Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes.

ABSTRACT: Translocation in the single subunit T7 RNA polymerase elongation complex was studied by molecular dynamics simulations using the posttranslocated crystal structure with the fingers domain open, an intermediate stable in the absence of pyrophosphate, magnesium ions, and nucleotide substrate. Unconstrained and umbrella sampling simulations were performed to examine the energetics of translocations. The extent of translocation was quantified using reaction coordinates representing the average and individual displacements of the RNA-DNA hybrid base pairs with respect to a reference structure. In addition, an unconstrained simulation was also performed for the product complex with the fingers domain closed, but with the pyrophosphate and magnesium removed, in order to examine the local stabilit

SUBMITTER: Woo HJ 

PROVIDER: S-EPMC4447105 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature