{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:07:07Z","timestamp":1791180427088,"version":"4.1.0"},"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2012,12,17]],"date-time":"2012-12-17T00:00:00Z","timestamp":1355702400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0051676","type":"journal-article","created":{"date-parts":[[2012,12,17]],"date-time":"2012-12-17T16:59:36Z","timestamp":1355763576000},"page":"e51676","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach"],"prefix":"10.1371","volume":"7","author":[{"given":"Moitrayee","family":"Bhattacharyya","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roopali","family":"Upadhyay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saraswathi","family":"Vishveshwara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,12,17]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1016\/j.sbi.2008.05.007","article-title":"Exploring the structure and function paradigm","volume":"18","author":"OC Redfern","year":"2008","journal-title":"Curr Opin Struct Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.sbi.2006.04.003","article-title":"Evolution of protein fold in the presence of functional constraints","volume":"16","author":"A Andreeva","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that Govern the Folding of Protein Chains","volume":"181","author":"CB Anfinsen","year":"1973","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/372631a0","article-title":"Protein superfamilles and domain superfolds","volume":"372","author":"CA Orengo","year":"1994","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1002\/prot.10514","article-title":"The number of protein folds and their distribution over families in nature","volume":"54","author":"X Liu","year":"2004","journal-title":"Proteins: Struct Func Bioinfo"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1006\/jmbi.2000.3786","article-title":"Estimating the number of protein folds and families from complete genome data","volume":"299","author":"YI Wolf","year":"2000","journal-title":"J Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1073\/pnas.0407152101","article-title":"The protein structure prediction problem could be solved using the current PDB library","volume":"102","author":"Y Zhang","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1146\/annurev.biochem.74.082803.133029","article-title":"Protein families and their evolution-A structural perspective","volume":"74","author":"CA Orengo","year":"2005","journal-title":"Ann Rev Biochem"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1472-6807-11-2","article-title":"1,000 structures and more from the MCSG","volume":"11","author":"D Lee","year":"2011","journal-title":"BMC Struct Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.sbi.2007.06.002","article-title":"Evolutionary transitions in protein fold space","volume":"17","author":"T William R","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"16623","DOI":"10.1073\/pnas.0606843103","article-title":"A backbone-based theory of protein folding","volume":"103","author":"GD Rose","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"7960","DOI":"10.1073\/pnas.0402525101","article-title":"Geometry and symmetry presculpt the free-energy landscape of proteins","volume":"101","author":"TX Hoang","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e9391","DOI":"10.1371\/journal.pone.0009391","article-title":"Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds","volume":"5","author":"V Soundararajan","year":"2010","journal-title":"PLoS ONE"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1002\/j.1460-2075.1986.tb04288.x","article-title":"The relation between the divergence of sequence and structure in proteins","volume":"5","author":"C Chothia","year":"1986","journal-title":"EMBO J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1016\/S0022-2836(02)00649-6","article-title":"One Fold with Many Functions: The Evolutionary Relationships between TIM Barrel Families Based on their Sequences, Structures and Functions","volume":"321","author":"N Nagano","year":"2002","journal-title":"J Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"14056","DOI":"10.1073\/pnas.0606239103","article-title":"Evolution of protein structural classes and protein sequence families","volume":"103","author":"I-G Choi","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"14132","DOI":"10.1073\/pnas.202497999","article-title":"Expanding protein universe and its origin from the biological Big Bang","volume":"99","author":"NV Dokholyan","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/S0168-9525(03)00167-7","article-title":"Moonlighting proteins: old proteins learning new tricks","volume":"19","author":"J Constance J","year":"2003","journal-title":"Trends in Genetics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1016\/j.bpj.2009.07.016","article-title":"Understanding Protein Structure from a Percolation Perspective","volume":"97","author":"D Deb","year":"2009","journal-title":"Biophys J"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/nrm2762","article-title":"Structural and functional constraints in the evolution of protein families","volume":"10","author":"CL Worth","year":"2009","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref21","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":"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":"579","DOI":"10.1038\/nature03990","article-title":"Natural-like function in artificial WW domains","volume":"437","author":"WP Russ","year":"2005","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1016\/S0006-3495(00)76756-7","article-title":"Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior","volume":"78","author":"O Keskin","year":"2000","journal-title":"Biophys J"},{"key":"ref25","unstructured":"Raimondi F, Felline A, Portella G, Orozco M, Fanelli F (2012) Light on the structural communication in Ras GTPases. J Biomol Struct Dyn: 1\u201316."},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/bioinformatics\/btm270","article-title":"Predicting functionally important residues from sequence conservation","volume":"23","author":"JA Capra","year":"2007","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1038\/250194a0","article-title":"Chemical and biological evolution of a nucleotide-binding protein","volume":"250","author":"MG Rossmann","year":"1974","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/0959-440X(95)80010-7","article-title":"NAD-binding domains of dehydrogenases","volume":"5","author":"L Arthur M","year":"1995","journal-title":"Current Opinion in Structural Biology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0022-2836(02)00885-9","article-title":"GXXXG and GXXXA Motifs Stabilize FAD and NAD(P)-binding Rossmann Folds Through C(alpha)-H\u2026 O Hydrogen Bonds and van der Waals Interactions","volume":"323","author":"G Kleiger","year":"2002","journal-title":"J Mol Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1006\/jmbi.1999.2911","article-title":"Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function","volume":"291","author":"LA Mirny","year":"1999","journal-title":"J Mol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S1359-0278(96)00011-9","article-title":"Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2","volume":"1","author":"E L\u00f3pez-Hern\u00e9ndez","year":"1996","journal-title":"Folding and Design"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1107\/S0907444911007062","article-title":"Network approach for capturing ligand-induced subtle global changes in protein structures","volume":"67","author":"A Sukhwal","year":"2011","journal-title":"Acta Cryst Section D"},{"key":"ref33","doi-asserted-by":"crossref","unstructured":"Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, <etal>et al<\/etal>.. (2010) An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol 6.","DOI":"10.1038\/msb.2010.65"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e1002505","DOI":"10.1371\/journal.pcbi.1002505","article-title":"Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks","volume":"8","author":"MS Vijayabaskar","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"AG Murzin","year":"1995","journal-title":"J Mol Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/nar\/28.1.254","article-title":"The ASTRAL compendium for protein structure and sequence analysis","volume":"28","author":"SE Brenner","year":"2000","journal-title":"Nucl Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1093\/bioinformatics\/btg224","article-title":"PISCES: a protein sequence culling server","volume":"19","author":"G Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1002\/prot.22573","article-title":"Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks","volume":"78","author":"M Bhattacharyya","year":"2010","journal-title":"Proteins: Struct Func Bioinfo"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4159","DOI":"10.1529\/biophysj.105.064485","article-title":"A network representation of protein structures: implications for protein stability","volume":"89","author":"KV Brinda","year":"2005","journal-title":"Biophysical journal"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1006\/jmbi.1999.3058","article-title":"Identification of side-chain clusters in protein structures by a graph spectral method","volume":"292","author":"N Kannan","year":"1999","journal-title":"J Mol Biol"},{"key":"ref41","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: Struct Func Bioinfo"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nature03607","article-title":"Uncovering the overlapping community structure of complex networks in nature and society","volume":"435","author":"G Palla","year":"2005","journal-title":"Nature"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0051676","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,7]],"date-time":"2019-07-07T00:32:52Z","timestamp":1562459572000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0051676"}},"subtitle":[],"editor":[{"given":"Aleksey","family":"Porollo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,12,17]]},"references-count":42,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2012,12,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0051676","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,17]]}}}