A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.
Identifieur interne : 002B97 ( Main/Exploration ); 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
Affiliations:
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Le document en format XML
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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. 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