In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.
Identifieur interne : 000669 ( PubMed/Curation ); précédent : 000668; suivant : 000670In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.
Auteurs : Hao-Jen Hsu [Taïwan] ; Wolfgang B. FischerSource :
- Journal of molecular modeling [ 0948-5023 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Viral Structural Proteins.
- chemistry : SARS Virus.
- Animals, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization.
Abstract
ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since structural models from experiments are still lacking, computational methods can be challenged to generate such models. In this study, a 'sequential approach' for the assembly is proposed in which the individual TMDs are assembled one by one. This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously. The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated. Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment. The results suggest that bundles are likely with the second TMD facing the putative pore. All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossing.
DOI: 10.1007/s00894-011-1092-6
PubMed: 21541740
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000669
Links to Exploration step
pubmed:21541740Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.</title><author><name sortKey="Hsu, Hao Jen" sort="Hsu, Hao Jen" uniqKey="Hsu H" first="Hao-Jen" last="Hsu">Hao-Jen Hsu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei</wicri:regionArea></affiliation></author><author><name sortKey="Fischer, Wolfgang B" sort="Fischer, Wolfgang B" uniqKey="Fischer W" first="Wolfgang B" last="Fischer">Wolfgang B. Fischer</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:21541740</idno><idno type="pmid">21541740</idno><idno type="doi">10.1007/s00894-011-1092-6</idno><idno type="wicri:Area/PubMed/Corpus">000669</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000669</idno><idno type="wicri:Area/PubMed/Curation">000669</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000669</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.</title><author><name sortKey="Hsu, Hao Jen" sort="Hsu, Hao Jen" uniqKey="Hsu H" first="Hao-Jen" last="Hsu">Hao-Jen Hsu</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei</wicri:regionArea></affiliation></author><author><name sortKey="Fischer, Wolfgang B" sort="Fischer, Wolfgang B" uniqKey="Fischer W" first="Wolfgang B" last="Fischer">Wolfgang B. Fischer</name></author></analytic><series><title level="j">Journal of molecular modeling</title><idno type="eISSN">0948-5023</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Humans</term><term>Molecular Dynamics Simulation</term><term>Protein Folding</term><term>Protein Multimerization</term><term>SARS Virus (chemistry)</term><term>Viral Structural Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Multimérisation de protéines</term><term>Pliage des protéines</term><term>Protéines virales structurales ()</term><term>Simulation de dynamique moléculaire</term><term>Virus du SRAS ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Structural Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Humans</term><term>Molecular Dynamics Simulation</term><term>Protein Folding</term><term>Protein Multimerization</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Multimérisation de protéines</term><term>Pliage des protéines</term><term>Protéines virales structurales</term><term>Simulation de dynamique moléculaire</term><term>Virus du SRAS</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since structural models from experiments are still lacking, computational methods can be challenged to generate such models. In this study, a 'sequential approach' for the assembly is proposed in which the individual TMDs are assembled one by one. This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously. The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated. Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment. The results suggest that bundles are likely with the second TMD facing the putative pore. All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossing.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21541740</PMID><DateCompleted><Year>2012</Year><Month>05</Month><Day>31</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">0948-5023</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>2</Issue><PubDate><Year>2012</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Journal of molecular modeling</Title><ISOAbbreviation>J Mol Model</ISOAbbreviation></Journal><ArticleTitle>In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.</ArticleTitle><Pagination><MedlinePgn>501-14</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00894-011-1092-6</ELocationID><Abstract><AbstractText>ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since structural models from experiments are still lacking, computational methods can be challenged to generate such models. In this study, a 'sequential approach' for the assembly is proposed in which the individual TMDs are assembled one by one. This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously. The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated. Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment. The results suggest that bundles are likely with the second TMD facing the putative pore. All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossing.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hsu</LastName><ForeName>Hao-Jen</ForeName><Initials>HJ</Initials><AffiliationInfo><Affiliation>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fischer</LastName><ForeName>Wolfgang B</ForeName><Initials>WB</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>05</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>J Mol Model</MedlineTA><NlmUniqueID>9806569</NlmUniqueID><ISSNLinking>0948-5023</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C515313">ORF3A protein, SARS coronavirus</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015678">Viral Structural Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056004" MajorTopicYN="N">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017510" MajorTopicYN="N">Protein Folding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055503" MajorTopicYN="N">Protein Multimerization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015678" MajorTopicYN="N">Viral Structural Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2010</Year><Month>11</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>04</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>5</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>5</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>6</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21541740</ArticleId><ArticleId IdType="doi">10.1007/s00894-011-1092-6</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Biochim Biophys Acta. 2011 Feb;1808(2):572-9</Citation><ArticleIdList><ArticleId IdType="pubmed">20708597</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12540-5</Citation><ArticleIdList><ArticleId IdType="pubmed">16894145</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Struct Mol Biol. 2010 Jan;17(1):31-7</Citation><ArticleIdList><ArticleId IdType="pubmed">20010838</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Graph. 1996 Dec;14(6):354-60, 376</Citation><ArticleIdList><ArticleId IdType="pubmed">9195488</ArticleId></ArticleIdList></Reference><Reference><Citation>Protein Eng. 1993 Jan;6(1):65-74</Citation><ArticleIdList><ArticleId IdType="pubmed">7679490</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Membr Biol. 2009 Aug;26(5):309-20</Citation><ArticleIdList><ArticleId IdType="pubmed">19707940</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteins. 1997 Aug;28(4):556-67</Citation><ArticleIdList><ArticleId IdType="pubmed">9261871</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 2004 Jul 30;341(1):271-9</Citation><ArticleIdList><ArticleId IdType="pubmed">15312778</ArticleId></ArticleIdList></Reference><Reference><Citation>Eur Biophys J. 2005 Feb;34(1):52-66</Citation><ArticleIdList><ArticleId IdType="pubmed">15221235</ArticleId></ArticleIdList></Reference><Reference><Citation>FEBS Lett. 2003 Nov 27;555(1):122-5</Citation><ArticleIdList><ArticleId IdType="pubmed">14630331</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 1994 Mar;68(3):1551-63</Citation><ArticleIdList><ArticleId IdType="pubmed">7508997</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 1996 Oct;70(10):7108-15</Citation><ArticleIdList><ArticleId IdType="pubmed">8794357</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2003 May 30;300(5624):1399-404</Citation><ArticleIdList><ArticleId IdType="pubmed">12730501</ArticleId></ArticleIdList></Reference><Reference><Citation>Eur Biophys J. 2003 Mar;32(1):67-77</Citation><ArticleIdList><ArticleId IdType="pubmed">12632209</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 2004 Jul;78(13):6723-34</Citation><ArticleIdList><ArticleId IdType="pubmed">15194747</ArticleId></ArticleIdList></Reference><Reference><Citation>J Med Chem. 2006 Jan 26;49(2):648-55</Citation><ArticleIdList><ArticleId IdType="pubmed">16420050</ArticleId></ArticleIdList></Reference><Reference><Citation>J Infect Dis. 2007 Aug 1;196(3):405-15</Citation><ArticleIdList><ArticleId IdType="pubmed">17597455</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 2002 Jun 11;41(23):7359-65</Citation><ArticleIdList><ArticleId IdType="pubmed">12044168</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2010 Feb 4;463(7281):689-92</Citation><ArticleIdList><ArticleId IdType="pubmed">20130653</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Biophys Biomol Struct. 1999;28:319-65</Citation><ArticleIdList><ArticleId IdType="pubmed">10410805</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Dec 1;438(7068):581-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16319877</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2003 May 13;100(10):6104-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12719519</ArticleId></ArticleIdList></Reference><Reference><Citation>Virology. 1980 Dec;107(2):548-51</Citation><ArticleIdList><ArticleId IdType="pubmed">6256950</ArticleId></ArticleIdList></Reference><Reference><Citation>Biophys J. 2007 Feb 1;92(3):854-63</Citation><ArticleIdList><ArticleId IdType="pubmed">17085501</ArticleId></ArticleIdList></Reference><Reference><Citation>FEBS Lett. 2003 Jan 30;535(1-3):34-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12560074</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2000 Mar 24;275(12):8592-9</Citation><ArticleIdList><ArticleId IdType="pubmed">10722698</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2008 Jan 31;451(7178):591-5</Citation><ArticleIdList><ArticleId IdType="pubmed">18235503</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Chem. 2008 Nov 15;29(14):2416-24</Citation><ArticleIdList><ArticleId IdType="pubmed">18432615</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Pathog. 2009 Jul;5(7):e1000511</Citation><ArticleIdList><ArticleId IdType="pubmed">19593379</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2002 May 28;99(11):7432-7</Citation><ArticleIdList><ArticleId IdType="pubmed">12032300</ArticleId></ArticleIdList></Reference><Reference><Citation>Virology. 2010 Dec 5;408(1):89-102</Citation><ArticleIdList><ArticleId IdType="pubmed">20880565</ArticleId></ArticleIdList></Reference><Reference><Citation>Virology. 2011 Mar 1;411(1):65-77</Citation><ArticleIdList><ArticleId IdType="pubmed">21237475</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochim Biophys Acta. 2011 Feb;1808(2):561-71</Citation><ArticleIdList><ArticleId IdType="pubmed">20546700</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1999 Feb 26;286(3):951-62</Citation><ArticleIdList><ArticleId IdType="pubmed">10024461</ArticleId></ArticleIdList></Reference><Reference><Citation>Int Rev Cell Mol Biol. 2009;275:35-63</Citation><ArticleIdList><ArticleId IdType="pubmed">19491052</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 1990 May 1;29(17):4031-7</Citation><ArticleIdList><ArticleId IdType="pubmed">1694455</ArticleId></ArticleIdList></Reference><Reference><Citation>Acc Chem Res. 2010 Mar 16;43(3):388-96</Citation><ArticleIdList><ArticleId IdType="pubmed">20017540</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 1996 Jan 12;271(5246):163-8</Citation><ArticleIdList><ArticleId IdType="pubmed">8539615</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2003 Jan 10;278(2):1012-21</Citation><ArticleIdList><ArticleId IdType="pubmed">12244057</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteins. 2008 Feb 15;70(3):834-43</Citation><ArticleIdList><ArticleId IdType="pubmed">17729286</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Jun 4;459(7247):726-30</Citation><ArticleIdList><ArticleId IdType="pubmed">19421192</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochim Biophys Acta. 2001 Jun 6;1512(2):291-8</Citation><ArticleIdList><ArticleId IdType="pubmed">11406106</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochim Biophys Acta. 2011 Feb;1808(2):554-60</Citation><ArticleIdList><ArticleId IdType="pubmed">20727848</ArticleId></ArticleIdList></Reference><Reference><Citation>Biophys J. 2010 Oct 6;99(7):2217-24</Citation><ArticleIdList><ArticleId IdType="pubmed">20923656</ArticleId></ArticleIdList></Reference><Reference><Citation>Antiviral Res. 2011 Apr;90(1):64-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21356245</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 2001 Apr;75(8):3647-56</Citation><ArticleIdList><ArticleId IdType="pubmed">11264354</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochim Biophys Acta. 2002 Mar 19;1561(1):27-45</Citation><ArticleIdList><ArticleId IdType="pubmed">11988179</ArticleId></ArticleIdList></Reference><Reference><Citation>Virus Res. 2008 Apr;133(1):113-21</Citation><ArticleIdList><ArticleId IdType="pubmed">18045721</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Dec 10;462(7274):745-56</Citation><ArticleIdList><ArticleId IdType="pubmed">19946266</ArticleId></ArticleIdList></Reference><Reference><Citation>J Chem Theory Comput. 2009 Sep 8;5(9):2503-13</Citation><ArticleIdList><ArticleId IdType="pubmed">26616628</ArticleId></ArticleIdList></Reference><Reference><Citation>FEBS Lett. 1996 Nov 25;398(1):12-8</Citation><ArticleIdList><ArticleId IdType="pubmed">8946945</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2008 Mar 20;452(7185):375-9</Citation><ArticleIdList><ArticleId IdType="pubmed">18322461</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Jan 1;457(7225):115-8</Citation><ArticleIdList><ArticleId IdType="pubmed">18987630</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 2002 Oct 25;277(43):40434-41</Citation><ArticleIdList><ArticleId IdType="pubmed">12183456</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000669 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 000669 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= CovidV1
|flux= PubMed
|étape= Curation
|type= RBID
|clé= pubmed:21541740
|texte= In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:21541740" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a CovidV1
| This area was generated with Dilib version V0.6.33. |  |