Journal
CELL CHEMICAL BIOLOGY
Volume 26, Issue 6, Pages 901-+Publisher
CELL PRESS
DOI: 10.1016/j.chembiol.2019.03.007
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Funding
- Josie Robertson Foundation
- Stand Up to Cancer-Innovative Research grant [SU2C-AACR-IRG11-17]
- program of the Entertainment Industry Foundation
- Pew Charitable Trusts
- Pershing Square Sohn Cancer Research Alliance
- NIH [R01 AI137168, R21 CA188881, R01 CA204396, T32 GM007739]
- MSKCC Core Grant [P30 CA008748]
- Alfred P. Sloan Foundation Research Fellowship
- Burroughs Wellcome Fund
- Alex's Lemonade Stand Foundation
- Gabrielle's Angel Foundation
- Damon Runyon Cancer Research Foundation
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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.
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