1
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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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2
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Huppelschoten Y, Elhebieshy AF, Hameed DS, Sapmaz A, Buchardt J, Nielsen TE, Ovaa H, van der Heden van Noort GJ. Total Chemical Synthesis of a Functionalized GFP Nanobody. Chembiochem 2022; 23:e202200304. [PMID: 35920208 PMCID: PMC9804225 DOI: 10.1002/cbic.202200304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/05/2023]
Abstract
Chemical protein synthesis has proven to be a powerful tool to access homogenously modified proteins. The chemical synthesis of nanobodies (Nb) would create possibilities to design tailored Nbs with a range of chemical modifications such as tags, linkers, reporter groups, and subsequently, Nb-drug conjugates. Herein, we describe the total chemical synthesis of a 123 amino-acid Nb against GFP. A native chemical ligation- desulfurization strategy was successfully applied for the synthesis of this GFP Nb, modified with a propargyl (PA) moiety for on-demand functionalization. Biophysical characterization indicated that the synthetic GFP Nb-PA was correctly folded after internal disulfide bond formation. The synthetic Nb-PA was functionalized with a biotin or a sulfo-cyanine5 dye by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), resulting in two distinct probes used for functional in vitro validation in pull-down and confocal microscopy settings.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands,Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Angela F. Elhebieshy
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Dharjath S. Hameed
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Aysegul Sapmaz
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Jens Buchardt
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Thomas E. Nielsen
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Huib Ovaa
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
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3
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Nakatsu K, Okamoto A, Hayashi G, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation**. Angew Chem Int Ed Engl 2022; 61:e202206240. [DOI: 10.1002/anie.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Koki Nakatsu
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 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
| | - Gosuke Hayashi
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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4
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Hayashi G, Nakatsu K, Okamoto A, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gosuke Hayashi
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering Furo-choChikusa-ku 464-8603 Nagoya JAPAN
| | - Koki Nakatsu
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
| | - Akimitsu Okamoto
- The University of Tokyo Graduate School of Engineering Faculty of Engineering: Tokyo Daigaku Daigakuin Kogakukei Kenkyuka Kogakubu Chemistry and Biotechnology JAPAN
| | - Hiroshi Murakami
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
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5
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Hessefort H, Gross A, Seeleithner S, Hessefort M, Kirsch T, Perkams L, Bundgaard KO, Gottwald K, Rau D, Graf CGF, Rozanski E, Weidler S, Unverzagt C. Chemical and Enzymatic Synthesis of Sialylated Glycoforms of Human Erythropoietin. Angew Chem Int Ed Engl 2021; 60:25922-25932. [PMID: 34523784 PMCID: PMC9297946 DOI: 10.1002/anie.202110013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/31/2021] [Indexed: 01/15/2023]
Abstract
Recombinant human erythropoietin (EPO) is the main therapeutic glycoprotein for the treatment of anemia in cancer and kidney patients. The in‐vivo activity of EPO is carbohydrate‐dependent with the number of sialic acid residues regulating its circulatory half‐life. EPO carries three N‐glycans and thus obtaining pure glycoforms provides a major challenge. We have developed a robust and reproducible chemoenzymatic approach to glycoforms of EPO with and without sialic acids. EPO was assembled by sequential native chemical ligation of two peptide and three glycopeptide segments. The glycopeptides were obtained by pseudoproline‐assisted Lansbury aspartylation. Enzymatic introduction of the sialic acids was readily accomplished at the level of the glycopeptide segments but even more efficiently on the refolded glycoprotein. Biological recognition of the synthetic EPOs was shown by formation of 1:1 complexes with recombinant EPO receptor.
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Affiliation(s)
- Hendrik Hessefort
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Angelina Gross
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Simone Seeleithner
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Markus Hessefort
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Tanja Kirsch
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Lukas Perkams
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Klaus Ole Bundgaard
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Karen Gottwald
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - David Rau
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | | | - Elisabeth Rozanski
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Sascha Weidler
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Carlo Unverzagt
- University of Bayreuth, Bioorganic Chemistry, Universitätsstraße 30, 95447, Bayreuth, Germany
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6
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Hessefort H, Gross A, Seeleithner S, Hessefort M, Kirsch T, Perkams L, Bundgaard KO, Gottwald K, Rau D, Graf CGF, Rozanski E, Weidler S, Unverzagt C. Chemical and Enzymatic Synthesis of Sialylated Glycoforms of Human Erythropoietin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hendrik Hessefort
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Angelina Gross
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Simone Seeleithner
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Markus Hessefort
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Tanja Kirsch
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Lukas Perkams
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Klaus Ole Bundgaard
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Karen Gottwald
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - David Rau
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | | | - Elisabeth Rozanski
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Sascha Weidler
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
| | - Carlo Unverzagt
- University of Bayreuth Bioorganic Chemistry Universitätsstraße 30 95447 Bayreuth Germany
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7
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Yao G, Knittel CH, Kosol S, Wenz MT, Keller BG, Gruß H, Braun AC, Lutz C, Hechler T, Pahl A, Süssmuth RD. Iodine-Mediated Tryptathionine Formation Facilitates the Synthesis of Amanitins. J Am Chem Soc 2021; 143:14322-14331. [PMID: 34459587 DOI: 10.1021/jacs.1c06565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic methods on the macrocyclization of peptides are of high interest since they facilitate the synthesis of various types of potentially bioactive compounds, e.g. addressing targets like protein-protein-interactions. Herein, we report on an efficient method to construct tryptathionine-cross-links in peptides between the amino acids Trp and Cys. This reaction not only is the basis for the total synthesis of the death cap toxin α-amanitin but also provides rapid access to various new amanitin analogues. This study for the first time presents a systematic compilation of structure-activity relations (SAR) of amatoxins with regard to RNA polymerase II inhibition and cytotoxicity with one amanitin derivative of superior RNAP II inhibition. The present approach paves the way for the synthesis of structurally diverse amatoxins as future payloads for antibody-toxin conjugates in cancer therapy.
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Affiliation(s)
- Guiyang Yao
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Caroline H Knittel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T Wenz
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hendrik Gruß
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Alexandra C Braun
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Christian Lutz
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Torsten Hechler
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Andreas Pahl
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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8
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Abboud SA, Amoura M, Madinier J, Renoux B, Papot S, Piller V, Aucagne V. Enzyme‐Cleavable Linkers for Protein Chemical Synthesis through Solid‐Phase Ligations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Skander A. Abboud
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Mehdi Amoura
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Jean‐Baptiste Madinier
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Brigitte Renoux
- Institut de Chimie des Milieux et des Matériaux de Poitiers UMR-CNRS 7285 4 rue Michel Brunet 86073 Poitiers cedex 9 France
| | - Sébastien Papot
- Institut de Chimie des Milieux et des Matériaux de Poitiers UMR-CNRS 7285 4 rue Michel Brunet 86073 Poitiers cedex 9 France
| | - Véronique Piller
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
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9
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Abboud SA, Amoura M, Madinier JB, Renoux B, Papot S, Piller V, Aucagne V. Enzyme-Cleavable Linkers for Protein Chemical Synthesis through Solid-Phase Ligations. Angew Chem Int Ed Engl 2021; 60:18612-18618. [PMID: 34097786 DOI: 10.1002/anie.202103768] [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: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The total synthesis of long proteins requires the assembly of multiple fragments through successive ligations. The need for intermediate purification steps is a strong limitation, particularly in terms of overall yield. One solution to this problem would be solid-supported chemical ligation (SPCL), for which a first peptide segment must be immobilized on a SPCL-compatible solid support through a linker that can be cleaved under very mild conditions to release the assembled protein. The cleavage of SPCL linkers has previously required chemical conditions sometimes incompatible with sensitive protein targets. Herein, we describe an alternative enzymatic approach to trigger cleavage under extremely mild and selective conditions. Optimization of the linker structure and use of a small enzyme able to diffuse into the solid support were key to the success of the strategy. We demonstrated its utility by the assembly of three peptide segments on the basis of native chemical ligation to afford a 15 kDa polypeptide.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Mehdi Amoura
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Jean-Baptiste Madinier
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Brigitte Renoux
- Institut de Chimie des Milieux et des Matériaux de Poitiers, UMR-CNRS 7285, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Sébastien Papot
- Institut de Chimie des Milieux et des Matériaux de Poitiers, UMR-CNRS 7285, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Véronique Piller
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
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10
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Liang L, Chu G, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li Y, Liu L. Chemical Synthesis of Activity‐Based E2‐Ubiquitin Probes for the Structural Analysis of E3 Ligase‐Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- 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
| | - Guo‐Chao Chu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - 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
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Junxiong Mao
- 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
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yangwode Jing
- 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
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education 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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11
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Liang LJ, Chu GC, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li YM, Liu L. Chemical Synthesis of Activity-Based E2-Ubiquitin Probes for the Structural Analysis of E3 Ligase-Catalyzed Transthiolation. Angew Chem Int Ed Engl 2021; 60:17171-17177. [PMID: 34021957 DOI: 10.1002/anie.202105870] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 12/17/2022]
Abstract
Activity-based E2 conjugating enzyme (E2)-ubiquitin (Ub) probes have recently emerged as effective tools for studying the molecular mechanism of E3 ligase (E3)-catalyzed ubiquitination. However, the preparation of existing activity-based E2-Ub probes depends on recombination technology and bioconjugation chemistry, limiting their structural diversity. Herein we describe an expedient total chemical synthesis of an E2 enzyme variant through a hydrazide-based native chemical ligation, which enabled the construction of a structurally new activity-based E2-Ub probe to covalently capture the catalytic site of Cys-dependent E3s. Chemical cross-linking coupled with mass spectrometry (CXMS) demonstrated the utility of this new probe in structural analysis of the intermediates formed during Nedd4 and Parkin-mediated transthiolation. This study exemplifies the utility of chemical protein synthesis for the development of protein probes for biological studies.
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Affiliation(s)
- 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
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.,School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - 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
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junxiong Mao
- 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
| | - Jingnan Chen
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yangwode Jing
- 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
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, 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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12
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Vamisetti GB, Meledin R, Nawatha M, Suga H, Brik A. The Development of a Fluorescence-Based Competitive Assay Enabled the Discovery of Dimeric Cyclic Peptide Modulators of Ubiquitin Chains. Angew Chem Int Ed Engl 2021; 60:7018-7023. [PMID: 33326152 PMCID: PMC8048552 DOI: 10.1002/anie.202013392] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/13/2020] [Indexed: 12/15/2022]
Abstract
Development of modulators targeting specific interactions of ubiquitin-based conjugates with their partners is a formidable task since it requires a suitable screening assay and homogeneous ubiquitin conjugates. We developed a novel high-throughput strategy for screening ligands for Lys48-linked tetraubiquitin chain in a relatively simple, fast, and affordable manner. This approach combined with a state-of-the-art toolbox of chemical protein synthesis and a specially optimized Cys deprotection protocol enabled us to design highly potent, Lys48-linked tetraubiquitin chain selective "next generation" dimeric peptide modulators. The dimeric peptide exhibited cancer cell permeability and induced cell death with higher efficiency compared to its monocyclic analogue. These features make our dimeric peptide a promising candidate for further studies using in vivo models. Our assay can be adopted for other various ubiquitin chains in their free or anchored forms as well as conjugates for Ub-like modifiers.
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Affiliation(s)
- Ganga B. Vamisetti
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Roman Meledin
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Mickal Nawatha
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of TokyoTokyo113-0033Japan
| | - Ashraf Brik
- SchulichFaculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
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13
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Vamisetti GB, Meledin R, Nawatha M, Suga H, Brik A. The Development of a Fluorescence‐Based Competitive Assay Enabled the Discovery of Dimeric Cyclic Peptide Modulators of Ubiquitin Chains. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ganga B. Vamisetti
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Roman Meledin
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Mickal Nawatha
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Hiroaki Suga
- Department of Chemistry School of Science The University of Tokyo Tokyo 113-0033 Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry Technion-Israel Institute of Technology Haifa 3200008 Israel
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14
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Jiang S, Hsieh W, Chen W, Liao J, Chiang P, Lin YA. Synthesis of Thiol‐Containing Oligopeptides via Tandem Activation of γ‐Thiolactones by Silver‐DABCO Pair. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sheng‐Yuan Jiang
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
| | - Wen‐Tsai Hsieh
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
| | - Wei‐Shuo Chen
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
| | - Jia‐Shiang Liao
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
| | - Po‐Yu Chiang
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
| | - Yuya A. Lin
- Department of Chemistry National Sun Yat-sen University Kaohsiung 804 Taiwan
- Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung 807 Taiwan
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15
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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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16
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Zheng Q, Wang T, Chu G, Zuo C, Zhao R, Sui X, Ye L, Yu Y, Chen J, Wu X, Zhang W, Deng H, Shi J, Pan M, Li Y, Liu L. An E1‐Catalyzed Chemoenzymatic Strategy to Isopeptide‐
N
‐Ethylated Deubiquitylase‐Resistant Ubiquitin Probes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- 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
| | - Tian Wang
- 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
| | - Guo‐Chao Chu
- School of Food and Biological Engineering Hefei University of Technology Hefei 230009 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rui Zhao
- School of Food and Biological Engineering Hefei University of Technology Hefei 230009 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xin Sui
- 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
| | - Linzhi Ye
- 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
| | - Yuanyuan Yu
- 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
| | - Jingnan Chen
- School of Food and Biological Engineering Hefei University of Technology Hefei 230009 China
| | - Xiangwei Wu
- School of Food and Biological Engineering Hefei University of Technology Hefei 230009 China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Man Pan
- Department of Biochemistry and Molecular Biology University of Chicago Chicago IL 60637 USA
| | - Yi‐Ming Li
- School of Food and Biological Engineering Hefei University of Technology Hefei 230009 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University Beijing 100084 China
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17
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Zheng Q, Wang T, Chu GC, Zuo C, Zhao R, Sui X, Ye L, Yu Y, Chen J, Wu X, Zhang W, Deng H, Shi J, Pan M, Li YM, Liu L. An E1-Catalyzed Chemoenzymatic Strategy to Isopeptide-N-Ethylated Deubiquitylase-Resistant Ubiquitin Probes. Angew Chem Int Ed Engl 2020; 59:13496-13501. [PMID: 32346954 DOI: 10.1002/anie.202002974] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/12/2020] [Indexed: 12/22/2022]
Abstract
Triazole-based deubiquitylase (DUB)-resistant ubiquitin (Ub) probes have recently emerged as effective tools for the discovery of Ub chain-specific interactors in proteomic studies, but their structural diversity is limited. A new family of DUB-resistant Ub probes is reported based on isopeptide-N-ethylated dimeric or polymeric Ub chains, which can be efficiently prepared by a one-pot, ubiquitin-activating enzyme (E1)-catalyzed condensation reaction of recombinant Ub precursors to give various homotypic and even branched Ub probes at multi-milligram scale. Proteomic studies using label-free quantitative (LFQ) MS indicated that the isopeptide-N-ethylated Ub probes may complement the triazole-based probes in the study of Ub interactome. Our study highlights the utility of modern protein synthetic chemistry to develop structurally and new families of tool molecules needed for proteomic studies.
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Affiliation(s)
- 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
| | - Tian Wang
- 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
| | - Guo-Chao Chu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.,Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Rui Zhao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.,Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Xin Sui
- 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
| | - Linzhi Ye
- 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
| | - Yuanyuan Yu
- 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
| | - Jingnan Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xiangwei Wu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Man Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Yi-Ming Li
- School of Food and Biological Engineering, 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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18
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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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19
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He R, Pan J, Mayer JP, Liu F. Stepwise Construction of Disulfides in Peptides. Chembiochem 2020; 21:1101-1111. [PMID: 31886929 DOI: 10.1002/cbic.201900717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 12/12/2022]
Abstract
The disulfide bond plays an important role in biological systems. It defines global conformation, and ultimately the biological activity and stability of the peptide or protein. It is frequently present, singly or multiply, in biologically important peptide hormones and toxins. Numerous disulfide-containing peptides have been approved by the regulatory agencies as marketed drugs. Chemical synthesis is one of the prerequisite tools needed to gain deep insights into the structure-function relationships of these biomolecules. Along with the development of solid-phase peptide synthesis, a number of methods of disulfide construction have been established. This minireview will focus on the regiospecific, stepwise construction of multiple disulfides used in the chemical synthesis of peptides. We intend for this article to serve a reference for peptide chemists conducting complex peptide syntheses and also hope to stimulate the future development of disulfide methodologies.
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Affiliation(s)
- Rongjun He
- Novo Nordisk Research Center Indianapolis, 5225 Exploration Drive, Indianapolis, IN, 46241, USA
| | - Jia Pan
- Novo Nordisk Research Center China, 20 Life Science Road, Beijing, 102206, P. R. China
| | - John P Mayer
- Department of Molecular, Developmental & Cell Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Fa Liu
- Novo Nordisk Research Center Seattle, 530 Fairview Avenue North, Seattle, WA, 98109, USA
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20
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Ling J, Fan C, Qin H, Wang M, Chen J, Wittung‐Stafshede P, Zhu TF. Mirror‐Image 5S Ribonucleoprotein Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jun‐Jie Ling
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Chuyao Fan
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Hong Qin
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Min Wang
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Ji Chen
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
| | - Pernilla Wittung‐Stafshede
- Chemical Biology DivisionDepartment of Biology and Biological EngineeringChalmers University of Technology 41296 Gothenburg Sweden
| | - Ting F. Zhu
- School of Life SciencesTsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologyMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyMinistry of Education Key Laboratory of BioinformaticsTsinghua University Beijing 100084 China
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21
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Ling JJ, Fan C, Qin H, Wang M, Chen J, Wittung-Stafshede P, Zhu TF. Mirror-Image 5S Ribonucleoprotein Complexes. Angew Chem Int Ed Engl 2020; 59:3724-3731. [PMID: 31841243 PMCID: PMC7217020 DOI: 10.1002/anie.201914799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Indexed: 12/01/2022]
Abstract
After realizing mirror‐image genetic replication, transcription, and reverse transcription, the biggest challenge in establishing a mirror‐image version of the central dogma is to build a mirror‐image ribosome‐based translation machine. Here, we chemically synthesized the natural and mirror‐image versions of three ribosomal proteins (L5, L18, and L25) in the large subunit of the Escherichia coli ribosome with post‐translational modifications. We show that the synthetic mirror‐image proteins can fold in vitro despite limited efficiency and assemble with enzymatically transcribed mirror‐image 5S ribosomal RNA into ribonucleoprotein complexes. In addition, the RNA–protein interactions are chiral‐specific in that the mirror‐image ribosomal proteins do not bind with natural 5S ribosomal RNA and vice versa. The synthesis and assembly of mirror‐image 5S ribonucleoprotein complexes are important steps towards building a functional mirror‐image ribosome.
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Affiliation(s)
- Jun-Jie Ling
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Hong Qin
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Min Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Ji Chen
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
| | - Pernilla Wittung-Stafshede
- Chemical Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China
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22
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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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23
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Zhang B, Deng Q, Zuo C, Yan B, Zuo C, Cao XX, Zhu TF, Zheng JS, Liu L. Ligation of Soluble but Unreactive Peptide Segments in the Chemical Synthesis of Haemophilus Influenzae DNA Ligase. Angew Chem Int Ed Engl 2019; 58:12231-12237. [PMID: 31250514 DOI: 10.1002/anie.201905149] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Indexed: 01/28/2023]
Abstract
During the total chemical synthesis of the water-soluble globular Haemophilus Influenzae DNA ligase (Hin-Lig), we observed the surprising phenomenon of a soluble peptide segment that failed to undergo native chemical ligation. Based on dynamic light scattering and transmission electron microscopy experiments, we determined that the peptide formed soluble colloidal particles in a homogeneous solution containing 6 m guanidine hydrochloride. Conventional peptide performance-improving strategies, such as installation of a terminal/side-chain Arg tag or O-acyl isopeptide, failed to enable the reaction, presumably because of their inability to disrupt the formation of soluble colloidal particles. However, a removable backbone modification strategy recently developed for the synthesis of membrane proteins did disrupt the formation of the colloids, and the desired ligation of this soluble but unreactive system was eventually accomplished. This work demonstrates that an appropriate solution dispersion state, in addition to good peptide solubility, is a prerequisite for successful peptide ligation.
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Affiliation(s)
- Baochang Zhang
- Tsinghua-Peking Joint 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
| | - Qiang Deng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chong Zuo
- Tsinghua-Peking Joint 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
| | - Bingjia Yan
- Tsinghua-Peking Joint 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
| | - Chao Zuo
- Tsinghua-Peking Joint 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
| | - Xiu-Xiu Cao
- School of Life Sciences, University of Science and Technology of China, and High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230026, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ji-Shen Zheng
- School of Life Sciences, University of Science and Technology of China, and High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230026, China
| | - Lei Liu
- Tsinghua-Peking Joint 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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Zhang B, Deng Q, Zuo C, Yan B, Zuo C, Cao X, Zhu TF, Zheng J, Liu L. Ligation of Soluble but Unreactive Peptide Segments in the Chemical Synthesis of
Haemophilus Influenzae
DNA Ligase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Baochang Zhang
- Tsinghua–Peking Joint 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
| | - Qiang Deng
- School of Life SciencesTsinghua University Beijing 100084 China
| | - Chong Zuo
- Tsinghua–Peking Joint 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
| | - Bingjia Yan
- Tsinghua–Peking Joint 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
| | - Chao Zuo
- Tsinghua–Peking Joint 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
| | - Xiu‐Xiu Cao
- School of Life SciencesUniversity of Science and Technology of China, and High Magnetic Field LaboratoryChinese Academy of Sciences Hefei 230026 China
| | - Ting F. Zhu
- School of Life SciencesTsinghua University Beijing 100084 China
| | - Ji‐Shen Zheng
- School of Life SciencesUniversity of Science and Technology of China, and High Magnetic Field LaboratoryChinese Academy of Sciences Hefei 230026 China
| | - Lei Liu
- Tsinghua–Peking Joint 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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25
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Laps S, Sun H, Kamnesky G, Brik A. Palladium‐Mediated Direct Disulfide Bond Formation in Proteins Containing S‐Acetamidomethyl‐cysteine under Aqueous Conditions. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shay Laps
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Hao Sun
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Guy Kamnesky
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
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Laps S, Sun H, Kamnesky G, Brik A. Palladium‐Mediated Direct Disulfide Bond Formation in Proteins Containing S‐Acetamidomethyl‐cysteine under Aqueous Conditions. Angew Chem Int Ed Engl 2019; 58:5729-5733. [DOI: 10.1002/anie.201900988] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Shay Laps
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Hao Sun
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Guy Kamnesky
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
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27
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Kamo N, Hayashi G, Okamoto A. Corrigendum: Triple Function of 4-Mercaptophenylacetic Acid Promotes One-Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2019; 58:1540. [PMID: 30694014 DOI: 10.1002/anie.201814304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kamo N, Hayashi G, Okamoto A. Berichtigung: Triple Function of 4‐Mercaptophenylacetic Acid Promotes One‐Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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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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Kamo N, Hayashi G, Okamoto A. Triple Function of 4-Mercaptophenylacetic Acid Promotes One-Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2018; 57:16533-16537. [PMID: 30346110 DOI: 10.1002/anie.201809765] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 11/07/2022]
Abstract
One-pot multiple peptide ligation is a key technology to improve the efficiency of chemical protein synthesis. One-pot repetitive peptide ligation requires a cycle of three steps: peptide ligation, removal of a protecting group, and inactivation of the deprotection reagent. However, previous strategies are not sufficient because of harsh deprotection conditions, slow deprotection rates, and difficulty in quenching the deprotection reagent. To address these issues, we developed a rapid, efficient deprotection and subsequent quenching strategy using an allyloxycarbonyl group to protect the N-terminal cysteine residue. 4-Mercaptophenylacetic acid (MPAA), a thiol additive for native chemical ligation, functioned not only as a scavenger for π-allyl palladium complexes, but also as a quencher of palladium(0) complexes. By utilizing the multifunctionality of MPAA, we carried out a one-pot five-segment ligation to afford histone H2AX (142 amino acids), which was isolated in 59 % yield.
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Affiliation(s)
- Naoki Kamo
- 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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31
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Kamo N, Hayashi G, Okamoto A. Triple Function of 4-Mercaptophenylacetic Acid Promotes One-Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Naoki Kamo
- 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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32
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Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. Building and Breaking Bonds via a Compact S-Propargyl-Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl 2018; 57:12702-12706. [PMID: 30118570 PMCID: PMC6169525 DOI: 10.1002/anie.201806197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/30/2018] [Indexed: 02/03/2023]
Abstract
Analogous to reversible post-translational protein modifications, the ability to attach and subsequently remove modifications on proteins would be valuable for protein and biological research. Although bioorthogonal functionalities have been developed to conjugate or cleave protein modifications, they are introduced into proteins on separate residues and often with bulky side chains, limiting their use to one type of control and primarily protein surface. Here we achieved dual control on one residue by genetically encoding S-propargyl-cysteine (SprC), which has bioorthogonal alkyne and propargyl groups in a compact structure, permitting usage in protein interior in addition to surface. We demonstrated its incorporation at the dimer interface of glutathione transferase for in vivo crosslinking via thiol-yne click chemistry, and at the active site of human rhinovirus 3C protease for masking and then turning on enzyme activity via Pd-cleavage of SprC into Cys. In addition, we installed biotin onto EGFP via Sonogashira coupling of SprC and then tracelessly removed it via Pd cleavage. SprC is small in size, commercially available, nontoxic, and allows for bond building and breaking on a single residue. Genetically encoded SprC will be valuable for chemically controlling proteins with an essential Cys and for reversible protein modifications.
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Affiliation(s)
- Jun Liu
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Rujin Cheng
- R. Cheng, and Prof. S. Rozovsky.University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Haifan Wu
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Shanshan Li
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
- S. Li, Prof. P.G. Wang Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302
| | - Peng G. Wang
- S. Li, Prof. P.G. Wang Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302
| | - William F. DeGrado
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Sharon Rozovsky
- R. Cheng, and Prof. S. Rozovsky.University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Lei Wang
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
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Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. Building and Breaking Bonds via a Compact S‐Propargyl‐Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jun Liu
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Rujin Cheng
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Haifan Wu
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Shanshan Li
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
- Department of Chemistry and Center for Therapeutics and Diagnostics Georgia State University Atlanta GA 30302 USA
| | - Peng G. Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics Georgia State University Atlanta GA 30302 USA
| | - William F. DeGrado
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Sharon Rozovsky
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Lei Wang
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
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34
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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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35
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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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36
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Levengood MR, Zhang X, Hunter JH, Emmerton KK, Miyamoto JB, Lewis TS, Senter PD. Orthogonal Cysteine Protection Enables Homogeneous Multi‐Drug Antibody–Drug Conjugates. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Xinqun Zhang
- Seattle Genetics, Inc. 21823 30thDrive SE Bothell WA USA
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37
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Levengood MR, Zhang X, Hunter JH, Emmerton KK, Miyamoto JB, Lewis TS, Senter PD. Orthogonal Cysteine Protection Enables Homogeneous Multi-Drug Antibody-Drug Conjugates. Angew Chem Int Ed Engl 2016; 56:733-737. [PMID: 27966822 PMCID: PMC5299463 DOI: 10.1002/anie.201608292] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/27/2016] [Indexed: 02/05/2023]
Abstract
A strategy for the preparation of homogeneous antibody–drug conjugates (ADCs) containing multiple payloads has been developed. This approach utilizes sequential unmasking of cysteine residues with orthogonal protection to enable site‐specific conjugation of each drug. In addition, because the approach utilizes conjugation to native antibody cysteine residues, it is widely applicable and enables high drug loading for improved ADC potency. To highlight the benefits of ADC dual drug delivery, this strategy was applied to the preparation of ADCs containing two classes of auristatin drug‐linkers that have differing physiochemical properties and exert complementary anti‐cancer activities. Dual‐auristatin ADCs imparted activity in cell line and xenograft models that are refractory to ADCs comprised of the individual auristatin components. This work presents a facile method for construction of potent dual‐drug ADCs and demonstrates how delivery of multiple cytotoxic warheads can lead to improved ADC activities. Lastly, we anticipate that the conditions utilized herein for orthogonal cysteine unmasking are not restricted to ADCs and can be broadly utilized for site‐specific protein modification.
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Affiliation(s)
| | - Xinqun Zhang
- Seattle Genetics, Inc., 21823 30thDrive SE, Bothell, WA, USA
| | - Joshua H Hunter
- Seattle Genetics, Inc., 21823 30thDrive SE, Bothell, WA, USA
| | - Kim K Emmerton
- Seattle Genetics, Inc., 21823 30thDrive SE, Bothell, WA, USA
| | | | - Timothy S Lewis
- Seattle Genetics, Inc., 21823 30thDrive SE, Bothell, WA, USA
| | - Peter D Senter
- Seattle Genetics, Inc., 21823 30thDrive SE, Bothell, WA, USA
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38
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Exner MP, Kuenzl T, To TMT, Ouyang Z, Schwagerus S, Hoesl MG, Hackenberger CPR, Lensen MC, Panke S, Budisa N. Design ofS-Allylcysteine in Situ Production and Incorporation Based on a Novel Pyrrolysyl-tRNA Synthetase Variant. Chembiochem 2016; 18:85-90. [DOI: 10.1002/cbic.201600537] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Matthias P. Exner
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Tilmann Kuenzl
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
| | - Tuyet Mai T. To
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Zhaofei Ouyang
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 124 10623 Berlin Germany
| | - Sergej Schwagerus
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 BerlinBuch Germany
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Michael G. Hoesl
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Christian P. R. Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 BerlinBuch Germany
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marga C. Lensen
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 124 10623 Berlin Germany
| | - Sven Panke
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
| | - Nediljko Budisa
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
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39
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Jbara M, Laps S, Maity SK, Brik A. Palladium-Assisted Cleavage of Peptides and Proteins Containing a Backbone with Thiazolidine Linkage. Chemistry 2016; 22:14851-14855. [DOI: 10.1002/chem.201603676] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Indexed: 02/03/2023]
Affiliation(s)
- 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
| | - 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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