1
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Xia Q, Meng X, Wang Y, Yuan R, Li P, Liu L, Li YM. A cell-permeable Ub-Dha probe for profiling E1-E2-E3 enzymes in live cells. Chem Commun (Camb) 2024; 60:4342-4345. [PMID: 38545842 DOI: 10.1039/d4cc00415a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Activity-based ubiquitin probes (Ub-ABPs) have recently been developed as effective tools for studying the capabilities of E1-E2-E3 enzymes, but most of them can only be used in cell lysates. Here, we report the first cell-penetrating Ub-Dha probes based on thiazolidine-protected cysteines, which enable successful delivery into cells confirmed by a fluorophore at the N-terminus of Ub and live-cell fluorescence microscopy. A total of 18 E1-E2-E3 enzymes in live cells were labelled and enriched in combination with label-free quantification (LFQ) mass spectrometry. This work provided a new cell-penetrating Ub tool for studying the activity and function of Ub-related enzymes.
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Affiliation(s)
- Qiong Xia
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Wang
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Rujing Yuan
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Pincheng Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Liwen Liu
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
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2
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Hill CJ, Datta S, McCurtin NP, Kimball HZ, Kingsley MC, Bayer AL, Martin AC, Peng Q, Weerapana E, Scheck RA. A Modular Turn-On Strategy to Profile E2-Specific Ubiquitination Events in Living Cells. Angew Chem Int Ed Engl 2024; 63:e202319579. [PMID: 38291002 DOI: 10.1002/anie.202319579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
A cascade of three enzymes, E1-E2-E3, is responsible for transferring ubiquitin to target proteins, which controls many different aspects of cellular signaling. The role of the E2 has been largely overlooked, despite influencing substrate identity, chain multiplicity, and topology. Here we report a method-targeted charging of ubiquitin to E2 (tCUbE)-that can track a tagged ubiquitin through its entire enzymatic cascade in living mammalian cells. We use this approach to reveal new targets whose ubiquitination depends on UbcH5a E2 activity. We demonstrate that tCUbE can be broadly applied to multiple E2s and in different human cell lines. tCUbE is uniquely suited to examine E2-E3-substrate cascades of interest and/or piece together previously unidentified cascades, thereby illuminating entire branches of the UPS and providing critical insight that will be useful for identifying new therapeutic targets in the UPS.
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Affiliation(s)
- Caitlin J Hill
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Suprama Datta
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | | | - Hannah Z Kimball
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Molly C Kingsley
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Abraham L Bayer
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | | | - Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Rebecca A Scheck
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
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3
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Tang JH, Shu QY, Guo YY, Zhu H, Li YM. Cell-Permeable Ubiquitin and Histone Tools for Studying Post-translational Modifications. Chembiochem 2023; 24:e202300169. [PMID: 37060212 DOI: 10.1002/cbic.202300169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/16/2023]
Abstract
Protein post-translational modifications (PTMs) regulate nearly all biological processes in eukaryotic cells, and synthetic PTM protein tools are widely used to detect the activity of the related enzymes and identify the interacting proteins in cell lysates. Recently, the study of these enzymes and the interacting proteome has been accomplished in live cells using cell-permeable PTM protein tools. In this concept, we will introduce cell penetrating techniques, the syntheses of cell-permeable PTM protein tools, and offer some future perspective.
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Affiliation(s)
- Jia-Hui Tang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Qing-Yao Shu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Yan Guo
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Huixia Zhu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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4
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Currie MF, Singh SK, Ji M, Chatterjee C. The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes. Methods 2023; 215:28-37. [PMID: 37244506 PMCID: PMC10364803 DOI: 10.1016/j.ymeth.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Histone post-translational modifications (PTMs) on lysine residues, including methylation, ubiquitylation, and sumoylation, have been studied using semisynthetic histones reconstituted into nucleosomes. These studies have revealed the in vitro effects of histone PTMs on chromatin structure, gene transcription, and biochemical crosstalk. However, the dynamic and transient nature of most enzyme-chromatin interactions poses a challenge toward identifying specific enzyme-substrate interactions. To address this, we report methodology for the synthesis of two ubiquitylated activity-based probe histones, H2BK120ub(G76C) and H2BK120ub(G76Dha), that may be used to trap enzyme active-site cysteines as disulfides or in the form of thioether linkages, respectively. The general synthetic method we report for converting ubiquitylated nucleosomes into activity-based probes may also be applied to other histone sites of ubiquitylation in order to facilitate the identification of enzyme-chromatin interactions.
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Affiliation(s)
- Madeline F Currie
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Sumeet K Singh
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Meihuan Ji
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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5
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Huppelschoten Y, van der Heden van Noort GJ. State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools. Semin Cell Dev Biol 2022; 132:74-85. [PMID: 34961664 DOI: 10.1016/j.semcdb.2021.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; Global Research Technologies, Novo Nordisk Research Park, Måløv, Denmark
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6
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Bustos F, Mathur S, Espejo-Serrano C, Toth R, Hastie CJ, Virdee S, Findlay GM. Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome. Life Sci Alliance 2022; 5:5/11/e202101248. [PMID: 35764390 PMCID: PMC9240097 DOI: 10.26508/lsa.202101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Affiliation(s)
- Francisco Bustos
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Sunil Mathur
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Carmen Espejo-Serrano
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - C James Hastie
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Greg M Findlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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7
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Jing Y, Zuo C, Du YX, Mao J, Ding R, Zhang J, Liang LJ, Qu Q. Chemical tools for E3 ubiquitin ligase study. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022; 61:e202203792. [DOI: 10.1002/anie.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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9
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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10
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Zhou H, Carpenter T, Fu X, Jin B, Ody B, Hassan MS, Jacobs SE, Cheung J, Nicholson EM, Turlington M, Zhao B, Lorenz S, Cropp TA, Yin J. Linkage-Specific Synthesis of Di-ubiquitin Probes Enabled by the Incorporation of Unnatural Amino Acid ThzK. Chembiochem 2022; 23:e202200133. [PMID: 35263494 PMCID: PMC9129888 DOI: 10.1002/cbic.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 11/08/2022]
Abstract
Di-ubiquitin (diUB) conjugates of defined linkages are useful tools for probing the functions of UB ligases, UB-binding proteins and deubiquitinating enzymes (DUBs) in coding, decoding and editing the signals carried by the UB chains. Here we developed an efficient method for linkage-specific synthesis of diUB probes based on the incorporation of the unnatural amino acid (UAA) Nϵ -L-thiaprolyl-L-Lys (L-ThzK) into UB for ligation with another UB at a defined Lys position. The diUB formed by the UAA-mediated ligation reaction has a G76C mutation on the side of donor UB for conjugation with E2 and E3 enzymes or undergoing dethiolation to generate a covalent trap for DUBs. The development of UAA mutagenesis for diUB synthesis provides an easy route for preparing linkage-specific UB-based probes to decipher the biological signals mediated by protein ubiquitination.
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Affiliation(s)
- Han Zhou
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Tomaya Carpenter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Xuan Fu
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Bo Jin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Britton Ody
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Mohammad Sazid Hassan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Savannah E Jacobs
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny Cheung
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Eve M Nicholson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Mark Turlington
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA 30149, USA
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Jun Yin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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11
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Immel JR, Chilamari M, Bloom S. Combining flavin photocatalysis with parallel synthesis: a general platform to optimize peptides with non-proteinogenic amino acids. Chem Sci 2021; 12:10083-10091. [PMID: 34377401 PMCID: PMC8317666 DOI: 10.1039/d1sc02562g] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Most peptide drugs contain non-proteinogenic amino acids (NPAAs), born out through extensive structure-activity relationship (SAR) studies using solid-phase peptide synthesis (SPPS). Synthetically laborious and expensive to manufacture, NPAAs also can have poor coupling efficiencies allowing only a small fraction to be sampled by conventional SPPS. To gain general access to NPAA-containing peptides, we developed a first-generation platform that merges contemporary flavin photocatalysis with parallel synthesis to simultaneously make, purify, quantify, and even test up to 96 single-NPAA peptide variants via the unique combination of boronic acids and a dehydroalanine residue in a peptide. We showcase the power of our newly minted platform to introduce NPAAs of diverse chemotypes-aliphatic, aromatic, heteroaromatic-directly into peptides, including 15 entirely new residues, and to evolve a simple proteinogenic peptide into an unnatural inhibitor of thrombin by non-classical peptide SAR.
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Affiliation(s)
- Jacob R Immel
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Maheshwerreddy Chilamari
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Steven Bloom
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
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12
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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13
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Liang L, Chu G, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li Y, Liu L. Chemical Synthesis of Activity‐Based E2‐Ubiquitin Probes for the Structural Analysis of E3 Ligase‐Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lu‐Jun Liang
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Guo‐Chao Chu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Qian Qu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yangwode Jing
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
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14
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Liang LJ, Chu GC, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li YM, Liu L. Chemical Synthesis of Activity-Based E2-Ubiquitin Probes for the Structural Analysis of E3 Ligase-Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021; 60:17171-17177. [PMID: 34021957 DOI: 10.1002/anie.202105870] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 12/17/2022]
Abstract
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, the preparation of existing activity-based E2-Ub probes depends on recombination technology and bioconjugation chemistry, limiting their structural diversity. Herein we describe an expedient total chemical synthesis of an E2 enzyme variant through a hydrazide-based native chemical ligation, which enabled the construction of a structurally new activity-based E2-Ub probe to covalently capture the catalytic site of Cys-dependent E3s. Chemical 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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Affiliation(s)
- Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.,School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Qian Qu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jingnan Chen
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yangwode Jing
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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15
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Qiao Y, Yu G, Leeuwon SZ, Liu WR. Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid. Molecules 2021; 26:2619. [PMID: 33947165 PMCID: PMC8125731 DOI: 10.3390/molecules26092619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form S-cyano-cysteine, in which the S-Cβ bond is highly polarized. We explored the labile nature of this bond for triggering E2 elimination to generate dehydroalanine. Our results indicated that when cysteine is at the flexible C-terminal end of a protein, the dehydroalanine formation is highly effective. We produced ubiquitin and ubiquitin-like proteins with a C-terminal dehydroalanine residue with high yields. When cysteine is located at an internal region of a protein, the efficiency of the reaction varies with mainly hydrolysis products observed. Dehydroalanine in proteins such as ubiquitin and ubiquitin-like proteins can serve as probes for studying pathways involving ubiquitin and ubiquitin-like proteins and it is also a starting point to generate proteins with many PTM analogues; therefore, we believe that this NTCB-triggered dehydroalanine formation method will find broad applications in studying ubiquitin and ubiquitin-like protein pathways and the functional annotation of many PTMs in proteins such as histones.
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Affiliation(s)
- Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Ge Yu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Sunshine Z. Leeuwon
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.Q.); (G.Y.); (S.Z.L.)
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
- Molecular & Cellular Medicine Department, College of Medicine, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
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16
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Benns HJ, Wincott CJ, Tate EW, Child MA. Activity- and reactivity-based proteomics: Recent technological advances and applications in drug discovery. Curr Opin Chem Biol 2020; 60:20-29. [PMID: 32768892 DOI: 10.1016/j.cbpa.2020.06.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Activity-based protein profiling (ABPP) is recognized as a powerful and versatile chemoproteomic technology in drug discovery. Central to ABPP is the use of activity-based probes to report the activity of specific enzymes or reactivity of amino acid types in complex biological systems. Over the last two decades, ABPP has facilitated the identification of new drug targets and discovery of lead compounds in human and infectious disease. Furthermore, as part of a sustained global effort to illuminate the druggable proteome, the repertoire of target classes addressable with activity-based probes has vastly expanded in recent years. Here, we provide an overview of ABPP and summarise the major technological advances with an emphasis on probe development.
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Affiliation(s)
- Henry James Benns
- Department of Life Sciences, London, UK; Department of Chemistry, Imperial College London, London, UK
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17
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Sui X, Wang Y, Du YX, Liang LJ, Zheng Q, Li YM, Liu L. Development and application of ubiquitin-based chemical probes. Chem Sci 2020; 11:12633-12646. [PMID: 34123237 PMCID: PMC8163311 DOI: 10.1039/d0sc03295f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein ubiquitination regulates almost every process in eukaryotic cells. The study of the many enzymes involved in the ubiquitination system and the development of ubiquitination-associated therapeutics are important areas of current research. Synthetic tools such as ubiquitin-based chemical probes have been making an increasing contribution to deciphering various biochemical components involved in ubiquitin conjugation, recruitment, signaling, and deconjugation. In the present minireview, we summarize the progress of ubiquitin-based chemical probes with an emphasis on their various structures and chemical synthesis. We discuss the utility of the ubiquitin-based chemical probes for discovering and profiling ubiquitin-dependent signaling systems, as well as the monitoring and visualization of ubiquitin-related enzymatic machinery. We also show how the probes can serve to elucidate the molecular mechanism of recognition and catalysis. Collectively, the development and application of ubiquitin-based chemical probes emphasizes the importance and utility of chemical protein synthesis in modern chemical biology. This article reviews the design, synthesis, and application of different classes of Ub-based chemical probes.![]()
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China .,Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yu Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Yun-Xiang Du
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
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18
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19
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Bartoccini F, Mari M, Retini M, Galarini R, Bartolucci S, Piersanti G. Single‐Step Synthesis of Dehydroalanine Derivatives via a Brønsted Acid‐Catalyzed Multicomponent Reaction. ChemistrySelect 2020. [DOI: 10.1002/slct.202000898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Francesca Bartoccini
- Department of Biomolecular SciencesUniversity of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino, PU Italy
| | - Michele Mari
- Department of Biomolecular SciencesUniversity of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino, PU Italy
| | - Michele Retini
- Department of Biomolecular SciencesUniversity of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino, PU Italy
| | - Roberta Galarini
- Centro Sviluppo e Validazione MetodiIstituto Zooprofilattico Sperimentale dell'Umbria e delle Marche “Togo Rosati” Via G. Salvemini 1 06126 Perugia, PG Italy
| | - Silvia Bartolucci
- Department of Biomolecular SciencesUniversity of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino, PU Italy
| | - Giovanni Piersanti
- Department of Biomolecular SciencesUniversity of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino, PU Italy
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20
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Kliza K, Husnjak K. Resolving the Complexity of Ubiquitin Networks. Front Mol Biosci 2020; 7:21. [PMID: 32175328 PMCID: PMC7056813 DOI: 10.3389/fmolb.2020.00021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.
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Affiliation(s)
- Katarzyna Kliza
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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21
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Taylor NC, McGouran JF. Strategies to Target Specific Components of the Ubiquitin Conjugation/Deconjugation Machinery. Front Chem 2020; 7:914. [PMID: 31998698 PMCID: PMC6966607 DOI: 10.3389/fchem.2019.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
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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Affiliation(s)
- Neil C Taylor
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Joanna F McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
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22
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Sui X, Li YM. Development of Ubiquitin Tools for Studies of Complex Ubiquitin Processing Protein Machines. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191113161511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Ubiquitination is one of the most extensive post-translational modifications in
eukaryotes and is involved in various physiological processes such as protein degradation,
autophagy, protein interaction, and protein localization. The ubiquitin (Ub)-related protein
machines include Ub-activating enzymes (E1s), Ub-conjugating enzymes (E2s), Ub ligases
(E3s), deubiquitinating enzymes (DUBs), p97, and the proteasomes. In recent years,
the role of DUBs has been extensively studied and relatively well understood. On the
other hand, the functional mechanisms of the other more complex ubiquitin-processing
protein machines (e.g., E3, p97, and proteasomes) are still to be sufficiently well explored
due to their intricate nature. One of the hurdles facing the studies of these complex protein
machines is the challenge of developing tailor-designed structurally defined model substrates,
which unfortunately cannot be directly obtained using recombinant technology. Consequently, the acquisition
and synthesis of the ubiquitin tool molecules are essential for the elucidation of the functions and
structures of the complex ubiquitin-processing protein machines. This paper aims to highlight recent studies on
these protein machines based on the synthetic ubiquitin tool molecules.
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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23
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Chu GC, Hua X, Zuo C, Chen CC, Meng XB, Zhang Z, Fu Y, Shi J, Li YM. Efficient Semi-Synthesis of Atypical Ubiquitin Chains and Ubiquitin-Based Probes Forged by Thioether Isopeptide Bonds. Chemistry 2019; 25:16668-16675. [PMID: 31625216 DOI: 10.1002/chem.201904010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/16/2019] [Indexed: 01/24/2023]
Abstract
The development of powerful and general methods to acquire ubiquitin (Ub) chains has prompted the deciphering of Ub-mediated processes. Herein, the cysteine-aminoethylation assisted chemical ubiquitination (CAACU) strategy is extended and improved to enable the efficient semi-synthesis of atypical Ub chain analogues and Ub-based probes. Combining the Cys aminoethylation and the auxiliary-mediated protein ligation, several linkage- and length-defined atypical Ub chains including di-Ubs, K27C-linked tri-Ub, K11/K48C-branched tri-Ub, and even the SUMOlated Ub are successfully prepared from recombinantly expressed starting materials at about a 9-20 mg L-1 expression level. In addition, the utility of this strategy is demonstrated with the synthesis of a novel non-hydrolyzable di-Ub PA probe, which may provide a new useful tool for the mechanistic studies of deubiquitinase (DUB) recognition.
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Affiliation(s)
- Guo-Chao Chu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xiao Hua
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Chong Zuo
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chen-Chen Chen
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Xian-Bin Meng
- National Protein Science Technology Center, Tsinghua University, Beijing, 100084, P. R. China
| | - Zhongping Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, 230031, P. R. China
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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24
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Mathur S, Fletcher AJ, Branigan E, Hay RT, Virdee S. Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases. Cell Chem Biol 2019; 27:74-82.e6. [PMID: 31859248 PMCID: PMC6963778 DOI: 10.1016/j.chembiol.2019.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/13/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling is an invaluable technique for studying enzyme biology and facilitating the development of therapeutics. Ubiquitin E3 ligases (E3s) are one of the largest enzyme families and regulate a host of (patho)physiological processes. The largest subtype are the RING E3s of which there are >600 members. RING E3s have adaptor-like activity that can be subject to diverse regulatory mechanisms and have become attractive drug targets. Activity-based probes (ABPs) for measuring RING E3 activity do not exist. Here we re-engineer ubiquitin-charged E2 conjugating enzymes to produce photocrosslinking ABPs. We demonstrate activity-dependent profiling of two divergent cancer-associated RING E3s, RNF4 and c-Cbl, in response to their native activation signals. We also demonstrate profiling of endogenous RING E3 ligase activation in response to epidermal growth factor (EGF) stimulation. These photocrosslinking ABPs should advance E3 ligase research and the development of selective modulators against this important class of enzymes. Photoactivated activity-based probes developed for large class of ubiquitin E3 ligases ABPs are compatible with divergent RING E3 activation mechanisms Parallelized E3 profiling and detection of growth factor-induced E3 activation
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Affiliation(s)
- Sunil Mathur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Adam J Fletcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Emma Branigan
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Ronald T Hay
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.
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25
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Zhang Y, Hirota T, Kuwata K, Oishi S, Gramani SG, Bode JW. Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO-E2-E3 Ligase Ternary Complexes. J Am Chem Soc 2019; 141:14742-14751. [PMID: 31436980 DOI: 10.1021/jacs.9b06820] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
E2 conjugating enzymes are the key catalytic actors in the transfer of ubiquitin, SUMO, and other ubiquitin-like modifiers to their substrate proteins. Their high rates of transfer and promiscuous binding complicate studies of their interactions and binding partners. To access specific, covalently linked conjugates of the SUMO E2 conjugating enzyme Ubc9, we prepared synthetic variants bearing site-specific non-native modifications including the following: (1) replacement of Cys93 to 2,3-diaminopropionic acid to form the amide-linked stable E2-SUMO conjugate, which is known to have high affinity for E3 ligases; (2) a photoreactive group (diazirine) to trap E3 ligases upon UV irradiation; and (3) an N-terminal biotin for purification and detection. To construct these Ubc9 variants in a flexible, convergent manner, we combined the three leading methods: native chemical ligation (NCL), α-ketoacid-hydroxylamine (KAHA) ligation, and serine/threonine ligation (STL). Using the synthetic proteins, we demonstrated the selective formation of Ubc9-SUMO conjugates and the trapping of an E3 ligase (RanBP2) to form the stable, covalently linked SUMO1-Ubc9-RanBP2 ternary complex. The powerful combination of ligation methods-which minimizes challenges of functional group manipulations-will enable chemical probes based on E2 conjugating enzymes to trap E3 ligases and facilitate the synthesis of other protein classes.
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Affiliation(s)
- Yinfeng Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Subramanian G Gramani
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan
| | - Jeffrey W Bode
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Chikusa , Nagoya 464-8602 , Japan.,Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich 8093 , Switzerland
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