Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.

ABSTRACT: The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The princi

SUBMITTER: Gur M 

PROVIDER: S-EPMC3739829 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature