ArticleMolecular & cellular proteomics : MCP2016
Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 55 citations in OpenAlex.
- Article
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- Enzyme-free biochemical production of seamlessly N-to-C cyclized peptides from natural or recombinant proteins.Methods in enzymology · 2025Article
- Deep quantification of substrate turnover defines protease subsite cooperativity.Molecular systems biology · 2024Article
- Bioengineering secreted proteases converts divergent Rcr3 orthologs and paralogs into extracellular immune co-receptors.The Plant cell · 2024Article
- Motif mapping during chickpea germination reveals a complex sequential activation of different proteolytic activities.PloS one · 2024Article
- An Efficient Peptidomics Screening for Exogenous Substrates and Inhibitory Peptides of the Dipeptidase ACE from Milk Hydrolysate.Pharmaceutics · 2023Article
- Activity-Based Probes for Proteases Pave the Way to Theranostic Applications.Pharmaceutics · 2022Review
- TAILS Identifies Candidate Substrates and Biomarkers of ADAMTS7, a Therapeutic Protease Target in Coronary Artery Disease.Molecular & cellular proteomics : MCP · 2022Article
- Profiling Sequence Specificity of Proteolytic Activities Using Proteome-Derived Peptide Libraries.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches.International journal of molecular sciences · 2021Article
- The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities.ACS catalysis · 2021Article
- Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen.Nature communications · 2021Article
- Origin and Expansion of the Serine Protease Repertoire in the Myelomonocyte Lineage.International journal of molecular sciences · 2021Review
- Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates.Journal of the American Chemical Society · 2020Article
- Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis.Scientific reports · 2020Article
- Structural and functional studies ofThe Journal of biological chemistry · 2020Article
- Autocatalytic Processing and Substrate Specificity of Arabidopsis Chloroplast Glutamyl Peptidase.Plant physiology · 2020Article
- A fungal substrate mimicking molecule suppresses plant immunity via an inter-kingdom conserved motif.Nature communications · 2019Article
- Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets.Proteomes · 2019Article
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Authors and funding
13 authors at 7 institutions in 4 countries.
Funding
Abstract
We present protease specificity profiling based on quantitative proteomics in combination with proteome-derived peptide libraries. Peptide libraries are generated by endoproteolytic digestion of proteomes without chemical modification of primary amines before exposure to a protease under investigation. After incubation with a test protease, treated and control libraries are differentially isotope-labeled using cost-effective reductive dimethylation. Upon analysis by liquid chromatography-tandem mass spectrometry, cleavage products of the test protease appear as semi-specific peptides that are enriched for the corresponding isotope label. We validate our workflow with two proteases with well-characterized specificity profiles: trypsin and caspase-3. We provide the first specificity profile of a protease encoded by a human endogenous retrovirus and for chlamydial protease-like activity factor (CPAF). For CPAF, we also highlight the structural basis of negative subsite cooperativity between subsites S1 and S2'. For A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) -4, -5, and -15, we show a canonical preference profile, including glutamate in P1 and glycine in P3'. In total, we report nearly 4000 cleavage sites for seven proteases. Our protocol is fast, avoids enrichment or synthesis steps, and enables probing for lysine selectivity as well as subsite cooperativity. Due to its simplicity, we anticipate usability by most proteomic laboratories.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.