Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links

doi:10.1074/jbc.M116.761841

	Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links
	Ding, Yue-He 2; Gong, Zhou 1; Dong, Xu 1; Liu, Kan 1; Liu, Zhu 3; Liu, Chao 4; He, Si-Min 4; Dong, Meng-Qiu 2; Tang, Chun 1,3
	2017-01-27
发表期刊	JOURNAL OF BIOLOGICAL CHEMISTRY
ISSN	0021-9258
卷号	292 期号:4 页码:1187-1196
摘要	Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "overlength" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function.
DOI	10.1074/jbc.M116.761841
收录类别	SCI
语种	英语
资助项目	Chinese Ministry of Science and Technology[2013CB910200] ; Chinese Ministry of Science and Technology[2016YFA0501200] ; Chinese Ministry of Science and Technology[2014CB849800] ; Chinese Ministry of Science and Technology[2012CB910602] ; National Natural Science Foundation of China[31225007] ; National Natural Science Foundation of China[21375010] ; National Natural Science Foundation of China[31400735] ; National Natural Science Foundation of China[31400644]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000393339800004
出版者	AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
引用统计	被引频次：35[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/7603
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Dong, Meng-Qiu; Tang, Chun
作者单位	1.Chinese Acad Sci, State Key Lab Magnet Resonance & Atom Mol Phys, Natl Ctr Magnet Resonance Wuhan, Wuhan Inst Phys & Math,CAS Key Lab Magnet Resonan, Wuhan 430071, Hubei Province, Peoples R China 2.Natl Inst Biol Sci, 7 Sci Pk Rd,ZGC Life Sci Pk, Beijing 102206, Peoples R China 3.Zhejiang Univ, Sch Med, Dept Pharmacol, Hangzhou 310058, Zhejiang, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Ding, Yue-He,Gong, Zhou,Dong, Xu,et al. Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links[J]. JOURNAL OF BIOLOGICAL CHEMISTRY,2017,292(4):1187-1196.
APA	Ding, Yue-He.,Gong, Zhou.,Dong, Xu.,Liu, Kan.,Liu, Zhu.,...&Tang, Chun.(2017).Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.JOURNAL OF BIOLOGICAL CHEMISTRY,292(4),1187-1196.
MLA	Ding, Yue-He,et al."Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links".JOURNAL OF BIOLOGICAL CHEMISTRY 292.4(2017):1187-1196.