Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
Abstract
A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.
- Publication:
-
Journal of Chemical Physics
- Pub Date:
- March 2014
- DOI:
- 10.1063/1.4869594
- Bibcode:
- 2014JChPh.140l5103H