Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent

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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 α-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.