The intrinsic conformational features of amino acids from a protein coil   library and their applications in force field development

doi:10.1039/c2cp43633g

CORC > 北京大学 > 化学与分子工程学院

	The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development
	Jiang, Fan ; Han, Wei ; Wu, Yun-Dong
刊名	physical chemistry chemical physics
	2013
关键词	MOLECULAR-DYNAMICS SIMULATIONS ALANINE-BASED PEPTIDES GENERALIZED-ENSEMBLE SIMULATIONS QUANTUM-MECHANICAL CALCULATIONS RESIDUAL DIPOLAR COUPLINGS POLYPROLINE-II STRUCTURE SIDE-CHAIN AB-INITIO FOLDING SIMULATIONS SECONDARY-STRUCTURE
DOI	10.1039/c2cp43633g
英文摘要	The local conformational (phi, chi, chi) preferences of amino acid residues remain an active research area, which are important for the development of protein force fields. In this perspective article, we first summarize spectroscopic studies of alanine-based short peptides in aqueous solution. While most studies indicate a preference for the P-II conformation in the unfolded state over alpha and beta conformations, significant variations are also observed. A statistical analysis from various coil libraries of high-resolution protein structures is then summarized, which gives a more coherent view of the local conformational features. The phi, chi, chi distributions of the 20 amino acids have been obtained from a protein coil library, considering both backbone and side-chain conformational preferences. The intrinsic side-chain chi(1) rotamer preference and chi(1)-dependent Ramachandran plot can be generally understood by combining the interaction of the side-chain C gamma/O gamma atom with two neighboring backbone peptide groups. Current all-atom force fields such as AMBER ff99sb-ILDN, ff03 and OPLS-AA/ L do not reproduce these distributions well. A method has been developed by combining the phi, psi plot of alanine with the influence of side-chain chi(1) rotamers to derive the local conformational features of various amino acids. It has been further applied to improve the OPLS-AA force field. The modified force field (OPLS-AA/ C) reproduces experimental (3)J coupling constants for various short peptides quite well. It also better reproduces the temperature-dependence of the helix-coil transition for alanine-based peptides. The new force field can fold a series of peptides and proteins with various secondary structures to their experimental structures. MD simulations of several globular proteins using the improved force field give significantly less deviation (RMSD) to experimental structures. The results indicate that the local conformational features from coil libraries are valuable for the development of balanced protein force fields.; Chemistry, Physical; Physics, Atomic, Molecular & Chemical; SCI(E); PubMed; 9; ARTICLE; 10; 3413-3428; 15
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/190689]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Jiang, Fan,Han, Wei,Wu, Yun-Dong. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development[J]. physical chemistry chemical physics,2013.
APA	Jiang, Fan,Han, Wei,&Wu, Yun-Dong.(2013).The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.physical chemistry chemical physics.
MLA	Jiang, Fan,et al."The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development".physical chemistry chemical physics (2013).