title: 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.
authors.affiliation: Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Han
authors.affiliation: Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China.
authors.forename: Cheuk-Kin
authors.initials: CK
authors.lastname: Wan
authors.affiliation: Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Jiang
authors.affiliation: Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China.
authors.forename: Yun-Dong
authors.initials: YD
authors.lastname: Wu