A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.
Identifieur interne : 002B97 ( Main/Curation ); précédent : 002B96; suivant : 002B98A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.
Auteurs : Krongsakda Phakthanakanok [Thaïlande] ; Khanok Ratanakhanokchai ; Khin Lay Kyu ; Pornthep Sompornpisut ; Aaron Watts ; Surapong PinitglangSource :
- BMC bioinformatics [ 1471-2105 ] ; 2009.
Descripteurs français
- KwdFr :
- Biologie informatique (), Conformation des protéines, Cysteine endopeptidases (), Cysteine endopeptidases (métabolisme), Domaine catalytique, Inhibiteurs de la cystéine protéinase (), Inhibiteurs de la cystéine protéinase (métabolisme), Liaison hydrogène, Modèles moléculaires, Oligopeptides (), Oligopeptides (métabolisme), Protéines virales (), Protéines virales (métabolisme), Relation structure-activité, Sites de fixation, Spécificité du substrat, Virus du SRAS (enzymologie), Virus du SRAS (métabolisme).
- MESH :
- enzymologie : Virus du SRAS.
- métabolisme : Cysteine endopeptidases, Inhibiteurs de la cystéine protéinase, Oligopeptides, Protéines virales, Virus du SRAS.
- Biologie informatique, Conformation des protéines, Cysteine endopeptidases, Domaine catalytique, Inhibiteurs de la cystéine protéinase, Liaison hydrogène, Modèles moléculaires, Oligopeptides, Protéines virales, Relation structure-activité, Sites de fixation, Spécificité du substrat.
English descriptors
- KwdEn :
- Binding Sites, Catalytic Domain, Computational Biology (methods), Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (metabolism), Cysteine Proteinase Inhibitors (chemistry), Cysteine Proteinase Inhibitors (metabolism), Hydrogen Bonding, Models, Molecular, Oligopeptides (chemistry), Oligopeptides (metabolism), Protein Conformation, SARS Virus (enzymology), SARS Virus (metabolism), Structure-Activity Relationship, Substrate Specificity, Viral Proteins (chemistry), Viral Proteins (metabolism).
- MESH :
- chemical , chemistry : Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Oligopeptides, Viral Proteins.
- chemical , metabolism : Cysteine Endopeptidases, Cysteine Proteinase Inhibitors, Oligopeptides, Viral Proteins.
- enzymology : SARS Virus.
- metabolism : SARS Virus.
- methods : Computational Biology.
- Binding Sites, Catalytic Domain, Hydrogen Bonding, Models, Molecular, Protein Conformation, Structure-Activity Relationship, Substrate Specificity.
Abstract
SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to structural-based drug design. The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach.
DOI: 10.1186/1471-2105-10-S1-S48
PubMed: 19208150
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001952
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :001952
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001956
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :001E45
- to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :001E45
- to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001E45
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :002C51
Links to Exploration step
pubmed:19208150Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.</title>
<author><name sortKey="Phakthanakanok, Krongsakda" sort="Phakthanakanok, Krongsakda" uniqKey="Phakthanakanok K" first="Krongsakda" last="Phakthanakanok">Krongsakda Phakthanakanok</name>
<affiliation wicri:level="1"><nlm:affiliation>Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand. s7500802@st.kmutt.ac.th</nlm:affiliation>
<country xml:lang="fr">Thaïlande</country>
<wicri:regionArea>Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok</wicri:regionArea>
<wicri:noRegion>Bangkok</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ratanakhanokchai, Khanok" sort="Ratanakhanokchai, Khanok" uniqKey="Ratanakhanokchai K" first="Khanok" last="Ratanakhanokchai">Khanok Ratanakhanokchai</name>
</author>
<author><name sortKey="Kyu, Khin Lay" sort="Kyu, Khin Lay" uniqKey="Kyu K" first="Khin Lay" last="Kyu">Khin Lay Kyu</name>
</author>
<author><name sortKey="Sompornpisut, Pornthep" sort="Sompornpisut, Pornthep" uniqKey="Sompornpisut P" first="Pornthep" last="Sompornpisut">Pornthep Sompornpisut</name>
</author>
<author><name sortKey="Watts, Aaron" sort="Watts, Aaron" uniqKey="Watts A" first="Aaron" last="Watts">Aaron Watts</name>
</author>
<author><name sortKey="Pinitglang, Surapong" sort="Pinitglang, Surapong" uniqKey="Pinitglang S" first="Surapong" last="Pinitglang">Surapong Pinitglang</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2009">2009</date>
<idno type="RBID">pubmed:19208150</idno>
<idno type="pmid">19208150</idno>
<idno type="doi">10.1186/1471-2105-10-S1-S48</idno>
<idno type="wicri:Area/PubMed/Corpus">001952</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001952</idno>
<idno type="wicri:Area/PubMed/Curation">001952</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001952</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001956</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001956</idno>
<idno type="wicri:Area/Ncbi/Merge">001E45</idno>
<idno type="wicri:Area/Ncbi/Curation">001E45</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001E45</idno>
<idno type="wicri:Area/Main/Merge">002C51</idno>
<idno type="wicri:Area/Main/Curation">002B97</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.</title>
<author><name sortKey="Phakthanakanok, Krongsakda" sort="Phakthanakanok, Krongsakda" uniqKey="Phakthanakanok K" first="Krongsakda" last="Phakthanakanok">Krongsakda Phakthanakanok</name>
<affiliation wicri:level="1"><nlm:affiliation>Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand. s7500802@st.kmutt.ac.th</nlm:affiliation>
<country xml:lang="fr">Thaïlande</country>
<wicri:regionArea>Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok</wicri:regionArea>
<wicri:noRegion>Bangkok</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Ratanakhanokchai, Khanok" sort="Ratanakhanokchai, Khanok" uniqKey="Ratanakhanokchai K" first="Khanok" last="Ratanakhanokchai">Khanok Ratanakhanokchai</name>
</author>
<author><name sortKey="Kyu, Khin Lay" sort="Kyu, Khin Lay" uniqKey="Kyu K" first="Khin Lay" last="Kyu">Khin Lay Kyu</name>
</author>
<author><name sortKey="Sompornpisut, Pornthep" sort="Sompornpisut, Pornthep" uniqKey="Sompornpisut P" first="Pornthep" last="Sompornpisut">Pornthep Sompornpisut</name>
</author>
<author><name sortKey="Watts, Aaron" sort="Watts, Aaron" uniqKey="Watts A" first="Aaron" last="Watts">Aaron Watts</name>
</author>
<author><name sortKey="Pinitglang, Surapong" sort="Pinitglang, Surapong" uniqKey="Pinitglang S" first="Surapong" last="Pinitglang">Surapong Pinitglang</name>
</author>
</analytic>
<series><title level="j">BMC bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2009" type="published">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term>
<term>Catalytic Domain</term>
<term>Computational Biology (methods)</term>
<term>Cysteine Endopeptidases (chemistry)</term>
<term>Cysteine Endopeptidases (metabolism)</term>
<term>Cysteine Proteinase Inhibitors (chemistry)</term>
<term>Cysteine Proteinase Inhibitors (metabolism)</term>
<term>Hydrogen Bonding</term>
<term>Models, Molecular</term>
<term>Oligopeptides (chemistry)</term>
<term>Oligopeptides (metabolism)</term>
<term>Protein Conformation</term>
<term>SARS Virus (enzymology)</term>
<term>SARS Virus (metabolism)</term>
<term>Structure-Activity Relationship</term>
<term>Substrate Specificity</term>
<term>Viral Proteins (chemistry)</term>
<term>Viral Proteins (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique ()</term>
<term>Conformation des protéines</term>
<term>Cysteine endopeptidases ()</term>
<term>Cysteine endopeptidases (métabolisme)</term>
<term>Domaine catalytique</term>
<term>Inhibiteurs de la cystéine protéinase ()</term>
<term>Inhibiteurs de la cystéine protéinase (métabolisme)</term>
<term>Liaison hydrogène</term>
<term>Modèles moléculaires</term>
<term>Oligopeptides ()</term>
<term>Oligopeptides (métabolisme)</term>
<term>Protéines virales ()</term>
<term>Protéines virales (métabolisme)</term>
<term>Relation structure-activité</term>
<term>Sites de fixation</term>
<term>Spécificité du substrat</term>
<term>Virus du SRAS (enzymologie)</term>
<term>Virus du SRAS (métabolisme)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cysteine Endopeptidases</term>
<term>Cysteine Proteinase Inhibitors</term>
<term>Oligopeptides</term>
<term>Viral Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cysteine Endopeptidases</term>
<term>Cysteine Proteinase Inhibitors</term>
<term>Oligopeptides</term>
<term>Viral Proteins</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="metabolism" xml:lang="en"><term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cysteine endopeptidases</term>
<term>Inhibiteurs de la cystéine protéinase</term>
<term>Oligopeptides</term>
<term>Protéines virales</term>
<term>Virus du SRAS</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term>
<term>Catalytic Domain</term>
<term>Hydrogen Bonding</term>
<term>Models, Molecular</term>
<term>Protein Conformation</term>
<term>Structure-Activity Relationship</term>
<term>Substrate Specificity</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term>
<term>Conformation des protéines</term>
<term>Cysteine endopeptidases</term>
<term>Domaine catalytique</term>
<term>Inhibiteurs de la cystéine protéinase</term>
<term>Liaison hydrogène</term>
<term>Modèles moléculaires</term>
<term>Oligopeptides</term>
<term>Protéines virales</term>
<term>Relation structure-activité</term>
<term>Sites de fixation</term>
<term>Spécificité du substrat</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to structural-based drug design. The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002B97 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 002B97 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= SrasV1 |flux= Main |étape= Curation |type= RBID |clé= pubmed:19208150 |texte= A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Curation/RBID.i -Sk "pubmed:19208150" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \ | NlmPubMed2Wicri -a SrasV1
This area was generated with Dilib version V0.6.33. |