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

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Science  23 Oct 1998:
Vol. 282, Issue 5389, pp. 740-744
DOI: 10.1126/science.282.5389.740

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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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