Molecular dynamics simulations of p53 DNA-binding domain.

ABSTRACT: We have studied room-temperature structural and dynamic properties of the p53 DNA-binding domain in both DNA-bound and DNA-free states. A cumulative 55 ns of explicit solvent molecular dynamics simulations with the particle mesh Ewald treatment of electrostatics was performed. It was found that the mean structures in the production portions of the trajectories agree well with the crystal structure: backbone root-mean-square deviations are in the range of 1.6 and 2.0 A. In both simulations, noticeable backbone deviations from the crystal structure are observed only in loop L6, due to the lack of crystal packing in the simulations. More deviations are observed in the DNA-free simulation, apparently due to the absence of DNA. Computed backbone B-factor is also in qualitative agreement with th

SUBMITTER: Lu Q 

PROVIDER: S-EPMC2522240 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature