1
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Karandikar P, Gerstl JVE, Kappel AD, Won SY, Dubinski D, Garcia-Segura ME, Gessler FA, See AP, Peruzzotti-Jametti L, Bernstock JD. SUMOtherapeutics for Ischemic Stroke. Pharmaceuticals (Basel) 2023; 16:ph16050673. [PMID: 37242456 DOI: 10.3390/ph16050673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The small, ubiquitin-like modifier (SUMO) is a post-translational modifier with a profound influence on several key biological processes, including the mammalian stress response. Of particular interest are its neuroprotective effects, first recognized in the 13-lined ground squirrel (Ictidomys tridecemlineatus), in the context of hibernation torpor. Although the full scope of the SUMO pathway is yet to be elucidated, observations of its importance in managing neuronal responses to ischemia, maintaining ion gradients, and the preconditioning of neural stem cells make it a promising therapeutic target for acute cerebral ischemia. Recent advances in high-throughput screening have enabled the identification of small molecules that can upregulate SUMOylation, some of which have been validated in pertinent preclinical models of cerebral ischemia. Accordingly, the present review aims to summarize current knowledge and highlight the translational potential of the SUMOylation pathway in brain ischemia.
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Affiliation(s)
- Paramesh Karandikar
- T. H. Chan School of Medicine, University of Massachusetts, Worcester, MA 01655, USA
| | - Jakob V E Gerstl
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Ari D Kappel
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA 02215, USA
| | - Sae-Yeon Won
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Daniel Dubinski
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Monica Emili Garcia-Segura
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Florian A Gessler
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
| | - Alfred Pokmeng See
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Joshua D Bernstock
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
- Department of Neurosurgery, University Medicine Rostock, 18057 Rostock, Germany
- Koch Institute for Integrated Cancer Research, MIT, Cambridge, MA 02142, USA
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2
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Abboud SA, Cisse EH, Doudeau M, Bénédetti H, Aucagne V. A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation. Chem Sci 2021; 12:3194-3201. [PMID: 34164087 PMCID: PMC8179351 DOI: 10.1039/d0sc06001a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - El Hadji Cisse
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
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3
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Jiang HK, Kurkute P, Li CL, Wang YH, Chen PJ, Lin SY, Wang YS. Revealing USP7 Deubiquitinase Substrate Specificity by Unbiased Synthesis of Ubiquitin Tagged SUMO2. Biochemistry 2020; 59:3796-3801. [PMID: 33006472 DOI: 10.1021/acs.biochem.0c00701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ubiquitination and SUMOylation of protein are crucial for various biological responses. The recent unraveling of cross-talk between SUMO and ubiquitin (Ub) has shown the pressing needs to develop the platform for the synthesis of Ub tagged SUMO2 dimers to decipher its biological functions. Still, the platforms for facile synthesis of dimers under native condition are less explored and remain major challenges. Here, we have developed the platform that can expeditiously synthesize all eight Ub tagged SUMO2 and SUMOylated proteins under native condition. Expanding genetic code (EGC) method was employed to incorporate Se-alkylselenocysteine at lysine positions. Oxidative selenoxide elimination generates the electrophilic center, dehydroalanine, which upon Michael addition with C-terminal modified ubiquitin, a nucleophile, yield Ub tagged SUMO2. The dimers were further interrogated with USP7, a SUMO2 deubiquitinase, which is involved in DNA repair, to understand specificity toward the Ub tagged SUMO2 dimer. Our results have shown that the C-terminal domain of USP7 is crucial for USP7 efficiency and selectivity for the Ub tagged SUMO2 dimer.
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Affiliation(s)
- Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 30044, Taiwan
| | - Prashant Kurkute
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Lung Li
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Hui Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Jung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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4
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Sénéchal M, Bouchenna J, Vicogne J, Melnyk O. Comment on "N-terminal Protein Tail Acts as Aggregation Protective Entropic Bristles: The SUMO Case". Biomacromolecules 2020; 21:3480-3482. [PMID: 32702971 DOI: 10.1021/acs.biomac.0c00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SUMO-2 protein, SUMO-2 core domain, and the tail peptide corresponding to the first 14 residues were produced by chemical synthesis, and their secondary structures were analyzed by circular dichroism. The CD spectra of SUMO-2 and SUMO-2 core domain show distinct features and α-helical contents. In particular, the presence of the disordered tail in SUMO-2 lowers the α-helical content of the protein compared with SUMO-2 core domain and also explains the shift in the position of the minimum around 208 nm.
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Affiliation(s)
- Magalie Sénéchal
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jennifer Bouchenna
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
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5
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Bouchenna J, Sénéchal M, Drobecq H, Vicogne J, Melnyk O. Total Chemical Synthesis of All SUMO-2/3 Dimer Combinations. Bioconjug Chem 2019; 30:2967-2973. [PMID: 31702897 DOI: 10.1021/acs.bioconjchem.9b00661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One hallmark of protein chemical synthesis is its capacity to access proteins that living systems can hardly produce. This is typically the case for proteins harboring post-translational modifications such as ubiquitin or ubiquitin-like modifiers. Various methods have been developed for accessing polyubiquitin conjugates by semi- or total synthesis. Comparatively, the preparation of small-ubiquitin-like modifier (SUMO) conjugates, and more particularly of polySUMO scaffolds, is much less developed. We describe hereinafter a synthetic strategy for accessing all SUMO-2/3 dimer combinations.
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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
| | - 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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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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Witting KF, van der Heden van Noort GJ, Kofoed C, Talavera Ormeño C, el Atmioui D, Mulder MPC, Ovaa H. Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases. Angew Chem Int Ed Engl 2018; 57:14164-14168. [PMID: 30188611 PMCID: PMC6220884 DOI: 10.1002/anie.201809232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/04/2018] [Indexed: 12/15/2022]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a reversible post-translational modifier that is covalently attached to target proteins through an enzymatic cascade and removed by designated proteases. Abnormalities in this process, referred to as Ufmylation, have been associated with a variety of human diseases. Given this, the UFM1-specific enzymes represent potential therapeutic targets; however, understanding of their biological function has been hampered by the lack of chemical tools for activity profiling. To address this unmet need, a diversifiable platform for UFM1 activity-based probes (ABPs) utilizing a native chemical ligation (NCL) strategy was developed, enabling the generation of a variety of tools to profile both UFM1 conjugating and deconjugating enzymes. The use of the probes is demonstrated in vitro and in vivo for monitoring UFM1 enzyme reactivity, opening new research avenues.
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Affiliation(s)
- Katharina F. Witting
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Christian Kofoed
- Department of ChemistryCenter for Evolutionary Chemical BiologyUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Cami Talavera Ormeño
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Dris el Atmioui
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333 ZCLeidenThe Netherlands
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8
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Witting KF, van der Heden van Noort GJ, Kofoed C, Talavera Ormeño C, el Atmioui D, Mulder MPC, Ovaa H. Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katharina F. Witting
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Christian Kofoed
- Department of Chemistry; Center for Evolutionary Chemical Biology; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Cami Talavera Ormeño
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dris el Atmioui
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Monique P. C. Mulder
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
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9
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Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases. Angew Chem Int Ed Engl 2018; 57:8958-8962. [PMID: 29771001 PMCID: PMC6055820 DOI: 10.1002/anie.201803483] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/09/2018] [Indexed: 12/31/2022]
Abstract
SUMO is a post-translational modifier critical for cell cycle progression and genome stability that plays a role in tumorigenesis, thus rendering SUMO-specific enzymes potential pharmacological targets. However, the systematic generation of tools for the activity profiling of SUMO-specific enzymes has proven challenging. We developed a diversifiable synthetic platform for SUMO-based probes by using a direct linear synthesis method, which permits N- and C-terminal labelling to incorporate dyes and reactive warheads, respectively. In this manner, activity-based probes (ABPs) for SUMO-1, SUMO-2, and SUMO-3-specific proteases were generated and validated in cells using gel-based assays and confocal microscopy. We further expanded our toolbox with the synthesis of a K11-linked diSUMO-2 probe to study the proteolytic cleavage of SUMO chains. Together, these ABPs demonstrate the versatility and specificity of our synthetic SUMO platform for in vitro and in vivo characterization of the SUMO protease family.
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Affiliation(s)
- Monique P C Mulder
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Medicines Evaluation Board, Graadt van Roggenweg 500, 3531, AH, Utrecht, The Netherlands
| | - Katharina F Witting
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dharjath S Hameed
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Dris El Atmioui
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Lindsey Lelieveld
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Current address: Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300, RA, Leiden, The Netherlands
| | - Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
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10
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Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Monique P. C. Mulder
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Remco Merkx
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Current address: Medicines Evaluation Board; Graadt van Roggenweg 500 3531 AH Utrecht The Netherlands
| | - Katharina F. Witting
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dharjath S. Hameed
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Dris El Atmioui
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Lindsey Lelieveld
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Current address: Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Frauke Liebelt
- Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Ilana Berlin
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Huib Ovaa
- Division of Cell Biology; Netherlands Cancer Institute (NKI); Plesmanlaan 121 1066 CX Amsterdam The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology; Leiden University Medical Center (LUMC); Einthovenweg 20 2333 ZC Leiden The Netherlands
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11
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Hewings DS, Heideker J, Ma TP, AhYoung AP, El Oualid F, Amore A, Costakes GT, Kirchhofer D, Brasher B, Pillow T, Popovych N, Maurer T, Schwerdtfeger C, Forrest WF, Yu K, Flygare J, Bogyo M, Wertz IE. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Nat Commun 2018; 9:1162. [PMID: 29563501 PMCID: PMC5862848 DOI: 10.1038/s41467-018-03511-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms. Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
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Affiliation(s)
- David S Hewings
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.,Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Johanna Heideker
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Taylur P Ma
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - Andrew P AhYoung
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Alessia Amore
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Gregory T Costakes
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Daniel Kirchhofer
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Bradley Brasher
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Thomas Pillow
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Till Maurer
- Structural Biology, Genentech, South San Francisco, California, 94080, USA
| | | | - William F Forrest
- Bioinformatics, Genentech, South San Francisco, California, 94080, USA
| | - Kebing Yu
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - John Flygare
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Merck, 630 Gateway Boulevard, South San Francisco, California, 94080, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA. .,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.
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12
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Bondalapati S, Eid E, Mali SM, Wolberger C, Brik A. Total chemical synthesis of SUMO-2-Lys63-linked diubiquitin hybrid chains assisted by removable solubilizing tags. Chem Sci 2017; 8:4027-4034. [PMID: 28580118 PMCID: PMC5434752 DOI: 10.1039/c7sc00488e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022] Open
Abstract
We report the first total chemical synthesis of four different SUMO-2-Lys63-linked di-ubiquitin hybrid chains, in which the di-ubiquitin is linked to different lysines in SUMO.
Small ubiquitin like modifier (SUMO) proteins are known to regulate many important cellular processes such as transcription and apoptosis. Recently, hybrid SUMO-ubiquitin chains containing SUMO-2 linked to Lys63-di-ubiquitin were found to play a major role in DNA repair. Despite some progress in understanding the role of these hybrid chains in DNA repair, there are various fundamental questions remaining to be answered. To further investigate the importance of hybrid SUMO-ubiquitin chains in DNA repair, the homogenous material of these chains, and their unique analogues, are needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the first total chemical synthesis of four different SUMO-2-Lys63-linked di-ubiquitin hybrid chains, in which the di-ubiquitin is linked to different lysines in SUMO. In these syntheses, the usefulness of removable solubilizing tags is demonstrated, and two different approaches were examined in terms of reliability and efficiency. In the first approach, a poly-Arg tag was attached to the C-terminus of SUMO via a 3,4-diaminobenzoic acid cleavable linker, whereas in the second we attached the tag via a phenylacetamidomethyl linker, which can be cleaved by PdCl2. The comparison between these different strategies offers guidelines for future scale-up preparation of these analogues and other proteins, which currently use synthetic peptide intermediates that are difficult to handle and purify. The availability of the SUMO-ubiquitin hybrid chains opens up new opportunities for studying the role of these chains in DNA repair and other cellular processes.
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Affiliation(s)
- Somasekhar Bondalapati
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Emad Eid
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Ashraf Brik
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
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13
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Bacchi M, Fould B, Jullian M, Kreiter A, Maurras A, Nosjean O, Coursindel T, Puget K, Ferry G, Boutin JA. Screening ubiquitin specific protease activities using chemically synthesized ubiquitin and ubiquitinated peptides. Anal Biochem 2017; 519:57-70. [PMID: 27993553 DOI: 10.1016/j.ab.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated. We chose the model protein "murine double minute 2" (mdm2), a ubiquitin ligase, itself ubiquitinated and deubiquitinated. We folded the ubiquitinated peptides and checked their tridimensional conformation. We assessed the use of these substrates with a series of fifteen deubiquitinases to show the potentiality of such an enzymological technique. By manipulating the sequence of the peptide on which ubiquitin is attached, we were able to detect differences in the enzyme/substrate recognition, and to determine that these differences are deubiquitinase-dependent. This approach could be used to understand the substrate/protein relationship between the protagonists of this reaction. The methodology could be customized for a given substrate and used to advance our understanding of the key amino acids responsible for the deubiquitinase specificities.
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Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Magali Jullian
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Aude Kreiter
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Amélie Maurras
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | | | - Karine Puget
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France.
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