Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins.
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.
RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Ryuhei
R
Harada
JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
Yu
Y
Takano
JST, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
Yasuteru
Y
Shigeta
D017122:Bacteriophage T4 / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation
D009113:Muramidase