pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.
Identifieur interne : 002341 ( PubMed/Checkpoint ); précédent : 002340; suivant : 002342pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.
Auteurs : Jinzhi Tan [République populaire de Chine] ; Koen H G. Verschueren ; Kanchan Anand ; Jianhua Shen ; Maojun Yang ; Yechun Xu ; Zihe Rao ; Janna Bigalke ; Burkhard Heisen ; Jeroen R. Mesters ; Kaixian Chen ; Xu Shen ; Hualiang Jiang ; Rolf HilgenfeldSource :
- Journal of molecular biology [ 0022-2836 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Cysteine Endopeptidases.
- chemical , metabolism : Cysteine Endopeptidases.
- enzymology : SARS Virus.
- Binding Sites, Computer Simulation, Crystallography, X-Ray, Dimerization, Hydrogen-Ion Concentration, Models, Molecular, Protein Conformation.
Abstract
The SARS coronavirus main proteinase (M(pro)) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the M(pro) by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the M(pro) monomer and the need for dimerization are also discussed.
DOI: 10.1016/j.jmb.2005.09.012
PubMed: 16242152
Affiliations:
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pubmed:16242152Le document en format XML
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Verschueren</name></author><author><name sortKey="Anand, Kanchan" sort="Anand, Kanchan" uniqKey="Anand K" first="Kanchan" last="Anand">Kanchan Anand</name></author><author><name sortKey="Shen, Jianhua" sort="Shen, Jianhua" uniqKey="Shen J" first="Jianhua" last="Shen">Jianhua Shen</name></author><author><name sortKey="Yang, Maojun" sort="Yang, Maojun" uniqKey="Yang M" first="Maojun" last="Yang">Maojun Yang</name></author><author><name sortKey="Xu, Yechun" sort="Xu, Yechun" uniqKey="Xu Y" first="Yechun" last="Xu">Yechun Xu</name></author><author><name sortKey="Rao, Zihe" sort="Rao, Zihe" uniqKey="Rao Z" first="Zihe" last="Rao">Zihe Rao</name></author><author><name sortKey="Bigalke, Janna" sort="Bigalke, Janna" uniqKey="Bigalke J" first="Janna" last="Bigalke">Janna Bigalke</name></author><author><name sortKey="Heisen, Burkhard" sort="Heisen, Burkhard" uniqKey="Heisen B" first="Burkhard" last="Heisen">Burkhard Heisen</name></author><author><name sortKey="Mesters, Jeroen R" sort="Mesters, Jeroen R" uniqKey="Mesters J" first="Jeroen R" last="Mesters">Jeroen R. Mesters</name></author><author><name sortKey="Chen, Kaixian" sort="Chen, Kaixian" uniqKey="Chen K" first="Kaixian" last="Chen">Kaixian Chen</name></author><author><name sortKey="Shen, Xu" sort="Shen, Xu" uniqKey="Shen X" first="Xu" last="Shen">Xu Shen</name></author><author><name sortKey="Jiang, Hualiang" sort="Jiang, Hualiang" uniqKey="Jiang H" first="Hualiang" last="Jiang">Hualiang Jiang</name></author><author><name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Crystallography, X-Ray</term><term>Cysteine Endopeptidases (chemistry)</term><term>Cysteine Endopeptidases (metabolism)</term><term>Dimerization</term><term>Hydrogen-Ion Concentration</term><term>Models, Molecular</term><term>Protein Conformation</term><term>SARS Virus (enzymology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Concentration en ions d'hydrogène</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Cysteine endopeptidases ()</term><term>Cysteine endopeptidases (métabolisme)</term><term>Dimérisation</term><term>Modèles moléculaires</term><term>Simulation numérique</term><term>Sites de fixation</term><term>Virus du SRAS (enzymologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine Endopeptidases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cysteine Endopeptidases</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cysteine endopeptidases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Crystallography, X-Ray</term><term>Dimerization</term><term>Hydrogen-Ion Concentration</term><term>Models, Molecular</term><term>Protein Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Concentration en ions d'hydrogène</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Cysteine endopeptidases</term><term>Dimérisation</term><term>Modèles moléculaires</term><term>Simulation numérique</term><term>Sites de fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The SARS coronavirus main proteinase (M(pro)) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the M(pro) by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the M(pro) monomer and the need for dimerization are also discussed.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16242152</PMID><DateCompleted><Year>2005</Year><Month>12</Month><Day>20</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0022-2836</ISSN><JournalIssue CitedMedium="Print"><Volume>354</Volume><Issue>1</Issue><PubDate><Year>2005</Year><Month>Nov</Month><Day>18</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.</ArticleTitle><Pagination><MedlinePgn>25-40</MedlinePgn></Pagination><Abstract><AbstractText>The SARS coronavirus main proteinase (M(pro)) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the M(pro) by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the M(pro) monomer and the need for dimerization are also discussed.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Jinzhi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Verschueren</LastName><ForeName>Koen H G</ForeName><Initials>KH</Initials></Author><Author ValidYN="Y"><LastName>Anand</LastName><ForeName>Kanchan</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Jianhua</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Maojun</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yechun</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Rao</LastName><ForeName>Zihe</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Bigalke</LastName><ForeName>Janna</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Heisen</LastName><ForeName>Burkhard</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Mesters</LastName><ForeName>Jeroen R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Kaixian</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Xu</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Hualiang</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Hilgenfeld</LastName><ForeName>Rolf</ForeName><Initials>R</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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UI="D003546">Cysteine Endopeptidases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003546" MajorTopicYN="N">Cysteine Endopeptidases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019281" MajorTopicYN="N">Dimerization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006863" MajorTopicYN="N">Hydrogen-Ion Concentration</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2005</Year><Month>04</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2005</Year><Month>08</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2005</Year><Month>09</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>10</Month><Day>26</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>12</Month><Day>21</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a SrasV1
| This area was generated with Dilib version V0.6.33. |  |