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LinX: A Software Tool for Uncommon Cross-Linking Chemistry.

Zdeněk Kukačka1, Michal Rosůlek1,2, Jan Jelínek1,3

  • 1Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.

Journal of Proteome Research
|March 4, 2021
PubMed
Summary

A new algorithm, LinX, identifies and quantifies intermolecular cross-links in homodimer protein interactions using mass spectrometry. This tool aids structural biology by analyzing protein-nucleic acid complexes and homodimer interfaces.

Keywords:
chemical cross-linkingdata interpretationhigh resolutionhomo oligomersmass spectrometrynucleic acidsproteins

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Area of Science:

  • Structural biology
  • Biochemistry
  • Proteomics

Background:

  • Chemical cross-linking mass spectrometry (CXMS) is vital for determining protein structures.
  • Existing algorithms struggle to identify cross-links at homodimer interaction interfaces.

Purpose of the Study:

  • To develop a novel algorithm for identifying and quantifying intermolecular cross-links in homodimer proteins.
  • To enable analysis of protein-nucleic acid complexes using CXMS.

Main Methods:

  • Utilized high mass accuracy for ion identification.
  • Developed the LinX algorithm implemented in Java.
  • Applied 14N/15N labeling for quantitative analysis of homodimers.

Main Results:

  • LinX successfully identifies cross-linked peptides at homodimer interaction interfaces.
  • The algorithm quantifies cross-links and their ratios.
  • Enabled analysis of protein-nucleic acid complexes.

Conclusions:

  • LinX addresses a critical gap in CXMS data analysis for homodimers.
  • The software provides a valuable tool for structural biology research.
  • LinX is freely available with source code and user guide.