Ten-microsecond MD simulation of a fast-folding WW domain
Peter L. Freddolino 1, Feng Liu 1, Martin H. Gruebele 1 and Klaus Schulten 2*
1 University of Illinois at Urbana-Champaign
2 University of Illinois 3143 Beckman Institute
* To whom correspondence should be addressed. E-mail: kschulte{at}ks.uiuc.edu.
Submitted on February 17, 2008
Revised on March 2, 2008
Accepted on 4 March 2008
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Abstract |
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All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the folded structure. The ongoing study of protein folding through computational methods thus requires both improvements in the performance of molecular dynamics programs to make longer timescales accessible, and testing of force fields in the context of folding simulations. We report a ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds, respectively. The protein simulated in explicit solvent exhibits several metastable states with incorrect topology and does not assume the native state during the present simulations.
Key Words:
WW domain, kinetics, molecular dynamics, protein folding
