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Kar A, Mannuthodikayil J, Singh S, Biswas A, Dubey P, Das A, Mandal K. Efficient Chemical Protein Synthesis using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments. Angew Chem Int Ed Engl 2020; 59:14796-14801. [PMID: 32333711 PMCID: PMC7891605 DOI: 10.1002/anie.202000491] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Indexed: 01/23/2023]
Abstract
We report an operationally simple method to facilitate chemical protein synthesis by fully convergent and one-pot native chemical ligations utilizing the fluorenylmethyloxycarbonyl (Fmoc) moiety as an N-masking group of the N-terminal cysteine of the middle peptide thioester segment(s). The Fmoc group is stable to the harsh oxidative conditions frequently used to generate peptide thioesters from peptide hydrazide or o-aminoanilide. The ready availability of Fmoc-Cys(Trt)-OH, which is routinely used in Fmoc solid-phase peptide synthesis, where the Fmoc group is pre-installed on cysteine residue, minimizes additional steps required for the temporary protection of the N-terminal cysteinyl peptides. The Fmoc group is readily removed after ligation by short exposure (<7 min) to 20 % piperidine at pH 11 in aqueous conditions at room temperature. Subsequent native chemical ligation reactions can be performed in presence of piperidine in the same solution at pH 7.
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Affiliation(s)
- Abhisek Kar
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Jamsad Mannuthodikayil
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Sameer Singh
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Anamika Biswas
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Puneet Dubey
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Amit Das
- Protein Crystallography Section, Radiation Biology and Health Sciences DivisionBhabha Atomic Research CentreTrombayMumbai400085India
- Homi Bhabha National InstituteAnushaktinagarMumbai400094India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
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2
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Kar A, Mannuthodikayil J, Singh S, Biswas A, Dubey P, Das A, Mandal K. Efficient Chemical Protein Synthesis using Fmoc‐Masked N‐Terminal Cysteine in Peptide Thioester Segments. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abhisek Kar
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Jamsad Mannuthodikayil
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Sameer Singh
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Anamika Biswas
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Puneet Dubey
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Amit Das
- Protein Crystallography Section, Radiation Biology and Health Sciences Division Bhabha Atomic Research Centre Trombay Mumbai 400085 India
- Homi Bhabha National Institute Anushaktinagar Mumbai 400094 India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
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3
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Dardashti RN, Kumar S, Sternisha SM, Reddy PS, Miller BG, Metanis N. Selenolysine: A New Tool for Traceless Isopeptide Bond Formation. Chemistry 2020; 26:4952-4957. [PMID: 31960982 PMCID: PMC7184786 DOI: 10.1002/chem.202000310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/14/2023]
Abstract
Despite their biological importance, post-translationally modified proteins are notoriously difficult to produce in a homogeneous fashion by using conventional expression systems. Chemical protein synthesis or semisynthesis offers a solution to this problem; however, traditional strategies often rely on sulfur-based chemistry that is incompatible with the presence of any cysteine residues in the target protein. To overcome these limitations, we present the design and synthesis of γ-selenolysine, a selenol-containing form of the commonly modified proteinogenic amino acid, lysine. The utility of γ-selenolysine is demonstrated with the traceless ligation of the small ubiquitin-like modifier protein, SUMO-1, to a peptide segment of human glucokinase. The resulting polypeptide is poised for native chemical ligation and chemoselective deselenization in the presence of unprotected cysteine residues. Selenolysine's straightforward synthesis and incorporation into synthetic peptides marks it as a universal handle for conjugating any ubiquitin-like modifying protein to its target.
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Affiliation(s)
- Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shailesh Kumar
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shawn M Sternisha
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Post Sai Reddy
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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4
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Zhao Z, Metanis N. Copper‐Mediated Selenazolidine Deprotection Enables One‐Pot Chemical Synthesis of Challenging Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
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5
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Zhao Z, Metanis N. Copper-Mediated Selenazolidine Deprotection Enables One-Pot Chemical Synthesis of Challenging Proteins. Angew Chem Int Ed Engl 2019; 58:14610-14614. [PMID: 31408267 DOI: 10.1002/anie.201909484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Indexed: 12/25/2022]
Abstract
While chemical protein synthesis has granted access to challenging proteins, the synthesis of longer proteins is often limited by low abundance or non-strategic placement of cysteine residues, which are essential for native chemical ligations, as well as multiple purification and isolation steps. We describe the one-pot total synthesis of human thiosulfate:glutathione sulfurtransferase (TSTD1). WT-TSTD1 was synthesized in a C-to-N synthetic approach involving multiple NCL reactions, CuII -mediated deprotection of selenazolidine (Sez), and chemoselective deselenization. The seleno-analog Se-TSTD1, in which the active site Cys is replaced with selenocysteine, was also synthesized with a kinetically controlled ligation with an N-to-C synthetic approach. The catalytic activity of the two proteins indicated that Se-TSTD1 possessed only four-fold lower activity than WT-TSTD1, thus suggesting that selenoproteins can have physiologically comparable sulfutransferase activity to their cysteine counterparts.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
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6
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Jbara M, Maity SK, Brik A. Examining Several Strategies for the Chemical Synthesis of Phosphorylated Histone H3 Reveals the Effectiveness of the Convergent Approach. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; 3200008 Haifa Israel
| | - Suman Kumar Maity
- 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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7
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Asahina Y, Kawakami T, Hojo H. Glycopeptide Synthesis Based on a TFA-Labile Protection Strategy and One-Pot Four-Segment Ligation for the Synthesis of O-Glycosylated Histone H2A. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801885] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuya Asahina
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
| | - Toru Kawakami
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
| | - Hironobu Hojo
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
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8
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Ellmer D, Brehs M, Haj-Yahya M, Lashuel HA, Becker CFW. Single Posttranslational Modifications in the Central Repeat Domains of Tau4 Impact its Aggregation and Tubulin Binding. Angew Chem Int Ed Engl 2019; 58:1616-1620. [PMID: 30549369 PMCID: PMC6391969 DOI: 10.1002/anie.201805238] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Indexed: 12/22/2022]
Abstract
A variety of methods have been employed to study the impact of posttranslational modifications on Tau protein function. Here, a semisynthesis strategy is described that enables selective modification within the central repeat domain of Tau4 (residues 291‐321), comprising a major interaction motive with tubulin as well as one of the key hexapeptides involved in Tau aggregation. This strategy has led to the preparation of four semisynthetic Tau variants with phosphoserine residues in different positions and one with a so far largely ignored carboxymethyllysine modification that results from a non‐enzymatic posttranslational modification (nPTM). The latter modification inhibits tubulin polymerization but exhibits an aggregation behavior very similar to unmodified Tau. In contrast, phosphorylated Tau variants exhibit similar binding to tubulin as unmodified Tau4 but show lower tendencies to aggregate.
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Affiliation(s)
- Doris Ellmer
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090, Vienna, Austria
| | - Manuel Brehs
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090, Vienna, Austria
| | - Mahmood Haj-Yahya
- École Polytechnique Fédérale de Lausanne (EPFL), Brain Mind Institute, Laboratory of Molecular and Chemical Biology of Neurodegeneration, 1015, Lausanne, Switzerland
| | - Hilal A Lashuel
- École Polytechnique Fédérale de Lausanne (EPFL), Brain Mind Institute, Laboratory of Molecular and Chemical Biology of Neurodegeneration, 1015, Lausanne, Switzerland
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090, Vienna, Austria
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9
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Ellmer D, Brehs M, Haj‐Yahya M, Lashuel HA, Becker CFW. Single Posttranslational Modifications in the Central Repeat Domains of Tau4 Impact its Aggregation and Tubulin Binding. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201805238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Doris Ellmer
- University of ViennaFaculty of ChemistryInstitute of Biological Chemistry Währinger Str. 38 1090 Vienna Austria
| | - Manuel Brehs
- University of ViennaFaculty of ChemistryInstitute of Biological Chemistry Währinger Str. 38 1090 Vienna Austria
| | - Mahmood Haj‐Yahya
- École Polytechnique Fédérale de Lausanne (EPFL), Brain Mind InstituteLaboratory of Molecular and Chemical Biology of Neurodegeneration 1015 Lausanne Switzerland
| | - Hilal A. Lashuel
- École Polytechnique Fédérale de Lausanne (EPFL), Brain Mind InstituteLaboratory of Molecular and Chemical Biology of Neurodegeneration 1015 Lausanne Switzerland
| | - Christian F. W. Becker
- University of ViennaFaculty of ChemistryInstitute of Biological Chemistry Währinger Str. 38 1090 Vienna Austria
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10
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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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11
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Boekhoven J, Didier D. Vereinigung von Kunst und Wissenschaft: Die 53. Bürgenstock-Konferenz. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Job Boekhoven
- Fakultät für Chemie und Institute for Advanced Study; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Dorian Didier
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität; Butenandtstraße 5-13 81377 München Deutschland
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12
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Boekhoven J, Didier D. Merging Art and Science-The 53rd Bürgenstock Conference. Angew Chem Int Ed Engl 2018; 57:10011-10014. [PMID: 30003659 DOI: 10.1002/anie.201806142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
For the 53rd time, the Bürgenstock Conference gathered some of the most gifted scientists and rising stars in organic, physical, and bioorganic chemistry. Orchestrated by Ilan Marek (President) and his successor, Véronique Gouverneur, the synergy between art and science took place in Brunnen, Switzerland, with a beatiful view over Lake Lucerne.
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Affiliation(s)
- Job Boekhoven
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Dorian Didier
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
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13
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Sueoka T, Koyama K, Hayashi G, Okamoto A. Chemistry-Driven Epigenetic Investigation of Histone and DNA Modifications. CHEM REC 2018; 18:1727-1744. [PMID: 30070422 DOI: 10.1002/tcr.201800040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022]
Abstract
In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site-specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification-specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single-base resolution.
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Affiliation(s)
- Takuma Sueoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenta Koyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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14
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Jbara M, Maity SK, Brik A. Palladium in der chemischen Synthese und Modifizierung von Proteinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702370] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
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15
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Jbara M, Maity SK, Brik A. Palladium in the Chemical Synthesis and Modification of Proteins. Angew Chem Int Ed Engl 2017; 56:10644-10655. [DOI: 10.1002/anie.201702370] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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16
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Liang J, Zhang L, Tan XL, Qi YK, Feng S, Deng H, Yan Y, Zheng JS, Liu L, Tian CL. Chemical Synthesis of Diubiquitin-Based Photoaffinity Probes for Selectively Profiling Ubiquitin-Binding Proteins. Angew Chem Int Ed Engl 2017; 56:2744-2748. [DOI: 10.1002/anie.201611659] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Xiang-Long Tan
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yun-Kun Qi
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Feng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Yijing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
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17
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Liang J, Zhang L, Tan XL, Qi YK, Feng S, Deng H, Yan Y, Zheng JS, Liu L, Tian CL. Chemical Synthesis of Diubiquitin-Based Photoaffinity Probes for Selectively Profiling Ubiquitin-Binding Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611659] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Xiang-Long Tan
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yun-Kun Qi
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Shan Feng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Yijing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
| | - Lei Liu
- Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale; University of Science and University of Science and Technology of China; Hefei 230026 China
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18
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Li J, He Q, Liu Y, Liu S, Tang S, Li C, Sun D, Li X, Zhou M, Zhu P, Bi G, Zhou Z, Zheng JS, Tian C. Chemical Synthesis of K34-Ubiquitylated H2B for Nucleosome Reconstitution and Single-Particle Cryo-Electron Microscopy Structural Analysis. Chembiochem 2016; 18:176-180. [PMID: 27976477 DOI: 10.1002/cbic.201600551] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/14/2022]
Abstract
Post-translational modifications (e.g., ubiquitylation) of histones play important roles in dynamic regulation of chromatin. Histone ubiquitylation has been speculated to directly influence the structure and dynamics of nucleosomes. However, structural information for ubiquitylated nucleosomes is still lacking. Here we report an alternative strategy for total chemical synthesis of homogenous histone H2B-K34-ubiquitylation (H2B-K34Ub) by using acid-cleavable auxiliary-mediated ligation of peptide hydrazides for site-specific ubiquitylation. Synthetic H2B-K34Ub was efficiently incorporated into nucleosomes and further used for single-particle cryo-electron microscopy (cryo-EM) imaging. The cryo-EM structure of the nucleosome containing H2B-K34Ub suggests that two flexible ubiquitin domains protrude between the DNA chains of the nucleosomes. The DNA chains around the H2B-K34 sites shift and provide more space for ubiquitin to protrude. These analyses indicated local and slight structural influences on the nucleosome with ubiquitylation at the H2B-K34 site.
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Affiliation(s)
- Jiabin Li
- Key Laboratory of Bioorganic Phosphorus Chemistry, Chemical Biology, Ministry of Education), Department of Chemistry and School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Qiaoqiao He
- Key Laboratory of Bioorganic Phosphorus Chemistry, Chemical Biology, Ministry of Education), Department of Chemistry and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuntao Liu
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Sanling Liu
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Shan Tang
- Key Laboratory of Bioorganic Phosphorus Chemistry, Chemical Biology, Ministry of Education), Department of Chemistry and School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chengmin Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Demeng Sun
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Xiaorun Li
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Min Zhou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ping Zhu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guoqiang Bi
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Zhenghong Zhou
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China.,Department of Microbiology, Immunology and Molecular Genetics and, California NanoSystems Systems, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Ji-Shen Zheng
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
| | - Changlin Tian
- Hefei National Laboratory of Physical Sciences at MicroScale and, School of Life Sciences, University of Science and Technology of China and, High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230027, China
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19
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Raj R, Lercher L, Mohammed S, Davis BG. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex. Angew Chem Int Ed Engl 2016; 55:8918-22. [PMID: 27272618 PMCID: PMC5111754 DOI: 10.1002/anie.201603106] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 12/28/2022]
Abstract
Transcriptional regulation can be established by various post-translational modifications (PTMs) on histone proteins in the nucleosome and by nucleobase modifications on chromosomal DNA. Functional consequences of histone O-GlcNAcylation (O-GlcNAc=O-linked β-N-acetylglucosamine) are largely unexplored. Herein, we generate homogeneously GlcNAcylated histones and nucleosomes by chemical post-translational modification. Mass-spectrometry-based quantitative interaction proteomics reveals a direct interaction between GlcNAcylated nucleosomes and the "facilitates chromatin transcription" (FACT) complex. Preferential binding of FACT to GlcNAcylated nucleosomes may point towards O-GlcNAcylation as one of the triggers for FACT-driven transcriptional control.
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Affiliation(s)
- Ritu Raj
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lukas Lercher
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.
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20
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Raj R, Lercher L, Mohammed S, Davis BG. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ritu Raj
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Lukas Lercher
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Shabaz Mohammed
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
| | - Benjamin G. Davis
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA UK
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21
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Maity SK, Jbara M, Laps S, Brik A. Efficient Palladium-Assisted One-Pot Deprotection of (Acetamidomethyl)Cysteine Following Native Chemical Ligation and/or Desulfurization To Expedite Chemical Protein Synthesis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603169] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Shay Laps
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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22
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Maity SK, Jbara M, Laps S, Brik A. Efficient Palladium-Assisted One-Pot Deprotection of (Acetamidomethyl)Cysteine Following Native Chemical Ligation and/or Desulfurization To Expedite Chemical Protein Synthesis. Angew Chem Int Ed Engl 2016; 55:8108-12. [PMID: 27126503 DOI: 10.1002/anie.201603169] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/09/2022]
Abstract
The acetamidomethyl (Acm) moiety is a widely used cysteine protecting group for the chemical synthesis and semisynthesis of peptide and proteins. However, its removal is not straightforward and requires harsh reaction conditions and additional purification steps before and after the removal step, which extends the synthetic process and reduces the overall yield. To overcome these shortcomings, a method for rapid and efficient Acm removal using Pd(II) complexes in aqueous medium is reported. We show, for the first time, the assembly of three peptide fragments in a one-pot fashion by native chemical ligation where the Acm moiety was used to protect the N-terminal Cys of the middle fragment. Importantly, an efficient synthesis of the ubiquitin-like protein UBL-5, which contains two native Cys residues, was accomplished through the one-pot operation of three key steps, namely ligation, desulfurization, and Acm deprotection, highlighting the great utility of the new approach in protein synthesis.
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Affiliation(s)
- Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Shay Laps
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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23
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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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24
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Jbara M, Maity SK, Morgan M, Wolberger C, Brik A. Chemical Synthesis of Phosphorylated Histone H2A at Tyr57 Reveals Insight into the Inhibition Mode of the SAGA Deubiquitinating Module. Angew Chem Int Ed Engl 2016; 55:4972-6. [PMID: 26960207 DOI: 10.1002/anie.201600638] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Abstract
Monoubiquitination of histone H2B plays a central role in transcription activation and is required for downstream histone-methylation events. Deubiquitination of H2B by the Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex is regulated by a recently discovered histone mark, phosphorylated H2AY57 (H2AY57p), which inhibits deubiquitination of H2B by the SAGA complex as well as restricting demethylation of H3 and increasing its acetylation. Evidence for the effect of H2AY57p, however, was indirect and was investigated in vivo by monitoring the effects of chemical inhibition of Tyr kinase CK2 or by mutating the phosphorylation site. We applied the total chemical synthesis of proteins to prepare H2AY57p efficiently and study the molecular details of this regulation. This analogue, together with semisynthetically prepared ubiquitinated H2B, enabled us to provide direct evidence for the cross-talk between those two marks and the inhibition of SAGA activity by H2AY57p.
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Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Michael Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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25
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Jbara M, Maity SK, Morgan M, Wolberger C, Brik A. Chemical Synthesis of Phosphorylated Histone H2A at Tyr57 Reveals Insight into the Inhibition Mode of the SAGA Deubiquitinating Module. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Michael Morgan
- Department of Biophysics and Biophysical Chemistry; Johns Hopkins University School of Medicine; 725 North Wolfe Street Baltimore MD 21205-2185 USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry; Johns Hopkins University School of Medicine; 725 North Wolfe Street Baltimore MD 21205-2185 USA
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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