Abstract:
BACKGROUND: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. RESULTS:The one turn alpha-helix chain (residues 47-54) of the SARS CoVMpro was directly involved in the induced-fit model of the enzyme-substrate complex. The S3 subsite of the enzyme had a negatively charged region due to the presence of Glu47. During MD simulations, Glu47 of the enzyme was shown to play a key role in electrostatic bonding with the P3Lys of the octapeptide. CONCLUSION:MD simulations were carried out on the SARS CoVMpro-octapeptide complex. The hypothesis proposed that Glu47 of SARS CoVMpro is an important residue in the S3 subsite and is involved in binding with P3Lys of the octapeptide.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Phakthanakanok K,Ratanakhanokchai K,Kyu KL,Sompornpisut P,Watts A,Pinitglang Sdoi
10.1186/1471-2105-10-S1-S48subject
Has Abstractpub_date
2009-01-30 00:00:00pages
S48issn
1471-2105pii
1471-2105-10-S1-S48journal_volume
10 Suppl 1pub_type
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