Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases
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ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Velos, instrument model
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Petra Van Damme
PROVIDER: PRD000727 | Pride | 2013-05-14
REPOSITORIES: Pride
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Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases.
Tanco Sebastian S Lorenzo Julia J Garcia-Pardo Javier J Degroeve Sven S Martens Lennart L Aviles Francesc Xavier FX Gevaert Kris K Van Damme Petra P
Molecular & cellular proteomics : MCP 20130425 8
Through processing peptide and protein C termini, carboxypeptidases participate in the regulation of various biological processes. Few tools are however available to study the substrate specificity profiles of these enzymes. We developed a proteome-derived peptide library approach to study the substrate preferences of carboxypeptidases. Our COFRADIC-based approach takes advantage of the distinct chromatographic behavior of intact peptides and the proteolytic products generated by the action of c ...[more]
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Project description:Through processing peptide and protein C termini, carboxypeptidases participate in the regulation of various biological processes. Few tools are however available to study the substrate specificity profiles of these enzymes. We developed a proteome-derived peptide library approach to study the substrate preferences of carboxypeptidases. Our COFRADIC-based approach takes advantage of the distinct chromatographic behavior of intact peptides and the proteolytic products generated by the action of carboxypeptidases, to enrich the latter and facilitate its MS-based identification. Two different peptide libraries, generated either by chymotrypsin or by metalloendopeptidase Lys-N, were used to determine the substrate preferences of human metallocarboxypeptidases A1 (hCPA1), A2 (hCPA2), and A4 (hCPA4). In addition, our approach allowed us to delineate the substrate specificity profile of mouse mast cell carboxypeptidase (MC-CPA or mCPA3), a carboxypeptidase suggested to function in innate immune responses regulation and mast cell granule homeostasis, but which thus far lacked a detailed analysis of its substrate preferences. mCPA3 was here shown to preferentially remove bulky aromatic amino acids, similar to hCPA2. This was also shown by a hierarchical cluster analysis, grouping hCPA1 close to hCPA4 in terms of its P1 primed substrate specificity, whereas hCPA2 and mCPA3 cluster separately. The specificity profile of mCPA3 may further aid to elucidate the function of this mast cell carboxypeptidase and its biological substrate repertoire. Finally, we used this approach to evaluate the substrate preferences of prolylcarboxypeptidase, a serine carboxypeptidase shown to cleave C-terminal amino acids linked to proline and alanine.
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Project description:Proteome-derived peptide libraries are a powerful tool for the investigation of protease specificity, conventionally involving the biotinylation of cleavage products to enable for their enrichment. Here we present a modified strategy for protease specificity profiling using proteome-derived peptide libraries in a tag-free manner. In comparison to the original method the new protocol is faster, avoids cost- and time-intensive enrichment steps, and enables probing for lysine selectivity. In the new workflow, peptide libraries are generated by endoproteolytic digestion of proteomes without chemical modification of primary amines prior to exposure to a protease under investigation. After incubation with the test protease, treated and control library are differentially labeled using stable isotopes by means of reductive dimethylation. Upon analysis by liquid chromatography mass spectrometry, cleavage products of the test protease appear as peptides enriched for the respective isotopic label. With “PICS 2.0” we identified more than 2800 cleavage sites in five specificity experiments for four proteases, including trypsin, caspase-3, and chlamydial protease-like activity factor (CPAF). Hence, this method is a valuable addition to the different strategies currently employed for specificity profiling of proteases
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