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Free-energy-driven folding and thermodynamics of the 67-residue protein GS-α3W—A large-scale Monte Carlo study
Article first published online: 4 JUN 2009
DOI: 10.1002/jcc.21321
Copyright © 2009 Wiley Periodicals, Inc.
Issue
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
Journal of Computational Chemistry
Special Issue: Free Energy Simulations: Methods and Applications
Volume 30, Issue 11, pages 1642–1648, August 2009
Additional Information
How to Cite
Meinke, J. H. and Hansmann, U. H. E. (2009), Free-energy-driven folding and thermodynamics of the 67-residue protein GS-α3W—A large-scale Monte Carlo study. Journal of Computational Chemistry, 30: 1642–1648. doi: 10.1002/jcc.21321
Publication History
- Issue published online: 12 JUN 2009
- Article first published online: 4 JUN 2009
- Manuscript Accepted: 8 APR 2009
- Manuscript Received: 20 JAN 2009
Funded by
- National Science Foundation. Grant Number: CHE-0809002
- Abstract
- Article
- References
- Cited By
Keywords:
- protein folding;
- Monte Carlo simulation;
- supercomputing
Graphical Abstract
Abstract
Utilizing the computational power of a few thousand processors on a BlueGene/P, we have explored the folding mechanism of the 67-residue protein GS-α3W. Results from our large-scale simulation indicate a diffusion-collision mechanism for folding. However, the lower-than-expected frequency of native-like configurations at physiological temperatures indicates shortcomings of our energy function. Our results suggest that computational studies of large proteins call for redevelopment and reparametrization of force fields that in turn require extensive simulations only possible with the newly available supercomputers with computing powers reaching the petaflop range. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009