the chloroplast transit peptide and its product acts as C4-PPDK in chloroplasts, while the smaller one does not contain the sequence and its product may function as a C3-enzyme in the cytosol. This unusual dual promoter system is not unique to the maize C4-type ppdk gene since the same organization is also observed in the rice (C3 plant) ppdk gene and in Flaveria. Thus, the two-promoter system is common to plant ppdk genes from C3 and C4, monocot and dicot plants. A discussion is also presented of the generation of a system for regulation of the expression of the C4-type ppdk gene. A chimeric gene consisting of a reporter gene under the control of the promoter of maize C4-ppdk is exclusively expressed in photosynthetic tissues and not in roots or stems of transgenic rice. The expression of the introduced gene is also regulated by light: it is low in etiolated leaves and is enhanced by illumination. These results indicate that the regulatory system that controls ppdk expression in maize is not unique to C4 plants.},
author = {Matsuoka, M},
file = {:home/alex/Dokumente/Mendeley Desktop/Matsuoka/Plant \& cell physiology/Matsuoka - 1995 - The gene for pyruvate, orthophosphate dikinase in C4 plants structure, regulation and evolution.pdf:pdf},
issn = {0032-0781},
journal = {Plant \& cell physiology},
keywords = {Amino Acid,Amino Acid Sequence,Biological Evolution,Enzymologic,Gene Expression Regulation,Molecular Sequence Data,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Plant,Pyruvate,Sequence Homology,Zea mays,Zea mays: enzymology,Zea mays: genetics},
month = sep,
number = {6},
pages = {937--43},
pmid = {8528609},
title = {{The gene for pyruvate, orthophosphate dikinase in C4 plants: structure, regulation and evolution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8528609},
volume = {36},
year = {1995}
}
@incollection{Ashton1990,
abstract = {The history of the resolution of C4 photosynthesis follows a pattern of demonstrating the operation of unique photosynthetic biochemistry by various means and then identifying the enzymes necessary to support that biochemistry. Critical to the developing understanding of this process was the recognition of two types of photosynthetic cells in C4 plants (mesophyll and bundle sheath) with quite different enzyme complements and distinct biochemical roles (see Fig. 3.1). As currently interpreted (see Edwards and Walker, 1983; Hatch, 1987) the reactions unique to the C4 pathway serve, in association with some remarkable modifications of leaf anatomy and ultrastructure, to concentrate CO2 in bundle sheath cells for utilisatiqn by the photosynthetic carbon reduction cycle carboxylase, ribulose L5-bisphosphate carboxylase-oxygenase (Rubisco). The Rubisco-mediated oxygenase reaction and associated photorespiration are thereby eliminated.},
address = {London},
author = {Ashton, AR and Burnell, JN and Furbank, RT and Jenkins, CLD and Hatch, MD},
booktitle = {Methods in Plant Biochemistry. Enzymes of Primary Metabolism},
editor = {Dey, P.M. and Harborne, J.B.},
isbn = {978-0-12-461017-0},
pages = {39--72},
publisher = {Academic Press},
title = {{The enzymes in C4 photosynthesis}},
year = {1990}
}
@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{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{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{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{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{Johnson1999,
abstract = {We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3\% for alpha-helix, 2.6\% for 3(10)-helix, 4.2\% for beta-strand, 4.2\% for beta-turn, 2.7\% for poly(L-proline) II type 3(1)-helix, and 5.1\% for other structures when compared with the X-ray structure.},
author = {Johnson, W C},
doi = {10.1002/(SICI)1097-0134(19990515)35:3<307::AID-PROT4>3.0.CO;2-3},
file = {:home/alex/Dokumente/Mendeley Desktop/Johnson/Proteins/Johnson - 1999 - Analyzing protein circular dichroism spectra for accurate secondary structures.pdf:pdf},
issn = {0887-3585},
journal = {Proteins},
keywords = {Algorithms,Circular Dichroism,Protein Structure,Secondary,X-Ray Diffraction},
month = may,
number = {3},
pages = {307--12},
pmid = {10328265},
title = {{Analyzing protein circular dichroism spectra for accurate secondary structures.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10328265},
volume = {35},
year = {1999}
}
@article{Chastain1997a,
abstract = {Pyruvate, orthophosphate dikinase (PPDK; E.C. 2.7.9.1) catalyzes the synthesis of the primary inorganic carbon acceptor, phosphoenolpyruvate in the C4 photosynthetic pathway and is reversibly regulated by light. PPDK regulatory protein (RP), a bifunctional serine/threonine kinase-phosphatase, catalyzes both the ADP-dependent inactivation and the Pi-dependent activation of PPDK. Attempts to clone the RP have to date proven unsuccessful. A bioinformatics approach was taken to identify the nucleotide and amino acid sequence of the protein. Based on previously established characteristics including molecular mass, known inter- and intracellular location, functionality, and low level of expression, available databases were interrogated to ultimately identify a single candidate gene. In this paper, we describe the nucleotide and deduced amino acid sequence of this gene and establish its identity as maize PPDK RP by in vitro analysis of its catalytic properties via the cloning and expression of the recombinant protein.},
author = {Burnell, Jim N and Chastain, Chris J.},
doi = {10.1016/j.bbrc.2006.04.150},
file = {:home/alex/Dokumente/Mendeley Desktop/Burnell, Chastain/Biochemical and biophysical research communications/Burnell, Chastain - 2006 - Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.pdf:pdf},
issn = {0006-291X},
journal = {Biochemical and biophysical research communications},
keywords = {Amino Acid Sequence,Base Sequence,Catalysis,Cloning,Computational Biology,Extracellular Space,Extracellular Space: metabolism,Gene Expression Regulation,Intracellular Space,Intracellular Space: metabolism,Molecular Sequence Data,Organism,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Orthophosphate Dikinase: metabolism,Plant,Plant Leaves,Plant Leaves: genetics,Plant Leaves: metabolism,Pyruvate,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Zea mays,Zea mays: genetics},
month = jun,
number = {2},
pages = {675--80},
pmid = {16696949},
publisher = {Federation of European Biochemical Societies},
title = {{Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene.}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397008843 http://www.ncbi.nlm.nih.gov/pubmed/16696949},
volume = {345},
year = {2006}
}
@article{Sali1993a,
abstract = {We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.},
author = {Sali, A and Blundell, T L},
doi = {10.1006/jmbi.1993.1626},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Amino Acid,Amino Acid Sequence,Animals,Enzymes,Enzymes: chemistry,Humans,Kallikreins,Kallikreins: chemistry,Mathematics,Models,Molecular Sequence Data,Pancreatic Elastase,Pancreatic Elastase: chemistry,Probability,Protein Conformation,Proteins,Proteins: chemistry,Sequence Homology,Software,Theoretical,Thermodynamics,Tissue Kallikreins,Trypsin,Trypsin: chemistry},
month = dec,
number = {3},
pages = {779--815},
pmid = {8254673},
title = {{Comparative protein modelling by satisfaction of spatial restraints.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8254673},
volume = {234},
year = {1993}
}
@article{Pieper2011,
abstract = {ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains 10,355,444 reliable models for domains in 2,421,920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are available through the ModBase interface as well as the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment (http://salilab.org/salign), the ModEval server for predicting the accuracy of protein structure models (http://salilab.org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs).},
author = {Pieper, Ursula and Webb, Benjamin M and Barkan, David T and Schneidman-Duhovny, Dina and Schlessinger, Avner and Braberg, Hannes and Yang, Zheng and Meng, Elaine C and Pettersen, Eric F and Huang, Conrad C and Datta, Ruchira S and Sampathkumar, Parthasarathy and Madhusudhan, Mallur S and Sj\"{o}lander, Kimmen and Ferrin, Thomas E and Burley, Stephen K and Sali, Andrej},
doi = {10.1093/nar/gkq1091},
file = {:home/alex/Dokumente/Mendeley Desktop/Pieper et al/Nucleic acids research/Pieper et al. - 2011 - ModBase, a database of annotated comparative protein structure models, and associated resources.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Bacterial Proteins,Bacterial Proteins: chemistry,Computer Graphics,Databases, Protein,Models, Molecular,Peptides,Peptides: chemistry,Protein Interaction Mapping,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Scattering, Small Angle,Sequence Alignment,Software,Structural Homology, Protein,User-Computer Interface,X-Ray Diffraction},
month = jan,
number = {Database issue},
pages = {D465--74},
pmid = {21097780},
title = {{ModBase, a database of annotated comparative protein structure models, and associated resources.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013688\&tool=pmcentrez\&rendertype=abstract},
volume = {39},
year = {2011}
}
@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{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{Datta2008,
abstract = {Structural studies of caspase-1 reveal that the dimeric thiol protease can exist in two states: in an on-state, when the active site is occupied, or in an off-state, when the active site is empty or when the enzyme is bound by a synthetic allosteric ligand at the dimer interface approximately 15 A from the active site. A network of 21 hydrogen bonds from nine side chains connecting the active and allosteric sites change partners when going between the on-state and the off-state. Alanine-scanning mutagenesis of these nine side chains shows that only two of them-Arg286 and Glu390, which form a salt bridge-have major effects, causing 100- to 200-fold reductions in catalytic efficiency (k(cat)/K(m)). Two neighbors, Ser332 and Ser339, have minor effects, causing 4- to 7-fold reductions. A more detailed mutational analysis reveals that the enzyme is especially sensitive to substitutions of the salt bridge: even a homologous R286K substitution causes a 150-fold reduction in k(cat)/K(m). X-ray crystal structures of these variants suggest the importance of both the salt bridge interaction and the coordination of solvent water molecules near the allosteric binding pocket. Thus, only a small subset of side chains from the larger hydrogen bonding network is critical for activity. These form a contiguous set of interactions that run from one active site through the allosteric site at the dimer interface and onto the second active site. This subset constitutes a functional allosteric circuit or "hot wire" that promotes site-to-site coupling.},
author = {Datta, Debajyoti and Scheer, Justin M and Romanowski, Michael J and Wells, James a},
doi = {10.1016/j.jmb.2008.06.040},
file = {:home/alex/Dokumente/Mendeley Desktop/Datta et al/Journal of molecular biology/Datta et al. - 2008 - An allosteric circuit in caspase-1.pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Allosteric Regulation,Amino Acid Substitution,Arginine,Caspase 1,Caspase 1: chemistry,Caspase 1: metabolism,Conserved Sequence,Crystallography, X-Ray,DNA Mutational Analysis,Glutamic Acid,Humans,Hydrogen Bonding,Kinetics,Models, Molecular,Mutant Proteins,Mutant Proteins: chemistry,Mutant Proteins: metabolism,Protein Structure, Secondary},
month = sep,
number = {5},
pages = {1157--67},
pmid = {18590738},
title = {{An allosteric circuit in caspase-1.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2626611\&tool=pmcentrez\&rendertype=abstract},
volume = {381},
year = {2008}
}
@article{Formaneck2006,
abstract = {A combination of thirty-two 10-ns-scale molecular dynamics simulations were used to explore the coupling between conformational transition and phosphorylation in the bacteria chemotaxis Y protein (CheY), as a simple but representative example of protein allostery. Results from these simulations support an activation mechanism in which the beta4-alpha4 loop, at least partially, gates the isomerization of Tyr106. The roles of phosphorylation and the conserved Thr87 are deemed indirect in that they stabilize the active configuration of the beta4-alpha4 loop. The indirect role of the activation event (phosphorylation) and/or conserved residues in stabilizing, rather than causing, specific conformational transition is likely a feature in many signaling systems. The current analysis of CheY also helps to make clear that neither the "old" (induced fit) nor the "new" (population shift) views for protein allostery are complete, because they emphasize the kinetic (mechanistic) and thermodynamic aspects of allosteric transitions, respectively. In this regard, an issue that warrants further analysis concerns the interplay of concerted collective motion and sequential local structural changes in modulating cooperativity between distant sites in biomolecules.},
author = {Formaneck, Mark S and Ma, Liang and Cui, Qiang},
doi = {10.1002/prot.20893},
file = {:home/alex/Dokumente/Mendeley Desktop/Formaneck, Ma, Cui/Proteins/Formaneck, Ma, Cui - 2006 - Reconciling the old and new views of protein allostery a molecular simulation study of chemotaxis Y protein (CheY).pdf:pdf},
issn = {1097-0134},
journal = {Proteins},
keywords = {Allosteric Regulation,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Chemotaxis,Computer Simulation,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Membrane Proteins: metabolism,Models,Molecular,Mutation,Mutation: genetics,Phosphorylation,Protein Binding,Protein Structure,Tertiary,Threonine,Threonine: genetics,Threonine: metabolism,Tyrosine,Tyrosine: metabolism},
month = jun,
number = {4},
pages = {846--67},
pmid = {16475196},
title = {{Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16475196},
volume = {63},
year = {2006}
}
@article{Ellington2009,
author = {Ellington, A. D and Chen, X. and Robertson, M. and Syrett, A.},
file = {:home/alex/Dokumente/Mendeley Desktop/Ellington et al/The international journal of biochemistry \& cell biology/Ellington et al. - 2009 - Evolutionary origins and directed evolution of RNA.pdf:pdf},
journal = {The international journal of biochemistry \& cell biology},
number = {2},
pages = {254--265},
title = {{Evolutionary origins and directed evolution of RNA}},
volume = {41},
year = {2009}
}
@article{Lawlor2002,
author = {Lawlor, D. W.},
doi = {10.1093/aob/mcf110},
file = {:home/alex/Dokumente/Mendeley Desktop/Lawlor/Annals of Botany/Lawlor - 2002 - Limitation to Photosynthesis in Water-stressed Leaves Stomata vs. Metabolism and the Role of ATP.pdf:pdf},
issn = {03057364},
journal = {Annals of Botany},
keywords = {amino acid metabolism,atp synthesis,bisphosphate synthesis,chaperones,photosynthesis,protein synthesis,relative water content,ribulose,rwc,stomata},
month = jun,
number = {7},
pages = {871--885},
title = {{Limitation to Photosynthesis in Water-stressed Leaves: Stomata vs. Metabolism and the Role of ATP}},
url = {http://aob.oupjournals.org/cgi/doi/10.1093/aob/mcf110},
volume = {89},
year = {2002}
}
@article{Thompson1994,
abstract = {The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.},
author = {Thompson, Julie D and Higgins, Desmond G and Gibson, Toby J},
doi = {10.1093/nar/22.22.4673},
file = {:home/alex/Dokumente/Mendeley Desktop/Thompson, Higgins, Gibson/Nucleic Acids Research/Thompson, Higgins, Gibson - 1994 - CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
keywords = {Algorithms,Amino Acid Sequence,Globins,Globins: genetics,Molecular Sequence Data,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,Secondary,Sensitivity and Specificity,Sequence Alignment,Sequence Alignment: methods,Software},
month = nov,
number = {22},
pages = {4673--4680},
pmid = {7984417},
title = {{CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308517\&tool=pmcentrez\&rendertype=abstract http://nar.oxfordjournals.org/cgi/doi/10.1093/nar/22.22.4673},
volume = {22},
year = {1994}
}
@article{Chastain2003,
author = {Chastain, Chris J and Chollet, Raymond},
doi = {10.1016/S0981-9428(03)00065-2},
file = {:home/alex/Dokumente/Mendeley Desktop/Chastain, Chollet/Plant Physiology and Biochemistry/Chastain, Chollet - 2003 - Regulation of pyruvate, orthophosphate dikinase by ADP-Pi-dependent reversible phosphorylation in C3 and C4 plants.pdf:pdf},
issn = {09819428},
journal = {Plant Physiology and Biochemistry},
keywords = {c 3 plant,c 4 photosynthesis,dephosphorylation,pi dikinase,ppdk,ppdk regulatory protein,protein phosphorylation,pyruvate,rp},
month = jun,
number = {6-7},
pages = {523--532},
title = {{Regulation of pyruvate, orthophosphate dikinase by ADP-/Pi-dependent reversible phosphorylation in C3 and C4 plants}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0981942803000652},
volume = {41},
year = {2003}
}
@article{Bleecker2000,
author = {Bleecker, A. B and Kende, H.},
file = {:home/alex/Dokumente/Mendeley Desktop/Bleecker, Kende/Annual Review of Cell and Developmental Biology/Bleecker, Kende - 2000 - ETHYLENE A Gaseous Signal Molecule in Plants.1:1},
journal = {Annual Review of Cell and Developmental Biology},
keywords = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper},
mendeley-tags = {Folder - Biochemie,Folder - Pflanzenphysiologie,Paper},
number = {1},
pages = {1--18},
shorttitle = {ETHYLENE},
title = {{ETHYLENE: A Gaseous Signal Molecule in Plants}},
volume = {16},
year = {2000}
}
@article{Sali1993,
abstract = {We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.},
author = {Sali, A and Blundell, T. L.},
doi = {10.1006/jmbi.1993.1626},
file = {:home/alex/Dokumente/Mendeley Desktop/Sali, Blundell/Journal of molecular biology/Sali, Blundell - 1993 - Comparative protein modelling by satisfaction of spatial restraints.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Amino Acid,Amino Acid Sequence,Animals,Enzymes,Enzymes: chemistry,Humans,Kallikreins,Kallikreins: chemistry,Mathematics,Models,Molecular Sequence Data,Pancreatic Elastase,Pancreatic Elastase: chemistry,Probability,Protein Conformation,Proteins,Proteins: chemistry,Sequence Homology,Software,Theoretical,Thermodynamics,Tissue Kallikreins,Trypsin,Trypsin: chemistry},
month = dec,
number = {3},
pages = {779--815},
pmid = {8254673},
title = {{Comparative protein modelling by satisfaction of spatial restraints.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8254673},
volume = {234},
year = {1993}
}
@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},
doi = {10.1038/nchembio.98},
file = {:home/alex/Dokumente/Mendeley Desktop/Goodey, Benkovic/Nature chemical biology/Goodey, Benkovic - 2008 - Allosteric regulation and catalysis emerge via a common route.pdf:pdf},
issn = {1552-4469},
journal = {Nature chemical biology},
keywords = {Allosteric Regulation,Catalysis,Folder - Allostery - Theory,Mechanism,Protein Conformation,Proteins,Proteins: chemistry,Proteins: metabolism},
mendeley-tags = {Folder - Allostery - Theory,Mechanism},
month = aug,
number = {8},
pages = {474--82},
pmid = {18641628},
title = {{Allosteric regulation and catalysis emerge via a common route.}},
url = {http://www.nature.com/doifinder/10.1038/nchembio.98 http://www.ncbi.nlm.nih.gov/pubmed/18641628},
volume = {4},
year = {2008}
}
@article{Resnick2008,
author = {Resnick, J. S and Rivarola, M. and Chang, C.},
file = {:home/alex/Dokumente/Mendeley Desktop/Resnick, Rivarola, Chang/The Plant journal for cell and molecular biology/Resnick, Rivarola, Chang - 2008 - Involvement of RTE1 in conformational changes promoting ETR1 ethylene receptor signaling in Arabidopsis.fulltext:fulltext},
journal = {The Plant journal: for cell and molecular biology},
keywords = {Folder - RTE1},
mendeley-tags = {Folder - RTE1},
number = {3},
pages = {423},
title = {{Involvement of RTE1 in conformational changes promoting ETR1 ethylene receptor signaling in Arabidopsis}},
volume = {56},
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{Pieper2004,
abstract = {MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).},
author = {Pieper, Ursula and Eswar, Narayanan and Braberg, Hannes and Madhusudhan, M S and Davis, Fred P and Stuart, Ashley C and Mirkovic, Nebojsa and Rossi, Andrea and Marti-Renom, Marc a and Fiser, Andras and Webb, Ben and Greenblatt, Daniel and Huang, Conrad C and Ferrin, Thomas E and Sali, Andrej},
doi = {10.1093/nar/gkh095},
file = {:home/alex/Dokumente/Mendeley Desktop/Pieper et al/Nucleic acids research/Pieper et al. - 2004 - MODBASE, a database of annotated comparative protein structure models, and associated resources.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Amino Acid Sequence,Animals,Binding Sites,Computational Biology,Databases, Protein,Genomics,Humans,Internet,Ligands,Models, Molecular,Molecular Sequence Data,Polymorphism, Single Nucleotide,Protein Binding,Protein Conformation,Proteins,Proteins: chemistry,Proteins: genetics,Sequence Alignment,Software,User-Computer Interface},
month = jan,
number = {Database issue},
pages = {D217--22},
pmid = {14681398},
title = {{MODBASE, a database of annotated comparative protein structure models, and associated resources.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308829\&tool=pmcentrez\&rendertype=abstract},
volume = {32},
year = {2004}
}
@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{Smith1985,
author = {Smith, P and Krohn, R and Hermanson, G and Mallia, A and Gartner, F and Provenzano, M and Fujimoto, E and Goeke, N and Olson, B and Klenk, D},
doi = {10.1016/0003-2697(85)90442-7},
file = {:home/alex/Dokumente/Mendeley Desktop/Smith et al/Analytical Biochemistry/Smith et al. - 1985 - Measurement of protein using bicinchoninic acid.pdf:pdf},
issn = {00032697},
journal = {Analytical Biochemistry},
keywords = {Folder - Methoden},
mendeley-tags = {Folder - Methoden},
month = oct,
number = {1},
pages = {76--85},
title = {{Measurement of protein using bicinchoninic acid}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0003269785904427},
volume = {150},
year = {1985}
}
@article{Wu2004,
author = {Wu, Xiaoqiu and J\"{o}rnvall, Hans and Berndt, Kurt D and Oppermann, Udo},
doi = {10.1016/j.bbrc.2003.11.091},
file = {:home/alex/Dokumente/Mendeley Desktop/Wu et al/Biochemical and Biophysical Research Communications/Wu et al. - 2004 - Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli RNA stability and secondary structure but not tRNA abundance.pdf:pdf},
issn = {0006291X},
journal = {Biochemical and Biophysical Research Communications},
keywords = {all gene products a,and functional analysis of,archaeal proteins,completed genome se-,demand-,fusion protein,heterologous protein expression,makes the structural,quences from numerous organisms,rare codon gene,rna stability,structural genomics,the current availability of},
month = jan,
number = {1},
pages = {89--96},
title = {{Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X03024653},
volume = {313},
year = {2004}
}
@article{Cooper1984,
abstract = {A general model is presented whereby ligand-induced changes in protein dynamics could produce allosteric communication between distinct binding sites, even in the absence of a macromolecular conformational change. Theoretical analysis, based on the statistical thermodynamics of ligand binding, shows that cooperative interaction free energies amounting to several kJ . mol-1 may be generated by this means. The effect arises out of the possible changes in frequencies and amplitudes of macromolecular thermal fluctuations in response to ligand attachment, and can involve all forms of dynamic behaviour, ranging from highly correlated, low-frequency normal mode vibrations to random local anharmonic motions of individual atoms or groups. Dynamic allostery of this form is primarily an entropy effect, and we derive approximate expressions which might allow the magnitude of the interaction in real systems to be calculated directly from experimental observations such as changes in normal mode frequencies and mean-square atomic displacements. Long-range influence of kinetic processes at different sites might also be mediated by a similar mechanism. We suggest that proteins and other biological macromolecules may have evolved to take functional advantage not only of mean conformational states but also of the inevitable thermal fluctuations about the mean.},
author = {Cooper, A and Dryden, D T},
issn = {0175-7571},
journal = {European biophysics journal : EBJ},
keywords = {Allosteric Regulation,Biological,Kinetics,Models,Protein Conformation,Proteins,Proteins: metabolism,Thermodynamics},
month = jan,
number = {2},
pages = {103--9},
pmid = {6544679},
title = {{Allostery without conformational change. A plausible model.}},
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{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.},
author = {Whiteley, Walter},
doi = {10.1088/1478-3975/2/4/S06},
file = {:home/alex/Dokumente/Mendeley Desktop/Whiteley/Physical biology/Whiteley - 2005 - Counting out to the flexibility of molecules.pdf:pdf},
issn = {1478-3975},
journal = {Physical biology},
keywords = {Algorithms,Animals,Biophysics,Biophysics: methods,Humans,Hydrogen Bonding,Immunoglobulins,Immunoglobulins: chemistry,Models, Molecular,Models, Statistical,Models, Theoretical,Molecular Conformation,Motion,Pliability,Protein Conformation,Protein Structure, Secondary},
month = nov,
number = {4},
pages = {S116--26},
pmid = {16280617},
title = {{Counting out to the flexibility of molecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16280617},
volume = {2},
year = {2005}
}
@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{Craig2011,
abstract = {The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/  or  http://cpclab.uni-duesseldorf.de/downloads ).},
author = {Craig, Ian R and Pfleger, Christopher and Gohlke, Holger and Essex, Jonathan W and Spiegel, Katrin},
doi = {10.1021/ci200168b},
file = {:home/alex/Dokumente/Mendeley Desktop/Craig et al/Journal of chemical information and modeling/Craig et al. - 2011 - Pocket-space maps to identify novel binding-site conformations in proteins.pdf:pdf},
issn = {1549-960X},
journal = {Journal of chemical information and modeling},
month = oct,
number = {10},
pages = {2666--79},
pmid = {21910474},
title = {{Pocket-space maps to identify novel binding-site conformations in proteins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21910474},
volume = {51},
year = {2011}
}
@article{Hatch1975,
author = {Hatch, M D and Slack, C R},
doi = {10.1016/0076-6879(75)42117-6},
journal = {Methods in Enzymology},
pages = {212--219},
title = {{Pyruvate, P1 dikinase from leaves}},
volume = {42},
year = {1975}
}
@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,Pi Dikinase in Flaveria Species.pdf:pdf},
journal = {Plant Cell Physiol.},
keywords = {1,7,9,c 4,c 4 plants,catalyses,cold lability,ec 2,flaveria,ic carbon acceptor in,pi dikinase,pj dikinase,ppdk,pyruvate,slack and hatch 1967,the primary inorgan-,the synthesis of phosphoenolpyruvate},
number = {2},
pages = {295--297},
title = {{A Comparative Study of the Cold-Sensitivity of Pyruvate,Pi Dikinase in Flaveria Species}},
volume = {31},
year = {1990}
}
@article{Kang2005,
abstract = {We have isolated a floury endosperm-4 (flo4) rice mutant with a floury-white endosperm but a normal outer portion. Scanning electron microscopic analysis revealed that this abnormal endosperm consisted of loosely packed starch granules. The mutant phenotype was generated by T-DNA insertion into the fifth intron of the OsPPDKB gene encoding pyruvate orthophosphate dikinase (PPDK). Plants containing flo4-1 produced no OsPPDKB transcript or the OsPPDKB protein in their developing kernels and leaves. We obtained two additional alleles, flo4-2 and flo4-3, that also showed the same white-core endosperm phenotype. The flo4 kernels weighed about 6\% less than wild-type ones. Starch contents in both kernel types were similar, but the total protein content was slightly higher in the mutant kernels. Moreover, lipid contents were significantly increased in the flo4 kernels. Expression analyses demonstrated that the cytosolic mRNA of OsPPDKB was induced in the reproductive organs after pollination, and greatly increased until about 10 days after fertilization. This mRNA was localized mainly in the endosperm, aleurone, and scutellum of the developing kernel. Our results suggest that cytosolic PPDK functions in rice to modulate carbon metabolism during grain filling.},
author = {Kang, Hong-Gyu and Park, Sunhee and Matsuoka, Makoto and An, Gynheung},
doi = {10.1111/j.1365-313X.2005.02423.x},
file = {:home/alex/Dokumente/Mendeley Desktop/Kang et al/The Plant journal for cell and molecular biology/Kang et al. - 2005 - White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB).pdf:pdf},
issn = {0960-7412},
journal = {The Plant journal : for cell and molecular biology},
keywords = {Lipids,Lipids: biosynthesis,Mutagenesis, Insertional,Oryza sativa,Oryza sativa: enzymology,Oryza sativa: genetics,Oryza sativa: growth \& development,Phenotype,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: genetics,Pyruvate, Orthophosphate Dikinase: metabolism,Seeds,Seeds: genetics,Seeds: growth \& development,Starch,Starch: biosynthesis},
month = jun,
number = {6},
pages = {901--11},
pmid = {15941402},
title = {{White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15941402},
volume = {42},
year = {2005}
}
@article{Laskowski1993,
author = {Laskowski, R. A. and MacArthur, M. W. and Moss, D. S. and Thornton, J. M.},
doi = {10.1107/S0021889892009944},
issn = {00218898},
journal = {Journal of Applied Crystallography},
month = apr,
number = {2},
pages = {283--291},
title = {{PROCHECK: a program to check the stereochemical quality of protein structures}},
url = {http://scripts.iucr.org/cgi-bin/paper?S0021889892009944},
volume = {26},
year = {1993}
}
@article{Laskowski1996,
abstract = {The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.},
author = {Laskowski, RomanA. and Rullmann, J.AntoonC. and MacArthur, MalcolmW. and Kaptein, Robert and Thornton, JanetM.},
doi = {10.1007/BF00228148},
issn = {0925-2738},
journal = {Journal of Biomolecular NMR},
keywords = {Amino Acid Sequence,Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: genetics,Evaluation Studies as Topic,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,Models,Molecular,Molecular Sequence Data,Molecular Structure,Protein Structure,Proteins,Proteins: chemistry,Proteins: genetics,Quality Control,Reproducibility of Results,Secondary,Software,Solutions},
month = dec,
number = {4},
pages = {477--86},
pmid = {9008363},
title = {{AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9008363 http://www.springerlink.com/index/10.1007/BF00228148},
volume = {8},
year = {1996}
}
@article{Cornic2000,
author = {Cornic, G},
doi = {10.1016/S1360-1385(00)01625-3},
file = {:home/alex/Dokumente/Mendeley Desktop/Cornic/Trends in Plant Science/Cornic - 2000 - Drought stress inhibits photosynthesis by decreasing stomatal aperture \^{a}€“ not by affecting ATP synthesis.pdf:pdf},
issn = {13601385},
journal = {Trends in Plant Science},
keywords = {Drought stress,Photosynthesis,Stomata},
month = may,
number = {5},
pages = {187--188},
title = {{Drought stress inhibits photosynthesis by decreasing stomatal aperture \^{a}€“ not by affecting ATP synthesis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1360138500016253},
volume = {5},
year = {2000}
}
@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},
doi = {10.1007/s11038-006-9089-3},
issn = {0167-9295},
journal = {Earth, Moon, and Planets},
month = oct,
number = {1-4},
pages = {153--203},
title = {{5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)}},
url = {http://www.springerlink.com/index/10.1007/s11038-006-9089-3},
volume = {98},
year = {2006}
}
@article{Monod1965,
author = {Monod, Jacque and Wyman, Jeffries and Changeux, Jean-Pierre},
doi = {10.1016/S0022-2836(65)80285-6},
file = {:home/alex/Dokumente/Mendeley Desktop/Monod, Wyman, Changeux/Journal of Molecular Biology/Monod, Wyman, Changeux - 1965 - On the nature of allosteric transitions A plausible model.pdf:pdf},
issn = {00222836},
journal = {Journal of Molecular Biology},
keywords = {Folder - Allostery - Theory,Mechanism},
mendeley-tags = {Folder - Allostery - Theory,Mechanism},
month = may,
number = {1},
pages = {88--118},
shorttitle = {On the nature of allosteric transitions},
title = {{On the nature of allosteric transitions: A plausible model}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283665802856},
volume = {12},
year = {1965}
}
@book{Berg2007,
address = {M\"{u}nchen; Heidelberg},
author = {Berg, Jeremy and Stryer, Lubert and Tymoczko, John L},
edition = {6. Aufl.},
isbn = {9783827418005},
keywords = {Folder - Biochemie},
mendeley-tags = {Folder - Biochemie},
publisher = {Spektrum Akademischer Verlag},
title = {{Biochemie}},
year = {2007}
}
@article{Geourjon1995a,
abstract = {Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins. In this paper we report improvements brought about by predicting all the sequences of a set of aligned proteins belonging to the same family. This improved SOPM method (SOPMA) correctly predicts 69.5\% of amino acids for a three-state description of the secondary structure (alpha-helix, beta-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25\% identity) proteins. Joint prediction with SOPMA and a neural networks method (PHD) correctly predicts 82.2\% of residues for 74\% of co-predicted amino acids. Predictions are available by Email to deleage@ibcp.fr or on a Web page (http:@www.ibcp.fr/predict.html).},
author = {Geourjon, C. and Del\'{e}age, G.},
doi = {10.1093/bioinformatics/11.6.681},
issn = {0266-7061},
journal = {Computer applications in the biosciences : CABIOS},
keywords = {Amino Acid,Databases,Factual,Neural Networks (Computer),Protein Structure,Proteins,Proteins: chemistry,Secondary,Sequence Alignment,Sequence Alignment: methods,Sequence Alignment: statistics \& numerical data,Sequence Homology,Software},
month = dec,
number = {6},
pages = {681--4},
pmid = {8808585},
title = {{SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments.}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/11.6.681 http://www.ncbi.nlm.nih.gov/pubmed/8808585},
volume = {11},
year = {1995}
}
@article{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}
}
@book{Madigan2009,
address = {München [u.a.]},
author = {Madigan, Michael and Martinko, John M},
edition = {11., aktua},
isbn = {9783827373588},
keywords = {Folder - Mikrobiologie},
mendeley-tags = {Folder - Mikrobiologie},
publisher = {Pearson Studium},
title = {{Brock - Mikrobiologie}},
year = {2009}
}
@book{Lakowicz2006,
address = {Boston, MA},
editor = {Lakowicz, Joseph R.},
isbn = {978-0-387-31278-1},
publisher = {Springer US},
title = {{Principles of Fluorescence Spectroscopy}},
url = {http://www.springerlink.com/index/10.1007/978-0-387-46312-4},
year = {2006}
}
@article{Orgel2008,
author = {Orgel, Leslie E.},
doi = {10.1371/journal.pbio.0060018},
file = {:home/alex/Dokumente/Mendeley Desktop/Orgel/PLoS Biology/Orgel - 2008 - The Implausibility of Metabolic Cycles on the Prebiotic Earth.pdf:pdf},
issn = {1544-9173},
journal = {PLoS Biology},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
number = {1},
pages = {e18},
title = {{The Implausibility of Metabolic Cycles on the Prebiotic Earth}},
url = {http://biology.plosjournals.org/perlserv/?request=get-document\&doi=10.1371/journal.pbio.0060018},
volume = {6},
year = {2008}
}
@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{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{Lazcano2008,
author = {Lazcano, A.},
file = {:home/alex/Dokumente/Mendeley Desktop/Lazcano/Chemistry \& Biodiversity/Lazcano - 2008 - What Is Life.pdf:pdf},
journal = {Chemistry \& Biodiversity},
number = {1},
pages = {1--15},
title = {{What Is Life?}},
volume = {5},
year = {2008}
}
@article{LeslieE.2004,
author = {{Leslie E.}, Orgel},
doi = {10.1080/10409230490460765},
file = {:home/alex/Dokumente/Mendeley Desktop/Leslie E/Critical Reviews in Biochemistry and Molecular Biology/Leslie E. - 2004 - Prebiotic Chemistry and the Origin of the RNA World.pdf:pdf},
issn = {1040-9238},
journal = {Critical Reviews in Biochemistry and Molecular Biology},
month = jan,
number = {2},
pages = {99--123},
title = {{Prebiotic Chemistry and the Origin of the RNA World}},
url = {http://informahealthcare.com/doi/abs/10.1080/10409230490460765},
volume = {39},
year = {2004}
}
@article{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{Tsai2009,
abstract = {Allostery has come of age; the number, breadth and functional roles of documented protein allostery cases are rising quickly. Since all dynamic proteins are potentially allosteric and allostery plays crucial roles in all cellular pathways, sorting and classifying allosteric mechanisms in proteins should be extremely useful in understanding and predicting how the signals are regulated and transmitted through the dynamic multi-molecular cellular organizations. Classification organizes the complex information thereby unraveling relationships and patterns in molecular activation and repression. In signaling, current classification schemes consider classes of molecules according to their functions; for example, epinephrine and norepinephrine secreted by the central nervous system are classified as neurotransmitters. Other schemes would account for epinephrine when secreted by the adrenal medulla to be hormone-like. Yet, such classifications account for the global function of the molecule; not for the molecular mechanism of how the signal transmission initiates and how it is transmitted. Here we provide a unified view of allostery and the first classification framework. We expect that a classification scheme would assist in comprehension of allosteric mechanisms, in prediction of signaling on the molecular level, in better comprehension of pathways and regulation of the complex signals, in translating them to the cascading events, and in allosteric drug design. We further provide a range of examples illustrating mechanisms in protein allostery and their classification from the cellular functional standpoint.},
author = {Tsai, Chung-Jung and {Del Sol}, Antonio and Nussinov, Ruth},
doi = {10.1039/b819720b},
file = {:home/alex/Dokumente/Mendeley Desktop/Tsai, Del Sol, Nussinov/Molecular bioSystems/Tsai, Del Sol, Nussinov - 2009 - Protein allostery, signal transmission and dynamics a classification scheme of allosteric mechanisms.b819720b:b819720b},
issn = {1742-2051},
journal = {Molecular bioSystems},
keywords = {Allosteric Regulation,Animals,Folder - Allostery - Theory,Humans,Mechanism,Signal Transduction,Thermodynamics},
mendeley-tags = {Folder - Allostery - Theory,Mechanism},
month = mar,
number = {3},
pages = {207--16},
pmid = {19225609},
shorttitle = {Protein allostery, signal transmission and dynamic},
title = {{Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms.}},
url = {http://xlink.rsc.org/?DOI=b819720b http://www.ncbi.nlm.nih.gov/pubmed/19225609},
volume = {5},
year = {2009}
}
@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},
issn = {0022-2836},
journal = {Journal of Molecular Biology},
keywords = {Amino Acids,Astronomical Phenomena,Astronomy,Biological Evolution,Folder - Vortrag RNA-Welt,Genetic Code,Geological Phenomena,Geology,Macromolecular Substances,Nucleic Acids,Nucleotides,Paleontology,RNA- Transfer},
mendeley-tags = {Amino Acids,Astronomical Phenomena,Astronomy,Biological Evolution,Folder - Vortrag RNA-Welt,Genetic Code,Geological Phenomena,Geology,Macromolecular Substances,Nucleic Acids,Nucleotides,Paleontology,RNA- Transfer},
month = dec,
number = {3},
pages = {381--393},
title = {{Evolution of the genetic apparatus}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/5718557 http://www.sciencedirect.com/science?\_ob=MImg\&\_imagekey=B6WK7-4DM29RS-BJ-1\&\_cdi=6899\&\_user=2665780\&\_pii=0022283668903938\&\_origin=\&\_coverDate=12/28/1968\&\_sk=999619996\&view=c\&wchp=dGLbVzW-zSkWl\&md5=e474c541454450eb7df9ef6da762f505\&ie=/sdarticle.pdf},
volume = {38},
year = {1968}
}
@inproceedings{Joyce2009,
author = {Joyce, G. F},
file = {:home/alex/Dokumente/Mendeley Desktop/Joyce/Unknown/Joyce - 2009 - Evolution in an RNA World.pdf:pdf},
keywords = {Folder - Vortrag RNA-Welt},
mendeley-tags = {Folder - Vortrag RNA-Welt},
pages = {17},
title = {{Evolution in an RNA World}},
volume = {74},
year = {2009}
}
@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}
}
@misc{Rullmann1996,
author = {Rullmann, J A C},
publisher = {Department of NMR Spectroscopy, Utrecht University},
title = {{AQUA}},
year = {1996}
}
@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},
doi = {10.1074/jbc.273.15.9119},
file = {:home/alex/Dokumente/Mendeley Desktop/Mellet/Journal of Biological Chemistry/Mellet - 1998 - Stopped Flow Fluorescence Energy Transfer Measurement of the Rate Constants Describing the Reversible Formation and the Irreversible Rearrangement of the Elastase-alpha 1-Proteinase Inhibitor Complex.pdf:pdf},
issn = {00219258},
journal = {Journal of Biological Chemistry},
keywords = {Animals,Chemical,Energy Transfer,Fluorescein-5-isothiocyanate,Fluorescence,Fluorescent Dyes,Kinetics,Leukocyte Elastase,Leukocyte Elastase: chemistry,Leukocyte Elastase: metabolism,Models,Pancreas,Pancreas: enzymology,Proteins,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,Serpins,Serpins: metabolism,Serpins: pharmacology,Spectrometry,Swine,Time Factors,alpha 1-Antitrypsin,alpha 1-Antitrypsin: chemistry,alpha 1-Antitrypsin: metabolism},
month = apr,
number = {15},
pages = {9119--9123},
pmid = {9535901},
title = {{Stopped Flow Fluorescence Energy Transfer Measurement of the Rate Constants Describing the Reversible Formation and the Irreversible Rearrangement of the Elastase-alpha 1-Proteinase Inhibitor Complex}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9535901 http://www.jbc.org/cgi/doi/10.1074/jbc.273.15.9119},
volume = {273},
year = {1998}
}
@article{Larkin2007,
abstract = {SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/},
author = {Larkin, M A and Blackshields, G and Brown, N P and Chenna, R and McGettigan, P A and McWilliam, H and Valentin, F and Wallace, I M and Wilm, A and Lopez, R and Thompson, J D and Gibson, T J and Higgins, D G},
doi = {10.1093/bioinformatics/btm404},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Algorithms,Amino Acid Sequence,Cluster Analysis,Computer Graphics,Molecular Sequence Data,Programming Languages,Protein,Protein: methods,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,User-Computer Interface},
month = nov,
number = {21},
pages = {2947--8},
pmid = {17846036},
title = {{Clustal W and Clustal X version 2.0.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17846036},
volume = {23},
year = {2007}
}
@article{Wang1988,
abstract = {The kinetic mechanism of pyruvate phosphate dikinase (PPDK) from Bacteroides symbiosus was investigated with several different kinetic diagnostics. Initial velocity patterns were intersecting for AMP/PPi and ATP/Pi substrate pairs and parallel for all other substrate pairs. PPDK was shown to catalyze [14C]pyruvate in equilibrium phosphoenolpyruvate (PEP) exchange in the absence of cosubstrates, [14C]AMP in equilibrium ATP exchange in the presence of Pi/PPi but not in their absence, and [32P]Pi in equilibrium PPi exchange in the presence of ATP/AMP but not in their absence. The enzyme was also shown, by using [alpha beta-18O, beta, beta-18O2]ATP and [beta gamma-18O, gamma, gamma, gamma-18O3]ATP and 31P NMR techniques, to catalyze exchange in ATP between the alpha beta-bridge oxygen and the alpha-P nonbridge oxygen and also between the beta gamma-bridge oxygen and the beta-P nonbridge oxygen. The exchanges were catalyzed by PPDK in the presence of Pi but not in its absence. These results were interpreted to support a bi(ATP,Pi) bi(AMP,PPi) uni(pyruvate) uni(PEP) mechanism. AMP and Pi binding order was examined by carrying out dead-end inhibition studies. The dead-end inhibitor adenosine 5'-monophosphorothioate (AMPS) was found to be competitive vs AMP, noncompetitive vs PPi, and uncompetitive vs PEP. The dead-end inhibitor imidodiphosphate (PNP) was found to be competitive vs PPi, uncompetitive vs AMP, and uncompetitive vs PEP. These results showed that AMP binds before PPi. The ATP and Pi binding order was studied by carrying out inhibition, positional isotope exchange, and alternate substrate studies.(ABSTRACT TRUNCATED AT 250 WORDS)},
author = {Wang, Hsuei Chin and Ciskanik, Lawrence and Dunaway-Mariano, Debra and {Von der Saal}, Wolfgang and Villafranca, Joseph J},
doi = {10.1021/bi00402a020},
issn = {0006-2960},
journal = {Biochemistry},
keywords = {Adenine Nucleotides,Adenine Nucleotides: metabolism,Adenine Nucleotides: pharmacology,Bacteroides,Bacteroides: enzymology,Carbon Radioisotopes,Kinetics,Magnetic Resonance Spectroscopy,Magnetic Resonance Spectroscopy: methods,Mathematics,Orthophosphate Dikinase,Orthophosphate Dikinase: isolation \& purification,Orthophosphate Dikinase: metabolism,Phosphates,Phosphates: pharmacology,Phosphorus Radioisotopes,Phosphotransferases,Phosphotransferases: metabolism,Pyruvate,purification},
mendeley-tags = {purification},
month = jan,
number = {2},
pages = {625--633},
pmid = {2831971},
title = {{Investigations of the partial reactions catalyzed by pyruvate phosphate dikinase}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2831971 http://pubs.acs.org/doi/abs/10.1021/bi00402a020},
volume = {27},
year = {1988}
}
@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{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{Kang2002,
abstract = {Coomassie Brilliant Blue (CBB) is a dye commonly used for the visualization of proteins separated by SDS-PAGE, offering a simple staining procedure and high quantitation. Furthermore, it is completely compatible with mass spectrometric protein identification. But despite these advantages, CBB is regarded to be less sensitive than silver or fluorescence stainings and therefore rarely used for the detection of proteins in analytical gel-based proteomic approaches. Several improvements of the original Coomassie protocol(1) have been made to increase the sensitivity of CBB. Two major modifications were introduced to enhance the detection of low-abundant proteins by converting the dye molecules into colloidal particles: In 1988, Neuhoff and colleagues applied 20\% methanol and higher concentrations of ammonium sulfate into the CBB G-250 based staining solution(2), and in 2004 Candiano et al. established Blue Silver using CBB G-250 with phosphoric acid in the presence of ammonium sulfate and methanol(3). Nevertheless, all these modifications just allow a detection of approximately 10 ng protein. A widely fameless protocol for colloidal Coomassie staining was published by Kang et al. in 2002 where they modified Neuhoff's colloidal CBB staining protocol regarding the complexing substances. Instead of ammonium sulfate they used aluminum sulfate and methanol was replaced by the less toxic ethanol(4). The novel aluminum-based staining in Kang's study showed superior sensitivity that detects as low as 1 ng/band (phosphorylase b) with little sensitivity variation depending on proteins. Here, we demonstrate application of Kang's protocol for fast and sensitive colloidal Coomassie staining of proteins in analytical purposes. We will illustrate the quick and easy protocol using two-dimensional gels routinely performed in our working group.},
author = {Kang, D and Gho, YS},
doi = {10.5012/bkcs.2002.23.11.1511},
file = {:home/alex/Dokumente/Mendeley Desktop/Kang, Gho/Bulletin of the Korean Chemical Society/Kang, Gho - 2002 - Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis.pdf:pdf},
issn = {0253-2964},
journal = {Bulletin of the Korean Chemical Society},
keywords = {Acrylic Resins,Acrylic Resins: chemistry,Colloids,Colloids: chemistry,Electrophoresis,Gel,Indicators and Reagents,Indicators and Reagents: chemistry,Proteins,Proteins: analysis,Proteins: chemistry,Rosaniline Dyes,Rosaniline Dyes: chemistry,Sensitivity and Specificity,Staining and Labeling,Staining and Labeling: methods,Two-Dimensional,Two-Dimensional: methods},
month = nov,
number = {11},
pages = {1511--1512},
title = {{Highly Sensitive and Fast Protein Detection with Coomassie Brilliant Blue in Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis}},
url = {http://koreascience.or.kr/journal/view.jsp?issn=0253-2964\&vol=23\&no=11\&sp=1511},
volume = {23},
year = {2002}
}
@article{Nechushtai2011a,
abstract = {Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.},
author = {Nechushtai, Rachel and Lammert, Heiko and Michaeli, Dorit and Eisenberg-Domovich, Yael and Zuris, John A and Luca, Maria A and Capraro, Dominique T and Fish, Alex and Shimshon, Odelia and Roy, Melinda and Schug, Alexander and Whitford, Paul C and Livnah, Oded and Onuchic, Jos\'{e} N and Jennings, Patricia A},
doi = {10.1073/pnas.1019502108},
file = {:home/alex/Dokumente/Mendeley Desktop/Nechushtai et al/Proceedings of the National Academy of Sciences of the United States of America/Nechushtai et al. - 2011 - Allostery in the ferredoxin protein motif does not involve a conformational switch.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Allosteric Regulation,Allosteric Regulation: physiology,Amino Acid Motifs,Ferredoxins,Ferredoxins: chemistry,Ferredoxins: genetics,Ferredoxins: metabolism,Humans,Iron,Iron: chemistry,Iron: metabolism,Models,Molecular,Mutation,Protein Folding,Protein Stability,Protein Structure,Sulfur,Sulfur: chemistry,Sulfur: metabolism,Tertiary},
month = feb,
number = {6},
pages = {2240--5},
pmid = {21266547},
title = {{Allostery in the ferredoxin protein motif does not involve a conformational switch.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=pmcentrez\&rendertype=abstract},
volume = {108},
year = {2011}
}
@article{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},
doi = {10.1016/j.bmcl.2008.08.061},
file = {:home/alex/Dokumente/Mendeley Desktop/Guckian et al/Bioorganic \& medicinal chemistry letters/Guckian et al. - 2008 - Design and synthesis of a series of meta aniline-based LFA-1 ICAM inhibitors.pdf:pdf},
issn = {1464-3405},
journal = {Bioorganic \& medicinal chemistry letters},
keywords = {Administration, Oral,Aniline Compounds,Aniline Compounds: chemical synthesis,Aniline Compounds: chemistry,Aniline Compounds: pharmacology,Animals,Chemistry, Pharmaceutical,Chemistry, Pharmaceutical: methods,Combinatorial Chemistry Techniques,Crystallography, X-Ray,Drug Design,Inhibitory Concentration 50,Intercellular Adhesion Molecule-1,Intercellular Adhesion Molecule-1: drug effects,Lymphocyte Function-Associated Antigen-1,Lymphocyte Function-Associated Antigen-1: chemistr,Molecular Conformation,Rats,Stereoisomerism},
month = oct,
number = {19},
pages = {5249--51},
pmid = {18778938},
title = {{Design and synthesis of a series of meta aniline-based LFA-1 ICAM inhibitors.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18778938},
volume = {18},
year = {2008}
}
@article{Huang2008,
abstract = {Oxygen deficit is an important abiotic stress influencing plants, because this condition results in an 'energy crisis'. Most species only survive short periods of anoxia, but several wetland species tolerate prolonged anoxia. Transcriptomic and proteomic studies, using anoxia-tolerant rice and anoxia-intolerant Arabidopsis, have provided evidence for the selective adoption of pyrophosphate (PPi) over ATP as high-energy donor molecules, which may contribute to anoxia tolerance. The use of PPi in some tolerant plant species is similar to that observed in many anaerobic prokaryotes. Investigations are being performed to better understand the origin and regulation of reversible PPi-dependent glycolytic enzymes such as cytosolic pyruvate phosphate dikinase, as well as PPi-consuming enzymes, which are engaged during the anoxic energy crisis. This will be crucial in unraveling this currency switch and its contribution to anoxia tolerance.},
author = {Huang, Shaobai and Colmer, Timothy D and Millar, a Harvey},
doi = {10.1016/j.tplants.2008.02.007},
file = {:home/alex/Dokumente/Mendeley Desktop/Huang, Colmer, Millar/Trends in plant science/Huang, Colmer, Millar - 2008 - Does anoxia tolerance involve altering the energy currency towards PPi.pdf:pdf},
issn = {1360-1385},
journal = {Trends in plant science},
keywords = {Adaptation, Physiological,Adenosine Triphosphate,Adenosine Triphosphate: metabolism,Anaerobiosis,Anaerobiosis: physiology,Diphosphates,Diphosphates: metabolism,Eukaryotic Cells,Eukaryotic Cells: metabolism,Glycolysis,Glycolysis: physiology,Oxygen,Oxygen: physiology,Plants,Plants: enzymology,Plants: metabolism,Prokaryotic Cells,Prokaryotic Cells: metabolism,Pyruvate, Orthophosphate Dikinase,Pyruvate, Orthophosphate Dikinase: metabolism},
month = may,
number = {5},
pages = {221--7},
pmid = {18439868},
title = {{Does anoxia tolerance involve altering the energy currency towards PPi?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18439868},
volume = {13},
year = {2008}
}
@article{Nechushtai2011,
abstract = {Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.},
author = {Nechushtai, Rachel and Lammert, Heiko and Michaeli, Dorit and Eisenberg-Domovich, Yael and Zuris, John A and Luca, Maria A and Capraro, Dominique T and Fish, Alex and Shimshon, Odelia and Roy, Melinda and Schug, Alexander and Whitford, Paul C and Livnah, Oded and Onuchic, Jos\'{e} N and Jennings, Patricia A},
doi = {10.1073/pnas.1019502108},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Allosteric Regulation,Allosteric Regulation: physiology,Amino Acid Motifs,Ferredoxins,Ferredoxins: chemistry,Ferredoxins: genetics,Ferredoxins: metabolism,Humans,Iron,Iron: chemistry,Iron: metabolism,Models,Molecular,Mutation,Protein Folding,Protein Stability,Protein Structure,Sulfur,Sulfur: chemistry,Sulfur: metabolism,Tertiary},
month = feb,
number = {6},
pages = {2240--5},
pmid = {21266547},
title = {{Allostery in the ferredoxin protein motif does not involve a conformational switch.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3038707\&tool=pmcentrez\&rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Komar1999,
abstract = {To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site-directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell-free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20\% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding.},
author = {Komar, Anton a and Lesnik, Thierry and Reiss, Claude},
doi = {10.1016/S0014-5793(99)01566-5},
file = {:home/alex/Dokumente/Mendeley Desktop/Komar, Lesnik, Reiss/FEBS Letters/Komar, Lesnik, Reiss - 1999 - Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation.pdf:pdf},
issn = {00145793},
journal = {FEBS Letters},
keywords = {Amino Acid Sequence,Base Sequence,Chloramphenicol O-Acetyltransferase,Chloramphenicol O-Acetyltransferase: genetics,Chloramphenicol O-Acetyltransferase: metabolism,Codon,Escherichia coli,Escherichia coli: metabolism,Molecular Sequence Data,Mutagenesis,Plasmids,Plasmids: metabolism,Protein Biosynthesis,Protein Folding,Ribosomes,Ribosomes: metabolism,Time Factors},
month = dec,
number = {3},
pages = {387--391},
pmid = {10622731},
title = {{Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10622731 http://linkinghub.elsevier.com/retrieve/pii/S0014579399015665},
volume = {462},
year = {1999}
}
@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},
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{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{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{Ernst2008,
author = {Ernst, R. and Kueppers, P. and Klein, C. M. and Schwarzmueller, T. and Kuchler, K. and Schmitt, L.},
doi = {10.1073/pnas.0800191105},
file = {:home/alex/Dokumente/Mendeley Desktop/Ernst et al/Proceedings of the National Academy of Sciences/Ernst et al. - 2008 - A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Folder - Biochemie},
mendeley-tags = {Folder - Biochemie},
month = mar,
number = {13},
pages = {5069--5074},
title = {{A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0800191105},
volume = {105},
year = {2008}
}
@book{Purves2006a,
address = {M\"{u}nchen; Heidelberg},
author = {Purves, William K and Sadava, David and Orians, Gordon H and Heller, H. Craig},
edition = {7},
isbn = {9783827420077},
keywords = {Folder - Allgemein},
mendeley-tags = {Folder - Allgemein},
month = aug,
publisher = {Spektrum Akademischer Verlag},
title = {{Biologie}},
year = {2006}
}
@article{Rosche1990,
abstract = {We have isolated and characterized cDNA clones encoding the entire precursor for the leafspecific isoform of pyruvate, orthophosphate dikinase (PPDK) from the dicotyledonous C4 plant Flaveria trinervia. The deduced amino acid sequence reveals a high degree of similarity to the corresponding maize protein indicating a common evolutionary basis. However, no significant similarities are apparent upon comparison of the putative transit peptides. The implications of this divergence are discussed with respect to the evolution of PPDK genes.},
author = {Rosche, Elke and Westhoff, Peter},
file = {:home/alex/Dokumente/Mendeley Desktop/Rosche, Westhoff/FEBS letters/Rosche, Westhoff - 1990 - Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.pdf:pdf},
issn = {0014-5793},
journal = {FEBS letters},
keywords = {Amino Acid Sequence,Base Sequence,Cloning,DNA,DNA: genetics,DNA: isolation \& purification,Molecular,Molecular Sequence Data,Nucleic Acid,Orthophosphate Dikinase,Orthophosphate Dikinase: genetics,Plants,Plants: enzymology,Plants: genetics,Protein Conformation,Pyruvate,Restriction Mapping,Sequence Homology},
month = oct,
number = {1-2},
pages = {116--21},
pmid = {2172023},
title = {{Primary structure of pyruvate, orthophosphate dikinase in the dicotyledonous C4 plant Flaveria trinervia.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2172023},
volume = {273},
year = {1990}
}
@article{Sievers2011,
abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.},
author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S\"{o}ding, Johannes and Thompson, Julie D and Higgins, Desmond G},
doi = {10.1038/msb.2011.75},
issn = {1744-4292},
journal = {Molecular systems biology},
keywords = {Algorithms,Amino Acid Sequence,Base Sequence,Data Mining,Data Mining: methods,Databases,Factual,Molecular Sequence Data,Protein,Protein: methods,Proteins,Proteins: analysis,Proteins: chemistry,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis,Software,Systems Biology,Systems Biology: instrumentation,Systems Biology: methods},
month = jan,
pages = {539},
pmid = {21988835},
title = {{Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21988835},
volume = {7},
year = {2011}
}
@misc{TheMendeleySupportTeam2011,
abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.},
address = {London},
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{MadisonL.Sheely1932,
author = {{Madison L. Sheely}},
file = {:home/alex/Dokumente/Mendeley Desktop/Madison L. Sheely/Industrial an Engineering Chemistry/Madison L. Sheely - 1932 - Glycerol Viscosity Tables.pdf:pdf},
journal = {Industrial an Engineering Chemistry},
month = apr,
number = {24},
pages = {1060--1063},
title = {{Glycerol Viscosity Tables}},
volume = {9},
year = {1932}
}
@article{Balzi1994,
abstract = {The complete sequence of the pleiotropic drug resistance gene PDR5 from Saccharomyces cerevisiae is reported and analyzed. PDR5 encodes a 160-kDa protein with a predicted duplicated six membrane-span domain and a repeated putative ATP-binding domain. PDR5 shares this structural feature with the mammalian multidrug resistance pumps as well as the functional capacity of conferring resistance to various inhibitors upon amplification (Leppert, G., McDevitt, R., Falco, S. C., Van Dyk, T. K., Ficke, M. B., and Golin, J. (1990) Genetics 125, 13-20). The yeast PDR5 is thus a new member of the ABC (ATP-binding cassette) protein superfamily. Mutations in another yeast pleiotropic drug resistance gene, PDR1, encoding a putative transcription regulator (Balzi, E., Chen, W., Ulaszewski, S., Capieaux, E., and Goffeau, A. (1987) J. Biol. Chem. 262, 16871-16879), increase markedly the mRNA levels of the PDR5 and STE6 genes. The multidrug resistance mutations pdr1-3 and pdr1-6 also lead to considerable overexpression of the PDR5 plasma membrane protein.},
author = {Balzi, E and Wang, M and Leterme, S and {Van Dyck}, L and Goffeau, A},
file = {:home/alex/Dokumente/Mendeley Desktop/Balzi et al/The Journal of Biological Chemistry/Balzi et al. - 1994 - PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of Biological Chemistry},
keywords = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic},
mendeley-tags = {ATP-Binding Cassette Transporters,Amino Acid Sequence,Animals,Base Sequence,Carrier Proteins,Cloning- Molecular,DNA-Binding Proteins,Drug Resistance- Microbial,Folder - Mikrobiologie,Fungal Proteins,Gene Expression,Genes- Fungal,Glycoproteins,Humans,Membrane Proteins,Molecular Sequence Data,Molecular Weight,Mutagenesis,Protein Structure- Secondary,RNA- Messenger,Restriction Mapping,Saccharomyces cerevisiae,Saccharomyces cerevisiae Proteins,Sequence Homology- Amino Acid,Terminator Regions- Genetic,Trans-Activators,Transcription Factors,Transcription- Genetic},
month = jan,
number = {3},
pages = {2206--2214},
title = {{PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8294477},
volume = {269},
year = {1994}
}
@article{Studies1967,
abstract = {1. The activity per unit of chlorophyll of certain carboxylases, and of other enzymes involved in photosynthesis, was determined in leaf extracts of the tropical grasses, sugar-cane, maize and sorghum, and compared with the activities for wheat, oat and silver-beet. Maximum rates of photosynthetic carbon dioxide uptake were also measured for comparison with enzyme activities. 2. Phosphopyruvate carboxylase activity was about 60 times greater in the tropical grasses than in wheat, oat and silver-beet and was severalfold higher than the rates of photosynthetic carbon dioxide uptake. Most of the enzyme was located in the chloroplast fraction of cell extracts. 3. Phosphopyruvate carboxylase was apparently the major photosynthetic carbon dioxide-fixing enzyme in the tropical grasses, although malic enzyme may contribute to a lesser extent. 4. Tropical grasses contained less than one-tenth of the ribulose diphosphate carboxylase activity present in wheat, oat and silver-beet. For the tropical grasses this activity, determined with a saturating concentration of bicarbonate, was approx. 10\% of the rate of photosynthesis. 5. The fraction-1 protein content of leaf extracts paralleled the ribulose diphosphate carboxylase activity. 6. In contrast, the activity of several other enzymes of the Calvin cycle was similar in the different species examined.},
author = {Slack, C R and Hatch, M D},
file = {:home/alex/Dokumente/Mendeley Desktop/Slack, Hatch/The Biochemical journal/Slack, Hatch - 1967 - Comparative studies on the activity of carboxylases and other enzymes in relation to the new pathway of photosynthetic carbon dioxide fixation in tropical grasses.pdf:pdf},
issn = {0264-6021},
journal = {The Biochemical journal},
keywords = {Acid Phosphatase,Acid Phosphatase: metabolism,Alcohol Oxidoreductases,Alcohol Oxidoreductases: metabolism,Aspartate Aminotransferases,Aspartate Aminotransferases: metabolism,Carbon Dioxide,Carbon Dioxide: metabolism,Carboxy-Lyases,Carboxy-Lyases: metabolism,Cereals,Cereals: metabolism,Fructose-Bisphosphatase,Fructose-Bisphosphatase: metabolism,Glyceraldehyde-3-Phosphate Dehydrogenases,Glyceraldehyde-3-Phosphate Dehydrogenases: metabol,Glycoside Hydrolases,Glycoside Hydrolases: metabolism,Malate Dehydrogenase,Malate Dehydrogenase: metabolism,Photosynthesis,Poaceae,Poaceae: enzymology,Poaceae: metabolism,Triticum,Triticum: metabolism,Ultracentrifugation,Zea mays,Zea mays: metabolism},
month = jun,
number = {3},
pages = {660--5},
pmid = {4292834},
title = {{Comparative studies on the activity of carboxylases and other enzymes in relation to the new pathway of photosynthetic carbon dioxide fixation in tropical grasses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1270465 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1270465\&tool=pmcentrez\&rendertype=abstract},
volume = {103},
year = {1967}
}
@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{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},
journal = {Nobel lectures in chemistry, 1922-1941},
pages = {165},
title = {{On haemin and the relationships between haemin and chlorophyll}},
year = {1999}
}
@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},
journal = {Geochimica et cosmochimica acta},
number = {5},
pages = {1087--1097},
shorttitle = {Thiols in hydrothermal solution},
title = {{Thiols in hydrothermal solution: standard partial molal properties and their role in the organic geochemistry of hydrothermal environments3}},
volume = {68},
year = {2004}
}
@article{Barford1994,
abstract = {Protein tyrosine phosphatases (PTPs) constitute a family of receptor-like and cytoplasmic signal transducing enzymes that catalyze the dephosphorylation of phosphotyrosine residues and are characterized by homologous catalytic domains. The crystal structure of a representative member of this family, the 37-kilodalton form (residues 1 to 321) of PTP1B, has been determined at 2.8 A resolution. The enzyme consists of a single domain with the catalytic site located at the base of a shallow cleft. The phosphate recognition site is created from a loop that is located at the amino-terminus of an alpha helix. This site is formed from an 11-residue sequence motif that is diagnostic of PTPs and the dual specificity phosphatases, and that contains the catalytically essential cysteine and arginine residues. The position of the invariant cysteine residue within the phosphate binding site is consistent with its role as a nucleophile in the catalytic reaction. The structure of PTP1B should serve as a model for other members of the PTP family and as a framework for understanding the mechanism of tyrosine dephosphorylation.},
author = {Barford, D and Flint, A J and Tonks, N K},
doi = {10.1126/science.8128219},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
keywords = {Amino Acid Sequence,Binding Sites,Computer Graphics,Crystallography,Humans,Models,Molecular,Molecular Sequence Data,Phosphates,Phosphates: metabolism,Protein Conformation,Protein Folding,Protein Structure,Protein Tyrosine Phosphatases,Protein Tyrosine Phosphatases: chemistry,Protein Tyrosine Phosphatases: isolation \& purific,Protein Tyrosine Phosphatases: metabolism,Secondary,Substrate Specificity,Tungsten Compounds,Tungsten Compounds: metabolism,X-Ray},
month = mar,
number = {5152},
pages = {1397--404},
pmid = {8128219},
title = {{Crystal structure of human protein tyrosine phosphatase 1B.}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.8128219 http://www.ncbi.nlm.nih.gov/pubmed/8128219},
volume = {263},
year = {1994}
}
@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{McComb1976,
abstract = {The molar absorptivity of NADH at 340 nm has been determined by an indirect procedure in which high-purity glucose is phosphorylated by ATP in the presence of hexokinase, coupled to oxidation of the glucose-6-phosphate by NAD+ in the presence of glucose-6-phosphate dehydrogenase. The average value from 85 independent determinations is 6317 liter mol-1 cm-1 at 25 degrees C and pH 7.8. The overall uncertainty is -4.0 to +5.5 ppt (6292 to 6352 liter mol-1 cm-1), based on a standard error of the mean of 0.48 ppt and an estimate of systematic error of -2.6 to +4.1 ppt. Effects of pH, buffer, and temperature on the molar absorptivity are also reported.},
author = {McComb, R B and Bond, L W and Burnett, R W and Keech, R C and Bowers, G N},
file = {:home/alex/Dokumente/Mendeley Desktop/McComb et al/Clinical chemistry/McComb et al. - 1976 - Determination of the molar absorptivity of NADH.pdf:pdf},
issn = {0009-9147},
journal = {Clinical chemistry},
keywords = {Absorption,Adenosine Triphosphate,Evaluation Studies as Topic,Glucose,Glucosephosphate Dehydrogenase,Hexokinase,Hydrogen-Ion Concentration,NAD,NAD: analysis,Osmolar Concentration,Oxidation-Reduction,Spectrophotometry,Temperature,Ultraviolet},
month = mar,
number = {2},
pages = {141--50},
pmid = {2388},
title = {{Determination of the molar absorptivity of NADH.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2388},
volume = {22},
year = {1976}
}
@article{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},
doi = {10.1128/AEM.02479-06},
file = {:home/alex/Dokumente/Mendeley Desktop/Motti et al/Applied and environmental microbiology/Motti et al. - 2007 - Screening marine fungi for inhibitors of the C4 plant enzyme pyruvate phosphate dikinase unguinol as a potential novel herbicide candidate.pdf:pdf},
issn = {0099-2240},
journal = {Applied and environmental microbiology},
keywords = {18S,18S: genetics,3-Ring,3-Ring: isolation \& purification,3-Ring: pharmacology,DNA,Digitaria,Digitaria: drug effects,Enzyme Inhibitors,Enzyme Inhibitors: isolation \& purification,Enzyme Inhibitors: pharmacology,Fungal,Fungal: chemistry,Fungal: genetics,Fungi,Fungi: classification,Fungi: isolation \& purification,Fungi: metabolism,Herbicides,Herbicides: isolation \& purification,Herbicides: pharmacology,Heterocyclic Compounds,Hordeum,Hordeum: drug effects,Kinetics,Molecular Sequence Data,Orthophosphate Dikinase,Orthophosphate Dikinase: antagonists \& inhibitors,Phylogeny,Protein Binding,Pyruvate,RNA,Ribosomal,Ribosomal Spacer,Ribosomal Spacer: chemistry,Ribosomal Spacer: genetics,Ribosomal: chemistry,Ribosomal: genetics,Sequence Analysis},
month = mar,
number = {6},
pages = {1921--7},
pmid = {17220253},
title = {{Screening marine fungi for inhibitors of the C4 plant enzyme pyruvate phosphate dikinase: unguinol as a potential novel herbicide candidate.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1828816\&tool=pmcentrez\&rendertype=abstract},
volume = {73},
year = {2007}
}
@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{Salahas1990,
abstract = {Phosphoenolpyruvate carboxylase (EC 4.1.1.31), used as a coupling enzyme in the assay of the pyruvate, orthophosphate dikinase (EC 2.7.9.1) forward reaction, is a serious limiting factor for the overall rate when added at a level of 0.2–0.3 unit/ml of assay medium. Nonlimiting assay conditions are obtained by either increasing the level of the coupling enzyme to 3 units/ml or adding 6mM glucose-6-phosphate as an activator/stabilizer of phosphoenolpyruvate carboxylase.},
author = {Salahas, G and Manetas, Y},
doi = {10.1007/BF00032598},
file = {:home/alex/Dokumente/Mendeley Desktop/Salahas, Manetas/Photosynthesis Research/Salahas, Manetas - 1990 - Assaying for pyruvate, orthophosphate dikinase activity Necessary precautions with.pdf:pdf},
journal = {Photosynthesis Research},
keywords = {assaying technique,dikinase,glucose-6-phosphate,orthophosphate,phosphoenolpyruvate carboxylase,pi,pyruvate},
number = {2},
pages = {183--188},
title = {{Assaying for pyruvate, orthophosphate dikinase activity: Necessary precautions with}},
url = {http://www.springerlink.com/content/rkt60781642pw447/},
volume = {24},
year = {1990}
}
@article{Lawrence2009,
author = {Lawrence, Ann-Marie and Besir, H\"{u}seyin},
doi = {10.3791/1350},
issn = {1940-087X},
journal = {Journal of Visualized Experiments},
month = aug,
number = {30},
title = {{Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid}},
url = {http://www.jove.com/index/Details.stp?ID=1350},
year = {2009}
}
@article{Leeuw2010,
author = {de Leeuw, Nora H. and Catlow, C. Richard A. and King, Helen E. and Putnis, Andrew and Muralidharan, Krishna and Deymier, Pierre and Stimpfl, Marilena and Drake, Michael J.},
doi = {10.1039/c0cc02312d},
file = {:home/alex/Dokumente/Mendeley Desktop/Leeuw et al/Chemical Communications/Leeuw et al. - 2010 - Where on Earth has our water come from.pdf:pdf},
issn = {1359-7345},
journal = {Chemical Communications},
number = {47},
pages = {8923},
title = {{Where on Earth has our water come from?}},
url = {http://xlink.rsc.org/?DOI=c0cc02312d},
volume = {46},
year = {2010}
}
@book{Malach2009,
author = {Malach, Anuschka},
publisher = {Heinrich-Heine-Universit\"{a}t D\"{u}sseldorf},
title = {{Expression und Reinigung von RTE1 aus Arabidopsis thaliana [Diplomarbeit, unver\"{o}ffentlicht]}},
year = {2009}
}
@article{Galperin2009,
abstract = {The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).},
author = {Galperin, Michael Y and Cochrane, Guy R},
doi = {10.1093/nar/gkn942},
file = {:home/alex/Dokumente/Mendeley Desktop/Galperin, Cochrane/Nucleic acids research/Galperin, Cochrane - 2009 - Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Databases, Genetic,Databases, Genetic: standards,Databases, Genetic: statistics \& numerical data,Internet,Molecular Biology},
month = jan,
number = {Database issue},
pages = {D1--4},
pmid = {19033364},
title = {{Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21487621},
volume = {37},
year = {2009}
}