期刊
JOURNAL OF STRUCTURAL BIOLOGY
卷 157, 期 3, 页码 514-523出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2006.10.002
关键词
replica exchange; molecular dynamics; protein folding; protein dynamics; Trp-cage; all-atom; explicit solvent
资金
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM050789] Funding Source: NIH RePORTER
- NIGMS NIH HHS [R01 GM050789] Funding Source: Medline
Two independent replica-exchange molecular dynamics (REMD) simulations with an explicit water model were performed of the Trp-cage mini-protein. In the first REMD simulation, the replicas started from the native conformation, while in the second they started from a normative conformation. Initially, the first simulation yielded results qualitatively similar to those of two previously published REMD simulations: the protein appeared to be over-stabilized, with the predicted melting temperature 50-150 K higher than the experimental value of 315 K. However, as the first REMD simulation progressed, the protein unfolded at all temperatures. In our second REMD simulation, which starts from a normative conformation, there was no evidence of significant folding. Transitions from the unfolded to the folded state did not occur on the timescale of these simulations, despite the expected improvement in sampling of REMD over conventional molecular dynamics (MD) simulations. The combined 1.42 mu s of simulation time was insufficient for REMD simulations with different starting structures to converge. Conventional MID simulations at a range of temperatures were also performed. In contrast to REMD, the conventional MD simulations provide an estimate of Tm in good agreement with experiment. Furthermore, the conventional MD is a fraction of the cost of REMD and continuous, realistic pathways of the unfolding process at atomic resolution are obtained. (c) 2006 Elsevier Inc. All rights reserved.
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