{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T23:11:23Z","timestamp":1777763483604,"version":"3.51.4"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2011,2,24]],"date-time":"2011-02-24T00:00:00Z","timestamp":1298505600000},"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.1001084","type":"journal-article","created":{"date-parts":[[2011,2,24]],"date-time":"2011-02-24T22:10:31Z","timestamp":1298585431000},"page":"e1001084","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":41,"title":["Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain"],"prefix":"10.1371","volume":"7","author":[{"given":"Jiahai","family":"Shi","sequence":"first","affiliation":[]},{"given":"Nanyu","family":"Han","sequence":"additional","affiliation":[]},{"given":"Liangzhong","family":"Lim","sequence":"additional","affiliation":[]},{"given":"Shixiong","family":"Lua","sequence":"additional","affiliation":[]},{"given":"J.","family":"Sivaraman","sequence":"additional","affiliation":[]},{"given":"Lushan","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Yuguang","family":"Mu","sequence":"additional","affiliation":[]},{"given":"Jianxing","family":"Song","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,2,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1093\/emboj\/cdf327","article-title":"Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain.","volume":"21","author":"K Anand","year":"2002","journal-title":"EMBO J"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1126\/science.1085658","article-title":"Coronavirus main proteinase (3CLpro) structure: basis for design of anti- SARS drugs.","volume":"300","author":"K Anand","year":"2003","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/369072a0","article-title":"Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases.","volume":"369","author":"M Allaire","year":"1994","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"13190","DOI":"10.1073\/pnas.1835675100","article-title":"The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor.","volume":"100","author":"H Yang","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"14908","DOI":"10.1021\/bi0616302","article-title":"Long-range cooperative interactions modulate dimerization in SARS 3CLpro.","volume":"45","author":"J Barrila","year":"2006","journal-title":"Biochemistry"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1529\/biophysj.106.091736","article-title":"Reversible unfolding of the severe acute respiratory syndrome coronavirus main protease in guanidinium chloride.","volume":"92","author":"HP Chang","year":"2007","journal-title":"Biophys J"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1074\/jbc.M408211200","article-title":"Severe acute respiratory syndrome coronavirus 3C-like proteinase N terminus is indispensable for proteolytic activity but not for enzyme dimerization. Biochemical and thermodynamic investigation in conjunction with molecular dynamics simulations.","volume":"280","author":"S Chen","year":"2005","journal-title":"J Biol Chem"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"14958","DOI":"10.1021\/bi0490237","article-title":"Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease.","volume":"43","author":"CY Chou","year":"2004","journal-title":"Biochemistry"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1074\/jbc.M310875200","article-title":"Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase.","volume":"279","author":"K Fan","year":"2004","journal-title":"J Biol Chem"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"14632","DOI":"10.1021\/bi061746y","article-title":"SARS CoV main proteinase: The monomer-dimer equilibrium dissociation constant.","volume":"45","author":"V Graziano","year":"2006","journal-title":"Biochemistry"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.virusres.2007.02.015","article-title":"Evaluating the 3C-like protease activity of SARS-Coronavirus: recommendations for standardized assays for drug discovery.","volume":"133","author":"V Grum-Tokars","year":"2008","journal-title":"Virus Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"22741","DOI":"10.1074\/jbc.M502556200","article-title":"Critical assessment of important regions in the subunit association and catalytic action of the severe acute respiratory syndrome coronavirus main protease.","volume":"280","author":"WC Hsu","year":"2005","journal-title":"J Biol Chem"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1016\/j.bbrc.2004.04.098","article-title":"Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate.","volume":"318","author":"CJ Kuo","year":"2004","journal-title":"Biochem Biophys Res Commun"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1111\/j.1742-4658.2006.05130.x","article-title":"The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain.","volume":"273","author":"J Shi","year":"2006","journal-title":"FEBS J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"24765","DOI":"10.1074\/jbc.M311744200","article-title":"Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors.","volume":"279","author":"J Shi","year":"2004","journal-title":"J Biol Chem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1016\/j.bbrc.2005.11.102","article-title":"The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase.","volume":"339","author":"P Wei","year":"2006","journal-title":"Biochem Biophys Res Commun"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/j.jmb.2006.11.073","article-title":"Production of authentic SARS-CoV M(pro) with enhanced activity: application as a novel tag-cleavage endopeptidase for protein overproduction.","volume":"366","author":"X Xue","year":"2007","journal-title":"J Mol Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1128\/JVI.02114-07","article-title":"Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design.","volume":"82","author":"X Xue","year":"2008","journal-title":"J Virol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"4227","DOI":"10.1128\/JVI.02612-07","article-title":"Without its N-finger, the main protease of severe acute respiratory syndrome coronavirus can form a novel dimer through its C-terminal domain.","volume":"82","author":"N Zhong","year":"2008","journal-title":"J Virol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"4308","DOI":"10.1021\/bi1002585","article-title":"Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro).","volume":"49","author":"J Barrila","year":"2010","journal-title":"Biochemistry"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4620","DOI":"10.1128\/JVI.02680-07","article-title":"Mechanism for controlling the dimer-monomer switch and coupling dimerization to catalysis of the severe acute respiratory syndrome coronavirus 3C-like protease.","volume":"82","author":"J Shi","year":"2008","journal-title":"J Virol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1074\/jbc.M705240200","article-title":"Mutation of Gly-11 on the dimer interface results in the complete crystallographic dimer dissociation of severe acute respiratory syndrome coronavirus 3C-like protease: crystal structure with molecular dynamics simulations.","volume":"283","author":"S Chen","year":"2008","journal-title":"J Biol Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.virol.2009.03.034","article-title":"Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure.","volume":"388","author":"T Hu","year":"2009","journal-title":"Virology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1016\/j.jmb.2006.11.078","article-title":"Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase.","volume":"366","author":"TW Lee","year":"2007","journal-title":"J Mol Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1016\/j.bbrc.2005.04.072","article-title":"Mutational and inhibitive analysis of SARS coronavirus 3C-like protease by fluorescence resonance energy transfer-based assays.","volume":"331","author":"WF Kuang","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1107\/S0021889807021206","article-title":"Phaser crystallographic software.","volume":"40","author":"AJ McCoy","year":"2007","journal-title":"J Appl Crystallogr"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1007\/978-1-60327-058-8_28","article-title":"Automated structure solution with the PHENIX suite.","volume":"426","author":"PH Zwart","year":"2008","journal-title":"Methods Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1107\/S0907444994003112","article-title":"The CCP4 suite: programs for protein crystallography.","volume":"50","year":"1994","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures.","volume":"26","author":"RA Laskowski","year":"1993","journal-title":"J Appl Cryst"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref31","article-title":"The PyMOL Molecular Graphics System.","author":"LD Warren","year":"2007"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.","volume":"4","author":"B Hess","year":"2008","journal-title":"J Chem Theory Comput"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","article-title":"A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.","volume":"24","author":"Y Duan","year":"2003","journal-title":"J Comput Chem"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-22464-0","article-title":"Molecular Modeling and Simulation: An Interdisciplinary Guide","author":"T Schlick","year":"2002"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations.","volume":"18","author":"B Hess","year":"1997","journal-title":"J Comput Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/j.chembiol.2008.04.011","article-title":"A structural view of the inactivation of the SARS coronavirus main proteinase by benzotriazole esters.","volume":"15","author":"KH Verschueren","year":"2008","journal-title":"Chem Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"31257","DOI":"10.1074\/jbc.M502577200","article-title":"Mechanism of the maturation process of SARS-CoV 3CL protease.","volume":"280","author":"MF Hsu","year":"2005","journal-title":"J Biol Chem"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1016\/j.jmb.2005.09.004","article-title":"Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide.","volume":"353","author":"TW Lee","year":"2005","journal-title":"J Mol Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.jmb.2005.09.012","article-title":"pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.","volume":"354","author":"J Tan","year":"2005","journal-title":"J Mol Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1016\/j.jmb.2007.06.001","article-title":"A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-CoV 3C-like peptidase.","volume":"371","author":"J Yin","year":"2007","journal-title":"J Mol Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"13894","DOI":"10.1074\/jbc.M510745200","article-title":"Only one protomer is active in the dimer of SARS 3C-like proteinase.","volume":"281","author":"H Chen","year":"2006","journal-title":"J Biol Chem"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1002\/prot.20249","article-title":"Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding.","volume":"57","author":"YP Pang","year":"2004","journal-title":"Proteins"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1002\/prot.21160","article-title":"Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme.","volume":"66","author":"K Zheng","year":"2007","journal-title":"Proteins"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1128\/JVI.02114-07","article-title":"Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design.","volume":"82","author":"X Xue","year":"2008","journal-title":"J Virol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/35051723","article-title":"Modular enzymes.","volume":"409","author":"C Khosla","year":"2001","journal-title":"Nature"},{"key":"ref46","first-page":"42","article-title":"To the problem of proteolytic enzyme evolution.","volume":"54","author":"NN Nemova","year":"2008","journal-title":"Biomed Khim"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1002\/pro.76","article-title":"C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer.","volume":"18","author":"N Zhong","year":"2009","journal-title":"Protein Sci"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s13238-010-0011-4","article-title":"Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode.","volume":"1","author":"S Chen","year":"2010","journal-title":"Protein Cell"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1016\/j.cbpa.2010.08.012","article-title":"Enzyme dynamics point to stepwise conformational selection in catalysis.","volume":"14","author":"B Ma","year":"2010","journal-title":"Curr Opin Chem Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e1000487","DOI":"10.1371\/journal.pcbi.1000487","article-title":"Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.","volume":"5","author":"A Dixit","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1002\/prot.20794","article-title":"Mutations in alpha-helical solvent-exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations.","volume":"63","author":"JS Fetrow","year":"2006","journal-title":"Proteins"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"4078","DOI":"10.1529\/biophysj.107.121913","article-title":"Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase.","volume":"94","author":"S Saen-Oon","year":"2008","journal-title":"Biophys J"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"3745","DOI":"10.1021\/ja028487u","article-title":"Effect of mutation on enzyme motion in dihydrofolate reductase.","volume":"125","author":"JB Watney","year":"2003","journal-title":"J Am Chem Soc"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001084","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,4]],"date-time":"2024-04-04T14:09:37Z","timestamp":1712239777000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001084"}},"subtitle":[],"editor":[{"given":"Ruth","family":"Nussinov","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,2,24]]},"references-count":53,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2011,2,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1001084","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,24]]}}}