A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: Implication for structure and active site binding mechanism
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Author list: Phakthanakanok K., Ratanakhanokchai K., Kyu K.L., Sompornpisut P., Watts A., Pinitglang S.
Publisher: BioMed Central
Publication year: 2009
Volume number: 10
Issue number: SUPPL. 1
ISSN: 1471-2105
eISSN: 1471-2105
Languages: English-Great Britain (EN-GB)
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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 α-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. © 2009 Phakthanakanok et al; licensee BioMed Central Ltd.
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