Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism.

ABSTRACT: Molecular dynamics simulations of a total duration of 30 ns in explicit solvent were carried out on the BPV-1-E2 protein complexed to a high-affinity DNA target containing the two hydrogen-bonded ACCG.CGGT half-sites separated by the noncontacted ACGT sequence. The analysis of the trajectories focuses on the DNA structure and on the dynamics. The data are compared to those issued from recent simulations made on three free targets that recognize E2 with different affinities. E2 does not drastically perturb the mechanic properties of the free DNA: the structural relationships between the BI/BII backbone substates and some helical parameters are preserved in the complex despite a severe slowing down of the phosphate group motions. The structures of both free and bound half-sites are very clos

SUBMITTER: Djuranovic D 

PROVIDER: S-EPMC1366753 | biostudies-literature | 2005 Oct

REPOSITORIES: biostudies-literature