Document Detail


Ten-microsecond molecular dynamics simulation of a fast-folding WW domain.
MedLine Citation:
PMID:  18339748     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Peter L Freddolino; Feng Liu; Martin Gruebele; Klaus Schulten
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Publication Detail:
Type:  Letter; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2008-03-13
Journal Detail:
Title:  Biophysical journal     Volume:  94     ISSN:  1542-0086     ISO Abbreviation:  Biophys. J.     Publication Date:  2008 May 
Date Detail:
Created Date:  2008-04-24     Completed Date:  2008-05-21     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  L75-7     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation
Models, Chemical*
Models, Molecular*
Peptidylprolyl Isomerase / chemistry*,  ultrastructure*
Protein Conformation
Protein Folding
Protein Structure, Tertiary*
Tryptophan / chemistry*
Grant Support
ID/Acronym/Agency:
P41RR05969/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/NIMA-interacting peptidylprolyl isomerase; 73-22-3/Tryptophan; EC 5.2.1.8/Peptidylprolyl Isomerase
Comments/Corrections

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