Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained   Solvent Model: Solvation Free Energies of Amino Acid Side Chains

doi:10.1021/ct800184c

CORC > 北京大学 > 化学与分子工程学院

	Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains
	Han, Wei ; Wan, Cheuk-Kin ; Wu, Yun-Dong
刊名	journal of chemical theory and computation
	2008
关键词	INTERMOLECULAR POTENTIAL FUNCTIONS MOLECULAR-DYNAMICS SIMULATIONS ELECTRON CORRELATION-ENERGY ATOM FORCE-FIELD MEMBRANE-PROTEINS THERMODYNAMIC PROPERTIES LIPOPROTEIN PARTICLES PERTURBATION-THEORY AQUEOUS-SOLUTION TRP-CAGE
DOI	10.1021/ct800184c
英文摘要	Recently, we reported that molecular dynamics (MD) simulations using a coarse-grained (CG) peptide model coupled with a CG water model are able to reproduce many of the structural and thermodynamic features of short peptides with nonpolar side chains at 103 times the normal speed (JCTC, 2007, 3, 2146-2161). To further develop a CG protein model for MD simulations, we systematically parametrized the side chains of all 20 naturally occurring amino acids. We developed the parameters by fitting the dihedral potentials of 13 small molecules, the densities and self-solvation free energies of liquids of eight organic molecules, and the hydration free energies of 35 small organic molecules. In a set of 11 classes of compounds (105 in total) including alkanes, alcohols, ethers, ketones/aldehydes, amines, amides, aromatics, carboxylic acids, sulfides/thiols, alkyl ammoniums, and carboxylate ions, the average error in the calculated hydration free energies compared with experimental results is about 1.4 kJ/mol. The average error in the calculated transfer free energies of the 19 side-chain analogues of amino acids from cyclohexane to water is about 2.2 kJ/mol. These results are comparable to the results of all-atom models.; Chemistry, Physical; Physics, Atomic, Molecular & Chemical; SCI(E); PubMed; 0; ARTICLE; 11; 1891-1901; 4
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/248483]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Han, Wei,Wan, Cheuk-Kin,Wu, Yun-Dong. Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains[J]. journal of chemical theory and computation,2008.
APA	Han, Wei,Wan, Cheuk-Kin,&Wu, Yun-Dong.(2008).Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains.journal of chemical theory and computation.
MLA	Han, Wei,et al."Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains".journal of chemical theory and computation (2008).