Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

ABSTRACT: The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. We used two computational methods to examine the protein's thermal fluctuations, including both the large-scale interdomain movements that contribute to the receptor's mechanism of action, as well as smaller-scale motions. We primarily employ extremely fast, "semi-atomistic" Library-Based Monte Carlo (LBMC) simulations, which include all backbone atoms but "implicit" side chains. Our results were compared with previous experiments and all-atom molecular dynamics (MD) simulation. Both LBMC and MD simulations were performed using both the apo and glucose-bound form of the protein, with LBMC exhibiting significantly larger fluctuations. The LBMC simulations are i

SUBMITTER: Cashman DJ 

PROVIDER: S-EPMC3021764 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature