Bioinformatics Analysis of Mutant Structure and Functional Sites of Foot-and-Mouth Disease Virus RNA-Dependent RNA Polymerase

Authors: Zeng, Tao; Mo, Zhongxi

Source: Journal of Computational and Theoretical Nanoscience, Volume 4, Numbers 7-8, November/December 2007 , pp. 1330-1336(7)

Publisher: American Scientific Publishers

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Abstract:

Foot-and-mouth disease virus (FMDV) RNA polymerase is an RNA-dependent RNA polymerase (RdRp). The efficiency of RdRp is critical to the replication of the viral genomic RNA. In this article, the three-dimensional structure and functional sites of four mutants of the FMDV RdRp were predicted using bioinformatic approaches. Our prediction revealed that the active cavity of RdRp is composed of three functional domains and two highly conserved regions in RdRp—the known catalytic site Asp245 and a possible binding site at 294-304:GGmpsGCsaTS. Through molecular docking, we also found that after the protein primer VPg was binds to the RNA polymerase, VPg's orientation determines the catalytic activity of FMDV RdRp.

Keywords: RNA-DEPENDENT RNA POLYMERASE (RDRP); STRUCTURAL ALIGNMENT; MOLECULAR DOCKING; QUATERNION

Document Type: Research article

DOI: 10.1166/jctn.2007.020