{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,25]],"date-time":"2025-05-25T12:42:36Z","timestamp":1748176956605},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2012,11,29]],"date-time":"2012-11-29T00:00:00Z","timestamp":1354147200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002794","type":"journal-article","created":{"date-parts":[[2012,11,29]],"date-time":"2012-11-29T22:40:24Z","timestamp":1354228824000},"page":"e1002794","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e"],"prefix":"10.1371","volume":"8","author":[{"given":"Elisa","family":"Cilia","sequence":"first","affiliation":[]},{"given":"Geerten W.","family":"Vuister","sequence":"additional","affiliation":[]},{"given":"Tom","family":"Lenaerts","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2012,11,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1002\/bies.950190606","article-title":"PDZ domains: targeting signalling molecules to sub-membranous sites","volume":"19","author":"CP Ponting","year":"1997","journal-title":"BioEssays"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1073\/pnas.98.3.787","article-title":"PDZ domains: More than just a glue","volume":"98","author":"I Bezprozvanny","year":"2001","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.jmb.2003.11.010","article-title":"Ligand-dependent dynamics and intramolecular signaling in a PDZ domain","volume":"335","author":"EJ Fuentes","year":"2004","journal-title":"Journal of molecular biology"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1016\/j.str.2006.10.010","article-title":"Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering","volume":"14","author":"S Gianni","year":"2006","journal-title":"Structure"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"18249","DOI":"10.1073\/pnas.0904492106","article-title":"Hidden dynamic allostery in a PDZ domain","volume":"106","author":"CM Petit","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1016\/S1097-2765(04)00086-3","article-title":"Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition","volume":"13","author":"FC Peterson","year":"2004","journal-title":"Molecular cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"13629","DOI":"10.1021\/bi700954e","article-title":"An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificity","volume":"46","author":"LC van den Berk","year":"2007","journal-title":"Biochemistry"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"116","DOI":"10.2174\/138920309787847563","article-title":"Frameworks for understanding long-range intra-protein communication","volume":"10","author":"MJ Whitley","year":"2009","journal-title":"Current protein & peptide science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.44.2.98","article-title":"Application of a Theory of Enzyme Specificity to Protein Synthesis","volume":"44","author":"DE Koshland","year":"1958","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","article-title":"On the Nature of Allosteric Transitions: A Plausible Model","volume":"12","author":"J Monod","year":"1965","journal-title":"Journal of molecular biology"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1039\/b819720b","article-title":"Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms","volume":"5","author":"CJ Tsai","year":"2009","journal-title":"Molecular bioSystems"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1126\/science.1169377","article-title":"Sending signals dynamically","volume":"324","author":"RG Smock","year":"2009","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2008.02.034","article-title":"Allostery: absence of a change in shape does not imply that allostery is not at play","volume":"378","author":"CJ Tsai","year":"2008","journal-title":"Journal of molecular biology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.sbi.2006.01.003","article-title":"The changing landscape of protein allostery","volume":"16","author":"JF Swain","year":"2006","journal-title":"Current opinion in structural biology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1002\/prot.20232","article-title":"Is allostery an intrinsic property of all dynamic proteins?","volume":"57","author":"K Gunasekaran","year":"2004","journal-title":"Proteins"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1126\/science.1186121","article-title":"Biochemistry. An ensemble view of allostery","volume":"327","author":"VJ Hilser","year":"2010","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"9280","DOI":"10.1021\/bi101131f","article-title":"Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E","volume":"49","author":"J Zhang","year":"2010","journal-title":"Biochemistry"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.jmb.2006.08.076","article-title":"Evaluation of energetic and dynamic coupling networks in a PDZ domain protein","volume":"364","author":"EJ Fuentes","year":"2006","journal-title":"Journal of molecular biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"6322","DOI":"10.1021\/ja809915a","article-title":"Conservation of side-chain dynamics within a protein family","volume":"131","author":"AB Law","year":"2009","journal-title":"Journal of the American Chemical Society"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/prot.22139","article-title":"Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis","volume":"74","author":"Y Kong","year":"2009","journal-title":"Proteins"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1002154","DOI":"10.1371\/journal.pcbi.1002154","article-title":"Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning","volume":"7","author":"ZN Gerek","year":"2011","journal-title":"PLoS computational biology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.cell.2009.07.038","article-title":"Protein sectors: evolutionary units of three-dimensional structure","volume":"138","author":"N Halabi","year":"2009","journal-title":"Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1021\/bi991913c","article-title":"Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor","volume":"39","author":"G Kozlov","year":"2000","journal-title":"Biochemistry"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/S0022-2836(02)00544-2","article-title":"Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions","volume":"320","author":"G Kozlov","year":"2002","journal-title":"Journal of molecular biology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"8931","DOI":"10.1021\/ja0752080","article-title":"Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein","volume":"130","author":"A Dhulesia","year":"2008","journal-title":"Journal of the American Chemical Society"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1472-6807-8-43","article-title":"Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure","volume":"8","author":"T Lenaerts","year":"2008","journal-title":"BMC structural biology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1006\/jmbi.2002.5402","article-title":"Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL","volume":"316","author":"T Walma","year":"2002","journal-title":"Journal of molecular biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1002168","DOI":"10.1371\/journal.pcbi.1002168","article-title":"Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone","volume":"7","author":"KH Dubay","year":"2011","journal-title":"PLoS computational biology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1126\/science.286.5438.295","article-title":"Evolutionarily conserved pathways of energetic connectivity in protein families","volume":"286","author":"SW Lockless","year":"1999","journal-title":"Science"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/S0022-2836(02)00544-2","article-title":"Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta 2-beta 3 loop to PDZ domain-ligand interactions","volume":"320","author":"G Kozlov","year":"2002","journal-title":"Journal of molecular biology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1021\/bi991913c","article-title":"Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptors","volume":"39","author":"G Kozlov","year":"2000","journal-title":"Biochemistry"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1002\/prot.20251","article-title":"Making optimal use of empirical energy functions: Force-field parameterization in crystal space","volume":"57","author":"E Krieger","year":"2004","journal-title":"Proteins-Structure Function and Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/0263-7855(90)80070-V","article-title":"WHAT IF: a molecular modeling and drug design program","volume":"8","author":"G Vriend","year":"1990","journal-title":"J Mol Graph"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0022-2836(02)00442-4","article-title":"Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations","volume":"320","author":"R Guerois","year":"2002","journal-title":"Journal of molecular biology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"W382","DOI":"10.1093\/nar\/gki387","article-title":"The FoldX web server: an online force field","volume":"33","author":"J Schymkowitz","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"066138","DOI":"10.1103\/PhysRevE.69.066138","article-title":"Estimating mutual information","volume":"69","author":"A Kraskov","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s10994-008-5083-5","article-title":"Discretization for naive-Bayes learning: managing discretization bias and variance","volume":"74","author":"Y Yang","year":"2009","journal-title":"Machine Learning"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1089\/106652799318274","article-title":"Clustering gene expression patterns","volume":"6","author":"A Ben-Dor","year":"1999","journal-title":"Journal of Computational Biology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/30918","article-title":"Collective dynamics of \u2018small-world\u2019 networks","volume":"393","author":"DJ Watts","year":"1998","journal-title":"Nature"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1002\/prot.20348","article-title":"Small-world network approach to identify key residues in protein-protein interaction","volume":"58","author":"A del Sol","year":"2005","journal-title":"Proteins"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"2006 0019","DOI":"10.1038\/msb4100063","article-title":"Residues crucial for maintaining short paths in network communication mediate signaling in proteins","volume":"2","author":"A del Sol","year":"2006","journal-title":"Molecular systems biology"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1002\/prot.20921","article-title":"MUSTANG: a multiple structural alignment algorithm","volume":"64","author":"AS Konagurthu","year":"2006","journal-title":"Proteins"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"Journal of computational chemistry"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"ME Smoot","year":"2011","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002794","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,6]],"date-time":"2019-07-06T07:40:46Z","timestamp":1562398846000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002794"}},"subtitle":[],"editor":[{"given":"Michael","family":"Nilges","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2012,11,29]]},"references-count":44,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2012,11,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002794","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11,29]]}}}