Dataset Information

Deep quantification of substrate turnover definesprotease subsite cooperativity. Working title: Massively parallel mapping of dipeptidyl peptidase cleavage sites reveals substrate motifs

ABSTRACT: Proteases play a crucial role in processing or breaking down proteins. They exhibit varying levels of substrate specificity that determine their physiological or pharmacological functions. However, this specificity is not well-understood. To address this, we have developed hiMAPS (high-throughput mapping of protease cleavage sites), a mass spectrometry-based method that can survey tens of thousands of distinct peptides. By applying this approach to human DPP4 and C. elegans DPF-3, two prolyl peptidases from the Dipeptidyl Peptidase IV (DPPIV) family, we have derived quantitative models that confirm a strong preference for Pro and Ala in the penultimate (P1) position from the N-terminus, but also reveal differences in the relative preferences for other residues. The hiMAPS approach can be applied to other exoproteases using various cheap sources of highly diverse peptides. Additionally, we have observed that these proteases tolerate and accept substrates containing Thr and Ser at P1 position.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jan Seebacher

LAB HEAD: Helge Grosshans

PROVIDER: PXD042089 | Pride | 2024-11-01

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2003_2083_HeLa_DPPs_ExpDesign.txt	Txt
	L2_201119_JS_2003_HeLa_DPF3_TMT15plex_Fr01.raw	Raw
	L2_201119_JS_2003_HeLa_DPF3_TMT15plex_Fr02.raw	Raw
	L2_201119_JS_2003_HeLa_DPF3_TMT15plex_Fr03.raw	Raw
	L2_201119_JS_2003_HeLa_DPF3_TMT15plex_Fr04.raw	Raw

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Publications

Deep quantification of substrate turnover defines protease subsite cooperativity.

Gudipati Rajani Kanth RK Gaidatzis Dimos D Seebacher Jan J Muehlhaeusser Sandra S Kempf Georg G Cavadini Simone S Hess Daniel D Soneson Charlotte C Großhans Helge H

Molecular systems biology 20241028

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 pepti ...[more]

PMID: 39468329

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