Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers

doi:10.1021/acs.analchem.6b00281

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	Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers
	Ding, Yue-He 1,2,3; Fan, Sheng-Bo 4; Li, Shuang 1; Feng, Bo-Ya 5,6; Gao, Ning 5,6; Ye, Keqiong 1; He, Si-Min 4; Dong, Meng-Qiu 1,2,3
刊名	ANALYTICAL CHEMISTRY
	2016-04-19
卷号	88 期号:8 页码:4461-4469
ISSN号	0003-2700
DOI	10.1021/acs.analchem.6b00281
英文摘要	Chemical cross-linking of proteins coupled with mass spectrometry (CXMS) is a powerful tool to study protein folding and to map the interfaces between interacting proteins. The most commonly used cross-linkers in CXMS are BS3 and DSS, which have similar structures and generate the same linkages between pairs of lysine residues in spatial proximity. However, there are cases where no cross-linkable lysine pairs are present at certain regions of a protein or at the interface of two interacting proteins. In order to find the cross-linkers that can best complement the performance of BS3 and DSS, we tested seven additional cross-linkers that either have different spacer arm structures or that target different amino acids (BS(2)G, EGS, AMAS, GMBS, Sulfo-GMBS, EDC, and TFCS). Using BSA, aldolase, the yeast H/ACA protein complex, and E. coli 70S ribosomes, we showed that, in terms of providing structural information not obtained through the use of BS3 and DSS, EGS and Sulfo-GMBS worked better than the other cross-linkers that we tested. EGS generated a large number of cross-links not seen with the other amine-specific cross-linkers, possibly due to its hydrophilic spacer arm. We demonstrate that incorporating the cross-links contributed by the EGS and amine-sulfhydryl cross-linkers greatly increased the accuracy of Rosetta in docking the structure of the yeast H/ACA protein complex. Given the improved depth of useful information it can provide, we suggest that the multilinker CXMS approach should be used routinely when the amount of a sample permits.
资助项目	National Scientific Instrumentation Grant Program[2011YQ09000506] ; National Natural Science Foundation of China[21375010] ; National Natural Science Foundation of China[21475141] ; National Natural Science Foundation of China[31422016] ; National Natural Science Foundation of China[31325007] ; Chinese Academy of Sciences (CAS Interdisciplinary Innovation Team grant)
WOS研究方向	Chemistry
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000374706000041
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/8566]
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
作者单位	1.Nat Inst Biol Sci, Beijing 102206, Peoples R China 2.Chinese Acad Med Sci, Grad Program, Beijing 100730, Peoples R China 3.Peking Union Med Coll, Beijing 100730, Peoples R China 4.Chinese Acad Sci, Univ CAS, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100049, Peoples R China 5.Tsinghua Univ, Sch Life Sci, Struct Biol Ctr, Prot Sci Lab,Minist Educ, Beijing 100084, Peoples R China 6.Tsinghua Univ, Dept Chem, Beijing 100084, Peoples R China
推荐引用方式 GB/T 7714	Ding, Yue-He,Fan, Sheng-Bo,Li, Shuang,et al. Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers[J]. ANALYTICAL CHEMISTRY,2016,88(8):4461-4469.
APA	Ding, Yue-He.,Fan, Sheng-Bo.,Li, Shuang.,Feng, Bo-Ya.,Gao, Ning.,...&Dong, Meng-Qiu.(2016).Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers.ANALYTICAL CHEMISTRY,88(8),4461-4469.
MLA	Ding, Yue-He,et al."Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers".ANALYTICAL CHEMISTRY 88.8(2016):4461-4469.