ArticleMolecular & cellular proteomics : MCP2013
The DegraBase: a database of proteolysis in healthy and apoptotic human cells.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.
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82 citing papers in PubMed, 1 synthesis or guideline pooled it, 145 citations in OpenAlex.
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- Atypical contribution of caspase-3 to melanoma cancer cell motility by regulation of coronin 1B activity.Cell death & disease · 2025Article
- Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.Chemical reviews · 2025Review
- Apoptotic Caspases-3 and -7 Cleave Extracellular Domains of Membrane-Bound Proteins from MDA-MB-231 Breast Cancer Cells.International journal of molecular sciences · 2025Article
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- Caspases compromise SLU7 and UPF1 stability and NMD activity during hepatocarcinogenesis.JHEP reports : innovation in hepatology · 2024Article
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- A glimpse into viral warfare: decoding the intriguing role of highly pathogenic coronavirus proteins in apoptosis regulation.Journal of biomedical science · 2024Review
- Defining PANoptosis: Biochemical and Mechanistic Evaluation of Innate Immune Cell Death Activation.Current protocols · 2024Article
- Evolution of Caspases and the Invention of Pyroptosis.International journal of molecular sciences · 2024Review
- An N terminomics toolbox combining 2-pyridinecarboxaldehyde probes and click chemistry for profiling protease specificity.Cell chemical biology · 2024Article
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- Spautin-1 Protects Against Mild TBI-Induced Anxiety-Like Behavior in Mice via Immunologically Silent Apoptosis.Neuromolecular medicine · 2023Article
- In-Depth Characterization of Apoptosis N-Terminome Reveals a Link Between Caspase-3 Cleavage and Posttranslational N-Terminal Acetylation.Molecular & cellular proteomics : MCP · 2023Review
- Identification of Human Host Substrates of the SARS-CoV-2 MACS infectious diseases · 2023Article
- Executioner caspases restrict mitochondrial RNA-driven Type I IFN induction during chemotherapy-induced apoptosis.Nature communications · 2023Article
- Proteome integral solubility alteration high-throughput proteomics assay identifies Collectin-12 as a non-apoptotic microglial caspase-3 substrate.Cell death & disease · 2023Article
22 more citing papers are in PubMed but not listed here.
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12 authors at 1 institution in 1 country.
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Abstract
Proteolysis is a critical post-translational modification for regulation of cellular processes. Our lab has previously developed a technique for specifically labeling unmodified protein N termini, the α-aminome, using the engineered enzyme, subtiligase. Here we present a database, called the DegraBase (http://wellslab.ucsf.edu/degrabase/), which compiles 8090 unique N termini from 3206 proteins directly identified in subtiligase-based positive enrichment mass spectrometry experiments in healthy and apoptotic human cell lines. We include both previously published and unpublished data in our analysis, resulting in a total of 2144 unique α-amines identified in healthy cells, and 6990 in cells undergoing apoptosis. The N termini derive from three general categories of proteolysis with respect to cleavage location and functional role: translational N-terminal methionine processing (∼10% of total proteolysis), sites close to the translational N terminus that likely represent removal of transit or signal peptides (∼25% of total), and finally, other endoproteolytic cuts (∼65% of total). Induction of apoptosis causes relatively little change in the first two proteolytic categories, but dramatic changes are seen in endoproteolysis. For example, we observed 1706 putative apoptotic caspase cuts, more than double the total annotated sites in the CASBAH and MEROPS databases. In the endoproteolysis category, there are a total of nearly 3000 noncaspase nontryptic cleavages that are not currently reported in the MEROPS database. These studies significantly increase the annotation for all categories of proteolysis in human cells and allow public access for investigators to explore interesting proteolytic events in healthy and apoptotic human cells.
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