A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin.

ABSTRACT: Atomically detailed simulations are used to compute the kinetics of the R-to-T transition in deoxy Scapharca hemoglobin. A computational approach called milestoning is utilized that combines 1), an efficient reaction path algorithm; and 2), a "fragment and glue" approach for classical trajectories. Milestoning computes the R-to-T transition kinetics on the microsecond timescale based on atomically detailed trajectories that rarely exceed a nanosecond. Eleven reference hypersurfaces (milestones) are constructed along the reaction coordinate, which is computed with a global path optimization algorithm. Two-hundred classical trajectories are calculated for each of the milestones to collect local distributions of first passage times. These local distributions are used in a non-Markovian theory

SUBMITTER: Elber R 

PROVIDER: S-EPMC1852362 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature