CovidV2, Main, Exploration, bibRecord, 001428

In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV

Identifieur interne : 001428 ( Main/Exploration ); précédent : 001427; suivant : 001429

In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV

Auteurs : Hao-Jen Hsu [Taïwan] ; Wolfgang B. Fischer [Taïwan]

Source :

Journal of Molecular Modeling [ 1610-2940 ] ; 2012-02-01.

RBID : ISTEX:5A6E845FD1DA81AF5C42B2F1A7FC9CFDD24DD3F6

Descripteurs français

KwdFr :
- Animaux, Humains, Multimérisation de protéines, Pliage des protéines, Protéines virales structurales (), Simulation de dynamique moléculaire, Virus du SRAS ().
MESH :
- Animaux, Humains, Multimérisation de protéines, Pliage des protéines, Protéines virales structurales, Simulation de dynamique moléculaire, Virus du SRAS.

English descriptors

KwdEn :
- 3a of SARS-CoV, Animals, Docking, Humans, Ion channel, Membrane protein, Molecular Dynamics Simulation, Molecular dynamics, Protein Folding, Protein Multimerization, Protein assembly, SARS Virus (chemistry), Viral Structural Proteins (chemistry).
MESH :
- chemical , chemistry : Viral Structural Proteins.
- chemistry : SARS Virus.
- Animals, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization.

Abstract

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.

Url:

DOI: 10.1007/s00894-011-1092-6

Affiliations:

Taïwan

Le document en format XML

<record><TEI wicri:istexFullTextTei="biblStruct"><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>
</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">ISTEX</idno>
<idno type="RBID">ISTEX:5A6E845FD1DA81AF5C42B2F1A7FC9CFDD24DD3F6</idno>
<date when="2011" year="2011">2011</date>
<idno type="doi">10.1007/s00894-011-1092-6</idno>
<idno type="url">https://api.istex.fr/ark:/67375/VQC-V243NB9M-3/fulltext.pdf</idno>
<idno type="wicri:Area/Istex/Corpus">000421</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000421</idno>
<idno type="wicri:Area/Istex/Curation">000388</idno>
<idno type="wicri:Area/Istex/Checkpoint">000088</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000088</idno>
<idno type="wicri:doubleKey">1610-2940:2011:Hsu H:in:silico:investigations</idno>
<idno type="wicri:source">PMC</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087964</idno>
<idno type="RBID">PMC:7087964</idno>
<idno type="wicri:Area/Pmc/Corpus">000279</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000279</idno>
<idno type="wicri:Area/Pmc/Curation">000279</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000279</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000800</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000800</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:21541740</idno>
<idno type="wicri:Area/PubMed/Corpus">000D23</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D23</idno>
<idno type="wicri:Area/PubMed/Curation">000D23</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D23</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000D00</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000D00</idno>
<idno type="wicri:Area/Ncbi/Merge">000263</idno>
<idno type="wicri:Area/Ncbi/Curation">000263</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000263</idno>
<idno type="wicri:doubleKey">1610-2940:2011:Hsu H:in:silico:investigations</idno>
<idno type="wicri:Area/Main/Merge">001430</idno>
<idno type="wicri:Area/Main/Curation">001428</idno>
<idno type="wicri:Area/Main/Exploration">001428</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" 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"><country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei</wicri:regionArea>
<wicri:noRegion>Taipei</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Fischer, Wolfgang B" sort="Fischer, Wolfgang B" uniqKey="Fischer W" first="Wolfgang B." last="Fischer">Wolfgang B. Fischer</name>
<affiliation wicri:level="1"><country xml:lang="fr">Taïwan</country>
<wicri:regionArea>Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei</wicri:regionArea>
<wicri:noRegion>Taipei</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><country wicri:rule="url">Taïwan</country>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Journal of Molecular Modeling</title>
<title level="j" type="sub">Computational Chemistry - Life Science - Advanced Materials - New Methods</title>
<title level="j" type="abbrev">J Mol Model</title>
<idno type="ISSN">1610-2940</idno>
<idno type="eISSN">0948-5023</idno>
<imprint><publisher>Springer-Verlag</publisher>
<pubPlace>Berlin/Heidelberg</pubPlace>
<date type="published" when="2012-02-01">2012-02-01</date>
<biblScope unit="volume">18</biblScope>
<biblScope unit="issue">2</biblScope>
<biblScope unit="page" from="501">501</biblScope>
<biblScope unit="page" to="514">514</biblScope>
</imprint>
<idno type="ISSN">1610-2940</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">1610-2940</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>3a of SARS-CoV</term>
<term>Animals</term>
<term>Docking</term>
<term>Humans</term>
<term>Ion channel</term>
<term>Membrane protein</term>
<term>Molecular Dynamics Simulation</term>
<term>Molecular dynamics</term>
<term>Protein Folding</term>
<term>Protein Multimerization</term>
<term>Protein assembly</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>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
<affiliations><list><country><li>Taïwan</li>
</country>
</list>
<tree><country name="Taïwan"><noRegion><name sortKey="Hsu, Hao Jen" sort="Hsu, Hao Jen" uniqKey="Hsu H" first="Hao-Jen" last="Hsu">Hao-Jen Hsu</name>
</noRegion>
<name sortKey="Fischer, Wolfgang B" sort="Fischer, Wolfgang B" uniqKey="Fischer W" first="Wolfgang B." last="Fischer">Wolfgang B. Fischer</name>
<name sortKey="Fischer, Wolfgang B" sort="Fischer, Wolfgang B" uniqKey="Fischer W" first="Wolfgang B." last="Fischer">Wolfgang B. Fischer</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001428 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001428 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Sante
   |area=    CovidV2
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     ISTEX:5A6E845FD1DA81AF5C42B2F1A7FC9CFDD24DD3F6
   |texte=   In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV
}}

This area was generated with Dilib version V0.6.33.
Data generation: Sat Mar 28 17:51:24 2020. Site generation: Sun Jan 31 15:35:48 2021

Serveur d'exploration Covid (26 mars)

In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV

In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

	Serveur d'exploration Covid (26 mars)
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.