Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB

J Phys Chem B. 2015 Jan 22;119(3):1035-47. doi: 10.1021/jp5064676. Epub 2014 Oct 30.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Dipeptides / chemistry
  • Entropy
  • Molecular Dynamics Simulation*
  • Peptides / chemistry
  • Protein Denaturation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Transition Temperature

Substances

  • Dipeptides
  • Peptides
  • Proteins
  • polyalanine