title: Coupled two-dimensional main-chain torsional potential for protein dynamics II: performance and validation.
abstract: The accuracy of force fields is of utmost importance in molecular modeling of proteins. Despite successful applications of force fields for about the past 30 years, some inherent flaws lying in force fields, such as biased secondary propensities and fixed atomic charges, have been observed in different aspects of biomolecular research; hence, a correction to current force fields is desirable. Because of the simplified functional form and the limited number of parameters for main chain torsion (MCT) in traditional force fields, it is not easy to propose an exquisite force field that is well-balanced among various conformations. Recently, AMBER-compatible force fields with coupled MCT term have been proposed, which show some improvement over AMBER03 and AMBER99SB force fields. In this work, further calibration of the torsional parameters has been conducted by changing the solvation model in quantum mechanical calculation and minimizing the deviation from the nuclear magnetic resonance experiments for some benchmark model systems and a folded protein. The results show that the revised force fields give excellent agreement with experiments in J coupling, chemical shifts, and secondary structure populations. In addition, the polarization effect is found to be crucial for the systems with ordered secondary structures.
authors.affiliation: †College of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Gao
authors.affiliation: †College of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China.|¶Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education, Hubei Province, South-Central University for Nationalities, Wuhan 430074, China.
authors.forename: Yongxiu
authors.initials: Y
authors.lastname: Li
authors.affiliation: §Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062, China.
authors.forename: Lirong
authors.initials: L
authors.lastname: Mou
authors.forename: Wenxin
authors.initials: W
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Zheng
authors.affiliation: †College of Fundamental Studies, Shanghai University of Engineering Science, Shanghai 201620, China.|⊥NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: ‡Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.|⊥NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
mesh_terms: D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D011789:Quantum Theory; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism
chemical_list: D009842:Oligopeptides; D011506:Proteins; D025801:Ubiquitin