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

Yong Duan and Peter A. Kollman
Science
New Series, Vol. 282, No. 5389 (Oct. 23, 1998), pp. 740-744
Stable URL: http://www.jstor.org/stable/2899265
Page Count: 5
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Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
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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.

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