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TitleDeep quantification of substrate turnover defines protease subsite cooperativity.
Journal, issue, pagesMol Syst Biol, Vol. 20, Issue 12, Page 1303-1328, Year 2024
Publish dateOct 28, 2024
AuthorsRajani Kanth Gudipati / Dimos Gaidatzis / Jan Seebacher / Sandra Muehlhaeusser / Georg Kempf / Simone Cavadini / Daniel Hess / Charlotte Soneson / Helge Großhans /
PubMed AbstractSubstrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to ...Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to a small number of events. Here, we develop qPISA (quantitative Protease specificity Inference from Substrate Analysis) to study Dipeptidyl Peptidase Four (DPP4), a key regulator of blood glucose levels. We use mass spectrometry to quantify >40,000 peptides from a complex, commercially available peptide mixture. By analyzing changes in substrate levels quantitatively instead of focusing on qualitative product identification through a binary classifier, we can reveal cooperative interactions within DPP4's active pocket and derive a sequence motif that predicts activity quantitatively. qPISA distinguishes DPP4 from the related C. elegans DPF-3 (a DPP8/9-orthologue), and we relate the differences to the structural features of the two enzymes. We demonstrate that qPISA can direct protein engineering efforts like the stabilization of GLP-1, a key DPP4 substrate used in the treatment of diabetes and obesity. Thus, qPISA offers a versatile approach for profiling protease and especially exopeptidase specificity, facilitating insight into enzyme mechanisms and biotechnological and clinical applications.
External linksMol Syst Biol / PubMed:39468329 / PubMed Central
MethodsEM (single particle)
Resolution2.64 Å
Structure data

17582

8pba

EMDB-17582, PDB-8pba:
Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo)
Method: EM (single particle) / Resolution: 2.64 Å

Source
  • caenorhabditis elegans (invertebrata)
KeywordsHYDROLASE / Dipeptidylpeptidase

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