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Related Experiment Video

Updated: Feb 17, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL.

Zhou Gong1,2, Zhu Liu3, Xu Dong1,2

  • 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.

Biophysics Reports
|December 15, 2017
PubMed
Summary

Chemical cross-linking coupled with mass spectrometry (CXMS) can reveal protein dynamics. A new method, DynaXL, extracts this information from over-length cross-links to visualize protein ensemble structures.

Keywords:
Chemical cross-linkingDynaXLEnsemble refinementMulti-domain proteinProtein–protein complexSolvent accessible surface distance

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Proteomics

Background:

  • Chemical cross-linking coupled with mass spectrometry (CXMS) is a key technique for protein structure determination.
  • Traditional CXMS analysis often discards cross-links inconsistent with a single protein structure, potentially losing valuable data.

Purpose of the Study:

  • To introduce DynaXL, a novel method for extracting protein dynamics information from over-length cross-links.
  • To enable the visualization of protein ensemble structures using this previously overlooked data.

Main Methods:

  • The DynaXL protocol involves five key steps: identifying confident cross-links, delineating protein domains/subunits, performing ensemble rigid-body refinement, and final validation/assessment.
  • This method leverages over-length cross-links, which contain hidden protein dynamics information.

Main Results:

  • DynaXL successfully extracts dynamic information from over-length cross-links.
  • The method facilitates the visualization of protein ensemble structures, offering a more comprehensive view of protein conformations.

Conclusions:

  • DynaXL provides a powerful approach to analyze protein dynamics and ensemble structures.
  • This method is broadly applicable to multi-domain proteins and protein-protein complexes, enhancing structural biology insights.