Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes

Gong, Ping; Davidson, Gregory A.; Gui, Weijun; Yang, Kun; Bozza, William P.; Zhuang, Zhihao

doi:10.1039/c8sc01573b

Cited by 27 publications

(30 citation statements)

References 50 publications

(45 reference statements)

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“…Such probes usually contain one or more Ub units and an enrichment/purication tag. [33][34][35][36][37][38][39][40] Ub units can be either natural or mimetics that do not impact the interaction with linkage-specic interactors ( Fig. 4a).…”

Section: Probes Capturing Ub Interactorsmentioning

confidence: 99%

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Development and application of ubiquitin-based chemical probes

Sui

Wang

et al. 2020

Chem. Sci.

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Section: Probes Capturing Ub Interactorsmentioning

confidence: 99%

“…Biochemical studies showed that the H2AK119Ub specic DUB Calypso/ASX can be efficiently captured by this probe. 25 Another Ub-substrate probe, Ub-PCNA-MAL, was developed by Zhuang et al 40 (Fig. 11b).…”

Section: This Journal Is © the Royal Society Of Chemistry 2020mentioning

confidence: 99%

Development and application of ubiquitin-based chemical probes

Sui

Wang

et al. 2020

Chem. Sci.

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“…To further unpick DUB specificity the challenging aim of generating Ubiquitin-protein conjugate probes has been addressed. In 2018 Brick and Zhuang (Gong et al, 2018) both extended their conjugation methodologies to create Ub-protein probes. Brik and co-workers targeted ubiquitinated α-globin, forming DHA at the single cysteine (104) present in α-globin and coupling to a thiol bearing thiazolidine.…”

Section: Ubiquitin-protein Conjugate Probes For Deubiquitinating Enzymesmentioning

confidence: 99%

Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Taylor

McGouran

2020

Front. Chem.

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The regulation of ubiquitination status in the cell is controlled by ubiquitin ligases acting in tandem with deubiquitinating enzymes. Ubiquitination controls many key processes in the cell from division to death making its tight regulation key to optimal cell function. Activity based protein profiling has emerged as a powerful technique to study these important enzymes. With around 100 deubiquitinating enzymes and 600 ubiquitin ligases in the human genome targeting a subclass of these enzymes or even a single enzyme is a compelling strategy to unpick this complex system. In this review we will discuss different approaches adopted, including activity-based probes centered around ubiquitin-protein, ubiquitin-peptide and mutated ubiquitin scaffolds. We examine challenges faced and opportunities presented to increase specificity in activity-based protein profiling of the ubiquitin conjugation/deconjugation machinery.

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“…In addition, the ubiquitin chain linkage specificity of DUBs may be determined by the development of di-Ub ABPs [79]. However, despite various efforts, ABPs are still limited in the analysis of DUB specificity towards target proteins and the selectivity between DUBs [80][81][82].…”

Section: Limitationsmentioning

confidence: 99%

Assay Systems for Profiling Deubiquitinating Activity

Cho

Park

Kim

et al. 2020

IJMS

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Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein–protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.

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Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes

Abstract: Activity-based Ub-PCNA probes identify deubiquitinating enzymes (DUBs) specific for PCNA and demonstrate site-specific deubiquitination by DUBs.

Cited by 27 publications

References 50 publications

Development and application of ubiquitin-based chemical probes

Development and application of ubiquitin-based chemical probes

Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery

Assay Systems for Profiling Deubiquitinating Activity

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