Decoding the messaging of the ubiquitin system using chemical and protein probes

Henneberg, Lukas T.; Schulman, Brenda A.

doi:10.1016/j.chembiol.2021.03.009

Cited by 41 publications

(38 citation statements)

References 120 publications

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“…Target ubiquitination is sequentially catalyzed by three enzymes: ubiquitin (Ub) J o u r n a l P r e -p r o o f activating enzyme (E1), Ub conjugating enzyme (E2), and ligase enzyme (E3) (22). PROTACs are involved in the E2/E3 Ub conjugation cascade where E2/Ub binds E3 resulting in the transfer of Ub to a lysine (Lys) residue on the surface of the target protein (23)(24)(25). Although intuitively, ternary complex formation should correlate with ubiquitination, Vieux et al demonstrated that for a Brd4 BD1 /CRBN targeted series of PROTACs, there was no correlation between ternary complex formation and target ubiquitination rate (26).…”

Section: Introductionmentioning

confidence: 99%

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

Bai

Riching

Makaju

et al. 2022

Journal of Biological Chemistry

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Section: Introductionmentioning

confidence: 99%

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

Bai

Riching

Makaju

et al. 2022

Journal of Biological Chemistry

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“…Firstly, the specific substrate of E3 ligase had been elucidated in few studies and needs to be identified, especially in the process of breast cancer metastasis. Recent advances in high-throughput screening chemical methods have revolutionized our ability to match E3 ubiquitin ligases with their cellular targets (134), like the UBAIT (ubiquitin-activated interaction traps strategy), which relies on a ubiquitin molecule covalently fused to the E3 ligase of interest being charged onto E2 enzymes. Using the affinity enrichment of tagged UBAITs with following mass spectrometry can identify substrates of several E3s (135).…”

Section: Discussionmentioning

confidence: 99%

“…Secondly, the substrate recognition specificity of E3 ligases needs to be understand more deeply in breast cancer metastasis, which is critical for the efficient small-molecule inhibition of substrate degradation. Comparing proteins modified in cell lysates versus when an E3 ligase is depleted will allow the identification of substrates (134,136). Thirdly, structural bases and ubiquitin mechanisms facilitate with further exploit pharmacological strategy.…”

Section: Discussionmentioning

confidence: 99%

“…Thirdly, structural bases and ubiquitin mechanisms facilitate with further exploit pharmacological strategy. For example, typical HECT family E3s harbor catalytic cysteines that first receive ubiquitin molecule from a bound E2~Ub intermediate and then directly deliver the ubiquitin to the substrate protein, which can pharmacologically target the catalytic cysteines of E3s (134). Instead, there are still several non-classical E3s whose structure and specific ubiquitin transfer mechanisms remain unknown.…”

Section: Discussionmentioning

confidence: 99%

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E3 Ubiquitin Ligases in Breast Cancer Metastasis: A Systematic Review of Pathogenic Functions and Clinical Implications

et al. 2021

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Female breast cancer has become the most commonly occurring cancer worldwide. Although it has a good prognosis under early diagnosis and appropriate treatment, breast cancer metastasis drastically causes mortality. The process of metastasis, which includes cell epithelial–mesenchymal transition, invasion, migration, and colonization, is a multistep cascade of molecular events directed by gene mutations and altered protein expressions. Ubiquitin modification of proteins plays a common role in most of the biological processes. E3 ubiquitin ligase, the key regulator of protein ubiquitination, determines the fate of ubiquitinated proteins. E3 ubiquitin ligases target a broad spectrum of substrates. The aberrant functions of many E3 ubiquitin ligases can affect the biological behavior of cancer cells, including breast cancer metastasis. In this review, we provide an overview of these ligases, summarize the metastatic processes in which E3s are involved, and comprehensively describe the roles of E3 ubiquitin ligases. Furthermore, we classified E3 ubiquitin ligases based on their structure and analyzed them with the survival of breast cancer patients. Finally, we consider how our knowledge can be used for E3s’ potency in the therapeutic intervention or prognostic assessment of metastatic breast cancer.

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“…[10f] These applications exemplify the power and utility of activity-based E2-Ub probes,a nd also suggest that E2-Ub probes with different structural tuning may be needed for elucidating the mechanistic details of diverse E3s. [11] However,fine structural tuning of the previously reported activitybased E2-Ub probes has been limited by the reliance of their syntheses on recombination technology and bioconjugation chemistry.C hemical protein synthesis is ap owerful platform to access proteins of almost any amino acid sequence,and has been widely used to obtain customized proteins for the study of biochemical and structural mechanisms. [12] We are therefore interested in the total chemical synthesis of E2 enzyme variants [13] to facilitate the construction of structurallydiverse,a tomically tailored activity-based E2-Ub probes.…”

Section: Introductionmentioning

confidence: 99%

Chemical Synthesis of Activity‐Based E2‐Ubiquitin Probes for the Structural Analysis of E3 Ligase‐Catalyzed Transthiolation

Liang

Chu

et al. 2021

Angew Chem Int Ed

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Activity-based E2 conjugating enzyme (E2)-ubiquitin (Ub) probes have recently emerged as effective tools for studying the molecular mechanism of E3 ligase (E3)-catalyzed ubiquitination. However,t he preparation of existing activitybased E2-Ub probes depends on recombination technology and bioconjugation chemistry,l imiting their structural diversity.H erein we describe an expedient total chemical synthesis of an E2 enzyme variant through ah ydrazide-based native chemical ligation, which enabled the construction of astructurally new activity-based E2-Ub probe to covalentlycapture the catalytic site of Cys-dependent E3s.C hemical cross-linking coupled with mass spectrometry (CXMS) demonstrated the utility of this new probe in structural analysis of the intermediates formed during Nedd4 and Parkin-mediated transthiolation. This study exemplifies the utility of chemical protein synthesis for the development of protein probes for biological studies.

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Decoding the messaging of the ubiquitin system using chemical and protein probes

Cited by 41 publications

References 120 publications

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

E3 Ubiquitin Ligases in Breast Cancer Metastasis: A Systematic Review of Pathogenic Functions and Clinical Implications

Chemical Synthesis of Activity‐Based E2‐Ubiquitin Probes for the Structural Analysis of E3 Ligase‐Catalyzed Transthiolation

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