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