Bioinformatical detection of recognition factors for ubiquitin and SUMO

Methods in Molecular Biology
Benjamin Vogt, Kay Hofmann

Abstract

The specific recognition of ubiquitin, small ubiquitin-like modifier (SUMO), and related proteins is absolutely crucial for the signaling capacity of these modifiers. Most ubiquitin receptor proteins employ dedicated ubiquitin binding domains (UBDs), of which about 15 families have been described. By contrast, SUMO is recognized by short linear motifs that comprise only a few residues and do not require a defined tertiary structure. At the moment, three classes of SUMO-interacting motifs (SIMs) have been described. The recognition modes of most other modifiers remain poorly understood. When working with ubiquitin-family modifiers, a frequently occurring task is to assess a given protein sequence for the presence of known ubiquitin- or SUMO-binding elements. Due to the different nature of UBDs and SIMs, completely different approaches have to be used. This chapter addresses the bioinformatical detection of UBDs and SIMs through Web-based methods that are freely accessible and do not require a particular bioinformatics infrastructure.

Citations

Oct 23, 2012·The Journal of Biological Chemistry·Huaiyu Sun, Tony Hunter
Nov 21, 2013·Proceedings of the National Academy of Sciences of the United States of America·Nabil ElroubyGeorge Coupland
Sep 11, 2014·The FEBS Journal·Simone CallegariMaria G Masucci
Feb 25, 2018·Nature Communications·Thomas HermannsKay Hofmann
Nov 3, 2015·Nature Structural & Molecular Biology·Nathalie EisenhardtAndrea Pichler
Oct 1, 2019·Proteomics·Ramesh Kumar, Kanaga Sabapathy
Dec 25, 2019·Biochemical Society Transactions·Nathalia VarejãoDavid Reverter
Jul 20, 2012·Biochemistry Research International·Elisa Da Silva-FerradaRune Matthiesen
Nov 24, 2012·Biopolymers·Renee Garza, Lorraine Pillus
Aug 10, 2020·Computational Biology and Chemistry·Urmi Roy
Aug 14, 2020·ACS Chemical Biology·Kira BrüninghoffHenning D Mootz
Mar 2, 2019·Trends in Biochemical Sciences·Michael MatternManuel S Rodriguez
Jun 16, 2021·Plant Cell Reports·Moumita SrivastavaAnjil Kumar Srivastava
Oct 14, 2014·Molecular Cell·Konstantinos ParaskevopoulosColin Gordon

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