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Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

Pu Liu·Xuhui Huang·Ruhong Zhou·B J Berne
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Abstract

A hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect of various protein amino acids in water by attenuating the protein-water attractive interactions (mimicking the Chaperon effect) while leaving other interactions among protein atoms and water molecules unchanged. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein within 4 ns, while the regular replica exchange method does not fold the same protein within 5 ns, even with many more replicas.

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AlgorithmsHydrophobic and Hydrophilic InteractionsKineticsMethodsProtein FoldingSolventsWaterJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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Pu Liu, Xuhui Huang, Ruhong Zhou, B J Berne. 2006-09-28. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.. https://doi.org/10.1021/jp060365r

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