期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 385, 期 1, 页码 312-329出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2008.10.018
关键词
principal component analysis; 1E0L; UNRES force field; folding dynamics; anomalous diffusion
资金
- National Institutes of Health [GM-14312]
- National Science Foundation [MCB05-41633]
- Fogarty Foundation [Fogarty Foundation (TW7193]
- Beowulf cluster at the Baker Laboratory of Chemistry and Chemical Biology, Cornell University
- National Science Foundation Terascale Computing System at the Pittsburgh Supercomputer Center
- John von Neumanri Institute for Computing at the Central Institute for Applied Mathematics, Forschungszentrum Juelich, Germany
- Department of Computer Science, Cornell University
- Center for Computation and Technology at Louisiana State University
- Louisiana legislature
- Faculty of Chemistry, University of Gdansk
Protein folding is considered here by studying the dynamics of the folding of the triple beta-strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and ending either in the native or normative conformational states, trajectories are generated with the coarse-grained united residue (UNRES) force field. The effectiveness of principal components analysis (PCA), an already established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories. The problems related to PCA and their solutions are discussed. The folding and nonfolding of proteins are examined with free-energy landscapes. Detailed analyses of many folding and nonfolding trajectories at different temperatures show that PCA is very efficient for characterizing the general folding and nonfolding features of proteins. It is shown that the first principal component captures and describes in detail the dynamics of a system. Anomalous diffusion in the folding/nonfolding dynamics is examined by the mean-square displacement (MSD) and the fractional diffusion and fractional kinetic equations. The collisionless (or ballistic) behavior of a polypeptide undergoing Brownian motion along the first few principal components is accounted for. (C) 2008 Elsevier Ltd. All rights reserved.
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