Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.
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.
Liu
Pu
P
Department of Chemistry, Columbia University, New York, New York 10027, USA.
Huang
Xuhui
X
Zhou
Ruhong
R
Berne
B J
BJ
D000465:Algorithms; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008722:Methods; D017510:Protein Folding; D012997:Solvents; D014867:Water / Q000737:chemistry
D012997:Solvents; D014867:Water