We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: Quantitative cross-linking/mass spectrometry ; conformation changes ; human C3 ; activation of complement system
Principal Investigators: (in alphabetical order) |
Dr Juri Rappsilber |
Submitting User: | ccms |
Chen ZA, Fischer L, Cox J, Rappsilber J.
Quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers and MaxQuant.
Mol. Cell Proteomics. Epub 2016 Jun 14.
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