Chemical cross-linking in the structural analysis of protein assemblies

•Chemical cross-linking and mass spectrometry (CXMS) reveals residues in spatial proximity.•When used at low concentrations, cross-linkers do not substantially alter protein structures.•CXMS analysis is fast, sensitive, robust and compatible with other in vitro and in vivo methods.•Quantitative CXMS...

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Bibliographic Details
Published in:Methods (San Diego, Calif.) Calif.), 2018-07, Vol.144, p.53-63
Main Authors: Chu, Feixia, Thornton, Daniel T., Nguyen, Hieu T.
Format: Article
Language:English
Subjects:
Chemical cross-linking
Cross-Linking Reagents
Integrative modeling
Mass spectrometry
Mass Spectrometry - methods
Models, Molecular
Protein Binding
Protein Conformation
Protein Interaction Mapping
Proteins - chemistry
Proteins - metabolism
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Summary:•Chemical cross-linking and mass spectrometry (CXMS) reveals residues in spatial proximity.•When used at low concentrations, cross-linkers do not substantially alter protein structures.•CXMS analysis is fast, sensitive, robust and compatible with other in vitro and in vivo methods.•Quantitative CXMS analysis elucidates conformational changes and equilibria of proteins. For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
ISSN:1046-2023
1095-9130
DOI:10.1016/j.ymeth.2018.05.023