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ABSTRACT: Protease specificity profiling

PROVIDER: PRJNA586896 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10381637_1.fastq.gz	Fastqsanger.gz
	SRR10381637_2.fastq.gz	Fastqsanger.gz
	SRR10381638_1.fastq.gz	Fastqsanger.gz
	SRR10381638_2.fastq.gz	Fastqsanger.gz
	SRR10381639_1.fastq.gz	Fastqsanger.gz

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Protease specificity profiling in a pipette tip using “charge-synchronized” proteome-derived peptide libraries

Project description:About 2% of the genome of human and other organisms codes for proteases. An important step toward deciphering the biological function of a protease and designing inhibitors is the profiling of protease specificity. In this work we present a novel, label-free, proteomics-based protease specificity profiling method that only requires simple sample preparation steps. It uses proteome-derived peptide libraries and enriches the cleaved sequences using strong cation exchange chromatography (SCX) material in a pipette tip. As a demonstration of the method’s versatility, we successfully determined the specificity of GluC, caspase-3, chymotrypsin and cathepsin G from several hundreds to almost 2000 cleavage events per proteases. Interestingly, we also found and confirmed a novel intrinsic preference of cathepsin G for Asn at the P1 subsite, explaining the reported cleavage position on the P. aeruginosa aeruginosa flagellin by human cathepsin G . Overall, this method is straightforward and requires so far the lowest investment in material and equipment for protease specificity profiling. Therefore, we think it will be applicable in any biochemistry laboratory and promote an increased understanding of protease specificity.

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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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