title: Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB.
abstract: 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 α-helical structures such as polyalanine peptides, Trp-cage miniprotein, and villin headpiece subdomain and β-sheet structures such as Trpzip-2, GB1 β-hairpins, and the WW domain, simultaneously. The properties of various popular force fields in balancing between α-helix and β-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 α-helix and β-sheet, RSFF2 gives melting curves of α-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.
authors.affiliation: College of Chemistry and Molecular Engineering, Peking University , Beijing, 100871, China.
authors.forename: Chen-Yang
authors.initials: CY
authors.lastname: Zhou
authors.forename: Fan
authors.initials: F
authors.lastname: Jiang
authors.forename: Yun-Dong
authors.initials: YD
authors.lastname: Wu
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D019277:Entropy; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D011489:Protein Denaturation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D004151:Dipeptides; D010455:Peptides; D011506:Proteins; C019529:polyalanine