Journal
JOURNAL OF STRUCTURAL BIOLOGY
Volume 157, Issue 3, Pages 491-499Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2006.10.001
Keywords
molecular dynamics; simulation; protein folding; alpha-helix; distributed computing
Funding
- NCRR NIH HHS [P41 RR006009] Funding Source: Medline
- NIGMS NIH HHS [R01 GM062868, GM62868] Funding Source: Medline
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Massively parallel all-atom, explicit solvent molecular dynamics simulations were used to explore the formation and existence of local structure in two small a-helical proteins, the villin headpiece and the helical fragment B of protein A. We report on the existence of transient helices and combinations of helices in the unfolded ensemble, and on the order of formation of helices, which appears to largely agree with previous experimental results. Transient local structure is observed even in the absence of overall native structure. We also calculate sets of residue-residue pairs that are statistically predictive of the formation of given local structures in our simulations. (c) 2006 Elsevier Inc. All rights reserved.
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