期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 119, 期 3, 页码 1035-1047出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp5064676
关键词
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资金
- National Natural Science Foundation of China [21133002, 21203004]
- Shenzhen Peacock Program [KQTD201103]
- Peking University Shenzhen Graduate School
Recently, we developed a residue-specific force field (RSFF1) based on conformational free-energy distributions of the 20 amino acid residues from a protein coil library. Most parameters in RSFF1 were adopted from the OPLS-AA/L force field, but some van der Waals and torsional parameters that effectively affect local conformational preferences were introduced specifically for individual residues to fit the coil library distributions. Here a similar strategy has been applied to modify the Amber ff99SB force field, and a new force field named RSFF2 is developed. It can successfully fold a-helical structures such as polyalanine peptides, Trp-cage miniprotein, and villin headpiece subdomain and beta-sheet structures such as Trpzip-2, GB1 beta-hairpins, and the WW domain, simultaneously. The properties of various popular force fields in balancing between a-helix and beta-sheet are analyzed based on their descriptions of local conformational features of various residues, and the analysis reveals the importance of accurate local free-energy distributions. Unlike the RSFF1, which overestimates the stability of both alpha-helix and beta-sheet, RSFF2 gives melting curves of alpha-helical peptides and Trp-cage in good agreement with experimental data. Fitting to the two-state model, RSFF2 gives folding enthalpies and entropies in reasonably good agreement with available experimental results.
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