1
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Lander A, Kong Y, Jin Y, Wu C, Luk LYP. Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery. ACS BIO & MED CHEM AU 2024; 4:68-76. [PMID: 38404743 PMCID: PMC10885103 DOI: 10.1021/acsbiomedchemau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 02/27/2024]
Abstract
Many cell-surface receptors are promising targets for chemical synthesis because of their critical roles in disease development. This synthetic approach enables investigations by racemic protein crystallography and ligand discovery by mirror-image methodologies. However, due to their complex nature, the chemical synthesis of a receptor can be a significant challenge. Here, we describe the chemical synthesis and folding of a central, cysteine-rich domain of the cell-surface receptor tumor necrosis factor 1 which is integral to binding of the cytokine TNF-α, namely, TNFR-1 CRD2. Racemic protein crystallography at 1.4 Å confirmed that the native binding conformation was preserved, and TNFR-1 CRD2 maintained its capacity to bind to TNF-α (KD ≈ 7 nM). Encouraged by this discovery, we carried out mirror-image phage display using the enantiomeric receptor mimic and identified a d-peptide ligand for TNFR-1 CRD2 (KD = 1 μM). This work demonstrated that cysteine-rich domains, including the central domains, can be chemically synthesized and used as mimics for investigations.
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Affiliation(s)
- Alexander
J. Lander
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Yifu Kong
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Yi Jin
- Manchester
Institute of Biotechnology, University of
Manchester, Manchester M1 7DN, U.K.
| | - Chuanliu Wu
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Louis Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
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2
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Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
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Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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3
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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4
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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5
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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6
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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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7
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Wu X, Malinčík J, Prescimone A, Sparr C. X‐Ray Crystallographic Studies of Quasi‐Racemates for Absolute Configuration Determinations. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xingxing Wu
- Department of Chemistry University of Basel St. Johanns-Ring 19 CH-4056 Basel Switzerland
| | - Juraj Malinčík
- Department of Chemistry University of Basel St. Johanns-Ring 19 CH-4056 Basel Switzerland
| | - Alessandro Prescimone
- Department of Chemistry University of Basel, BPR 1096 Mattenstrasse 24a, CH-4058 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 CH-4056 Basel Switzerland
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8
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Structural Insights into the Phosphorylation-Enhanced Deubiquitinating Activity of UCHL3 and Ubiquitin Chain Cleavage Preference Analysis. Int J Mol Sci 2022; 23:ijms231810789. [PMID: 36142702 PMCID: PMC9501053 DOI: 10.3390/ijms231810789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
Ubiquitin C-terminal hydrolase-L3 (UCHL3), an important member of the ubiquitin C-terminal hydrolase family, is involved in DNA repair and cancer development. UCHL3 can cleave only complexes of monoubiquitin and its conjugates, such as Ub-AMC, His, or small ubiquitin-like modifier, but not polyubiquitin chains. Phosphorylation of Ser75 promotes the cleavage activity of UCHL3 toward poly-ubiquitin chains in vivo, but biochemical evidence in vitro is still lacking. Here, we first analyzed the structure of simulated phosphorylated UCHL3S75E and the complex of UCHL3S75E with Ub-PA and preliminarily explained the structural mechanism of phosphorylation-enhanced UCHL3 deubiquitinating activity. Additionally, the cleavage activity of UCHL3 toward different types of synthesized poly-ubiquitin chains in vitro was tested. The results showed that purified UCHL3S75E enhanced the cleavage activity toward Ub-AMC compared to UCHL3WT. Meanwhile, UCHL3S75E and UCHL3WT did not show any cleavage activity for different types of di-ubiquitin and tri-ubiquitin chains. However, UCHL3 could hydrolyze the K48 tetra-ubiquitin chain, providing compelling in vitro evidence confirming previous in vivo results. Thus, this study shows that UCHL3 can hydrolyze and has a cleavage preference for polyubiquitin chains, which expands our understanding of the phosphorylation regulation of UCHL3 and lays a foundation for further elucidation of its physiological role.
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9
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Zheng Q, Su Z, Yu Y, Liu L. Recent progress in dissecting ubiquitin signals with chemical biology tools. Curr Opin Chem Biol 2022; 70:102187. [PMID: 35961065 DOI: 10.1016/j.cbpa.2022.102187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
Protein ubiquitination regulates almost all eukaryotic cellular processes, and is of very high complexity due to the diversity of ubiquitin (Ub) modifications including mono-, multiply mono-, homotypic poly-, and even heterotypic poly-ubiquitination. To accurately elucidate the role of each specific Ub signal in different cells with spatiotemporal resolutions, a variety of chemical biology tools have been developed. In this review, we summarize some recently developed chemical biology tools for ubiquitination studies and their applications in molecular and cellular biology.
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Affiliation(s)
- Qingyun Zheng
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China; Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zhen Su
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China
| | - Yuanyuan Yu
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China.
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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10
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Contiguously hydrophobic sequences are functionally significant throughout the human exome. Proc Natl Acad Sci U S A 2022; 119:e2116267119. [PMID: 35294280 PMCID: PMC8944643 DOI: 10.1073/pnas.2116267119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
SignificanceProteins rely on the hydrophobic effect to maintain structure and interactions with the environment. Surprisingly, natural selection on amino acid hydrophobicity has not been detected using modern genetic data. Analyses that treat each amino acid separately do not reveal significant results, which we confirm here. However, because the hydrophobic effect becomes more powerful as more hydrophobic molecules are introduced, we tested whether unbroken stretches of hydrophobic amino acids are under selection. Using genetic variant data from across the human genome, we find evidence that selection increases with the length of the unbroken hydrophobic sequence. These results could lead to improvements in a wide range of genomic tools as well as insights into protein-aggregation disease etiology and protein evolutionary history.
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11
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Zhou Y, Xie Q, Wang H, Sun H. Chemical approaches for the preparation of ubiquitinated proteins via natural linkages. J Pept Sci 2021; 28:e3367. [PMID: 34514672 DOI: 10.1002/psc.3367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
Ubiquitination is an important posttranslation modification (PTM) that regulates a variety of cellular processes, including protein degradation, DNA repair, and viral infections. In this process, the C-terminal carboxyl group of ubiquitin (Ub) or poly-Ub is attached to the ε-amine of lysine (Lys) side chain of an acceptor protein through an isopeptide bond. Studying a molecular mechanism of ubiquitination and deubiquitination is fundamental for unraveling its precise role in health and disease and hence crucial for drug development. Enzymatic approaches for protein ubiquitination possess limited ability to selectivity install Ub or Ub chain on the desired position of an acceptor protein and often lead to heterogeneous mixtures. In the past decades, chemical protein (semi)synthesis has been proved to be an efficient tool to facilitate site-specific protein ubiquitination, which significantly contributes to decode the Ub signal at molecular and structural levels. In this review, we summarize the synthetic strategies developed for protein ubiquitination, and the achievements to generate monoubiquitinated, di-ubiquitinated, and tetraubiquitinated proteins with native isopeptide and ester bonds.
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Affiliation(s)
- Yuhui Zhou
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qingsong Xie
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huagui Wang
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing, China
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12
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Ye Y, Wu X, Chu GC, Hua X, Wang J, Zheng X, Li YM. Semi-synthesis of K27-linked-mixed-triubiquitin chains through a combination of enzymatic reaction with CAACU strategy. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Craddock DE, Parks MJ, Taylor LA, Wagner BL, Ruf M, Wheeler KA. Increasing the structural boundary of quasiracemate formation: 4-substituted naphthylamides. CrystEngComm 2021. [DOI: 10.1039/d0ce01331e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Spatially larger naphthylamides than previously reported diarylamides promote greater structural variance of substituents during the pairwise assembly of quasienantiomers.
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14
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Tan Y, Wu H, Wei T, Li X. Chemical Protein Synthesis: Advances, Challenges, and Outlooks. J Am Chem Soc 2020; 142:20288-20298. [PMID: 33211477 DOI: 10.1021/jacs.0c09664] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Contemporary chemical protein synthesis has been dramatically advanced over the past few decades, which has enabled chemists to reach the landscape of synthetic biomacromolecules. Chemical synthesis can produce synthetic proteins with precisely controlled structures which are difficult or impossible to obtain via gene expression systems. Herein, we summarize the key enabling ligation technologies, major strategic developments, and some selected representative applications of synthetic proteins and provide an outlook for future development.
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Affiliation(s)
- Yi Tan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Tongyao Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China SAR
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15
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Yao L, Chen Z, Zhang K, Yam VW. Heterochiral Self‐Discrimination‐Driven Supramolecular Self‐Assembly of Decanuclear Gold(I)‐Sulfido Complexes into 2D Nanostructures with Chiral Anions‐Tuned Morphologies. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Liao‐Yuan Yao
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Zhen Chen
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Kaka Zhang
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Vivian Wing‐Wah Yam
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
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16
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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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17
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Yao L, Chen Z, Zhang K, Yam VW. Heterochiral Self‐Discrimination‐Driven Supramolecular Self‐Assembly of Decanuclear Gold(I)‐Sulfido Complexes into 2D Nanostructures with Chiral Anions‐Tuned Morphologies. Angew Chem Int Ed Engl 2020; 59:21163-21169. [DOI: 10.1002/anie.202009728] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Liao‐Yuan Yao
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Zhen Chen
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Kaka Zhang
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Vivian Wing‐Wah Yam
- Institute of Molecular Functional Materials and Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong P. R. China
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18
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Li Y, Cao X, Tian C, Zheng JS. Chemical protein synthesis-assisted high-throughput screening strategies for d-peptides in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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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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20
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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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21
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22
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Qu Q, Gao S, Wu F, Zhang M, Li Y, Zhang L, Bierer D, Tian C, Zheng J, Liu L. Synthesis of Disulfide Surrogate Peptides Incorporating Large‐Span Surrogate Bridges Through a Native‐Chemical‐Ligation‐Assisted Diaminodiacid Strategy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qian Qu
- Tsinghua-Peking Center for Life SciencesMinistry of Education Key Laboratory of Bioorganic Phosphorus, Chemistry and Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Shuai Gao
- Tsinghua-Peking Center for Life SciencesMinistry of Education Key Laboratory of Bioorganic Phosphorus, Chemistry and Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Fangming Wu
- High Magnetic Field LaboratoryChinese Academy of Sciences Hefei 230031 China
| | - Meng‐Ge Zhang
- School of Life SciencesHefei National Laboratory for Physical Sciences at the MicroscaleUniversity of Science and Technology of China Hefei 230027 China
| | - Ying Li
- School of Life SciencesHefei National Laboratory for Physical Sciences at the MicroscaleUniversity of Science and Technology of China Hefei 230027 China
| | - Long‐Hua Zhang
- School of Life SciencesHefei National Laboratory for Physical Sciences at the MicroscaleUniversity of Science and Technology of China Hefei 230027 China
| | - Donald Bierer
- Bayer AGDepartment of Medicinal Chemistry Aprather Weg 18A 42096 Wuppertal Germany
| | - Chang‐Lin Tian
- High Magnetic Field LaboratoryChinese Academy of Sciences Hefei 230031 China
- School of Life SciencesHefei National Laboratory for Physical Sciences at the MicroscaleUniversity of Science and Technology of China Hefei 230027 China
| | - Ji‐Shen Zheng
- School of Life SciencesHefei National Laboratory for Physical Sciences at the MicroscaleUniversity of Science and Technology of China Hefei 230027 China
| | - Lei Liu
- Tsinghua-Peking Center for Life SciencesMinistry of Education Key Laboratory of Bioorganic Phosphorus, Chemistry and Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
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23
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Qu Q, Gao S, Wu F, Zhang MG, Li Y, Zhang LH, Bierer D, Tian CL, Zheng JS, Liu L. Synthesis of Disulfide Surrogate Peptides Incorporating Large-Span Surrogate Bridges Through a Native-Chemical-Ligation-Assisted Diaminodiacid Strategy. Angew Chem Int Ed Engl 2020; 59:6037-6045. [PMID: 32060988 DOI: 10.1002/anie.201915358] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/19/2020] [Indexed: 12/17/2022]
Abstract
The use of synthetic bridges as surrogates for disulfide bonds has emerged as a practical strategy to obviate the poor stability of some disulfide-containing peptides. However, peptides incorporating large-span synthetic bridges are still beyond the reach of existing methods. Herein, we report a native chemical ligation (NCL)-assisted diaminodiacid (DADA) strategy that enables the robust generation of disulfide surrogate peptides incorporating surrogate bridges up to 50 amino acids in length. This strategy provides access to some highly desirable but otherwise impossible-to-obtain disulfide surrogates of bioactive peptide. The bioactivities and structures of the synthetic disulfide surrogates were verified by voltage clamp assays, NMR, and X-ray crystallography; and stability studies established that the disulfide replacements effectively overcame the problems of disulfide reduction and scrambling that often plague these pharmacologically important peptides.
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Affiliation(s)
- Qian Qu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus, Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Shuai Gao
- 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
| | - Fangming Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China
| | - Meng-Ge Zhang
- School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, China
| | - Ying Li
- School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, China
| | - Long-Hua Zhang
- School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, China
| | - Donald Bierer
- Bayer AG, Department of Medicinal Chemistry, Aprather Weg 18A, 42096, Wuppertal, Germany
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, China.,School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, China
| | - Ji-Shen Zheng
- School of Life Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, 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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24
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Zuo C, Zhang B, Wu M, Bierer D, Shi J, Fang GM. Chemical synthesis and racemic crystallization of rat C5a-desArg. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.08.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
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Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
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26
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Lithium chloride: An efficient additive for the synthesis of α-conotoxin PnIA(A10L) in the Fmoc solid phase strategy. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2019.151383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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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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28
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Gupta S, Ylä-Anttila P, Sandalova T, Sun R, Achour A, Masucci MG. 14-3-3 scaffold proteins mediate the inactivation of trim25 and inhibition of the type I interferon response by herpesvirus deconjugases. PLoS Pathog 2019; 15:e1008146. [PMID: 31710640 PMCID: PMC6874091 DOI: 10.1371/journal.ppat.1008146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/21/2019] [Accepted: 10/14/2019] [Indexed: 12/31/2022] Open
Abstract
The 14-3-3 molecular scaffolds promote type I interferon (IFN) responses by stabilizing the interaction of RIG-I with the TRIM25 ligase. Viruses have evolved unique strategies to halt this cellular response to support their replication and spread. Here, we report that the ubiquitin deconjugase (DUB) encoded in the N-terminus of the Epstein-Barr virus (EBV) large tegument protein BPLF1 harnesses 14-3-3 molecules to promote TRIM25 autoubiquitination and sequestration of the ligase into inactive protein aggregates. Catalytically inactive BPLF1 induced K48-linked autoubiquitination and degradation of TRIM25 while the ligase was mono- or di-ubiquitinated in the presence of the active viral enzyme and formed cytosolic aggregates decorated by the autophagy receptor p62/SQSTM1. Aggregate formation and the inhibition of IFN response were abolished by mutations of solvent exposed residues in helix-2 of BPLF1 that prevented binding to 14-3-3 while preserving both catalytic activity and binding to TRIM25. 14-3-3 interacted with the Coiled-Coil (CC) domain of TRIM25 in in vitro pulldown, while BPLF1 interacted with both the CC and B-box domains, suggesting that 14-3-3 positions BPLF1 at the ends of the CC dimer, close to known autoubiquitination sites. Our findings provide a molecular understanding of the mechanism by which a viral deubiquitinase inhibits the IFN response and emphasize the role of 14-3-3 proteins in modulating antiviral defenses.
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Affiliation(s)
- Soham Gupta
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Päivi Ylä-Anttila
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Campus Solna, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Campus Solna, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Campus Solna, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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29
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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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30
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Chimeric protein probes for C5a receptors through fusion of the anaphylatoxin C5a core region with a small-molecule antagonist. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9513-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Kurgan KW, Kleman AF, Bingman CA, Kreitler DF, Weisblum B, Forest KT, Gellman SH. Retention of Native Quaternary Structure in Racemic Melittin Crystals. J Am Chem Soc 2019; 141:7704-7708. [PMID: 31059253 DOI: 10.1021/jacs.9b02691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Racemic crystallography has been used to elucidate the secondary and tertiary structures of peptides and small proteins that are recalcitrant to conventional crystallization. It is unclear, however, whether racemic crystallography can capture native quaternary structure, which could be disrupted by heterochiral associations. We are exploring the use of racemic crystallography to characterize the self-assembly behavior of membrane-associated peptides, very few of which have been crystallized. We report a racemic crystal structure of the membrane-active peptide melittin; the new structure allows comparison with a previously reported crystal structure of L-melittin. The tetrameric assembly observed in crystalline L-melittin has been proposed to represent the tetrameric state detected in solution for this peptide. This tetrameric assembly is precisely reproduced in the racemic crystal, which strengthens the conclusion that the tetramer is biologically relevant. More broadly, these findings suggest that racemic crystallography can provide insight on native quaternary structure.
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Affiliation(s)
| | | | | | - Dale F Kreitler
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203-1102 , United States
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32
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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33
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Zhao DD, Fan XW, Hao H, Zhang HL, Guo Y. Temporary Solubilizing Tags Method for the Chemical Synthesis of Hydrophobic Proteins. CURR ORG CHEM 2019. [DOI: 10.2174/1385272822666181211121758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hydrophobic proteins, as one of the cellular protein classifications, play an essential function in maintaining the normal life cycle of living cells. Researches on the structure and function of hydrophobic proteins promote the exploration of the causes of major diseases, and development of new therapeutic agents for disease treatment. However, the poor water solubility of hydrophobic proteins creates problems for their preparation, separation, characterization and functional studies. The temporary solubilizing tags are considered a practical strategy to effectively solve the poor water solubility problem of hydrophobic proteins. This strategy can significantly improve the water solubility of hydrophobic peptides/proteins, making them like water-soluble peptides/proteins easy to be purified, characterized. More importantly, the temporary solubilizing tags can be removed after protein synthesis, so thus the structure and function of the hydrophobic proteins are not affected. At present, temporary solubilizing tags have been successfully used to prepare many important hydrophobic proteins such as membrane proteins, lipoproteins and chaperones. In this review, we summarize the recent researches and applications of temporary solubilizing tags.
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Affiliation(s)
- Dong-Dong Zhao
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Xiao-Wen Fan
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - He Hao
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Hong-Li Zhang
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Ye Guo
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
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34
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Conibear AC, Muttenthaler M. Advancing the Frontiers of Chemical Protein Synthesis-The 7 th CPS Meeting, Haifa, Israel. Cell Chem Biol 2019; 25:247-254. [PMID: 29547714 DOI: 10.1016/j.chembiol.2018.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 7th Chemical Protein Synthesis Meeting took place in September 2017 in Haifa, Israel, bringing together 100 scientists from 11 countries. The cutting-edge scientific program included new synthetic strategies and ligation auxiliaries, novel insights into protein signaling and post-translational modifications, and a range of promising therapeutic applications.
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Affiliation(s)
- Anne C Conibear
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, 4072 Brisbane, Australia.
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35
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Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L. Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27‐linked Ubiquitin Chains. Angew Chem Int Ed Engl 2019; 58:2627-2631. [DOI: 10.1002/anie.201810814] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/20/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Man Pan
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Shan Ding
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujia Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Qian Qu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Tian Wang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Danning Hong
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Yujing Ren
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujun Liang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Ziqing Mei
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lei Liu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
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36
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Wang CK, Craik DJ. Toward Structure Determination of Disulfide-Rich Peptides Using Chemical Shift-Based Methods. J Phys Chem B 2019; 123:1903-1912. [PMID: 30730741 DOI: 10.1021/acs.jpcb.8b10649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide-rich peptides are a class of molecules for which NMR spectroscopy has been the primary tool for structural characterization. Here, we explore whether the process can be achieved by using structural information encoded in chemical shifts. We examine (i) a representative set of five cyclic disulfide-rich peptides that have high-resolution NMR and X-ray structures and (ii) a larger set of 100 disulfide-rich peptides from the PDB. Accuracy of the calculated structures was dependent on the methods used for searching through conformational space and for identifying native conformations. Although Hα chemical shifts could be predicted reasonably well using SHIFTX, agreement between predicted and experimental chemical shifts was sufficient for identifying native conformations for only some peptides in the representative set. Combining chemical shift data with the secondary structure information and potential energy calculations improved the ability to identify native conformations. Additional use of sparse distance restraints or homology information to restrict the search space also improved the resolution of the calculated structures. This study demonstrates that abbreviated methods have potential for elucidation of peptide structures to high resolution and further optimization of these methods, e.g., improvement in chemical shift prediction accuracy, will likely help transition these methods into the mainstream of disulfide-rich peptide structural biology.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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37
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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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38
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Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L. Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27‐linked Ubiquitin Chains. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810814] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Man Pan
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Shan Ding
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujia Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Qian Qu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Tian Wang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Danning Hong
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Yujing Ren
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujun Liang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Ziqing Mei
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lei Liu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
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39
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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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40
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Kent SBH. Novel protein science enabled by total chemical synthesis. Protein Sci 2018; 28:313-328. [PMID: 30345579 DOI: 10.1002/pro.3533] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/01/2023]
Abstract
Chemical synthesis is a well-established method for the preparation in the research laboratory of multiple-tens-of-milligram amounts of correctly folded, high purity protein molecules. Chemically synthesized proteins enable a broad spectrum of novel protein science. Racemic mixtures consisting of d-protein and l-protein enantiomers facilitate crystallization and determination of protein structures by X-ray diffraction. d-Proteins enable the systematic development of unnatural mirror image protein molecules that bind with high affinity to natural protein targets. The d-protein form of a therapeutic target can also be used to screen natural product libraries to identify novel small molecule leads for drug development. Proteins with novel polypeptide chain topologies including branched, circular, linear-loop, and interpenetrating polypeptide chains can be constructed by chemical synthesis. Medicinal chemistry can be applied to optimize the properties of therapeutic protein molecules. Chemical synthesis has been used to redesign glycoproteins and for the a priori design and construction of covalently constrained novel protein scaffolds not found in nature. Versatile and precise labeling of protein molecules by chemical synthesis facilitates effective application of advanced physical methods including multidimensional nuclear magnetic resonance and time-resolved FTIR for the elucidation of protein structure-activity relationships. The chemistries used for total synthesis of proteins have been adapted to making artificial molecular devices and protein-inspired nanomolecular constructs. Research to develop mirror image life in the laboratory is in its very earliest stages, based on the total chemical synthesis of d-protein forms of polymerase enzymes.
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Affiliation(s)
- Stephen B H Kent
- Department of Chemistry and Department of Biochemistry and Molecular Biology; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, 60637
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41
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Ramalho SD, Wang CK, King GJ, Byriel KA, Huang YH, Bolzani VS, Craik DJ. Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. JOURNAL OF NATURAL PRODUCTS 2018; 81:2436-2445. [PMID: 30345754 DOI: 10.1021/acs.jnatprod.8b00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.
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Affiliation(s)
- Suelem D Ramalho
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Gordon J King
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Karl A Byriel
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Vanderlan S Bolzani
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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42
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Ai H, Guo Y, Sun D, Liu S, Qi Y, Guo J, Qu Q, Gong Q, Zhao S, Li J, Liu L. Examination of the Deubiquitylation Site Selectivity of USP51 by Using Chemically Synthesized Ubiquitylated Histones. Chembiochem 2018; 20:221-229. [PMID: 30192049 DOI: 10.1002/cbic.201800432] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Indexed: 12/25/2022]
Abstract
Histone ubiquitylation and deubiquitylation processes and the mechanisms of their regulation are closely relevant to the field of epigenetics. Recently, the deubiquitylating enzyme USP51 was reported to selectively cleave ubiquitylation on histone H2A at K13 or K15 (i.e., H2AK13Ub and H2AK15Ub), but not at K119 (i.e., H2AK119Ub), in nucleosomes in vivo. To elucidate the mechanism for the selectivity of USP51, we constructed structurally well-defined in vitro protein systems with a ubiquitin modification at precise sites. A total chemical protein synthesis procedure was developed, wherein hydrazide-based native chemical ligation was used to efficiently generate five ubiquitylated histones (H2AK13Ub, H2AK15Ub, H2AK119Ub, H2BK34Ub, and H2BK120Ub). These synthetic ubiquitylated histones were assembled into nucleosomes and subjected to in vitro USP51 deubiquitylation assays. Surprisingly, USP51 did not show preference between H2AK13/15Ub and H2AK119Ub, in contrast to previous in vivo observations. Accordingly, an understanding of the selectivity of USP51 may require consideration of other factors, such as alternative pre-existing histone modifications, competitive reader proteins, or different nucleosome quality among the in vivo extraction nucleosome and the in vitro reconstitution one. Further experiments established that USP51 in vitro could deubiquitylate a nucleosome carrying H2BK120Ub, but not H2BK34Ub. Molecular dynamics simulations suggested that USP51-catalyzed hydrolysis of ubiquitylated nucleosomes was affected by steric hindrance of the isopeptide bond.
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Affiliation(s)
- Huasong Ai
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
| | - Yu Guo
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P.R. China.,Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 201210, P.R. China
| | - Demeng Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Sanling Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Yunkun Qi
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
| | - Jing Guo
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
| | - Qian Qu
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
| | - Qingyue Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Suwen Zhao
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P.R. China
| | - Jiabin Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
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43
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Kent SBH. Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis. Curr Opin Chem Biol 2018; 46:1-9. [DOI: 10.1016/j.cbpa.2018.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/14/2018] [Accepted: 03/17/2018] [Indexed: 12/12/2022]
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44
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Qu Q, Gao S, Li YM. Racemic crystal structures of peptide toxins, GsMTx4 prepared by protein total synthesis. J Pept Sci 2018; 24:e3112. [PMID: 30009430 DOI: 10.1002/psc.3112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 01/28/2023]
Abstract
The Piezo channel is a versatile mechanosensitive cation channel that mediates tactile, vascular development, and proprioception. GsMTx4 is the only reported inhibitor specifically targeting Piezo channels. Although the sequence of GsMTx4 is reported, the crystal structure of GsMTx4 is still unknown. Here, we achieved the two-segment synthesis of GsMTx4 and its enantiomer, enGsMTx4, through hydrazide based Native Chemical Ligation, and analyzed the crystal structure of GsMTx4 through the racemic crystallization technology. By analyzing the structure, we found that there is a hydrophobic patch surrounded by aromatic residues and charged residues.
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Affiliation(s)
- Qian Qu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
| | - Shuai Gao
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
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45
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Liang LJ, Si Y, Tang S, Huang D, Wang ZA, Tian C, Zheng JS. Biochemical properties of K11,48-branched ubiquitin chains. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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46
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Total synthesis of snake toxin α-bungarotoxin and its analogues by hydrazide-based native chemical ligation. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Chen C, Gao S, Qu Q, Mi P, Tao A, Li YM. Chemical synthesis and structural analysis of guanylate cyclase C agonist linaclotide. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Yan B, Shi W, Ye L, Liu L. Acyl donors for native chemical ligation. Curr Opin Chem Biol 2018; 46:33-40. [PMID: 29654943 DOI: 10.1016/j.cbpa.2018.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/21/2018] [Accepted: 03/29/2018] [Indexed: 11/28/2022]
Abstract
Native chemical ligation (NCL) has become one of the most important methods in chemical syntheses of proteins. Recently, in order to expand its scope, considerable effort has been devoted to tuning the C-terminal acyl donor thioesters used in NCL. This article reviews the recent advances in the design of C-terminal acyl donors, their precursors and surrogates, and highlights some noteworthy progress that may lead the future direction of protein chemical synthesis.
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Affiliation(s)
- Bingjia Yan
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Weiwei Shi
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Linzhi Ye
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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49
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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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50
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Racemic X-ray structure of L-type calcium channel antagonist Calciseptine prepared by total chemical synthesis. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9198-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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