Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution

Author:

Duan Yong1,Kollman Peter A.1

Affiliation:

1. Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.

Abstract

An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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