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.
Keywords
MicrosecondMolecular dynamicsNanosecondProtein foldingAqueous solutionFolding (DSP implementation)SolvationChemical physicsChemistryCrystallographyNative stateIntermediate stateContact orderFolding funnelPhi value analysisDownhill foldingComputational chemistryMoleculePhysicsPhysical chemistryBiochemistryAtomic physics
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Publication Info
- Year
- 1998
- Type
- article
- Volume
- 282
- Issue
- 5389
- Pages
- 740-744
- Citations
- 1334
- Access
- Closed
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Cite This
Yong Duan,
Peter A. Kollman
(1998).
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution.
Science
, 282
(5389)
, 740-744.
https://doi.org/10.1126/science.282.5389.740
Identifiers
- DOI
- 10.1126/science.282.5389.740