期刊
PHYSICAL REVIEW LETTERS
卷 102, 期 23, 页码 -出版社
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevLett.102.238102
关键词
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资金
- National Institutes of Health [GM-14312]
- National Science Foundation [MCB05-41633]
- National Science Foundation Terascale Computing System at the Pittsburgh Supercomputer Center
- John von Neumann Institute for Computing at the Central Institute for Applied Mathematics
- Forschungszentrum Juelich, Germany
- Department of Computer Science
- Informatics Center of the Metropolitan Academic Network (IC MAN)
- Interdisciplinary Center of Mathematical and Computer Modeling
The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.
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