Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links
文献类型：期刊论文
| 作者 | Ding, Yue-He2; Gong, Zhou1; Dong, Xu1; Liu, Kan1; Liu, Zhu3; Liu, Chao4; He, Si-Min4; Dong, Meng-Qiu2; Tang, Chun1,3 |
| 刊名 | JOURNAL OF BIOLOGICAL CHEMISTRY
 |
| 出版日期 | 2017-01-27 |
| 卷号 | 292期号:4页码:1187-1196 |
| 英文摘要 | 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology |
| 关键词[WOS] | GLUTAMINE-BINDING-PROTEIN ; SUGAR PHOSPHOTRANSFERASE SYSTEM ; MASS-SPECTROMETRY ; ENZYME-I ; CONFORMATIONAL ENSEMBLES ; MOLECULAR ARCHITECTURE ; DISTANCE RESTRAINTS ; ANGSTROM RESOLUTION ; DYNAMIC EQUILIBRIUM ; INITIATION COMPLEX |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000393339800004 |
| 源URL | [http://ir.wipm.ac.cn/handle/112942/10036]  |
| 专题 | 武汉物理与数学研究所_磁共振应用研究部 |
| 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. |
入库方式： OAI收割
来源：武汉物理与数学研究所
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