1
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Li W, Cao P, Xu P, Sun F, Wang C, Zhang J, Dong S, Wilson JR, Xu D, Fan H, Feng Z, Zhang X, Zhu Q, Fan Y, Brown N, Justin N, Gamblin SJ, Li H, Zhang Y, He J. Rapid reconstitution of ubiquitinated nucleosome using a non-denatured histone octamer ubiquitylation approach. Cell Biosci 2024; 14:81. [PMID: 38886783 PMCID: PMC11184750 DOI: 10.1186/s13578-024-01265-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Histone ubiquitination modification is emerging as a critical epigenetic mechanism involved in a range of biological processes. In vitro reconstitution of ubiquitinated nucleosomes is pivotal for elucidating the influence of histone ubiquitination on chromatin dynamics. RESULTS In this study, we introduce a Non-Denatured Histone Octamer Ubiquitylation (NDHOU) approach for generating ubiquitin or ubiquitin-like modified histone octamers. The method entails the co-expression and purification of histone octamers, followed by their chemical cross-linking to ubiquitin using 1,3-dibromoacetone. We demonstrate that nucleosomes reconstituted with these octamers display a high degree of homogeneity, rendering them highly compatible with in vitro biochemical assays. These ubiquitinated nucleosomes mimic physiological substrates in function and structure. Additionally, we have extended this method to cross-linking various histone octamers and three types of ubiquitin-like proteins. CONCLUSIONS Overall, our findings offer an efficient strategy for producing ubiquitinated nucleosomes, advancing biochemical and biophysical studies in the field of chromatin biology.
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Affiliation(s)
- Weijie Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Peirong Cao
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Pengqi Xu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Fahui Sun
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chi Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jiale Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuqi Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jon R Wilson
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Difei Xu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Hengxin Fan
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China
| | - Qingjun Zhu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yingzhi Fan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nick Brown
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil Justin
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - He Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China
| | - Ying Zhang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Jun He
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China.
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2
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Raniszewski NR, Beyer JN, Noel MI, Burslem GM. Sortase mediated protein ubiquitination with defined chain length and topology. RSC Chem Biol 2024; 5:321-327. [PMID: 38576722 PMCID: PMC10989510 DOI: 10.1039/d3cb00229b] [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: 11/27/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024] Open
Abstract
Ubiquitination is a key post-translational modification on protein lysine sidechains known to impact protein stability, signal transduction cascades, protein-protein interactions, and beyond. Great strides have been made towards developing new methods to generate discrete chains of polyubiquitin and conjugate them onto proteins site-specifically, with methods ranging from chemical synthetic approaches, to enzymatic approaches and many in between. Previous work has demonstrated the utility of engineered variants of the bacterial transpeptidase enzyme sortase (SrtA) for conjugation of ubiquitin site-specifically onto target proteins. In this manuscript, we've combined the classical E1/E2-mediated polyubiquitin chain extension approach with sortase-mediated ligation and click chemistry to enable the generation of mono, di, and triubiquitinated proteins sfGFP and PCNA. We demonstrate the utility of this strategy to generate both K48-linked and K63-linked polyubiquitins and attach them both N-terminally and site-specifically to the proteins of interest. Further, we highlight differential activity between two commonly employed sortase variants, SrtA 5M and 7M, and demonstrate that while SrtA 7M can be used to conjugate these ubiquitins to substrates, SrtA 5M can be employed to release the ubiquitin from the substrates as well as to cleave C-terminal tags from the ubiquitin variants used. Overall, we envision that this approach is broadly applicable to readily generate discrete polyubiquitin chains of any linkage type that is accessible via E1/E2 systems and conjugate site-specifically onto proteins of interest, thus granting access to bespoke ubiquitinated proteins that are not currently possible.
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Affiliation(s)
- Nicole R Raniszewski
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Jenna N Beyer
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Myles I Noel
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
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3
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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4
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Kriegesmann J, Schlatzer T, Che K, Altdorf C, Huhmann S, Kählig H, Kurzbach D, Breinbauer R, Becker CFW. Constraining and Modifying Peptides Using Pd-Mediated Cysteine Allylation. Chembiochem 2023; 24:e202300098. [PMID: 36917494 PMCID: PMC10947015 DOI: 10.1002/cbic.202300098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
Over the past decades, several strategies for inducing and stabilizing secondary structure formation in peptides have been developed to increase their proteolytic stability and their binding affinity to specific interaction partners. Here, we report how our recently introduced chemoselective Pd-catalyzed cysteine allylation reaction can be extended to stapling and how the resulting alkene-containing staples themselves can be further modified to introduce additional probes into such stabilized peptides. The latter is demonstrated by introducing a fluorophore as well as a PEG moiety into different stapled peptides using bioorthogonal thiol-ene and Diels-Alder reactions. Furthermore, we investigated structural implications of our allyl staples when used to replace conformationally relevant disulfide bridges. To this end, we chose a selective binder of integrin α3 β1 (LXY3), which is only active in its cyclic disulfide form. We replaced the disulfide bridge by different stapling reagents in order to increase stability and binding affinity towards integrin α3 β1 .
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Affiliation(s)
- Julia Kriegesmann
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Thomas Schlatzer
- Institute of Organic ChemistryGraz University of Technology8010GrazAustria
| | - Kateryna Che
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Claudia Altdorf
- Syntab Therapeutics GmbHPauwelstrasse 17post code?AachenGermany
| | - Susanne Huhmann
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Hanspeter Kählig
- Department of Organic ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Dennis Kurzbach
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of Technology8010GrazAustria
| | - Christian F. W. Becker
- Institute of Biological ChemistryFaculty of ChemistryUniversity of Vienna1090ViennaAustria
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5
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Paudel P, Banos CM, Liu Y, Zhuang Z. Triubiquitin Probes for Identification of Reader and Eraser Proteins of Branched Polyubiquitin Chains. ACS Chem Biol 2023; 18:837-847. [PMID: 36972492 PMCID: PMC10894068 DOI: 10.1021/acschembio.2c00898] [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: 03/29/2023]
Abstract
The important roles played by branched polyubiquitin chains were recently uncovered in proteasomal protein degradation, mitotic regulation, and NF-κB signaling. With the new realization of a wide presence of branched ubiquitin chains in mammalian cells, there is an urgent need of identifying the reader and eraser proteins of the various branched ubiquitin chains. In this work, we report the generation of noncleavable branched triubiquitin probes with combinations of K11-, K48-, and K63-linkages. Through a pulldown approach using the branched triUb probes, we identified human proteins that recognize branched triubiquitin structures including ubiquitin-binding proteins and deubiquitinases (DUBs). Proteomics analysis of the identified proteins enriched by the branched triubiquitin probes points to possible roles of branched ubiquitin chains in cellular processes including DNA damage response, autophagy, and receptor endocytosis. In vitro characterization of several identified UIM-containing proteins demonstrated their binding to branch triubiquitin chains with moderate to high affinities. Availability of this new class of branched triubiquitin probes will enable future investigation into the roles of branched polyubiquitin chains through identification of specific reader and eraser proteins, and the modes of branched ubiquitin chain recognition and processing using biochemical and biophysical methods.
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Affiliation(s)
| | | | - Yujue Liu
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware, USA, 19716
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware, USA, 19716
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6
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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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7
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Waltho A, Sommer T. Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions. Methods Mol Biol 2023; 2602:19-38. [PMID: 36446964 DOI: 10.1007/978-1-0716-2859-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nearly 20 years since the first branched ubiquitin (Ub) chains were identified by mass spectrometry, our understanding of these chains and their function is still evolving. This is due to the limitations of classical Ub research techniques in identifying these chains and the vast complexity of potential branched chains. Considering only lysine or N-terminal methionine attachment sites, there are already 28 different possible branch points. Taking into account recently discovered ester-linked ubiquitination, branch points of more than two linkage types, and the higher-order chain structures within which branch points exist, the diversity of branched chains is nearly infinite. This review breaks down the complexity of these chains into their general functions, what we know so far about the different linkage combinations, branched chain-optimized methodologies, and the future perspectives of branched chain research.
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Affiliation(s)
- Anita Waltho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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Huppelschoten Y, van der Heden van Noort GJ. State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools. Semin Cell Dev Biol 2022; 132:74-85. [PMID: 34961664 DOI: 10.1016/j.semcdb.2021.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; Global Research Technologies, Novo Nordisk Research Park, Måløv, Denmark
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9
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Wang T, Li C, Wang M, Zhang J, Zheng Q, Liang L, Chu G, Tian X, Deng H, He W, Liu L, Li J. Expedient Synthesis of Ubiquitin‐like Protein ISG15 Tools through Chemo‐Enzymatic Ligation Catalyzed by a Viral Protease Lb
pro. Angew Chem Int Ed Engl 2022; 61:e202206205. [DOI: 10.1002/anie.202206205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Tian Wang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Chuntong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Meijing Wang
- School of Pharmaceutical Sciences Tsinghua University Beijing 100084 P. R. China
| | - Jiachen Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Qingyun Zheng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Lujun Liang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Guochao Chu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Wei He
- School of Pharmaceutical Sciences Tsinghua University Beijing 100084 P. R. China
| | - Lei Liu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
- Center for BioAnalytical Chemistry Hefei National Laboratory of Physical Science at Microscale University of Science and Technology of China Hefei 230026 P. R. China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 P. R. China
- Center for BioAnalytical Chemistry Hefei National Laboratory of Physical Science at Microscale University of Science and Technology of China Hefei 230026 P. R. China
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10
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Wang T, Li C, Wang M, Zhang J, Zheng Q, Liang L, Chu G, Tian X, Deng H, He W, Liu L, Li J. Expedient Synthesis of Ubiquitin‐like Protein ISG15 Tools Through Chemo‐Enzymatic Ligation Catalyzed by a Viral Protease Lbpro. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tian Wang
- Tsinghua University Department of Chemistry CHINA
| | - Chuntong Li
- Tsinghua University Department of Chemistry CHINA
| | - Meijing Wang
- Tsinghua University School of Pharmaceutical Sciences CHINA
| | | | | | - Lujun Liang
- Tsinghua University Department of Chemistry CHINA
| | - Guochao Chu
- Tsinghua University Department of Chemistry CHINA
| | - Xiaolin Tian
- Tsinghua University School of Life Sciences CHINA
| | - Haiteng Deng
- Tsinghua University School of Life Sciences CHINA
| | - Wei He
- Tsinghua University School of Pharmaceutical Sciences CHINA
| | - Lei Liu
- Tsinghua University Chemistry Tsinghua University 100084 Beijing CHINA
| | - Jinghong Li
- Tsinghua University Department of Chemistry CHINA
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11
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Posttranslational Chemical Mutagenesis Methods to Insert Posttranslational Modifications into Recombinant Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144389. [PMID: 35889261 PMCID: PMC9316245 DOI: 10.3390/molecules27144389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) dramatically expand the functional diversity of the proteome. The precise addition and removal of PTMs appears to modulate protein structure and function and control key regulatory processes in living systems. Deciphering how particular PTMs affect protein activity is a current frontier in biology and medicine. The large number of PTMs which can appear in several distinct positions, states, and combinations makes preparing such complex analogs using conventional biological and chemical tools challenging. Strategies to access homogeneous and precisely modified proteins with desired PTMs at selected sites and in feasible quantities are critical to interpreting their molecular code. Here, we summarize recent advances in posttranslational chemical mutagenesis and late-stage functionalization chemistry to transfer novel PTM mimicry into recombinant proteins with emphasis on novel transformations.
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12
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Wang R, Yang D, Tian T, An Y, Wan C, Chang Q, Liang M, Hou Z, Wang Y, Zhang L, Li Z. Low-Toxicity Sulfonium-Based Probes for Cysteine-Specific Profiling in Live Cells. Anal Chem 2022; 94:4366-4372. [PMID: 35244395 DOI: 10.1021/acs.analchem.1c05129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite being a low-abundance amino acid, cysteine plays an essential role in regulating protein function and serves as a satisfactory target of post-translational modifications and drug developments. To comprehensively assess reactive-cysteine-containing proteins, the development of chemical proteomic probes to label cysteine residues in human cells is an important objective. Cysteine modification using sulfonium-based probes is a novel method to identify reactive cysteine residues in proteins. Herein, we reported a set of "cysteine-reactive sulfonium-based (C-Sul)" probes to label the reactive cysteine sites in cellular proteins. Notably, water-soluble C-Sul probes have a significantly enhanced stability and cellular uptakes, displaying a high specificity toward reactive cysteines and compatibility with quantitative proteomic profiling. In comparison to the conventional iodoacetamide-based probe, C-Sul particularly has no inhibitory effects on cell viability, enabling its application in proteomic profiling of reactive cysteine residues under biorelevant conditions. We propose C-Sul probes as optimal tools of cysteine profiling for further broadly basic research.
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Affiliation(s)
- Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Dongyan Yang
- Innovative Institute for Plant Health, College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Tian Tian
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Qi Chang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
| | - Ying Wang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, PR China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, PR China
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13
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Burslem GM. The chemical biology of ubiquitin. Biochim Biophys Acta Gen Subj 2022; 1866:130079. [PMID: 34971772 PMCID: PMC10038182 DOI: 10.1016/j.bbagen.2021.130079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
This mini-review will cover the various chemical biology approaches employed to prepare and modulate ubiquitin chains and the ubiquitin-proteasome system. Emphasis will be given to the biochemistry and chemical biology of poly-ubiquitin chain preparation as a tool to elucidate its roles in biological systems as well as the hijacking of the ubiquitin proteasome system using heterobifunctional compounds to induce intracellular ubiquitination.
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Affiliation(s)
- George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
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14
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Wu D, Yang K, Zhang Z, Feng Y, Rao L, Chen X, Yu G. Metal-free bioorthogonal click chemistry in cancer theranostics. Chem Soc Rev 2022; 51:1336-1376. [PMID: 35050284 DOI: 10.1039/d1cs00451d] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry is a powerful tool to site-specifically activate drugs in living systems. Bioorthogonal reactions between a pair of biologically reactive groups can rapidly and specifically take place in a mild physiological milieu without perturbing inherent biochemical processes. Attributed to their high selectivity and efficiency, bioorthogonal reactions can significantly decrease background signals in bioimaging. Compared with metal-catalyzed bioorthogonal click reactions, metal-free click reactions are more biocompatible without the metal catalyst-induced cytotoxicity. Although a great number of bioorthogonal chemistry-based strategies have been reported for cancer theranostics, a comprehensive review is scarce to highlight the advantages of these strategies. In this review, recent progress in cancer theranostics guided by metal-free bioorthogonal click chemistry will be depicted in detail. The elaborate design as well as the advantages of bioorthogonal chemistry in tumor theranostics are summarized and future prospects in this emerging field are emphasized.
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Affiliation(s)
- Dan Wu
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China.
| | - Kuikun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, P. R. China
| | - Zhankui Zhang
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China.
| | - Yunxuan Feng
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Lang Rao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, P. R. China.
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 117597, Singapore.
| | - Guocan Yu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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15
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Fottner M, Weyh M, Gaussmann S, Schwarz D, Sattler M, Lang K. A modular toolbox to generate complex polymeric ubiquitin architectures using orthogonal sortase enzymes. Nat Commun 2021; 12:6515. [PMID: 34764289 PMCID: PMC8585875 DOI: 10.1038/s41467-021-26812-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 10/13/2021] [Indexed: 11/09/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin (Ub) and Ub-like modifiers (Ubls) represents one of the most important regulators in eukaryotic biology. Polymeric Ub/Ubl chains of distinct topologies control the activity, stability, interaction and localization of almost all cellular proteins and elicit a variety of biological outputs. Our ability to characterize the roles of distinct Ub/Ubl topologies and to identify enzymes and receptors that create, recognize and remove these modifications is however hampered by the difficulty to prepare them. Here we introduce a modular toolbox (Ubl-tools) that allows the stepwise assembly of Ub/Ubl chains in a flexible and user-defined manner facilitated by orthogonal sortase enzymes. We demonstrate the universality and applicability of Ubl-tools by generating distinctly linked Ub/Ubl hybrid chains, and investigate their role in DNA damage repair. Importantly, Ubl-tools guarantees straightforward access to target proteins, site-specifically modified with distinct homo- and heterotypic (including branched) Ub chains, providing a powerful approach for studying the functional impact of these complex modifications on cellular processes.
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Affiliation(s)
- Maximilian Fottner
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.5801.c0000 0001 2156 2780Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maria Weyh
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany
| | - Stefan Gaussmann
- grid.6936.a0000000123222966Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.4567.00000 0004 0483 2525Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Dominic Schwarz
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany
| | - Michael Sattler
- grid.6936.a0000000123222966Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.4567.00000 0004 0483 2525Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kathrin Lang
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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16
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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17
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Waddington MA, Zheng X, Stauber JM, Hakim Moully E, Montgomery HR, Saleh LMA, Král P, Spokoyny AM. An Organometallic Strategy for Cysteine Borylation. J Am Chem Soc 2021; 143:8661-8668. [PMID: 34060827 DOI: 10.1021/jacs.1c02206] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Cys-borylation proceeds at room temperature and tolerates a variety of functional groups present in complex polypeptides. Further, the bioconjugation strategy can be applied to a model protein modification of Cys-containing DARPin (designed ankyrin repeat protein). The resultant bioconjugates show no additional toxicity compared to their Cys alkyl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the resultant peptide bioconjugates while maintaining the binding affinity to a protein target.
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Affiliation(s)
- Mary A Waddington
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Xin Zheng
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Julia M Stauber
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Elamar Hakim Moully
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Liban M A Saleh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Alexander M Spokoyny
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States.,California NanoSystems Institute (CNSI), University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095, United States
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18
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Gui W, Davidson GA, Zhuang Z. Chemical methods for protein site-specific ubiquitination. RSC Chem Biol 2021; 2:450-467. [PMID: 34381999 PMCID: PMC8323803 DOI: 10.1039/d0cb00215a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Ubiquitination is an important protein post-translational modification regulating many cellular processes in eukaryotes. Ubiquitination is catalyzed by a three-enzyme cascade resulting in the conjugation of the C-terminal carboxylate of ubiquitin (Ub) to the ε-amino group of a lysine residue in the acceptor protein via an isopeptide bond. In vitro enzymatic ubiquitination utilizing Ub ligases has been successfully employed to generate Ub dimers and polymers. However, limitations of the enzymatic approach exist, particularly due to the requirement of specific Ub ligase for any given target protein and the low catalytic efficiency of the Ub ligase. To achieve an in-depth understanding of the molecular mechanism of Ub signaling, new methods are needed to generate mono- and poly-ubiquitinated proteins at a specific site with defined polyubiquitin chain linkage and length. Chemical methods offer an attractive solution to the above-described challenges. In this review, we summarize the recently developed chemical methods for generating ubiquitinated proteins using synthetic and semisynthetic approaches. These new tools and approaches, as an important part of the Ub toolbox, are crucial to our understanding and exploitation of the Ub system for novel therapeutics.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Gregory A Davidson
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware 214A Drake Hall Newark DE 19716 USA
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19
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Taylor NC, McGouran JF. Investigating eosin Y as a photocatalyst for the radical-dependent activity-based probing of deubiquitinating enzymes. Org Biomol Chem 2021; 19:2177-2181. [PMID: 33630007 DOI: 10.1039/d1ob00253h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eosin Y was assessed for its ability to induce a thiol-ene dependent protein-protein reaction in a metal-free, oxygen-tolerant, visible light mediated system. Protein-protein coupling efficiency under these mild conditions was comparable to previously reported UV-dependent conditions. The desired thiol-ene reaction was however limited within more complex biological systems.
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Affiliation(s)
- Neil C Taylor
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland.
| | - Joanna F McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland.
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20
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Guo AD, Wu KH, Chen XH. Light-induced efficient and residue-selective bioconjugation of native proteins via indazolone formation. RSC Adv 2021; 11:2235-2241. [PMID: 35424183 PMCID: PMC8693682 DOI: 10.1039/d0ra10154k] [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: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 12/03/2022] Open
Abstract
Chemical modification of proteins has emerged as a powerful tool to realize enormous applications, such as development of novel biologics and functional studies of individual protein. We report a light-induced lysine-selective native protein conjugation approach via indazolone formation, conferring reliable chemoselectivity, excellent efficiency, temporal control and biocompatibility under operationally simple and mild conditions, in vitro and in living systems. This straightforward protocol demonstrates the generality and accessibility for direct and rapid functionalization of diverse native proteins, which suggests a new avenue of great importance to bioconjugation, medicinal chemistry and chemical biology.
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Affiliation(s)
- An-Di Guo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke-Huan Wu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Xiao-Hua Chen
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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21
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Deol KK, Crowe SO, Du J, Bisbee HA, Guenette RG, Strieter ER. Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation. Mol Cell 2020; 80:796-809.e9. [PMID: 33156996 PMCID: PMC7718437 DOI: 10.1016/j.molcel.2020.10.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/13/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023]
Abstract
The linkage, length, and architecture of ubiquitin (Ub) chains are all important variables in providing tight control over many biological paradigms. There are clear roles for branched architectures in regulating proteasome-mediated degradation, but the proteins that selectively recognize and process these atypical chains are unknown. Here, using synthetic and enzyme-derived ubiquitin chains along with intact mass spectrometry, we report that UCH37/UCHL5, a proteasome-associated deubiquitinase, cleaves K48 branched chains. The activity and selectivity toward branched chains is markedly enhanced by the proteasomal Ub receptor RPN13/ADRM1. Using reconstituted proteasome complexes, we find that chain debranching promotes degradation of substrates modified with branched chains under multi-turnover conditions. These results are further supported by proteome-wide pulse-chase experiments, which show that the loss of UCH37 activity impairs global protein turnover. Our work therefore defines UCH37 as a debranching deubiquitinase important for promoting proteasomal degradation.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sean O Crowe
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Heather A Bisbee
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Robert G Guenette
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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22
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Nolan MD, Scanlan EM. Applications of Thiol-Ene Chemistry for Peptide Science. Front Chem 2020; 8:583272. [PMID: 33282831 PMCID: PMC7689097 DOI: 10.3389/fchem.2020.583272] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Radical thiol-ene chemistry has been demonstrated for a range of applications in peptide science, including macrocyclization, glycosylation and lipidation amongst a myriad of others. The thiol-ene reaction offers a number of advantages in this area, primarily those characteristic of "click" reactions. This provides a chemical approach to peptide modification that is compatible with aqueous conditions with high orthogonality and functional group tolerance. Additionally, the use of a chemical approach for peptide modification affords homogeneous peptides, compared to heterogeneous mixtures often obtained through biological methods. In addition to peptide modification, thiol-ene chemistry has been applied in novel approaches to biological studies through synthesis of mimetics and use in development of probes. This review will cover the range of applications of the radical-mediated thiol-ene reaction in peptide and protein science.
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Affiliation(s)
- Mark D Nolan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Eoin M Scanlan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
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23
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Wang YS, Wu KP, Jiang HK, Kurkute P, Chen RH. Branched Ubiquitination: Detection Methods, Biological Functions and Chemical Synthesis. Molecules 2020; 25:E5200. [PMID: 33182242 PMCID: PMC7664869 DOI: 10.3390/molecules25215200] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 11/16/2022] Open
Abstract
Ubiquitination is a versatile posttranslational modification that elicits signaling roles to impact on various cellular processes and disease states. The versatility is a result of the complexity of ubiquitin conjugates, ranging from a single ubiquitin monomer to polymers with different length and linkage types. Recent studies have revealed the abundant existence of branched ubiquitin chains in which one ubiquitin molecule is connected to two or more ubiquitin moieties in the same ubiquitin polymer. Compared to the homotypic ubiquitin chain, the branched chain is recognized or processed differently by readers and erasers of the ubiquitin system, respectively, resulting in a qualitative or quantitative alteration of the functional output. Furthermore, certain types of branched ubiquitination are induced by cellular stresses, implicating their important physiological role in stress adaption. In addition, the current chemical methodologies of solid phase peptide synthesis and expanding genetic code approach have been developed to synthesize different architectures of branched ubiquitin chains. The synthesized branched ubiquitin chains have shown their significance in understanding the topologies and binding partners of the branched chains. Here, we discuss the recent progresses on the detection, functional characterization and synthesis of branched ubiquitin chains as well as the future perspectives of this emerging field.
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Affiliation(s)
- Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- 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; (H.-K.J.); (P.K.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (H.-K.J.); (P.K.)
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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24
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Choi H, Kim M, Jang J, Hong S. Visible‐Light‐Induced Cysteine‐Specific Bioconjugation: Biocompatible Thiol–Ene Click Chemistry. Angew Chem Int Ed Engl 2020; 59:22514-22522. [DOI: 10.1002/anie.202010217] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Hangyeol Choi
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Myojeong Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Jaebong Jang
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Sungwoo Hong
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
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25
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Choi H, Kim M, Jang J, Hong S. Visible‐Light‐Induced Cysteine‐Specific Bioconjugation: Biocompatible Thiol–Ene Click Chemistry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Hangyeol Choi
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Myojeong Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Jaebong Jang
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
| | - Sungwoo Hong
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalizations Institute for Basic Science (IBS) Daejeon 34141 Korea
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26
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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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27
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Sui X, Wang Y, Du YX, Liang LJ, Zheng Q, Li YM, Liu L. Development and application of ubiquitin-based chemical probes. Chem Sci 2020; 11:12633-12646. [PMID: 34123237 PMCID: PMC8163311 DOI: 10.1039/d0sc03295f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein ubiquitination regulates almost every process in eukaryotic cells. The study of the many enzymes involved in the ubiquitination system and the development of ubiquitination-associated therapeutics are important areas of current research. Synthetic tools such as ubiquitin-based chemical probes have been making an increasing contribution to deciphering various biochemical components involved in ubiquitin conjugation, recruitment, signaling, and deconjugation. In the present minireview, we summarize the progress of ubiquitin-based chemical probes with an emphasis on their various structures and chemical synthesis. We discuss the utility of the ubiquitin-based chemical probes for discovering and profiling ubiquitin-dependent signaling systems, as well as the monitoring and visualization of ubiquitin-related enzymatic machinery. We also show how the probes can serve to elucidate the molecular mechanism of recognition and catalysis. Collectively, the development and application of ubiquitin-based chemical probes emphasizes the importance and utility of chemical protein synthesis in modern chemical biology. This article reviews the design, synthesis, and application of different classes of Ub-based chemical probes.![]()
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Affiliation(s)
- Xin Sui
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China .,Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yu Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Yun-Xiang Du
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University Beijing 100084 China
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28
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Hua X, Chu GC, Li YM. The Ubiquitin Enigma: Progress in the Detection and Chemical Synthesis of Branched Ubiquitin Chains. Chembiochem 2020; 21:3313-3318. [PMID: 32621561 DOI: 10.1002/cbic.202000295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/01/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitin chains with distinct topologies play essential roles in eukaryotic cells. Recently, it was discovered that multiple ubiquitin units can be ligated to more than one lysine residue in the same ubiquitin to form diverse branched ubiquitin chains. Although there is increasing evidence implicating these branched chains in a plethora of biological functions, few mechanistic details have been elucidated. This concept article introduces the function, detection and chemical synthesis of branched ubiquitin chains; and offers some future perspective for this exciting new field.
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Affiliation(s)
- Xiao Hua
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases, Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, China.,Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Guo-Chao Chu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases, Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
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29
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Baumann AL, Schwagerus S, Broi K, Kemnitz-Hassanin K, Stieger CE, Trieloff N, Schmieder P, Hackenberger CPR. Chemically Induced Vinylphosphonothiolate Electrophiles for Thiol–Thiol Bioconjugations. J Am Chem Soc 2020; 142:9544-9552. [DOI: 10.1021/jacs.0c03426] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alice L. Baumann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Sergej Schwagerus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Kevin Broi
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Kristin Kemnitz-Hassanin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Nils Trieloff
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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30
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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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31
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Taylor NC, Hessman G, Kramer HB, McGouran JF. Probing enzymatic activity - a radical approach. Chem Sci 2020; 11:2967-2972. [PMID: 34122797 PMCID: PMC8157568 DOI: 10.1039/c9sc05258e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) are known to have numerous important interactions with the ubiquitin cascade and their dysregulation is associated with several diseases, including cancer and neurodegeneration. They are an important class of enzyme, and activity-based probes have been developed as an effective strategy to study them. Existing activity-based probes that target the active site of these enzymes work via nucleophilic mechanisms. We present the development of latent ubiquitin-based probes that target DUBs via a site selective, photoinitiated radical mechanism. This approach differs from existing photocrosslinking probes as it requires a free active site cysteine. In contrast to existing cysteine reactive probes, control over the timing of the enzyme-probe reaction is possible as the alkene warhead is completely inert under ambient conditions, even upon probe binding. The probe's reactivity has been demonstrated against recombinant DUBs and to capture endogenous DUB activity in cell lysate. This allows more finely resolved investigations of DUBs.
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Affiliation(s)
- Neil C Taylor
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute 152-160 Pearse St. Dublin 2 Ireland
| | - Gary Hessman
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute 152-160 Pearse St. Dublin 2 Ireland
| | - Holger B Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford Parks Road Oxford OX1 3PT UK
| | - Joanna F McGouran
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute 152-160 Pearse St. Dublin 2 Ireland
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32
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Pacheco MR, Jacinto JP, Penas D, Calmeiro T, Almeida AV, Colaço M, Fortunato E, Jones NC, Hoffmann SV, Pereira MMA, Tavares P, Pereira AS. Supramolecular protein polymers using mini-ferritin Dps as the building block. Org Biomol Chem 2020; 18:9300-9307. [DOI: 10.1039/d0ob01702g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Production of long polymer chains with iron oxidation and storage activity, built from protein nanocages using a click chemistry approach.
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33
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Gui W, Paudel P, Zhuang Z. Activity-Based Ubiquitin Probes for Investigation of Deubiquitinases. COMPREHENSIVE NATURAL PRODUCTS III 2020. [PMCID: PMC7157470 DOI: 10.1016/b978-0-12-409547-2.14672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ubiquitination is emerging as an important post-translational modification (PTM) for numerous cellular functions including protein degradation, DNA damage repair and tolerance, and cell cycle progression. Compared with other small-molecule modifiers found in phosphorylation, acetylation and glycosylation, ubiquitin is a small protein modifier that exists as either a single ubiquitin or a polyubiquitin chain. Furthermore, the polyubiquitin chains are formed via various linkages imparting an additional layer of specificity in cellular signaling. In order to adequately study ubiquitin signaling and particularly deubiquitination, a number of ubiquitin activity-based probes (ABPs) were developed and utilized in understanding the deubiquitinase (DUBs) function. Here, we focus on the current state of the DUB ABP development and their application in understanding DUB function and specificity for polyubiquitin chains and ubiquitinated proteins.
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34
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Chu GC, Hua X, Zuo C, Chen CC, Meng XB, Zhang Z, Fu Y, Shi J, Li YM. Efficient Semi-Synthesis of Atypical Ubiquitin Chains and Ubiquitin-Based Probes Forged by Thioether Isopeptide Bonds. Chemistry 2019; 25:16668-16675. [PMID: 31625216 DOI: 10.1002/chem.201904010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/16/2019] [Indexed: 01/24/2023]
Abstract
The development of powerful and general methods to acquire ubiquitin (Ub) chains has prompted the deciphering of Ub-mediated processes. Herein, the cysteine-aminoethylation assisted chemical ubiquitination (CAACU) strategy is extended and improved to enable the efficient semi-synthesis of atypical Ub chain analogues and Ub-based probes. Combining the Cys aminoethylation and the auxiliary-mediated protein ligation, several linkage- and length-defined atypical Ub chains including di-Ubs, K27C-linked tri-Ub, K11/K48C-branched tri-Ub, and even the SUMOlated Ub are successfully prepared from recombinantly expressed starting materials at about a 9-20 mg L-1 expression level. In addition, the utility of this strategy is demonstrated with the synthesis of a novel non-hydrolyzable di-Ub PA probe, which may provide a new useful tool for the mechanistic studies of deubiquitinase (DUB) recognition.
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Affiliation(s)
- Guo-Chao Chu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xiao Hua
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Chong Zuo
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chen-Chen Chen
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Xian-Bin Meng
- National Protein Science Technology Center, Tsinghua University, Beijing, 100084, P. R. China
| | - Zhongping Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, 230031, P. R. China
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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35
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Hua X, Bai JS, Kong YF, Chu GC, Shi J, Li YM. Acid-sensitive auxiliary assisted atypical diubiquitin synthesis exploiting thiol-ene coupling. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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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] [MESH Headings] [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 KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Maite Mißun
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Tobias Schneider
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Franziska Müller
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Joachim Lutz
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Martin Scheffner
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Andreas Marx
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
| | - Michael Kovermann
- Universität KonstanzChemieUniversitätsstrasse 1078457KonstanzGermany
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37
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Oki Y, Kirita K, Ohta S, Ohba S, Horiguchi I, Sakai Y, Ito T. Switching of Cell Proliferation/Differentiation in Thiol–Maleimide Clickable Microcapsules Triggered by in Situ Conjugation of Biomimetic Peptides. Biomacromolecules 2019; 20:2350-2359. [DOI: 10.1021/acs.biomac.9b00333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yuichiro Oki
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Katsuhisa Kirita
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Seiichi Ohta
- Center for
Disease
Biology and Integrative Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Ohba
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Center for
Disease
Biology and Integrative Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikki Horiguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taichi Ito
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Center for
Disease
Biology and Integrative Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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38
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Chu GC, Pan M, Li J, Liu S, Zuo C, Tong ZB, Bai JS, Gong Q, Ai H, Fan J, Meng X, Huang YC, Shi J, Deng H, Tian C, Li YM, Liu L. Cysteine-Aminoethylation-Assisted Chemical Ubiquitination of Recombinant Histones. J Am Chem Soc 2019; 141:3654-3663. [PMID: 30758956 DOI: 10.1021/jacs.8b13213] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes through tightly regulated dynamic reversible processes. The efficient preparation of ubiquitinated histones and their analogs is important for biochemical and biophysical studies on histone ubiquitination. Here, we report the CAACU (cysteine-aminoethylation assisted chemical ubiquitination) strategy for the efficient synthesis of ubiquitinated histone analogs. The key step in the CAACU strategy is the installation of an N-alkylated 2-bromoethylamine derivative into a recombinant histone through cysteine aminoethylation, followed by native chemical ligation assisted by Seitz's auxiliary to produce mono- and diubiquitin (Ub) and small ubiquitin-like modifier (SUMO) modified histone analogs. This approach enables the rapid production of modified histones from recombinant proteins at about 1.5-6 mg/L expression. The thioether-containing isopeptide bonds in the products are chemically stable and bear only one atomic substitution in the structure, compared to their native counterparts. The ubiquitinated histone analogs prepared by CAACU can be readily reconstituted into nucleosomes and selectively recognized by relevant interacting proteins. The thioether-containing isopeptide bonds can also be recognized and hydrolyzed by deubiquitinases (DUBs). Cryo-electron microscopy (cryo-EM) of the nucleosome containing H2BKC34Ub indicated that the obtained CAACU histones were of good quality for structural studies. Collectively, this work exemplifies the utility of the CAACU strategy for the simple and efficient production of homogeneous ubiquitinated and SUMOylated histones for biochemical and biophysical studies.
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Affiliation(s)
- Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | | | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Jing-Si Bai
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | | | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | | | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
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39
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Recent advances in the chemical synthesis and semi-synthesis of poly-ubiquitin-based proteins and probes. Sci China Chem 2019. [DOI: 10.1007/s11426-018-9401-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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40
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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41
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Zhao X, Scheffner M, Marx A. Assembly of branched ubiquitin oligomers by click chemistry. Chem Commun (Camb) 2019; 55:13093-13095. [DOI: 10.1039/c9cc07303e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ubiquitin monomers functionalized with an azide or multiple alkynes were utilized for the assembly of branched ubiquitin oligomers that exhibit stability in eukaryotic cell lysates.
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Affiliation(s)
- Xiaohui Zhao
- Departments of Chemistry and Biology
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
| | - Martin Scheffner
- Departments of Chemistry and Biology
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
| | - Andreas Marx
- Departments of Chemistry and Biology
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
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42
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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43
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Robidillo CJT, Aghajamali M, Faramus A, Sinelnikov R, Veinot JGC. Interfacing enzymes with silicon nanocrystals through the thiol-ene reaction. NANOSCALE 2018; 10:18706-18719. [PMID: 30270384 DOI: 10.1039/c8nr05368e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study reports the preparation of functional bioinorganic hybrids, through application of the thiol-ene reaction, that exhibit catalytic activity and photoluminescent properties from enzymes and freestanding silicon nanocrystals. Thermal hydrosilylation of 1,7-octadiene and alkene-terminated poly(ethylene oxide)methyl ether with hydride-terminated silicon nanocrystals afforded nanocrystals functionalized with alkene residues and poly(ethylene oxide) moieties. These silicon nanocrystals were conjugated with representative enzymes through the photochemical thiol-ene reaction to afford bioinorganic hybrids that are dispersible and photostable in buffer, and that exhibit photoluminescence (λmax = 630 nm) and catalytic activity. They were characterized using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), dynamic light scattering analysis (DLS), absorption spectroscopy, steady-state and time-resolved photoluminescence spectroscopy, and pertinent enzyme activity assays. The general derivatization approach presented for interfacing enzymes with biocompatible silicon nanocrystals has far reaching implications for many applications ranging from sensors to therapeutic agents. The bioinorganic hybrids presented herein have potential applications in the chemical detection of nitrophenyl esters and urea. They can also be employed in enzyme-based theranostics as they combine long-lived silicon nanocrystal photoluminescence with substrate-specific enzymatic activity.
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44
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Abstract
Access to well-defined ubiquitin conjugates has been key to elucidating the biochemical functions of proteins in the ubiquitin signaling network. Yet, we have a poor understanding of how deubiquitinases and ubiquitin-binding proteins respond to ubiquitin modifications when anchored to a protein other than ubiquitin or a ubiquitin-like protein. This is due to the difficulty of synthesizing ubiquitinated proteins comprised of native isopeptide bonds. Here we report on the evolution of a deubiquitinase capable of site-specifically modifying itself with defined ubiquitin chains. Following mutagenesis and yeast display screening, we identify a variant of the yeast ubiquitin C-terminal hydrolase Yuh1 that has a 28-fold improvement in the transamidation to hydrolysis ratio relative to the wild type enzyme. The switch in activity enables robust autoubiquitination of a lysine in the crossover loop to form an isopeptide bond. We demonstrate the utility of autoubiquitinating the evolved Yuh1 variant by investigating the consequences of ubiquitin chain anchoring on the activities of other deubiquitinases. Much to our surprise, we find that certain deubiquitinases are exquisitely sensitive to chain anchoring. These results highlight the importance of investigating the biochemical activities of deubiquitinases with both substrate-anchored and unanchored ubiquitin chains.
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45
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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46
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Abstract
Dextrans are a versatile class of polysaccharides with applications that span medicine, cell biology, food science, and consumer goods. Here, we report on a new type of large monofunctionalized dextran that exhibits unusual properties: efficient cytosolic and nuclear uptake. This dextran permeates various human cell types without the use of transfection agents, electroporation, or membrane perturbation. Cellular uptake occurs primarily through active transport via receptor-mediated processes. These monofunctionalized dextrans could serve as intracellular delivery platforms for drugs or other cargos.
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Affiliation(s)
- Wen Chyan
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Henry R. Kilgore
- Graduate Program in Biophysics, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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47
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Leonen CJA, Upadhyay E, Chatterjee C. Studies of biochemical crosstalk in chromatin with semisynthetic histones. Curr Opin Chem Biol 2018; 45:27-34. [PMID: 29494828 DOI: 10.1016/j.cbpa.2018.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 01/26/2023]
Abstract
Reversible post-translational modifications of histone proteins in eukaryotic chromatin are closely tied to gene function and cellular development. Specific combinations of histone modifications, or marks, are implicated in distinct DNA-templated processes mediated by a range of chromatin-associated enzymes that install, erase and interpret the histone code. Mechanistic studies of the precise biochemical relationship between sets of marks and their effects on chromatin function are significantly complicated by the dynamic nature and heterogeneity of marks in cellular chromatin. Protein semisynthesis is a chemical technique that enables the piecewise assembly of uniformly and site-specifically modified histones in quantities sufficient for biophysical and biochemical analyses. Recent pioneering efforts in semisynthesis have yielded access to histones site-specifically modified by entire proteins, such as ubiquitin (Ub) and the small ubiquitin-like modifier (SUMO). Herein, we highlight key studies of biochemical crosstalk involving Ub and SUMO in chromatin that were enabled by histone semisynthesis.
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Affiliation(s)
| | - Esha Upadhyay
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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48
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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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49
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Xu L, Huang JF, Chen CC, Qu Q, Shi J, Pan M, Li YM. Chemical Synthesis of Natural Polyubiquitin Chains through Auxiliary-Mediated Ligation of an Expressed Ubiquitin Isomer. Org Lett 2017; 20:329-332. [DOI: 10.1021/acs.orglett.7b03515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ling Xu
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Jian-Feng Huang
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Chen-Chen Chen
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Qian Qu
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jing Shi
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Man Pan
- Department
of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Yi-Ming Li
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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50
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Zhao X, Lutz J, Höllmüller E, Scheffner M, Marx A, Stengel F. Identification of Proteins Interacting with Ubiquitin Chains. Angew Chem Int Ed Engl 2017; 56:15764-15768. [DOI: 10.1002/anie.201705898] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/01/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaohui Zhao
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Joachim Lutz
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Eva Höllmüller
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Martin Scheffner
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Andreas Marx
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Florian Stengel
- Departments of Chemistry and Biology; Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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