Significantly Improved Protein Folding Thermodynamics Using a   Dispersion-Corrected Water Model and a New Residue-Specific Force Field

doi:10.1021/acs.jpclett.7b01213

CORC > 北京大学 > 化学与分子工程学院

	Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field
	Wu, Hao-Nan ; Jiang, Fan ; Wu, Yun-Dong
刊名	JOURNAL OF PHYSICAL CHEMISTRY LETTERS
	2017
关键词	MOLECULAR-DYNAMICS SIMULATIONS INTRINSICALLY DISORDERED PROTEINS ALPHA-HELIX FORMATION SIDE-CHAIN BACKBONE PARAMETERS AMBER FF99SB PEPTIDES COOPERATIVITY ACCURACY EXCHANGE
DOI	10.1021/acs.jpclett.7b01213
英文摘要	An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature dependence of folding/unfolding equilibrium and overly collapsed unfolded or disordered states. For the latter problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage, and the GB1 hairpin). By using residue-specific parameters to achieve better match between amino acid sequences and native structures and adding a small H-bond correction to partially compensate the missing many-body effects in a-helix formation, the new RSFF2+ force field with the TIP4P-D water model can excellently reproduce experimental melting curves of both alpha-helical and beta-hairpin systems. The RSFF2+/TIP4P-D method also gives less collapsed unfolded structures and describes well folded proteins simultaneously.; National Natural Science Foundation of China [21573009]; SCI(E); ARTICLE; 14; 3199-3205; 8
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/472062]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Wu, Hao-Nan,Jiang, Fan,Wu, Yun-Dong. Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field[J]. JOURNAL OF PHYSICAL CHEMISTRY LETTERS,2017.
APA	Wu, Hao-Nan,Jiang, Fan,&Wu, Yun-Dong.(2017).Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field.JOURNAL OF PHYSICAL CHEMISTRY LETTERS.
MLA	Wu, Hao-Nan,et al."Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field".JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017).