title: Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry.
abstract: Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-µmol/L binding affinity. In contrast, we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular cross-links to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes.
authors.affiliation: CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 China.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Gong
authors.affiliation: National Institute of Biological Sciences, Beijing, 102206 China.
authors.forename: Yue-He
authors.initials: YH
authors.lastname: Ding
authors.affiliation: CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 China.
authors.forename: Xu
authors.initials: X
authors.lastname: Dong
authors.affiliation: National Institute of Biological Sciences, Beijing, 102206 China.
authors.forename: Na
authors.initials: N
authors.lastname: Liu
authors.affiliation: National Institute of Biological Sciences, Beijing, 102206 China.
authors.forename: E Erquan
authors.initials: EE
authors.lastname: Zhang
authors.affiliation: National Institute of Biological Sciences, Beijing, 102206 China.
authors.forename: Meng-Qiu
authors.initials: MQ
authors.lastname: Dong
authors.affiliation: CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 China.
authors.forename: Chun
authors.initials: C
authors.lastname: Tang
keywords: Ambiguous distance restraint; Encounter complex; Ensemble refinement; Fleeting complex; Protein–protein interaction