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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Proteomics evaluation of chemically cleavable activity-based probes.

Marko Fonović1, Steven H L Verhelst, Mark T Sorum

  • 1Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.

Molecular & Cellular Proteomics : MCP
|July 7, 2007
PubMed
Summary

Chemically cleavable linkers improve activity-based probes (ABPs) for proteomics. This method enhances protein release after affinity isolation, yielding better mass spectrometry data for serine and cysteine proteases.

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Area of Science:

  • Biochemistry and Proteomics
  • Chemical Biology

Background:

  • Activity-based probes (ABPs) are valuable tools in proteomics for targeting specific enzyme families.
  • Affinity isolation using biotin tags is a common application of ABPs, but protein release can be challenging.
  • Difficulties in releasing captured proteins limit downstream analysis, particularly for mass spectrometry.

Purpose of the Study:

  • To evaluate ABPs incorporating a chemically cleavable linker for improved protein release.
  • To compare the efficacy of chemoselective cleavage versus standard on-bead digestion for proteomics analysis.
  • To demonstrate the utility of cleavable linkers with ABPs targeting serine and cysteine proteases.

Main Methods:

  • Development and evaluation of activity-based probes with chemically cleavable linkers.
  • Affinity purification of probe-labeled target proteins.
  • Comparison of protein release using chemoselective cleavage versus standard on-bead digestion.
  • Mass spectrometric analysis of released proteins.

Main Results:

  • Chemically cleavable linkers enable mild elution of probe-labeled proteins compatible with mass spectrometry.
  • Chemoselective cleavage significantly improves the quality of proteomic data compared to standard on-bead digestion.
  • The cleavable linker system demonstrates effectiveness across multiple ABPs targeting serine and cysteine proteases.

Conclusions:

  • Activity-based probes with chemically cleavable linkers offer a superior method for affinity isolation and proteomic analysis.
  • This approach overcomes limitations associated with traditional biotin tags, enhancing data quality and compatibility with mass spectrometry.
  • The developed system represents a significant advancement for studying enzyme activity and function in complex biological samples.