Journal
BIOPHYSICAL JOURNAL
Volume 97, Issue 8, Pages 2338-2347Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2009.08.012
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Funding
- National Institutes of Health [P41-RR05969]
- National Science Foundation [PHY0822613]
- National Center for Supercomputing Applications [MCA93S028]
- Beckman Institute at the University of Illinois at Urbana-Champaign
- Direct For Mathematical & Physical Scien
- Division Of Physics [0822613] Funding Source: National Science Foundation
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Molecular dynamics simulations of protein folding can provide very high-resolution data on the folding process; however, due to computational challenges most studies of protein folding have been limited to small peptides, or made use of approximations such as Go potentials or implicit solvent models. We have performed a set of molecular dynamics simulations totaling >50 mu s on the villin headpiece subdomain, one of the most stable and fastest-folding naturally occurring proteins, in explicit solvent. We find that the wild-type villin headpiece reliably folds to a native conformation on timescales similar to experimentally observed folding, but that a fast folding double-norleucine mutant shows significantly more heterogeneous behavior. Along with other recent simulation studies, we note the occurrence of nonnative structures intermediates, which may yield a nativelike signal in the fluorescence measurements typically used to study villin folding. Based on the wild-type simulations, we propose alternative approaches to measure the formation of the native state.
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