Journal
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
Volume 5, Issue 7, Pages 1217-1224Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jz500179a
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Funding
- National Science Foundation [MCB-0953061]
- Georgia Research Alliance
- Georgia State's IBM System p7 supercomputer through a partnership of the Southeastern Universities Research Association
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0953061] Funding Source: National Science Foundation
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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 alpha-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed beta-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. RaiMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.
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