Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity.

ABSTRACT: The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30-74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function.

SUBMITTER: Moustafa IM 

PROVIDER: S-EPMC3114172 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature