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Dasovich M, Leung AKL. PARPs and ADP-ribosylation: Deciphering the complexity with molecular tools. Mol Cell 2023; 83:1552-1572. [PMID: 37119811 PMCID: PMC10202152 DOI: 10.1016/j.molcel.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
PARPs catalyze ADP-ribosylation-a post-translational modification that plays crucial roles in biological processes, including DNA repair, transcription, immune regulation, and condensate formation. ADP-ribosylation can be added to a wide range of amino acids with varying lengths and chemical structures, making it a complex and diverse modification. Despite this complexity, significant progress has been made in developing chemical biology methods to analyze ADP-ribosylated molecules and their binding proteins on a proteome-wide scale. Additionally, high-throughput assays have been developed to measure the activity of enzymes that add or remove ADP-ribosylation, leading to the development of inhibitors and new avenues for therapy. Real-time monitoring of ADP-ribosylation dynamics can be achieved using genetically encoded reporters, and next-generation detection reagents have improved the precision of immunoassays for specific forms of ADP-ribosylation. Further development and refinement of these tools will continue to advance our understanding of the functions and mechanisms of ADP-ribosylation in health and disease.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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2
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Anderson BA, Krishnamurthy R. Heterogeneous Pyrophosphate-Linked DNA-Oligonucleotides: Aversion to DNA but Affinity for RNA. Chemistry 2018. [PMID: 29532524 DOI: 10.1002/chem.201800538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by pyrophosphate as backbones of primordial oligomers, DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) were synthesized and investigated for their base-pairing properties. As expected, pyrophosphate inserts into the backbone compromised the thermal stability of ppDNA-DNA duplexes. In contrast, the ppDNA-RNA duplex exhibited, remarkably, duplex stability, even with accumulation of pyrophosphate linkages. This seems to be a consequence of an increase in the diameter of the double-helix with eight-bond-repeat units, and higher inclination of the base-pair axis with respect to the backbone in RNA (A-form), compared with that in DNA (B-form). These results suggest that pyrophosphate-linked oligonucleotides could harbor functional capabilities with implications for their roles in the origins of life and chemical biology.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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3
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A General Approach Towards Triazole-Linked Adenosine Diphosphate Ribosylated Peptides and Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Liu Q, Kistemaker HAV, Bhogaraju S, Dikic I, Overkleeft HS, van der Marel GA, Ovaa H, van der Heden van Noort GJ, Filippov DV. A General Approach Towards Triazole-Linked Adenosine Diphosphate Ribosylated Peptides and Proteins. Angew Chem Int Ed Engl 2018; 57:1659-1662. [PMID: 29215186 DOI: 10.1002/anie.201710527] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/24/2017] [Indexed: 01/03/2023]
Abstract
Current methods to prepare adenosine diphosphate ribosylated (ADPr) peptides are not generally applicable due to the labile nature of this post-translational modification and its incompatibility with strong acidic conditions used in standard solid-phase peptide synthesis. A general strategy is presented to prepare ADPr peptide analogues based on a copper-catalyzed click reaction between an azide-modified peptide and an alkyne-modified ADPr counterpart. The scope of this approach was expanded to proteins by preparing two ubiquitin ADPr analogues carrying the biological relevant α-glycosidic linkage. Biochemical validation using Legionella effector enzyme SdeA shows that clicked ubiquitin ADPr is well-tolerated and highlights the potential of this strategy to prepare ADPr proteins.
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Affiliation(s)
- Qiang Liu
- Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Hans A V Kistemaker
- Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands.,Current address: ProQR Therapeutics, Leiden, The Netherlands
| | - Sagar Bhogaraju
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany
| | - Herman S Overkleeft
- Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | | | - Huib Ovaa
- Department of Chemical Immunology, Leiden University Medical Centre, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | | | - Dmitri V Filippov
- Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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5
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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6
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017; 56:2955-2959. [DOI: 10.1002/anie.201611878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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7
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Kistemaker HAV, Nardozza AP, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Synthesis and Macrodomain Binding of Mono-ADP-Ribosylated Peptides. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Hans A. V. Kistemaker
- Leiden Institute of Chemistry; Dept. of Bio-organic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Aurelio Pio Nardozza
- Department of Physiological Chemistry, Biomedical Center; Faculty of Medicine; Ludwig-Maximilians-Universität München; Großhaderner Street 9 82152 Planegg-Martinsried Germany
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry; Dept. of Bio-organic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijs A. van der Marel
- Leiden Institute of Chemistry; Dept. of Bio-organic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Andreas G. Ladurner
- Department of Physiological Chemistry, Biomedical Center; Faculty of Medicine; Ludwig-Maximilians-Universität München; Großhaderner Street 9 82152 Planegg-Martinsried Germany
- Center for Integrated Protein Science Munich (CIPSM); Ludwig-Maximilians-Universität München; Butenandt Street 5 81377 Munich Germany
- Munich Cluster for Systems Neurology (SyNergy); Ludwig-Maximilians-Universität München; Feodor Lynen Street 17 81377 Munich Germany
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry; Dept. of Bio-organic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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8
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Kistemaker HAV, Nardozza AP, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Synthesis and Macrodomain Binding of Mono-ADP-Ribosylated Peptides. Angew Chem Int Ed Engl 2016; 55:10634-8. [PMID: 27464500 DOI: 10.1002/anie.201604058] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/06/2016] [Indexed: 11/06/2022]
Abstract
Mono-ADP-ribosylation is a dynamic posttranslational modification (PTM) with important roles in signaling. Mammalian proteins that recognize or hydrolyze mono-ADP-ribosylated proteins have been described. We report the synthesis of ADP-ribosylated peptides from the proteins histone H2B, RhoA and, HNP-1. An innovative procedure was applied that makes use of pre-phosphorylated amino acid building blocks. Binding assays revealed that the macrodomains of human MacroD2 and TARG1 exhibit distinct specificities for the different ADP-ribosylated peptides, thus showing that the sequence surrounding ADP-ribosylated residues affects the substrate selectivity of macrodomains.
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Affiliation(s)
- Hans A V Kistemaker
- Leiden Institute of Chemistry, Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Aurelio Pio Nardozza
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Street 9, 82152, Planegg-Martinsried, Germany
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs A van der Marel
- Leiden Institute of Chemistry, Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Street 9, 82152, Planegg-Martinsried, Germany. .,Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandt Street 5, 81377, Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Feodor Lynen Street 17, 81377, Munich, Germany.
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Dept. of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Sherstyuk YV, Abramova TV. How To Form a Phosphate Anhydride Linkage in Nucleotide Derivatives. Chembiochem 2015; 16:2562-70. [PMID: 26420042 DOI: 10.1002/cbic.201500406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 12/25/2022]
Abstract
The fundamental roles of nucleoside triphosphates and nucleotide cofactors such as NAD(+) in biochemistry are well known. In recent decades, continuing research has revealed the key role of 5'-capped RNA and 5',5'-dinucleoside polyphosphates in the regulation of vitally important physiological processes. Last but not least, the commercial potential of nucleoside triphosphate synthesis can hardly be overestimated. Nevertheless, despite decades of investigation and the obvious topicality of the research on the chemical synthesis of the nucleotide compounds containing phosphate anhydride linkages, none of the existing procedures can be considered an up-to-date "gold standard". However, there are a number of fruitful synthetic approaches to forming phosphate anhydride linkages in satisfactory yield. These are summarized in this concise review, organized by the type of active phosphorous intermediate and reagents used.
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Affiliation(s)
- Yuliya V Sherstyuk
- Laboratory of Organic Synthesis, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Avenue, 8, Novosibirsk, 630090, Russia
| | - Tatyana V Abramova
- Laboratory of Organic Synthesis, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Avenue, 8, Novosibirsk, 630090, Russia.
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Hofer A, Cremosnik GS, Müller AC, Giambruno R, Trefzer C, Superti-Furga G, Bennett KL, Jessen HJ. A Modular Synthesis of Modified Phosphoanhydrides. Chemistry 2015; 21:10116-22. [PMID: 26033174 DOI: 10.1002/chem.201500838] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/11/2022]
Abstract
Phosphoanhydrides (P-anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate-modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P-anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, (18) O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.
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Affiliation(s)
- Alexandre Hofer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Gregor S Cremosnik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA (UK)
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Henning J Jessen
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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