DEGRONOPEDIA: a web server for proteome-wide inspection of degrons
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Abstract
E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, a web server that searches for degrons and maps them to nearby residues that can undergo ubiquitination and disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment of degron conservation, the server also reports on post-translational modifications and mutations that may modulate degron availability. Acknowledging the prevalence of degrons at protein termini, DEGRONOPEDIA incorporates machine learning to assess N-/C-terminal stability, supplemented by simulations of proteolysis to identify degrons in newly formed termini. An experimental validation of a predicted C-terminal destabilizing motif, coupled with the confirmation of a post-proteolytic degron in another case, exemplifies its practical application. DEGRONOPEDIA can be freely accessed at degronopedia.com.
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Self-citation
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- Authors
- Szulc, N. A., Stefaniak, F., Piechota, M., Soszyńska, A., Piórkowska, G., Cappannini, A., Bujnicki, J. M., Maniaci, C., & Pokrzywa, W.
- Affiliations
- International Institute of Molecular and Cell Biology (PL)
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw , 4 Ks. Trojdena Str. , 02-109 Warsaw , Poland
- University of Dundee (GB)
- Corresponding author
- Szulc, Natalia A
- Pokrzywa, Wojciech
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-04-03
- Volume
- 52
- Issue
- W1
- Pages
- W221-W232
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11223883
- OpenAlex
- W4393902617
- Cited by
- 35
- References
- 117
- Citations by year
- 2026: 6 · 2025: 18 · 2024: 7 · 2023: 4
- FWCI
- 4.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion, cc-by)
- Funders
- National Science Centre, Poland (2021/41/N/NZ1/03473, 2021/42/E/NZ1/00190, 2020/39/B/NZ2/03127, 2017/26/A/NZ1/01083)
- European Commission (H2020-MSCA-ITN-2020, 956810, CA16120)
- BBSRC (BB/T009454/2)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- degron, E3 ubiquitin ligase, linear motifs, ubiquitination, protein degradation, protein disorder, protein unfolding, post-translational modification, web server
- MeSH terms
- Machine Learning, Degrons, Humans, Protein Processing, Post-Translational, Software, Internet, Proteome, Amino Acid Motifs, Ubiquitin-Protein Ligases, Ubiquitination, Proteolysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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