Tandem Ubiquitin Binding Entities (TUBEs) as Tools to Explore Ubiquitin-Proteasome System and PROTAC Drug Discovery

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 2365; p. 185
• Main Authors: Kadimisetty, Karteek, Sheets, Katie J, Gross, Patrick H, Zerr, Myra J, Ouazia, Dahmane
• Format: Journal Article
• Language: English
• Published: United States 2021
• Subjects: Drug Discovery; Intercellular Signaling Peptides and Proteins; Polyubiquitin - metabolism; Proteasome Endopeptidase Complex - metabolism; Protein Binding; Ubiquitin - metabolism; Ubiquitin; Protein degradation; PROTAC; Ubiquitin proteasome system; TUBEs; Polyubiquitin chains; Chain selectivity; High-throughput assay
• ISSN: 1940-6029
• DOI: 10.1007/978-1-0716-1665-9_10

The ubiquitin proteasome system (UPS) is a complex pathway that involves multiple enzymes and culminates in the formation of a polyubiquitin chain on a target protein. As its importance is becoming more evident in drug discovery, there is a renewed interest in understanding the role that polyubiquitin chains play. This has been a challenge, mostly due to the lack of experimental tools for detecting the polyubiquitinated forms of a protein of interest (POI). Tandem Ubiquitin Binding Entities (TUBEs) are engineered protein domains that bind specifically to polyubiquitin chains. These polyubiquitin affinity matrices are highly sensitive as they bind to polyubiquitin chains in the nanomolar range. They exist in two forms: pan-selective TUBEs and chain-selective TUBEs. The ability of TUBEs to be conjugated to different entities is truly what makes them unique. TUBEs are used in a wide variety of experiments such as in protein pulldowns to enrich for polyubiquitinated proteins. They are an alternative to ubiquitin antibodies in Western blots. Further, TUBEs are used as capture reagents for immobilizing polyubiquitinated proteins on a microtiter plate. The use of TUBEs as components of in vitro and cell-based assays presents the unique feature of confirming and assessing the polyubiquitination of a POI in response to inhibitors, activators, or PROTAC molecules. Therefore, TUBEs not only play a big role in studying the UPS but also have a huge potential for speeding up the drug discovery process.