Accurate Structure Prediction and Conformational Analysis of Cyclic   Peptides with Residue-Specific Force Fields

doi:10.1021/acs.jpclett.6b00452

CORC > 北京大学 > 化学与分子工程学院

	Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields
	Geng, Hao ; Pang, Fan ; Wu, Yun-Dong
刊名	JOURNAL OF PHYSICAL CHEMISTRY LETTERS
	2016
关键词	EXCHANGE MOLECULAR-DYNAMICS SMALL PROTEINS AMBER FF99SB MODELS CYCLOPEPTIDES OPTIMIZATION TEMPLATES SEARCH DESIGN MOTIFS
DOI	10.1021/acs.jpclett.6b00452
英文摘要	Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 angstrom. We also compared the backbone (phi, psi) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins.; National Natural Science Foundation of China [21133002, 21573009]; Shenzhen Science and Technology Innovation Committee [KQTD201103, JCYJ20140509093817689]; Nanshan District in Shenzhen [KC2014ZDZJ0026A]; Peking University Shenzhen Graduate School; NSFC; Guangzhou government; SCI(E); EI; PubMed; ARTICLE; jiangfan@pku.edu.cn; wuyd@pkusz.edu.cn; 10; 1805-1810; 7
语种	中文
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/433910]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Geng, Hao,Pang, Fan,Wu, Yun-Dong. Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields[J]. JOURNAL OF PHYSICAL CHEMISTRY LETTERS,2016.
APA	Geng, Hao,Pang, Fan,&Wu, Yun-Dong.(2016).Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields.JOURNAL OF PHYSICAL CHEMISTRY LETTERS.
MLA	Geng, Hao,et al."Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields".JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016).