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How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

ABSTRACT: 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.

SUBMITTER: Maisuradze GG

PROVIDER: S-EPMC2760970 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

Maisuradze Gia G GG Liwo Adam A Scheraga Harold A HA

Physical review letters 20090612 23

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. Simi ...[more]

PMID: 19658975

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