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Kriegesmann J, Brik A. Synthesis of ubiquitinated proteins for biochemical and functional analysis. Chem Sci 2023; 14:10025-10040. [PMID: 37772107 PMCID: PMC10529715 DOI: 10.1039/d3sc03664b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/27/2023] [Indexed: 09/30/2023] Open
Abstract
Ubiquitination plays a crucial role in controlling various biological processes such as translation, DNA repair and immune response. Protein degradation for example, is one of the main processes which is controlled by the ubiquitin system and has significant implications on human health. In order to investigate these processes and the roles played by different ubiquitination patterns on biological systems, homogeneously ubiquitinated proteins are needed. Notably, these conjugates that are made enzymatically in cells cannot be easily obtained in large amounts and high homogeneity by employing such strategies. Therefore, chemical and semisynthetic approaches have emerged to prepare different ubiquitinated proteins. In this review, we will present the key synthetic strategies and their applications for the preparation of various ubiquitinated proteins. Furthermore, the use of these precious conjugates in different biochemical and functional studies will be highlighted.
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Affiliation(s)
- Julia Kriegesmann
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
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2
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Iwase R, Dempsey DR, Whedon SD, Jiang H, Palanski BA, Deng B, Cole PA. Semisynthetic Approach to the Analysis of Tumor Suppressor PTEN Ubiquitination. J Am Chem Soc 2023; 145:6039-6044. [PMID: 36897111 PMCID: PMC10071500 DOI: 10.1021/jacs.2c13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Phosphatase and tensin homologue (PTEN) tumor suppressor protein is a PIP3 lipid phosphatase that is subject to multifaceted post-translational modifications. One such modification is the monoubiquitination of Lys13 that may alter its cellular localization but is also positioned in a manner that could influence several of its cellular functions. To explore the regulatory influence of ubiquitin on PTEN's biochemical properties and its interaction with ubiquitin ligases and a deubiquitinase, the generation of a site-specifically and stoichiometrically ubiquitinated protein could be beneficial. Here, we describe a semisynthetic method that relies upon sequential expressed protein ligation steps to install ubiquitin at a Lys13 mimic in near full-length PTEN. This approach permits the concurrent installation of C-terminal modifications in PTEN, thereby facilitating an analysis of the interplay between N-terminal ubiquitination and C-terminal phosphorylation. We find that the N-terminal ubiquitination of PTEN inhibits its enzymatic function, reduces its binding to lipid vesicles, modulates its processing by NEDD4-1 E3 ligase, and is efficiently cleaved by the deubiquitinase, USP7. Our ligation approach should motivate related efforts for uncovering the effects of ubiquitination of complex proteins.
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Affiliation(s)
- Reina Iwase
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel R. Dempsey
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Dermatology and Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Samuel D. Whedon
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brad A. Palanski
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Bedphiny Deng
- Dana-Farber/Harvard Cancer Center, Boston, Massachusetts 02115, United States
- College of Natural Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
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3
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Mandal S, Brik A. Probing the cell delivery of synthetic diubiquitin chains. Chem Commun (Camb) 2022; 58:8782-8785. [PMID: 35837864 PMCID: PMC9350984 DOI: 10.1039/d2cc02476d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, the live-cell delivery of structurally different synthetic diubiquitin chains was examined. We found that the combination of structural variations of the Ub chains (intrinsic factors); nature of CPP and CPP-protein linkage (extrinsic factors) influence their delivery. In this study, the live-cell delivery of structurally different synthetic diubiquitin chains was examined.![]()
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Affiliation(s)
- Shaswati Mandal
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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4
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Zhao B, Tsai YC, Jin B, Wang B, Wang Y, Zhou H, Carpenter T, Weissman AM, Yin J. Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond. Pharmacol Rev 2020; 72:380-413. [PMID: 32107274 PMCID: PMC7047443 DOI: 10.1124/pr.118.015651] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell. SIGNIFICANCE STATEMENT: The post-translational modification of proteins with ubiquitin alters the fate and function of proteins in diverse ways. Protein engineering is fundamentally transforming research in this area, providing new mechanistic insights and allowing for the exploration of concepts that can potentially be applied to therapeutic intervention.
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Affiliation(s)
- Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yien Che Tsai
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bufan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yiyang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Han Zhou
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Tomaya Carpenter
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Allan M Weissman
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Jun Yin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
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5
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Eid E, Boross GN, Sun H, Msallam M, Singh SK, Brik A. Total Chemical Synthesis of ISGylated-Ubiquitin Hybrid Chain Assisted by Acetamidomethyl Derivatives with Dual Functions. Bioconjug Chem 2020; 31:889-894. [PMID: 32069038 PMCID: PMC7086396 DOI: 10.1021/acs.bioconjchem.0c00026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Interferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like modifiers (ULM) family, which adopts a β-grasp fold domain(s) similar to ubiquitin (Ub) with only minor sequence homology. ISG15 consists of two Ub-like domains and aids the immune system in neutralizing infections by numerous pathogens and plays an important role in defending cells against many viruses including influenza A. Recently, Ub was found to be a substrate for ISG15, which can be ISGylated on Lys29 and Lys48, while the former is more dominant. The discovery of such hybrid ISG15-Ub chains brought forward various fundamental questions regarding the nature and effect of this conjugation. To further investigate the role of hybrid ISG15-Ub chains, the pure homogeneous material of these chains is needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the total chemical synthesis of a 231-residue ISG15-Lys29-Ub hybrid chain. During the synthesis we encountered insoluble peptide fragments, and therefore we developed a new reversible Acm based solubilizing tag to efficiently tackle this hurdle. This new Acm tag was compared with the known Arg based Acm solubilizing tag and was found to be more reliable in terms of incorporation and efficiency as demonstrated in the synthesis of the native ISG15-Ub hybrid chain.
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Affiliation(s)
- Emad Eid
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
| | - Gábor N Boross
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
| | - Hao Sun
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
| | - Muna Msallam
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
| | - Sumeet K Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008, Israel
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6
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Bouchenna J, Sénéchal M, Drobecq H, Stankovic-Valentin N, Vicogne J, Melnyk O. The Role of the Conserved SUMO-2/3 Cysteine Residue on Domain Structure Investigated Using Protein Chemical Synthesis. Bioconjug Chem 2019; 30:2684-2696. [PMID: 31532181 DOI: 10.1021/acs.bioconjchem.9b00598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While the semi or total synthesis of ubiquitin or polyubiquitin conjugates has attracted a lot of attention the past decade, the preparation of small ubiquitin-like modifier (SUMO) conjugates is much less developed. We describe hereinafter some important molecular features to consider when preparing SUMO-2/3 conjugates by chemical synthesis using the native chemical ligation and extended methods. In particular, we clarify the role of the conserved cysteine residue on SUMO-2/3 domain stability and properties. Our data reveal that SUMO-2 and -3 proteins behave differently from the Cys → Ala modification with SUMO-2 being less impacted than SUMO-3, likely due to a stabilizing interaction occurring in SUMO-2 between its tail and the SUMO core domain. While the Cys → Ala modification has no effect on the enzyme-catalyzed conjugation, it shows a deleterious effect on the enzyme-catalyzed deconjugation process, especially with the SUMO-3 conjugate. Whereas it is often stated that SUMO-2 and SUMO-3 are structurally and functionally indistinguishable, here we show that these proteins have specific structural and biochemical properties. This information is important to consider when designing and preparing SUMO-2/3 conjugates, and should help in making progress in the understanding of the specific role of SUMO-2 and/or SUMO-3 modifications on protein structure and function.
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Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) , DKFZ - ZMBH Alliance, 69120 , Heidelberg , Germany
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
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7
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Zhao X, Mißun M, Schneider T, Müller F, Lutz J, Scheffner M, Marx A, Kovermann M. Artificially Linked Ubiquitin Dimers Characterised Structurally and Dynamically by NMR Spectroscopy. Chembiochem 2019; 20:1772-1777. [PMID: 30920720 PMCID: PMC6771822 DOI: 10.1002/cbic.201900146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 12/23/2022]
Abstract
As one of the most prevalent post‐translational modifications in eukaryotic cells, ubiquitylation plays vital roles in many cellular processes, such as protein degradation, DNA metabolism, and cell differentiation. Substrate proteins can be tagged by distinct types of polymeric ubiquitin (Ub) chains, which determine the eventual fate of the modified protein. A facile, click chemistry based approach for the efficient generation of linkage‐defined Ub chains, including Ub dimers, was recently established. Within these chains, individual Ub moieties are connected through a triazole linkage, rather than the natural isopeptide bond. Herein, it is reported that the conformation of an artificially K48‐linked Ub dimer resembles that of the natively linked dimer, with respect to structural and dynamic characteristics, as demonstrated by means of high‐resolution NMR spectroscopy. Thus, it is proposed that artificially linked Ub dimers, as generated by this approach, represent potent tools for studying the inherently different properties and functions of distinct Ub chains.
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Affiliation(s)
- Xiaohui Zhao
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Maite Mißun
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Franziska Müller
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Joachim Lutz
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
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8
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Gopinath P, Ohayon S, Nawatha M, Brik A. Chemical and semisynthetic approaches to study and target deubiquitinases. Chem Soc Rev 2018; 45:4171-98. [PMID: 27049734 DOI: 10.1039/c6cs00083e] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a key posttranslational modification, which affects numerous biological processes and is reversed by a class of enzymes known as deubiquitinases (DUBs). This family of enzymes cleaves mono-ubiquitin or poly-ubiquitin chains from a target protein through different mechanisms and mode of interactions with their substrates. Studying the role of DUBs in health and diseases has been a major goal for many laboratories both in academia and in industry. However, the field has been challenged by the difficulties in obtaining native substrates and novel reagents using traditional enzymatic and molecular biology approaches. Recent advancements in the synthesis and semisynthesis of proteins made it possible to prepare several unique ubiquitin conjugates to study various aspects of DUBs such as their specificities and structures. Moreover, these approaches enable the preparation of novel activity based probes and assays to monitor DUB activities in vitro and in cellular contexts. Efforts made to bring new chemical entities for the selective inhibition of DUBs based on these tools are also highlighted with selected examples.
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Affiliation(s)
- Pushparathinam Gopinath
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shimrit Ohayon
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Mickal Nawatha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
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9
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Tang S, Liang LJ, Si YY, Gao S, Wang JX, Liang J, Mei Z, Zheng JS, Liu L. Practical Chemical Synthesis of Atypical Ubiquitin Chains by Using an Isopeptide-Linked Ub Isomer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708067] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shan Tang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yan-Yan Si
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jia-Xing Wang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jun Liang
- School of Life Sciences; University of Science and Technology of China; Hefei 230026 China
| | - Ziqing Mei
- Biotechnology Research Institute; Chinese Academy of Agricultural Sciences; Beijing 100081 China
| | - Ji-Shen Zheng
- School of Life Sciences; University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
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10
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Tang S, Liang LJ, Si YY, Gao S, Wang JX, Liang J, Mei Z, Zheng JS, Liu L. Practical Chemical Synthesis of Atypical Ubiquitin Chains by Using an Isopeptide-Linked Ub Isomer. Angew Chem Int Ed Engl 2017; 56:13333-13337. [DOI: 10.1002/anie.201708067] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Shan Tang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yan-Yan Si
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jia-Xing Wang
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Jun Liang
- School of Life Sciences; University of Science and Technology of China; Hefei 230026 China
| | - Ziqing Mei
- Biotechnology Research Institute; Chinese Academy of Agricultural Sciences; Beijing 100081 China
| | - Ji-Shen Zheng
- School of Life Sciences; University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences; Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education); Department of Chemistry; Tsinghua University; Beijing 100084 China
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11
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Chemical ubiquitination for decrypting a cellular code. Biochem J 2017; 473:1297-314. [PMID: 27208213 PMCID: PMC5298413 DOI: 10.1042/bj20151195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/15/2016] [Indexed: 02/06/2023]
Abstract
The modification of proteins with ubiquitin (Ub) is an important regulator of eukaryotic biology and deleterious perturbation of this process is widely linked to the onset of various diseases. The regulatory capacity of the Ub signal is high and, in part, arises from the capability of Ub to be enzymatically polymerised to form polyubiquitin (polyUb) chains of eight different linkage types. These distinct polyUb topologies can then be site-specifically conjugated to substrate proteins to elicit a number of cellular outcomes. Therefore, to further elucidate the biological significance of substrate ubiquitination, methodologies that allow the production of defined polyUb species, and substrate proteins that are site-specifically modified with them, are essential to progress our understanding. Many chemically inspired methods have recently emerged which fulfil many of the criteria necessary for achieving deeper insight into Ub biology. With a view to providing immediate impact in traditional biology research labs, the aim of this review is to provide an overview of the techniques that are available for preparing Ub conjugates and polyUb chains with focus on approaches that use recombinant protein building blocks. These approaches either produce a native isopeptide, or analogue thereof, that can be hydrolysable or non-hydrolysable by deubiquitinases. The most significant biological insights that have already been garnered using such approaches will also be summarized.
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12
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Liang J, Zhang L, Tan XL, Qi YK, Feng S, Deng H, Yan Y, Zheng JS, Liu L, Tian CL. Chemical Synthesis of Diubiquitin-Based Photoaffinity Probes for Selectively Profiling Ubiquitin-Binding Proteins. Angew Chem Int Ed Engl 2017; 56:2744-2748. [DOI: 10.1002/anie.201611659] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Xiang-Long Tan
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yun-Kun Qi
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Feng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Yijing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
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13
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Liang J, Zhang L, Tan XL, Qi YK, Feng S, Deng H, Yan Y, Zheng JS, Liu L, Tian CL. Chemical Synthesis of Diubiquitin-Based Photoaffinity Probes for Selectively Profiling Ubiquitin-Binding Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611659] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Xiang-Long Tan
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yun-Kun Qi
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Feng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Yijing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
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14
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Singh SK, Sahu I, Mali SM, Hemantha HP, Kleifeld O, Glickman MH, Brik A. Synthetic Uncleavable Ubiquitinated Proteins Dissect Proteasome Deubiquitination and Degradation, and Highlight Distinctive Fate of Tetraubiquitin. J Am Chem Soc 2016; 138:16004-16015. [PMID: 27960333 DOI: 10.1021/jacs.6b09611] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various hypotheses have been proposed regarding how chain length, linkage type, position on substrate, and susceptibility to deubiquitinases (DUBs) affect processing of different substrates by proteasome. Here we report a new strategy for the chemical synthesis of ubiquitinated proteins to generate a set of well-defined conjugates bearing an oxime bond between the chain and the substrate. We confirmed that this isopeptide replacement is resistant to DUBs and to shaving by proteasome. Analyzing products generated by proteasomes ranked how chain length governed degradation outcome. Our results support that (1) the cleavage of the proximal isopeptide bond is not a prerequisite for proteasomal degradation, (2) by overcoming trimming at the proteasome, tetraUb is a fundamentally different signal than shorter chains, and (3) the tetra-ubiquitin chain can be degraded with the substrate. Together these results highlight the usefulness of chemistry to dissect the contribution of proteasome-associated DUBs and the complexity of the degradation process.
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Affiliation(s)
- Sumeet K Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Indrajit Sahu
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Hosahalli P Hemantha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Oded Kleifeld
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Michael H Glickman
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
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15
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Stanley M, Virdee S. Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates. Chembiochem 2016; 17:1472-80. [PMID: 27197715 PMCID: PMC5094518 DOI: 10.1002/cbic.201600138] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/11/2022]
Abstract
We describe the genetically directed incorporation of aminooxy functionality into recombinant proteins by using a mutant Methanosarcina barkeri pyrrolysyl‐tRNA synthetase/tRNACUA pair. This allows the general production of nonhydrolysable ubiquitin conjugates of recombinant origin by bioorthogonal oxime ligation. This was exemplified by the preparation of nonhydrolysable versions of diubiquitin, polymeric ubiquitin chains and ubiquitylated SUMO. The conjugates exhibited unrivalled isostery with the native isopeptide bond, as inferred from structural and biophysical characterisation. Furthermore, the conjugates functioned as nanomolar inhibitors of deubiquitylating enzymes and were recognised by linkage‐specific antibodies. This technology should provide a versatile platform for the development of powerful tools for studying deubiquitylating enzymes and for elucidating the cellular roles of diverse polyubiquitin linkages.
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Affiliation(s)
- Mathew Stanley
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.
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16
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Meledin R, Mali SM, Singh SK, Brik A. Protein ubiquitination via dehydroalanine: development and insights into the diastereoselective 1,4-addition step. Org Biomol Chem 2016; 14:4817-23. [PMID: 27143624 DOI: 10.1039/c6ob00882h] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy for site-specific protein ubiquitination using dehydroalanine (Dha) chemistry for the preparation of ubiquitin conjugates bearing a very close mimic of the native isopeptide bond. Our approach relies on the selective formation of Dha followed by conjugation with hexapeptide bearing a thiol handle derived from the C-terminal of ubiquitin. Subsequently, the resulting synthetic intermediate undergoes native chemical ligation with the complementary part of the ubiquitin polypeptide. It has been proposed that the Michael addition step could result in the formation of a diastereomeric mixture as a result of unselective protonation of the enolate intermediate. It has also been proposed that the chiral protein environment may influence such an addition step. In the protein context these questions remain open and no experimental evidence was provided as to how such a protein environment affects the diastereoselectivity of the addition step. As was previously proposed for the conjugation step on protein bearing Dha, the isopeptide bond formation step in our study resulted in the construction of two protein diastereomers. To assign the ratio of these diastereomers, trypsinization coupled with high-pressure liquid chromatography analysis were performed. Moreover, the obtained peptide diastereomers were compared with identical synthetic peptides having defined stereogenic centers, which enabled the determination of the configuration of the isopeptide mimic in each diastereomer. Our study, which offers a new method for isopeptide bond formation and protein ubiquitination, gives insights into the parameters that affect the stereoselectivity of the addition step to Dha for chemical protein modifications.
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Affiliation(s)
- Roman Meledin
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008 Israel.
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17
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Xie RL, Xu L, Li JB, Chu GC, Wang T, Huang YC, Li YM. Chemical Synthesis of K48-Linked Diubiquitin by Incorporation of a Lysine-Linked Auxiliary Handle. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600292] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Affiliation(s)
- Suman Kumar Maity
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
| | - Shimrit Ohayon
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich
Faculty of Chemistry Technion—Israel Institute of Technology, 3200008 Haifa, Israel
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19
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Pham GH, Strieter ER. Peeling away the layers of ubiquitin signaling complexities with synthetic ubiquitin-protein conjugates. Curr Opin Chem Biol 2015; 28:57-65. [PMID: 26093241 DOI: 10.1016/j.cbpa.2015.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Abstract
Covalent attachment of ubiquitin, a process termed ubiquitination, affects the location, function, and stability of modified proteins. Significant advances have been made in building synthetic ubiquitin-protein conjugates that can be used to investigate how ubiquitin regulates diverse biological processes. Herein we describe recent advances and discuss how chemical methods have been implemented to address the molecular underpinnings of ubiquitin-dependent cellular signaling.
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Affiliation(s)
- Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States.
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20
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Yang R, Bi X, Li F, Cao Y, Liu CF. Native chemical ubiquitination using a genetically incorporated azidonorleucine. Chem Commun (Camb) 2015; 50:7971-4. [PMID: 24915456 DOI: 10.1039/c4cc03721a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A robust chemical ubiquitination method was developed. The method employed a genetically incorporated azidonorleucine as an orthogonal lysine precursor for the installation of a Gly residue bearing an Nα-auxiliary which mediated the ligation between ubiquitin(1-75)-thioester and the target protein. To demonstrate our methodology, a model protein, K48-linked diubiquitin, was synthesized with an overall yield of 35%.
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Affiliation(s)
- Renliang Yang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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21
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Bondalapati S, Mansour W, Nakasone MA, Maity SK, Glickman MH, Brik A. Chemical synthesis of phosphorylated ubiquitin and diubiquitin exposes positional sensitivities of e1-e2 enzymes and deubiquitinases. Chemistry 2015; 21:7360-4. [PMID: 25829361 DOI: 10.1002/chem.201500540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 12/22/2022]
Abstract
Modification of ubiquitin by phosphorylation extends the signaling possibilities of this dynamic signal, as it could affect the activity of ligases and the processing of ubiquitin chains by deubiquitinases. The first chemical synthesis of phosphorylated ubiquitin and of Lys63-linked diubiquitin at the proximal, distal or both ubiquitins is reported. This enabled the examination of how such a modification alters E1-E2 activities of the ubiquitination machinery. It is found that E1 charging was not affected, while the assembly of phosphorylated ubiquitin chains was differentially inhibited with E2 enzymes tested. Moreover, this study shows that phosphorylation interferes with the recognition of linkage specific antibodies and the activities of several deubiquitinases. Notably, phosphorylation in the proximal or distal ubiquitin unit has differential effects on specific deubiquitinases. These results support a unique role of phosphorylation in the dynamics of the ubiquitin signal.
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Affiliation(s)
- Somasekhar Bondalapati
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653 Beer-Sheva 8410501 (Israel); Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200008 Haifa (Israel)
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22
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Abeywardana T, Pratt MR. Using Chemistry to Investigate the Molecular Consequences of Protein Ubiquitylation. Chembiochem 2014; 15:1547-54. [DOI: 10.1002/cbic.201402117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 12/21/2022]
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23
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Boll E, Drobecq H, Ollivier N, Raibaut L, Desmet R, Vicogne J, Melnyk O. A novel PEG-based solid support enables the synthesis of >50 amino-acid peptide thioesters and the total synthesis of a functional SUMO-1 peptide conjugate. Chem Sci 2014. [DOI: 10.1039/c3sc53509f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bis(2-sulfanylethyl)amino PEG resin gives access to large peptide thioester segments and to functional SUMO-1 conjugates.
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Affiliation(s)
- Emmanuelle Boll
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Hervé Drobecq
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Nathalie Ollivier
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Laurent Raibaut
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Rémi Desmet
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Jérome Vicogne
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Oleg Melnyk
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
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24
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Haj-Yahya N, Hemantha HP, Meledin R, Bondalapati S, Seenaiah M, Brik A. Dehydroalanine-based diubiquitin activity probes. Org Lett 2013; 16:540-3. [PMID: 24364494 DOI: 10.1021/ol403416w] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A strategy for the synthesis of dehydroalanine based diubiquitin activity probes is described. The site-specific introduction of dehydroalanine was achieved from diubiquitin bearing Cys residue near the scissile bond between two ubiquitins linked through Lys48, Lys63 or in a head to tail fashion. The probes were characterized for their activities with various deubiquitinases, which open new opportunities in studying deubiquitinases in various settings.
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Affiliation(s)
- Najat Haj-Yahya
- Department of Chemistry, Ben-Gurion University of the Negev , Beer Sheva 84105, Israel
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25
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van Treel ND, Mootz HD. SUMOylated RanGAP1 prepared by click chemistry. J Pept Sci 2013; 20:121-7. [PMID: 24338848 DOI: 10.1002/psc.2591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 01/26/2023]
Abstract
Ubiquitin and ubiquitin-like proteins such as SUMO represent important and abundant post-translational modifications involved in many cellular processes. These modifiers are reversibly attached via an isopeptide bond to lysine side chains of their target proteins by the action of specific E1, E2, and E3 enzymes. A significant challenge in studying ubiquitylation and SUMOylation is the frequently encountered inability to access desired conjugates at a defined position of the target protein and in homogenous form by using enzymatic preparation. In recent years, several chemical conjugation approaches have been developed to overcome this limitation. In this study, we aimed to selectively SUMOylate a 189-amino acid fragment of human RanGAP1 (amino acids 398-587) at the position of Lys524 by applying two recently reported approaches based on the Cu(I)-catalyzed alkyne-azide cycloaddition. Because of low yields observed for the incorporation of an unnatural amino acid with an azide moiety by the tRNA suppression technology, this route was abandoned. However, installing a single cysteine at position 524 and its selective alkylation was successful to introduce the azide group. The triazole-linked SUMO1**RanGAP1 conjugate could be obtained in good yields, purified, and was shown to specifically interact with RanBP2/Ubc9. Thus, we expand the scope of proteins accessible to chemical conjugation with ubiquitin-like proteins and underline the importance of having alternative approaches to do so.
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Affiliation(s)
- Nadine D van Treel
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
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