Cell Chemical Biology
Volume 26, Issue 6, 20 June 2019, Pages 901-907.e6
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Brief Communication
A Chemical Strategy for Protease Substrate Profiling

https://doi.org/10.1016/j.chembiol.2019.03.007Get rights and content
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Highlights

  • A 2PCA-biotin probe enables chemical enrichment of protease substrates (CHOPS)

  • CHOPS rapidly identifies DPP substrates with a gel-based readout

  • DPP9 preferentially cleaves short peptides, not whole proteins (e.g., Nlrp1b)

  • CHOPS enables unbiased protease substrate profiling with quantitative proteomics

Summary

The dipeptidyl peptidases (DPPs) regulate hormones, cytokines, and neuropeptides by cleaving dipeptides after proline from their amino termini. Due to technical challenges, many DPP substrates remain unknown. Here, we introduce a simple method, termed CHOPS (chemical enrichment of protease substrates), for the discovery of protease substrates. CHOPS exploits a 2-pyridinecarboxaldehyde (2PCA)-biotin probe, which selectively biotinylates protein N-termini except those with proline in the second position. CHOPS can, in theory, discover substrates for any protease, but is particularly well suited to discover canonical DPP substrates, as cleaved but not intact DPP substrates can be identified by gel electrophoresis or mass spectrometry. Using CHOPS, we show that DPP8 and DPP9, enzymes that control the Nlrp1 inflammasome through an unknown mechanism, do not directly cleave Nlrp1. We further show that DPP9 robustly cleaves short peptides but not full-length proteins. More generally, this work delineates a practical technology for identifying protease substrates, which we anticipate will complement available “N-terminomic” approaches.

Keywords

protease substrates
mass spectrometry-based proteomics
N-terminal modification
chemical probes
Nlrp1 inflammasome

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