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Lutz J, Höllmüller E, Scheffner M, Marx A, Stengel F. The Length of a Ubiquitin Chain: A General Factor for Selective Recognition by Ubiquitin-Binding Proteins. Angew Chem Int Ed Engl 2020; 59:12371-12375. [PMID: 32301549 PMCID: PMC7384046 DOI: 10.1002/anie.202003058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Indexed: 12/16/2022]
Abstract
The attachment of ubiquitin (Ub) chains of various length to proteins is a prevalent posttranslational modification in eukaryotes. The fate of a modified protein is determined by Ub-binding proteins (UBPs), which interact with Ub chains in a linkage-selective manner. However, the impact and functional consequences of chain length on the binding selectivity of UBPs remain mostly elusive. We have generated Ub chains of defined length and linkage by using click chemistry and GELFrEE fractionation. These defined polymers were used in affinity-based enrichment assays to identify length- and linkage-selective interaction partners on a proteome-wide scale. For the first time, it is revealed that the length of a Ub chain generally has a major impact on its ability to be selectively recognized by UBPs.
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Affiliation(s)
- Joachim Lutz
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Eva Höllmüller
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Martin Scheffner
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Andreas Marx
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Florian Stengel
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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2
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Lutz J, Höllmüller E, Scheffner M, Marx A, Stengel F. Die Länge einer Ubiquitinkette: ein genereller Faktor für die selektive Erkennung durch Ubiquitin‐bindende Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003058] [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]
Affiliation(s)
- Joachim Lutz
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Eva Höllmüller
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Martin Scheffner
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Florian Stengel
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
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3
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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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4
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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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5
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Marx A. Science at the Chemistry Biology Interface, some Personal Thoughts. Isr J Chem 2019. [DOI: 10.1002/ijch.201800165] [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]
Affiliation(s)
- Andreas Marx
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of Konstanz Germany
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6
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Meledin R, Mali SM, Kleifeld O, Brik A. Activity-Based Probes Developed by Applying a Sequential Dehydroalanine Formation Strategy to Expressed Proteins Reveal a Potential α-Globin-Modulating Deubiquitinase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Roman Meledin
- Schulich Faculty of Chemistry; Technion Israel Institute of Technology; Haifa 3200008 Israel
| | - Sachitanand M. Mali
- Schulich Faculty of Chemistry; Technion Israel Institute of Technology; Haifa 3200008 Israel
| | - Oded Kleifeld
- Faculty of Biology; Technion Israel Institute of Technology; Haifa 3200003 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion Israel Institute of Technology; Haifa 3200008 Israel
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7
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Meledin R, Mali SM, Kleifeld O, Brik A. Activity-Based Probes Developed by Applying a Sequential Dehydroalanine Formation Strategy to Expressed Proteins Reveal a Potential α-Globin-Modulating Deubiquitinase. Angew Chem Int Ed Engl 2018. [PMID: 29527788 DOI: 10.1002/anie.201800032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report a general and novel semisynthetic strategy for the preparation of ubiquitinated protein-activity-based probes on the basis of sequential dehydroalanine formation on expressed proteins. We applied this approach to construct a physiologically and therapeutically relevant ubiquitinated α-globin probe, which was used for the enrichment and proteomic identification of α-globin-modulating deubiquitinases. We found USP15 as a potential deubiquitinase for the modulation of α-globin, an excess of which aggravates β-thalassemia symptoms. This development opens new opportunities for activity-based-probe design to shed light on the important aspects underlying ubiquitination and deubiquitination in health and disease.
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Affiliation(s)
- Roman Meledin
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, 3200008, Israel
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, 3200008, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, 3200008, Israel
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8
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Taupitz KF, Dörner W, Mootz HD. Covalent Capturing of Transient SUMO-SIM Interactions Using Unnatural Amino Acid Mutagenesis and Photocrosslinking. Chemistry 2017; 23:5978-5982. [PMID: 28121373 DOI: 10.1002/chem.201605619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 11/09/2022]
Abstract
The weak interaction between the post-translational modifier SUMO (small ubiquitin-like modifier) and proteins containing the SUMO-interacting motif (SIM) poses limitations to the identification of interaction partners of SUMOylated proteins and to the mapping of the interfaces. To overcome these limitations, genetically encoded photocrosslinker amino acids were incorporated close to the SIM-interaction groove in human SUMO1. UV irradiation resulted in the desired covalent crosslinks both in a purified protein environment and in cell extracts.
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Affiliation(s)
- Kim F Taupitz
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Wolfgang Dörner
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Henning D Mootz
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
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9
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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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10
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Bondalapati S, Mansour W, Nakasone MA, Maity SK, Glickman MH, Brik A. Chemical synthesis of phosphorylated ubiquitin and diubiquitin exposes positional sensitivities of e1-e2 enzymes and deubiquitinases. Chemistry 2015; 21:7360-4. [PMID: 25829361 DOI: 10.1002/chem.201500540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 12/22/2022]
Abstract
Modification of ubiquitin by phosphorylation extends the signaling possibilities of this dynamic signal, as it could affect the activity of ligases and the processing of ubiquitin chains by deubiquitinases. The first chemical synthesis of phosphorylated ubiquitin and of Lys63-linked diubiquitin at the proximal, distal or both ubiquitins is reported. This enabled the examination of how such a modification alters E1-E2 activities of the ubiquitination machinery. It is found that E1 charging was not affected, while the assembly of phosphorylated ubiquitin chains was differentially inhibited with E2 enzymes tested. Moreover, this study shows that phosphorylation interferes with the recognition of linkage specific antibodies and the activities of several deubiquitinases. Notably, phosphorylation in the proximal or distal ubiquitin unit has differential effects on specific deubiquitinases. These results support a unique role of phosphorylation in the dynamics of the ubiquitin signal.
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Affiliation(s)
- Somasekhar Bondalapati
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653 Beer-Sheva 8410501 (Israel); Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200008 Haifa (Israel)
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11
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Ohayon S, Refua M, Hendler A, Aharoni A, Brik A. Harnessing the Oxidation Susceptibility of Deubiquitinases for Inhibition with Small Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Ohayon S, Refua M, Hendler A, Aharoni A, Brik A. Harnessing the oxidation susceptibility of deubiquitinases for inhibition with small molecules. Angew Chem Int Ed Engl 2014; 54:599-603. [PMID: 25327786 DOI: 10.1002/anie.201408411] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 01/08/2023]
Abstract
Deubiquitinases (DUBs) counteract ubiquitination by removing or trimming ubiquitin chains to alter the signal. Their diverse role in biological processes and involvement in diseases have recently attracted great interest with regard to their mechanism and inhibition. It has been shown that some DUBs are regulated by reactive oxygen species (ROS) in which the catalytic Cys residue undergoes reversible oxidation, hence modulating DUBs activity under oxidative stress. Reported herein for the first time, the observation that small molecules, which are capable of generating ROS efficiently, inhibit DUBs by selective and nonreversible oxidation of the catalytic Cys residue. Interestingly, the small molecule beta-lapachone, which is currently in clinical trials for cancer, is among the potent inhibitors, thus suggesting possible new cellular targets for its therapeutic effects. Our study describes a novel mechanism of DUBs inhibition and opens new opportunities in exploiting them for cancer therapy.
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Affiliation(s)
- Shimrit Ohayon
- Department of Chemistry, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501 (Israel)
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13
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Schneider T, Schneider D, Rösner D, Malhotra S, Mortensen F, Mayer TU, Scheffner M, Marx A. Analyse des Ubiquitincodes durch proteasebeständige Ubiquitinketten mit definierter Verknüpfung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407192] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Schneider T, Schneider D, Rösner D, Malhotra S, Mortensen F, Mayer TU, Scheffner M, Marx A. Dissecting ubiquitin signaling with linkage-defined and protease resistant ubiquitin chains. Angew Chem Int Ed Engl 2014; 53:12925-9. [PMID: 25196034 DOI: 10.1002/anie.201407192] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 01/08/2023]
Abstract
Ubiquitylation is a complex posttranslational protein modification and deregulation of this pathway has been associated with different human disorders. Ubiquitylation comes in different flavors: Besides mono-ubiquitylation, ubiquitin chains of various topologies are formed on substrate proteins. The fate of ubiquitylated proteins is determined by the linkage-type of the attached ubiquitin chains, however, the underlying mechanism is poorly characterized. Herein, we describe a new method based on codon expansion and click-chemistry-based polymerization to generate linkage-defined ubiquitin chains that are resistant to ubiquitin-specific proteases and adopt native-like functions. The potential of these artificial chains for analyzing ubiquitin signaling is demonstrated by linkage-specific effects on cell-cycle progression.
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Affiliation(s)
- Tatjana Schneider
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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15
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Uprety R, Luo J, Liu J, Naro Y, Samanta S, Deiters A. Genetic Encoding of Caged Cysteine and Caged Homocysteine in Bacterial and Mammalian Cells. Chembiochem 2014; 15:1793-9. [DOI: 10.1002/cbic.201400073] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Indexed: 12/19/2022]
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16
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Abeywardana T, Pratt MR. Using Chemistry to Investigate the Molecular Consequences of Protein Ubiquitylation. Chembiochem 2014; 15:1547-54. [DOI: 10.1002/cbic.201402117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 12/21/2022]
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17
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Mulder MPC, El Oualid F, ter Beek J, Ovaa H. A native chemical ligation handle that enables the synthesis of advanced activity-based probes: diubiquitin as a case study. Chembiochem 2014; 15:946-9. [PMID: 24623714 PMCID: PMC4159580 DOI: 10.1002/cbic.201402012] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 01/08/2023]
Abstract
We present the development of a native chemical ligation handle that also functions as a masked electrophile that can be liberated during synthesis when required. This handle can thus be used for the synthesis of complex activity-based probes. We describe the use of this handle in the generation of linkage-specific activity-based deubiquitylating enzyme probes that contain substrate context and closely mimic the native ubiquitin isopeptide linkage. We have generated activity-based probes based on all seven isopeptide-linked diubiquitin topoisomers and demonstrated their structural integrity and ability to label DUBs in a linkage-specific manner.
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Affiliation(s)
- Monique P C Mulder
- Division of Cell Biology, Netherlands Cancer Institute (NKI)Plesmanlaan 121, 1066 CX Amsterdam (The Netherlands) E-mail: Homepage: http://research.nki.nl/Ovaalab/
| | - Farid El Oualid
- Division of Cell Biology, Netherlands Cancer Institute (NKI)Plesmanlaan 121, 1066 CX Amsterdam (The Netherlands) E-mail: Homepage: http://research.nki.nl/Ovaalab/
| | - Jarno ter Beek
- Division of Cell Biology, Netherlands Cancer Institute (NKI)Plesmanlaan 121, 1066 CX Amsterdam (The Netherlands) E-mail: Homepage: http://research.nki.nl/Ovaalab/
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute (NKI)Plesmanlaan 121, 1066 CX Amsterdam (The Netherlands) E-mail: Homepage: http://research.nki.nl/Ovaalab/
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18
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Singh RK, Sundar A, Fushman D. Nonenzymatic rubylation and ubiquitination of proteins for structural and functional studies. Angew Chem Int Ed Engl 2014; 53:6120-5. [PMID: 24764216 DOI: 10.1002/anie.201402642] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 11/07/2022]
Abstract
Uncovering the mechanisms that allow conjugates of ubiquitin (Ub) and/or Ub-like (UBL) proteins such as Rub1 to serve as distinct molecular signals requires the ability to make them with native connectivity and defined length and linkage composition. A novel, effective, and affordable strategy for controlled chemical assembly of fully natural UBL-Ub, Ub-UBL, and UBL-UBL conjugates from recombinant monomers is presented. Rubylation of Ub and Rub1 and ubiquitination of Rub1 was achieved without E2/E3 enzymes. New residue-specific information was obtained on the interdomain contacts in naturally-occurring K48-linked Rub1-Ub and Ub-Rub1, and K29-linked Rub1-Ub heterodimers, and their recognition by a K48-linkage-specific Ub receptor. The disassembly of these heterodimers by major deubiquitinating enzymes was examined and it was discovered that some deubiquitinases also possess derubylase activity. This unexpected result suggests possible crosstalk between Ub and Rub1/Nedd8 signaling pathways.
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Affiliation(s)
- Rajesh K Singh
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-3360 (USA)
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19
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Singh RK, Sundar A, Fushman D. Nonenzymatic Rubylation and Ubiquitination of Proteins for Structural and Functional Studies. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Wang XA, Kurra Y, Huang Y, Lee YJ, Liu WR. E1-Catalyzed Ubiquitin C-Terminal Amidation for the Facile Synthesis of Deubiquitinase Substrates. Chembiochem 2013; 15:37-41. [DOI: 10.1002/cbic.201300608] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Indexed: 11/05/2022]
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21
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Adams AL, Cowper B, Morgan RE, Premdjee B, Caddick S, Macmillan D. Cysteine Promoted C-Terminal Hydrazinolysis of Native Peptides and Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Adams AL, Cowper B, Morgan RE, Premdjee B, Caddick S, Macmillan D. Cysteine promoted C-terminal hydrazinolysis of native peptides and proteins. Angew Chem Int Ed Engl 2013; 52:13062-6. [PMID: 24123371 PMCID: PMC4065347 DOI: 10.1002/anie.201304997] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/31/2013] [Indexed: 11/23/2022]
Affiliation(s)
- Anna L Adams
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ (United Kingdom)
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23
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Haj-Yahya N, Haj-Yahya M, Castañeda CA, Spasser L, Hemantha HP, Jbara M, Penner M, Ciechanover A, Fushman D, Brik A. Modifying the Vicinity of the Isopeptide Bond To Reveal Differential Behavior of Ubiquitin Chains with Interacting Proteins: Organic Chemistry Applied to Synthetic Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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24
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Haj-Yahya N, Haj-Yahya M, Castañeda CA, Spasser L, Hemantha HP, Jbara M, Penner M, Ciechanover A, Fushman D, Brik A. Modifying the vicinity of the isopeptide bond to reveal differential behavior of ubiquitin chains with interacting proteins: organic chemistry applied to synthetic proteins. Angew Chem Int Ed Engl 2013; 52:11149-53. [PMID: 24006204 DOI: 10.1002/anie.201306118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 01/08/2023]
Abstract
In every direction: Chemical protein synthesis allows the construction of 14 di-ubiquitin analogues modified in the vicinity of the isopeptide bond to examine their behavior with deubiquitinases and ubiquitin binding domains. The results set the ground for the generation of unique probes for studying the interactions of these chains with various ubiquitin-interacting proteins.
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Affiliation(s)
- Najat Haj-Yahya
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105 (Israel) http://www.bgu.ac.il/∼abrik
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Forschungsprofessur der Royal Society: M. J. Rosseinsky / Sackler-Preis: J. Q. Yu und M. S. Sanford / Tetrahedron-Preis für Nachwuchswissenschaftler: A. Brik und M. S. Sanford. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303314] [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]
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Royal Society Research Professorship: M. J. Rosseinsky / Raymond and Beverly Sackler International Prize: J. Q. Yu and M. S. Sanford / Tetrahedron Young Investigator Award: A. Brik and M. S. Sanford. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201303314] [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]
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic polymerization of ubiquitin: single-step synthesis and isolation of discrete ubiquitin oligomers. Angew Chem Int Ed Engl 2012; 51:13085-8. [PMID: 23161800 PMCID: PMC4083817 DOI: 10.1002/anie.201207171] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/26/2012] [Indexed: 11/05/2022]
Abstract
Linked: a method based on thiol-ene chemistry enables the synthesis and purification of ubiquitin oligomers with ≥4 units. This approach, which employs free-radical polymerization, can be applied towards the synthesis of homogeneous Lys6-linked ubiquitin oligomers currently inaccessible by enzymatic methods. By using these chains, one can study their roles in the ubiquitin proteasome system and the DNA damage response pathway.
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Affiliation(s)
- Vivian H. Trang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Ellen M. Valkevich
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Shoko Minami
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Yi-Chen Chen
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Eric R. Strieter
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic Polymerization of Ubiquitin: Single-Step Synthesis and Isolation of Discrete Ubiquitin Oligomers. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-methylation of isopeptide bond as a strategy to resist deubiquitinases. Angew Chem Int Ed Engl 2012; 51:11535-9. [PMID: 23065695 DOI: 10.1002/anie.201205771] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Mahmood Haj-Yahya
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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Haj-Yahya M, Eltarteer N, Ohayon S, Shema E, Kotler E, Oren M, Brik A. N-Methylation of Isopeptide Bond as a Strategy to Resist Deubiquitinases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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