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Peng S, Liu X, Lu C, Wang H, Liu X, Gong Q, Tao H, Xu H, Tian C, Xu G, Li JB. Efficient Chemical Synthesis of Multi-Monoubiquitylated and Diubiquitylated Histones by the α-Halogen Ketone-Mediated Strategy. Bioconjug Chem 2024; 35:944-953. [PMID: 38954775 DOI: 10.1021/acs.bioconjchem.4c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The chemical synthesis of homogeneously ubiquitylated histones is a powerful approach to decipher histone ubiquitylation-dependent epigenetic regulation. Among the various methods, α-halogen ketone-mediated conjugation chemistry has recently been an attractive strategy to generate single-monoubiquitylated histones for biochemical and structural studies. Herein, we report the use of this strategy to prepare not only dual- and even triple-monoubiquitylated histones but also diubiquitin-modified histones. We were surprised to find that the synthetic efficiencies of multi-monoubiquitylated histones were comparable to those of single-monoubiquitylated ones, suggesting that this strategy is highly tolerant to the number of ubiquitin monomers installed onto histones. The facile generation of a series of single-, dual-, and triple-monoubiquitylated H3 proteins enabled us to evaluate the influence of ubiquitylation patterns on the binding of DNA methyltransferase 1 (DNMT1) to nucleosomes. Our study highlights the potential of site-specific conjugation chemistry to generate chemically defined histones for epigenetic studies.
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Affiliation(s)
- Shuai Peng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Xin Liu
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Haibo Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Xiaotong Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Qingyue Gong
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Huizhong Tao
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Hongrui Xu
- Suzhou Municipal Center for Disease Control and Prevention, Suzhou 215004, China
| | - Changlin Tian
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
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2
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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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3
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Galesic A, Pan B, Ramirez J, Rhoades E, Pratt MR, Petersson EJ. Combining non-canonical amino acid mutagenesis and native chemical ligation for multiply modifying proteins: A case study of α-synuclein post-translational modifications. Methods 2023; 218:101-109. [PMID: 37549799 PMCID: PMC10657485 DOI: 10.1016/j.ymeth.2023.08.002] [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] [Received: 06/24/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
The Parkinson's disease associated protein α-synuclein (αS) has been found to contain numerous post-translational modifications (PTMs), in both physiological and pathological states. One PTM site of particular interest is serine 87, which is subject to both O-linked β-N-acetylglucosamine (gS) modification and phosphorylation (pS), with αS-pS87 enriched in Parkinson's disease. An often-overlooked aspect of these PTMs is their effect on the membrane-binding properties of αS, which are important to its role in regulating neurotransmitter release. Here, we show how one can study these effects by synthesizing αS constructs containing authentic PTMs and labels for single molecule fluorescence correlation spectroscopy measurements. We synthesize αS-gS87 and αS-pS87 by combining native chemical ligation with genetic code expansion approaches. We introduce the fluorophore by a click reaction with a non-canonical amino acid. Beyond the specific problem of PTM effects on αS, our studies highlight the value of this combination of methods for multiply modifying proteins.
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Affiliation(s)
- Ana Galesic
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Jennifer Ramirez
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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4
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Kriegesmann J, Brik A. Synthesis of ubiquitinated proteins for biochemical and functional analysis. Chem Sci 2023; 14:10025-10040. [PMID: 37772107 PMCID: PMC10529715 DOI: 10.1039/d3sc03664b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/27/2023] [Indexed: 09/30/2023] Open
Abstract
Ubiquitination plays a crucial role in controlling various biological processes such as translation, DNA repair and immune response. Protein degradation for example, is one of the main processes which is controlled by the ubiquitin system and has significant implications on human health. In order to investigate these processes and the roles played by different ubiquitination patterns on biological systems, homogeneously ubiquitinated proteins are needed. Notably, these conjugates that are made enzymatically in cells cannot be easily obtained in large amounts and high homogeneity by employing such strategies. Therefore, chemical and semisynthetic approaches have emerged to prepare different ubiquitinated proteins. In this review, we will present the key synthetic strategies and their applications for the preparation of various ubiquitinated proteins. Furthermore, the use of these precious conjugates in different biochemical and functional studies will be highlighted.
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Affiliation(s)
- Julia Kriegesmann
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology Haifa Israel
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5
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Battis K, Xiang W, Winkler J. The Bidirectional Interplay of α-Synuclein with Lipids in the Central Nervous System and Its Implications for the Pathogenesis of Parkinson's Disease. Int J Mol Sci 2023; 24:13270. [PMID: 37686080 PMCID: PMC10487772 DOI: 10.3390/ijms241713270] [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: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
The alteration and aggregation of alpha-synuclein (α-syn) play a crucial role in neurodegenerative diseases collectively termed as synucleinopathies, including Parkinson's disease (PD). The bidirectional interaction of α-syn with lipids and biomembranes impacts not only α-syn aggregation but also lipid homeostasis. Indeed, lipid composition and metabolism are severely perturbed in PD. One explanation for lipid-associated alterations may involve structural changes in α-syn, caused, for example, by missense mutations in the lipid-binding region of α-syn as well as post-translational modifications such as phosphorylation, acetylation, nitration, ubiquitination, truncation, glycosylation, and glycation. Notably, different strategies targeting the α-syn-lipid interaction have been identified and are able to reduce α-syn pathology. These approaches include the modulation of post-translational modifications aiming to reduce the aggregation of α-syn and modify its binding properties to lipid membranes. Furthermore, targeting enzymes involved in various steps of lipid metabolism and exploring the neuroprotective potential of lipids themselves have emerged as novel therapeutic approaches. Taken together, this review focuses on the bidirectional crosstalk of α-syn and lipids and how alterations of this interaction affect PD and thereby open a window for therapeutic interventions.
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Affiliation(s)
| | | | - Jürgen Winkler
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany; (K.B.); (W.X.)
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6
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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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7
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Pancoe SX, Wang YJ, Shimogawa M, Perez RM, Giannakoulias S, Petersson EJ. Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation. J Mol Biol 2022; 434:167859. [PMID: 36270580 PMCID: PMC9922159 DOI: 10.1016/j.jmb.2022.167859] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Fibrillar aggregates of the α-synuclein (αS) protein are the hallmark of Parkinson's Disease and related neurodegenerative disorders. Characterization of the effects of mutations and post-translational modifications (PTMs) on the αS aggregation rate can provide insight into the mechanism of fibril formation, which remains elusive in spite of intense study. A comprehensive collection (375 examples) of mutant and PTM aggregation rate data measured using the fluorescent probe thioflavin T is presented, as well as a summary of the effects of fluorescent labeling on αS aggregation (20 examples). A curated set of 131 single mutant de novo aggregation experiments are normalized to wild type controls and analyzed in terms of structural data for the monomer and fibrillar forms of αS. These tabulated data serve as a resource to the community to help in interpretation of aggregation experiments and to potentially be used as inputs for computational models of aggregation.
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Affiliation(s)
- Samantha X Pancoe
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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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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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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10
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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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11
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Oliveira LMA, Gasser T, Edwards R, Zweckstetter M, Melki R, Stefanis L, Lashuel HA, Sulzer D, Vekrellis K, Halliday GM, Tomlinson JJ, Schlossmacher M, Jensen PH, Schulze-Hentrich J, Riess O, Hirst WD, El-Agnaf O, Mollenhauer B, Lansbury P, Outeiro TF. Alpha-synuclein research: defining strategic moves in the battle against Parkinson's disease. NPJ Parkinsons Dis 2021; 7:65. [PMID: 34312398 PMCID: PMC8313662 DOI: 10.1038/s41531-021-00203-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
With the advent of the genetic era in Parkinson's disease (PD) research in 1997, α-synuclein was identified as an important player in a complex neurodegenerative disease that affects >10 million people worldwide. PD has been estimated to have an economic impact of $51.9 billion in the US alone. Since the initial association with PD, hundreds of researchers have contributed to elucidating the functions of α-synuclein in normal and pathological states, and these remain critical areas for continued research. With this position paper the authors strive to achieve two goals: first, to succinctly summarize the critical features that define α-synuclein's varied roles, as they are known today; and second, to identify the most pressing knowledge gaps and delineate a multipronged strategy for future research with the goal of enabling therapies to stop or slow disease progression in PD.
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Affiliation(s)
- Luis M A Oliveira
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA.
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Robert Edwards
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, CA, USA
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ronald Melki
- Institut François Jacob, MIRCen, CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Leonidas Stefanis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- First Department of Neurology, Medical School of the National and Kapodistrian University of Athens, Athens, Greece
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Faculty of Life Sciences, EPFL, Lausanne, Switzerland
| | - David Sulzer
- Department of Psychiatry, Neurology, Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Kostas Vekrellis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Glenda M Halliday
- University of Sydney, Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, Sydney, NSW, Australia
| | - Julianna J Tomlinson
- Neuroscience Program, The Ottawa Hospital, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
| | - Michael Schlossmacher
- Neuroscience Program, The Ottawa Hospital, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
- Division of Neurology, The Ottawa Hospital, Ottawa, ON, Canada
| | - Poul Henning Jensen
- Aarhus University, Department of Biomedicine & DANDRITE, Danish Research Institute of Translational Neuroscience, Aarhus, Denmark
| | - Julia Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Warren D Hirst
- Neurodegenerative Diseases Research Unit, Biogen, Cambridge, MA, USA
| | - Omar El-Agnaf
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Paracelsus-Elena-Klinik, Kassel, Germany
| | | | - Tiago F Outeiro
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
- Max Planck Institute for Experimental Medicine, Göttingen, Germany.
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
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12
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Bell R, Vendruscolo M. Modulation of the Interactions Between α-Synuclein and Lipid Membranes by Post-translational Modifications. Front Neurol 2021; 12:661117. [PMID: 34335440 PMCID: PMC8319954 DOI: 10.3389/fneur.2021.661117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease is characterised by the presence in brain tissue of aberrant inclusions known as Lewy bodies and Lewy neurites, which are deposits composed by α-synuclein and a variety of other cellular components, including in particular lipid membranes. The dysregulation of the balance between lipid homeostasis and α-synuclein homeostasis is therefore likely to be closely involved in the onset and progression of Parkinson's disease and related synucleinopathies. As our understanding of this balance is increasing, we describe recent advances in the characterisation of the role of post-translational modifications in modulating the interactions of α-synuclein with lipid membranes. We then discuss the impact of these advances on the development of novel diagnostic and therapeutic tools for synucleinopathies.
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Affiliation(s)
| | - Michele Vendruscolo
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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13
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Moon SP, Balana AT, Pratt MR. Consequences of post-translational modifications on amyloid proteins as revealed by protein semisynthesis. Curr Opin Chem Biol 2021; 64:76-89. [PMID: 34175787 DOI: 10.1016/j.cbpa.2021.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/21/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022]
Abstract
Alterations to the global levels of certain types of post-translational modifications (PTMs) are commonly observed in neurodegenerative diseases. The net influence of these PTM changes to the progression of these diseases can be deduced from cellular and animal studies. However, at the molecular level, how one PTM influences a given protein is not uniform and cannot be easily generalized from systemic observations, thus requiring protein-specific interrogations. Given that protein aggregation is a shared pathological hallmark in neurodegeneration, it is important to understand how these PTMs affect the behavior of amyloid-forming proteins. For this purpose, protein semisynthesis techniques, largely via native chemical and expressed protein ligation, have been widely used. These approaches have thus far led to our increased understanding of the site-specific consequences of certain PTMs to amyloidogenic proteins' endogenous function, their propensity for aggregation, and the structural variations these PTMs induce toward the aggregates formed.
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Affiliation(s)
- Stuart P Moon
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Aaron T Balana
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matthew R Pratt
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA; Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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14
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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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15
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Chu GC, Zhao R, Wu X, Shi J, Li YM. One-Pot Synthesis of a Bis-Thio-Acetone Linked Ubiquitinated Histones Using 1,3-Dibromoacetone. J Org Chem 2020; 85:15631-15637. [PMID: 33191736 DOI: 10.1021/acs.joc.0c01851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes. Here, we reported a one-pot synthesis of ubiquitinated histone analogues using 1,3-dibromoacetone (DBA) as the cross-linking reagent. The key step is that under the acidic borate buffer, the DBA linker can be efficiently installed to the Cys of the recombinant Ub mutant, followed by the coupling between the Ub-DBA with histones at physiological pH. The process requires a single HPLC step or orthogonal affinity tag purification to obtain ubiquitinated histone at about 24-38 mg/L expression.
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Affiliation(s)
- Guo-Chao Chu
- 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, China.,Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Rui Zhao
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Xiangwei Wu
- 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, China
| | - Jing Shi
- 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 of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
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16
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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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17
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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18
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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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19
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Moon SP, Balana AT, Galesic A, Rakshit A, Pratt MR. Ubiquitination Can Change the Structure of the α-Synuclein Amyloid Fiber in a Site Selective Fashion. J Org Chem 2019; 85:1548-1555. [PMID: 31809571 DOI: 10.1021/acs.joc.9b02641] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxic amyloid aggregates are a feature of many neurodegenerative diseases. A number of biochemical and structural studies have demonstrated that not all amyloids of a given protein are equivalent but rather that an aggregating protein can form different amyloid structures or polymorphisms. Different polymorphisms can also induce different amounts of pathology and toxicity in cells and in mice, suggesting that the structural differences may play important roles in disease. However, the features that cause the formation of polymorphisms in vivo are still being uncovered. Posttranslational modifications on several amyloid forming proteins, including the Parkinson's disease causing protein α-synuclein, may be one such cause. Here, we explore whether ubiquitination can induce structural changes in α-synuclein aggregates in vitro. We used protein chemistry to first synthesize ubiquitinated analogues at three different positions using disulfide linkages. After aggregation, these linkages can be reversed, allowing us to make relative comparisons between the structures using a proteinase K assay. We find that, while ubiquitination at residue 6, 23, or 96 inhibits α-synuclein aggregation, only modification at residue 96 causes an alteration in the aggregate structure, providing further evidence that posttranslational modifications may be an important feature in amyloid polymorphism formation.
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20
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Chen H, Zhao YF, Chen YX, Li YM. Exploring the Roles of Post-Translational Modifications in the Pathogenesis of Parkinson's Disease Using Synthetic and Semisynthetic Modified α-Synuclein. ACS Chem Neurosci 2019; 10:910-921. [PMID: 30628768 DOI: 10.1021/acschemneuro.8b00447] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alpha-synuclein (α-syn), a small soluble protein containing 140 amino acids, is associated with the recycling pool of synaptic vesicles in presynaptic terminals. The misfolding and aggregation of α-syn is closely related to a group of neurodegenerative diseases, including Parkinson's disease (PD), which is one of the most common progressive neurodegenerative diseases. Varieties of the post-translational modifications (PTMs) of α-syn, including phosphorylation, ubiquitination, and glycosylation, have been detected in soluble and aggregated α-syn in vivo. These PTMs can have either positive or negative effects on α-syn aggregation and toxicity, which may play critical roles in PD pathogenesis. Herein, we review the advances in synthetic and semisynthetic chemistry to generate homogeneous α-syn variants with site-specific modifications. Using these modified α-syn, we gain insight into the consequences of PTMs on α-syn aggregation and other biophysical properties, which can help elucidate the role of PTMs in the pathogenesis of PD and develop potential therapies to PD.
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Affiliation(s)
- Huai Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yu-Fen Zhao
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yong-Xiang Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
- Beijing Institute
for Brain Disorders, Beijing 100069, P.R. China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, P.R. China
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21
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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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22
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Si Y, Liang L, Tang S, Qi Y, Huang Y, Liu L. Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9189-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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23
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Bi X, Pasunooti KK, Liu CF. Total chemical and semisynthetic approaches for the preparation of ubiquitinated proteins and their applications. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9122-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Muronetz VI, Melnikova AK, Seferbekova ZN, Barinova KV, Schmalhausen EV. Glycation, glycolysis, and neurodegenerative diseases: Is there any connection? BIOCHEMISTRY (MOSCOW) 2017; 82:874-886. [DOI: 10.1134/s0006297917080028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Mali SM, Singh SK, Eid E, Brik A. Ubiquitin Signaling: Chemistry Comes to the Rescue. J Am Chem Soc 2017; 139:4971-4986. [PMID: 28328208 DOI: 10.1021/jacs.7b00089] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Posttranslational modification of proteins by ubiquitin (Ub), i.e., ubiquitination, mediates a variety of cellular processes, including protein homeostasis, cell cycle, DNA repair, and viral infections. Understanding the molecular mechanism of ubiquitination in these events is the basis for unraveling its precise role in health and disease. However, the inherent complexity of Ub signaling due to the high atomic complexity of Ub conjugates, where Ub is attached to other Ub molecules and to protein substrates in various forms, imposes a major challenge for these studies. In this regard, the enzymatic approaches employed for the preparation of important Ub conjugates have severe limitations to deliver them in high homogeneity and in adequate amounts for the desired study. Recent developments in the area of chemical synthesis and semisynthesis of proteins offer great solutions to the enzymatic limitations and enabling the preparation of various Ub conjugates with precise control over the atomic structure. These conjugates significantly contribute to deciphering Ub signaling at the molecular level, and with the synthetic tools in hand, chemical biologists have become key players in efforts toward understanding the complexity of the Ub code. In this Perspective, we highlight the key contributions of these synthetic approaches and how the development of novel Ub-based reagents is greatly assisting in uncovering unknown aspects of Ub signaling. We also discuss future aspirations to address unresolved questions in this exciting area of research.
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Affiliation(s)
- Sachitanand M Mali
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Sumeet K Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Emad Eid
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
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26
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Stanley M, Virdee S. Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates. Chembiochem 2016; 17:1472-80. [PMID: 27197715 PMCID: PMC5094518 DOI: 10.1002/cbic.201600138] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/11/2022]
Abstract
We describe the genetically directed incorporation of aminooxy functionality into recombinant proteins by using a mutant Methanosarcina barkeri pyrrolysyl‐tRNA synthetase/tRNACUA pair. This allows the general production of nonhydrolysable ubiquitin conjugates of recombinant origin by bioorthogonal oxime ligation. This was exemplified by the preparation of nonhydrolysable versions of diubiquitin, polymeric ubiquitin chains and ubiquitylated SUMO. The conjugates exhibited unrivalled isostery with the native isopeptide bond, as inferred from structural and biophysical characterisation. Furthermore, the conjugates functioned as nanomolar inhibitors of deubiquitylating enzymes and were recognised by linkage‐specific antibodies. This technology should provide a versatile platform for the development of powerful tools for studying deubiquitylating enzymes and for elucidating the cellular roles of diverse polyubiquitin linkages.
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Affiliation(s)
- Mathew Stanley
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.
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27
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Hameed DS, Sapmaz A, Ovaa H. How Chemical Synthesis of Ubiquitin Conjugates Helps To Understand Ubiquitin Signal Transduction. Bioconjug Chem 2016; 28:805-815. [PMID: 27077728 DOI: 10.1021/acs.bioconjchem.6b00140] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ubiquitin (Ub) is a small post-translational modifier protein involved in a myriad of biochemical processes including DNA damage repair, proteasomal proteolysis, and cell cycle control. Ubiquitin signaling pathways have not been completely deciphered due to the complex nature of the enzymes involved in ubiquitin conjugation and deconjugation. Hence, probes and assay reagents are important to get a better understanding of this pathway. Recently, improvements have been made in synthesis procedures of Ub derivatives. In this perspective, we explain various research reagents available and how chemical synthesis has made an important contribution to Ub research.
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Affiliation(s)
- Dharjath S Hameed
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aysegul Sapmaz
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center , Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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Yang K, Li G, Gong P, Gui W, Yuan L, Zhuang Z. Chemical Protein Ubiquitylation with Preservation of the Native Cysteine Residues. Chembiochem 2016; 17:995-8. [PMID: 27113245 DOI: 10.1002/cbic.201600042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 12/22/2022]
Abstract
We report a cysteine-based ligation strategy for generating a monoubiquitylated protein while preserving the native cysteine residues on the acceptor protein. In monoubiquitylation of proliferating cell nuclear antigen (PCNA) this method circumvents the need to mutate the native cysteine residues on PCNA. The chemically ubiquitylated PCNA contains a noncleavable linkage of the same length as the native isopeptide linkage. It also retains the normal function of the native Ub-PCNA in stimulating the ATPase activity of replication factor C (RFC) and lesion bypass synthesis by Polη. This method may be adapted for chemical ubiquitylation of other proteins and for site-specific modification of a target protein at a specific site through sulfhydryl chemistry.
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Affiliation(s)
- Kun Yang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE, 19716, USA
| | - Guorui Li
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE, 19716, USA
| | - Ping Gong
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE, 19716, USA
| | - Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE, 19716, USA
| | - Libo Yuan
- 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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