Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability

Abstract

We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $ψ$ (N-C$^α$-C-N) and $ζ$ (C$^β$-C$^α$-C-N) of the backbone dihedral angles. We then performed folding simulations of $α$-helical and $β$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.

10 pages, (Revtex4.1), 6 figures. arXiv admin note: substantial text overlap with arXiv:1208.6150, arXiv:1206.3909