PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification

Abstract

A further parametrization of a united-atom protein model coupled with coarse-grained water has been carried out to cover all amino acids (AAs). The local conformational features of each AA have been fitted on the basis of restricted coil-library statistics of high-resolution X-ray crystal structures of proteins. Potential functions were developed on the basis of combined backbone and side chain rotamer conformational preferences, or rotamer Ramachandran plots (ϕ, Ψ, χ1). Side chain-side chain and side chain-backbone interaction potentials were parametrized to fit the potential mean forces of corresponding all-atom simulations. The force field has been applied in molecular dynamics simulations of several proteins of 56-108 AA residues whose X-ray crystal and/or NMR structures are available. Starting from the crystal structures, each protein was simulated for about 100 ns. The Cα RMSDs of the calculated structures are 2.4-4.2 Å with respect to the crystal and/or NMR structures, which are still larger than but close to those of all-atom simulations (1.1-3.6 Å). Starting from the PDB structure of malate synthase G of 723 AA residues, the wall-clock time of a 30 ns simulation is about three days on a 2.65 GHz dual-core CPU. The RMSD to the experimental structure is about 4.3 Å. These results implicate the applicability of the force field in the study of protein structures.