Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.

ABSTRACT: Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impac

SUBMITTER: Xue Y 

PROVIDER: S-EPMC3970899 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature