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The Proteasome Structure01:17

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New strategies to identify protease substrates.

Vahap Canbay1, Ulrich Auf dem Keller1

  • 1Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.

Current Opinion in Chemical Biology
|November 21, 2020
PubMed
Summary

Proteome dynamics involve protein modifications, including limited proteolysis. Mass spectrometry-based degradomics enables system-wide identification of protease substrates and cleavage sites for precision medicine and diagnostics.

Keywords:
COFRADICDegradomicsHUNTERIn silico enrichmentProteaseProteoformTAILSTargeted degradomics

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Area of Science:

  • Proteomics
  • Biochemistry
  • Molecular Biology

Background:

  • Proteome dynamics are regulated by transcription, translation, and post-translational modifications.
  • Limited proteolysis, an irreversible modification, generates diverse proteoforms from proteins.
  • Dysregulated proteolytic cleavage is linked to numerous pathologies.

Purpose of the Study:

  • To review current strategies in protease substrate degradomics.
  • To introduce mass spectrometry-based and in silico enrichment workflows for protein termini.
  • To highlight the potential for digital proteome map deconvolution in precision medicine and diagnostics.

Main Methods:

  • Mass spectrometry-based degradomics for global protease substrate identification.
  • Workflows for precise cleavage site determination.
  • In silico enrichment of protein termini.

Main Results:

  • Degradomics enables system-wide identification of protease substrates.
  • Precise cleavage sites can be resolved.
  • Enrichment strategies facilitate proteome deconvolution.

Conclusions:

  • Protease substrate degradomics is crucial for understanding proteome dynamics.
  • Advanced workflows offer a path toward comprehensive digital proteome maps.
  • Applications include precision medicine and degradomics biomarker diagnostics.