title: Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins.
abstract: Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2Dforce field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2Dforce fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.
authors.affiliation: College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China.
authors.forename: Ya
authors.identifier: 0000-0002-4391-430X
authors.initials: Y
authors.lastname: Gao
authors.affiliation: College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China.
authors.forename: Chaomin
authors.initials: C
authors.lastname: Zhang
authors.affiliation: College of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.|Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.|Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China.|State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
mesh_terms: D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation
chemical_list: D064267:Intrinsically Disordered Proteins