Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes: QCLMS reveals protein conformational changes

Zhuo Chen, Lutz Fischer, Salman Tahir, Jimi-Carlo Bukowski-Wills, Paul N. Barlow, Juri Rappsilber

Research output: Contribution to journalArticlepeer-review

Abstract

Quantitative cross-linking/mass spectrometry (QCLMS) probes protein structural dynamics in solution by quantitatively comparing the yields of cross-links between different conformational statuses. We have used QCLMS to understand the final maturation step of the proteasome lid and also to elucidate the structure of complement C3(H2O). Here we benchmark our workflow 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.
Original languageEnglish
Number of pages19
JournalWellcome Open Research
DOIs
Publication statusPublished - 15 Nov 2016

Keywords

  • cross-linking/mass spectrometry
  • quantitative protein structure
  • conformational change
  • isotope labeled cross-linkers
  • automated data process

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