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题名: The Challenge to the Rule of Homology Modeling: Folding Mechanism Study of Protein G(A) and G(B) with High Sequence Identity but Different Native Structures
作者: Wu, Xue1, 2, 3;  Jin, Zhong4;  Xiu, Zhilong3;  Li, Guohui1
关键词: Molecular dynamics simulation ;  Homology modeling ;  G(A)88 ;  G(B)88 ;  G(A)95 ;  G(B)95
刊名: CURRENT PHARMACEUTICAL DESIGN
发表日期: 2013-04-01
卷: 19, 期:12, 页:2282-2292
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine
类目[WOS]: Pharmacology & Pharmacy
研究领域[WOS]: Pharmacology & Pharmacy
英文摘要: As one of the most valuable methods for drug design, homology modeling shows that protein structures are more conserved than protein sequences, that is, the proteins with high sequence identity have high structural similarity, but protein pairs G(A)88/G(B)88 and G(A)95/G(B)95 prove the opposite. The pairs G(A)88 and G(B)88 shares the 88% sequence identity, but display different structures, and the pair G(A)95 and G(B)95 with 95% sequence identity yet presents different structures. The research on these proteins provides an opportunity of complementary study. In the process of protein folding, at which stage the protein final structure was determined and which residues were important for folding to a given structure were still unknown. Here we used OPLS all-atom force field for molecular dynamics simulations to study the unfolding of G(A)88, G(B)88, G(A)95 and G(B)95 at high temperatures, and used the process of protein unfolding to reverse the process of protein folding. G(B)88 and G(B)95 folded to the alpha+beta structure, but G(A)88 and G(A)95 folded to the all-alpha-helix structure. In the process of G(A)88 and G(A)95 folding, the helices folded earlier than the formation of tertiary interactions. In the process of folding to G(B)88 and G(B)95, the alpha-helix formed earlier. We showed that early along the folding pathway, the final protein structure was confirmed, and very small differences between protein sequences determined the protein structure.
关键词[WOS]: DESIGN ;  DYNAMICS ;  ALPHA ;  BETA
语种: 英语
WOS记录号: WOS:000316457700015
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/137799
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Beijing 100864, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
3.Dalian Univ Technol, Sch Environm & Biol Sci & Technol, Dept Biosci & Biotechnol, Dalian, Peoples R China
4.Chinese Acad Sci, Comp Network Informat Ctr, Supercomp Ctr, Beijing 100190, Peoples R China

Recommended Citation:
Wu, Xue,Jin, Zhong,Xiu, Zhilong,et al. The Challenge to the Rule of Homology Modeling: Folding Mechanism Study of Protein G(A) and G(B) with High Sequence Identity but Different Native Structures[J]. CURRENT PHARMACEUTICAL DESIGN,2013,19(12):2282-2292.
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