Residue-Specific Force Field Based on the Protein Coil Library. RSFF1:   Modification of OPLS-AA/L

doi:10.1021/jp5017449

CORC > 北京大学 > 化学与分子工程学院

	Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L
	Jiang, Fan ; Zhou, Chen-Yang ; Wu, Yun-Dong
刊名	journal of physical chemistry b
	2014
关键词	MOLECULAR-DYNAMICS SIMULATIONS FOLDING SIMULATIONS SIDE-CHAIN SECONDARY-STRUCTURE COUPLING-CONSTANTS AMINO-ACIDS ORGANIC-MOLECULES CONFORMATIONAL PREFERENCES BACKBONE CONFORMATIONS PEPTIDE BACKBONE
DOI	10.1021/jp5017449
英文摘要	Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil library were used as the target data. The dihedral angle (torsion) potentials and some local nonbonded (1-4/1-5/1-6) interactions in OPLS-AA/L force field were modified such that the target data can be excellently reproduced by molecular dynamics simulations of dipeptides (blocked AAs) in explicit water, resulting in a new force field with AA-specific parameters, RSFF1. An efficient free energy decomposition approach was developed to separate the corrections on phi and psi from the two-dimensional Ramachandran plots. RSFF1 is shown to reproduce the experimental NMR (3)J-coupling constants of AA dipeptides better than other force fields. It has a good balance between alpha-helical and beta-sheet secondary structures. It can successfully fold a set of alpha-helix proteins (Trp-cage and Homeodomain) and beta-hairpins (Trpzip-2, GB1 hairpin), which cannot be consistently stabilized by other state-of-the-art force fields. Interestingly, the RSFF1 force field systematically overestimates the melting temperature (and the stability of native state) of these peptides/proteins. It has a potential application in the simulation of protein folding and protein structure refinement.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000338184400001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Chemistry, Physical; SCI(E); EI; PubMed; 19; ARTICLE; jiangfan@pku.edu.cn; wuyd@pkusz.edu.cn; 25; 6983-6998; 118
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/189682]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Jiang, Fan,Zhou, Chen-Yang,Wu, Yun-Dong. Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L[J]. journal of physical chemistry b,2014.
APA	Jiang, Fan,Zhou, Chen-Yang,&Wu, Yun-Dong.(2014).Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L.journal of physical chemistry b.
MLA	Jiang, Fan,et al."Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L".journal of physical chemistry b (2014).