title: Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.
abstract: 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 "over-length" 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.
authors.affiliation: the National Institute of Biological Sciences, Beijing 102206.
authors.forename: Yue-He
authors.initials: YH
authors.lastname: Ding
authors.affiliation: From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Gong
authors.affiliation: From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071.
authors.forename: Xu
authors.initials: X
authors.lastname: Dong
authors.affiliation: From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071.
authors.forename: Kan
authors.initials: K
authors.lastname: Liu
authors.affiliation: the Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, and.
authors.forename: Zhu
authors.initials: Z
authors.lastname: Liu
authors.affiliation: the Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, CAS, Beijing 100190, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Liu
authors.affiliation: the Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, CAS, Beijing 100190, China.
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
authors.affiliation: the National Institute of Biological Sciences, Beijing 102206, dongmengqiu@nibs.ac.cn.
authors.forename: Meng-Qiu
authors.identifier: 0000-0002-6094-1182
authors.initials: MQ
authors.lastname: Dong
authors.affiliation: From the CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, tanglab@wipm.ac.cn.|the Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, and.
authors.forename: Chun
authors.identifier: 0000-0001-6477-6500
authors.initials: C
authors.lastname: Tang
mesh_terms: D003432:Cross-Linking Reagents / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D013058:Mass Spectrometry; D008956:Models, Chemical
chemical_list: D003432:Cross-Linking Reagents; D029968:Escherichia coli Proteins
keywords: calmodulin (CaM); mass spectrometry (MS); molecular dynamics; protein cross-linking; protein domain; protein dynamics; protein excited state; structural model