Abstract

DEGRONOPEDIA is a web server that combines experimental data on degron motifs with their multilayer context annotation. It allows the study of peptide motifs that can act as a primary degron in a tripartite degron architecture. In this model, the secondary degron refers to a lysine to which ubiquitin can be attached, while the tertiary degron points to a flexible, internally disordered region close to the secondary degron, acting as an initiating site for proteasomal degradation.

DEGRONOPEDIA annotates not only lysine as a potential ubiquitination site but also cysteine/threonine/serine, as ubiquitin can be attached to these. The server also provides information on post-translational modifications and pathogenic mutations within the degron and its flanking regions, as these can modulate degron accessibility. Since degrons can be formed after cleavage by proteases, we simulate sequence pruning based on user-defined sites, experimental data and theoretical predictions and search for emerging new degrons. Furthermore, DEGRONOPEDIA allows you to analyze your own sequence/structure to examine it for degrons and use machine learning to predict its N-/C-terminal stability.

See also ⚡ Quick start.

Availability

This website is free and open to all users, and there is no login required.

Feedback

If you would like to provide your feedback or report a bug, please contact Natalia Szulc or Wojciech Pokrzywa.

Laboratory

Pokrzywa Lab - Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw (IIMCB)

Acknowledgments

We thank Dr. Natalia Gumińska for preparing the logo of the DEGRONOPEDIA, see her blog Biorysunki.
All graphics in the Tutorial were created in BioRender.com.

Citing

Natalia A. Szulc, Filip Stefaniak, Małgorzata Piechota, Andrea Cappannini, Janusz M. Bujnicki, Wojciech Pokrzywa (2022).
DEGRONOPEDIA - a web server for proteome-wide inspection of degrons
doi: 10.1101/2022.05.19.492622