Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.
Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.
Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States.
Urmi
U
Doshi
Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302-3965, United States.
Donald
D
Hamelberg
Chignolin; RaMD; Trp-cage; aMD; accelerated molecular dynamics; enhanced conformational sampling method; protein folding