Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion.

ABSTRACT: Recent studies suggest that protein motions observed in molecular simulations are related to biochemical activities, although the computed time scales do not necessarily match those of the experimentally observed processes. The molecular origin of this conflicting observation is explored here for a test protein, cyanovirin-N (CV-N), through a series of molecular dynamics simulations that span a time range of three orders of magnitude up to 0.4 μs. Strikingly, increasing the simulation time leads to an approximately uniform amplification of the motional sizes, while maintaining the same conformational mechanics. Residue fluctuations exhibit amplitudes of 1-2 Å in the nanosecond simulations, whereas their average sizes increase by a factor of 4-5 in the microsecond regime. The mean-square di

SUBMITTER: Liu L 

PROVIDER: S-EPMC3290687 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature