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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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An integrated workflow for crosslinking mass spectrometry.

Marta L Mendes1, Lutz Fischer1,2, Zhuo A Chen1

  • 1Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.

Molecular Systems Biology
|September 27, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a workflow using sequential digestion and xiSEARCH software to improve crosslinked peptide detection in mass spectrometry. This method enhances the identification of dynamic protein-protein interactions for drug development.

Keywords:
crosslinking mass spectrometryprotein-protein interactionsproteomicssoftwarestructural biology

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Identifying protein-protein interactions is crucial for understanding cellular functions.
  • Crosslinked peptides in mass spectrometry provide insights into interaction sites.
  • Current methods for detecting crosslinked peptides can be limited in sensitivity and scope.

Purpose of the Study:

  • To develop a streamlined workflow for enhanced mass spectrometric detection of crosslinked peptides.
  • To improve the identification of dynamic protein-protein interaction sites.
  • To facilitate the discovery of novel targets for small molecule inhibitors.

Main Methods:

  • Implementation of a sequential digestion protocol to shorten long tryptic peptides.
  • Utilizing the crosslink identification software xiSEARCH for data analysis.
  • Demonstration of a 12-fraction protocol applicable to multi-protein complexes and cell lysates.

Main Results:

  • Enhanced detection of crosslinked peptides through sequential digestion.
  • Successful quantitative analysis and high-density crosslinking demonstrated.
  • The workflow does not require specific crosslinker features for effective application.

Conclusions:

  • The presented workflow offers a simple yet powerful approach to study protein-protein interactions.
  • Reveals accessible and functionally relevant dynamic interaction sites.
  • These findings are highly relevant for the development of targeted small molecule inhibitors.