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Hervé du Penhoat MA, Souchaud A, Rajpal A, Vuilleumier R, Gaigeot MP, Tavernelli I, Fujii K, Yokoya A, Díaz-Tendero S, Politis MF. Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment. Phys Chem Chem Phys 2024; 26:15693-15704. [PMID: 38766756 DOI: 10.1039/d4cp00489b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.
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Affiliation(s)
| | | | - Aashini Rajpal
- IMPMC, Sorbonne Université, UMR CNRS 7590, MNHN, Paris, France.
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | | | - Kentaro Fujii
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marie-Françoise Politis
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
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Jacinto MP, Greenberg MM. Histone Deacetylase 1 Inhibition by Peptides Containing a DNA Damage-Induced, Nonenzymatic, Histone Covalent Modification. Biochemistry 2023; 62:1388-1393. [PMID: 36972223 PMCID: PMC10124317 DOI: 10.1021/acs.biochem.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Treatment of HeLa cells with the DNA damaging agent, bleomycin (BLM), results in the formation of a nonenzymatic 5-methylene-2-pyrrolone histone covalent modification on lysine residues (KMP). KMP is much more electrophilic than other N-acyllysine covalent modifications and post-translational modifications, including N-acetyllysine (KAc). Using histone peptides containing KMP, we show that this modification inhibits the class I histone deacetylase, HDAC1, by reacting with a conserved cysteine (C261) located near the active site. HDAC1 is inhibited by histone peptides whose corresponding N-acetylated sequences are known deacetylation substrates, but not one containing a scrambled sequence. The HDAC1 inhibitor, trichostatin A, competes with covalent modification by the KMP-containing peptides. HDAC1 is also covalently modified by a KMP-containing peptide in a complex milieu. These data indicate that peptides containing KMP are recognized by HDAC1 and are bound in the active site. The effects on HDAC1 indicate that KMP formation in cells may contribute to the biological effects of DNA damaging agents, such as BLM, that form this nonenzymatic covalent modification.
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Affiliation(s)
- Marco Paolo Jacinto
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Jacinto MP, Heidenreich D, Müller S, Greenberg MM. Covalent Modification of Bromodomain Proteins by Peptides Containing a DNA Damage-Induced, Histone Post-Translational Modification. Chembiochem 2022; 23:e202200373. [PMID: 36173930 PMCID: PMC9675715 DOI: 10.1002/cbic.202200373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/28/2022] [Indexed: 02/03/2023]
Abstract
An electrophilic 5-methylene-2-pyrrolone modification (KMP ) is produced at lysine residues of histone proteins in nucleosome core particles upon reaction with a commonly formed DNA lesion (C4-AP). The nonenzymatic KMP modification is also generated in the histones of HeLa cells treated with the antitumor agent, bleomycin that oxidizes DNA and forms C4-AP. This nonenzymatic covalent histone modification has the same charge as the N-acetyllysine (KAc ) modification but is more electrophilic. In this study we show that KMP -containing histone peptides are recognized by, and covalently modify bromodomain proteins that are KAc readers. Distinct selectivity preferences for covalent bromodomain modification are observed following incubation with KMP -containing peptides of different sequence. MS/MS analysis of 3 covalently modified bromodomain proteins confirmed that Cys adduction was selective. The modified Cys was not always proximal to the KAc binding site, indicating that KMP -containing peptide interaction with bromodomain protein is distinct from the former. Analysis of protein adduction yields as a function of bromodomain pH at which the protein charge is zero (pI) or cysteine solvent accessible surface area are also consistent with non-promiscuous interaction between the proteins and electrophilic peptides. These data suggest that intracellular formation of KMP could affect cellular function and viability by modifying proteins that regulate genetic expression.
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Affiliation(s)
- Marco Paolo Jacinto
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Marc M Greenberg
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
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Liu Q, Li W, Qin S. Therapeutic effect of phycocyanin on acute liver oxidative damage caused by X-ray. Biomed Pharmacother 2020; 130:110553. [PMID: 32739742 DOI: 10.1016/j.biopha.2020.110553] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 12/18/2022] Open
Abstract
1) BACKGROUND: Phycocyanin (PC) is a type of natural protein in algae with antioxidant and anti-inflammatory properties. However, the protective effect of PC on hepatic damage induced by X-ray remains unknown. 2) METHODS: Male C57BL/6 mice were gavaged with 200mg/kg PC for consecutive 7 days before or after radiation. The blood samples and tissues were collected on days 1 and 7 after radiation exposure. 3) RESULTS: Pretreatment or treatment with PC decreased significantly the levels of alanine aminotransferase (ALT), aspartate aminotransferase(AST) in the plasma. Histological evaluation further confirmed the protection of PC against radiation-induced hepatotoxicity. PC-treatment also increased the relative mRNA expression of superoxide dismutase (SOD) and glutathione (GSH-PX), and descended the ROS in the liver. Moreover, the expression of H2AX, an indicator of DNA damage in mice, of the PC-intervention group was much smaller than that of the radiation group. In vivo, PC-treatment markedly up-regulated NF-E2-related factor 2(Nrf2) expression and downstream gene such as hemeoxygenase-1 (HO-1), NQO1. 4) Conclusion: PC could attenuate the radiation-induced oxidative stress damage by activating Nrf2/ HO-1 signaling pathway, and reduce the radiation-induced DNA damage. Therefore, PC is a protective agent against radiation-induced liver damage.
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Affiliation(s)
- Qi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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Stirling ER, Cook KL, Roberts DD, Soto-Pantoja DR. Metabolomic Analysis Reveals Unique Biochemical Signatures Associated with Protection from Radiation Induced Lung Injury by Lack of cd47 Receptor Gene Expression. Metabolites 2019; 9:E218. [PMID: 31597291 PMCID: PMC6835245 DOI: 10.3390/metabo9100218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 01/10/2023] Open
Abstract
The goal of this study was to interrogate biochemical profiles manifested in mouse lung tissue originating from wild type (WT) and cd47 null mice with the aim of revealing the in vivo role of CD47 in the metabolic response to ionizing radiation, especially changes related to the known association of CD47 deficiency with increased tissue viability and survival. For this objective, we performed global metabolomic analysis in mouse lung tissue collected from (C57Bl/6 background) WT and cd47 null mice with and without exposure to 7.6 Gy whole body radiation. Principal component analysis and hierarchical clustering revealed a consistent separation between genotypes following radiation exposure. Random forest analysis also revealed a unique biochemical signature in WT and cd47 null mice following treatment. Our data show that cd47 null irradiated lung tissue activates a unique set of metabolic pathways that facilitate the handling of reactive oxygen species, lipid metabolism, nucleotide metabolism and nutrient metabolites which may be regulated by microbial processing. Given that cd47 has pleiotropic effects on responses to ionizing radiation, we not only propose this receptor as a therapeutic target but postulate that the biomarkers regulated in this study associated with radioprotection are potential mitigators of radiation-associated pathologies, including the onset of pulmonary disease.
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Affiliation(s)
- Elizabeth R Stirling
- Department of Cancer Biology, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
| | - Katherine L Cook
- Department of Cancer Biology, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Department of Surgery, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
| | - David D Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - David R Soto-Pantoja
- Department of Cancer Biology, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Department of Surgery, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
- Department of Radiation Oncology, Wake Forest School of Medicine Comprehensive Cancer Center, Winston-Salem, NC 27101, USA.
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Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 771:99-127. [PMID: 28342455 DOI: 10.1016/j.mrrev.2017.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 02/07/2023]
Abstract
Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.
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Aparici-Espert I, Francés-Monerris A, Rodríguez-Muñiz GM, Roca-Sanjuán D, Lhiaubet-Vallet V, Miranda MA. A Combined Experimental and Theoretical Approach to the Photogeneration of 5,6-Dihydropyrimidin-5-yl Radicals in Nonaqueous Media. J Org Chem 2016; 81:4031-8. [DOI: 10.1021/acs.joc.6b00314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Isabel Aparici-Espert
- Instituto
Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos s/n, 46022 València, Spain
| | | | - Gemma M. Rodríguez-Muñiz
- Instituto
Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos s/n, 46022 València, Spain
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
| | - Virginie Lhiaubet-Vallet
- Instituto
Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos s/n, 46022 València, Spain
| | - Miguel A. Miranda
- Instituto
Universitario Mixto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Avda de los Naranjos s/n, 46022 València, Spain
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Dizdaroglu M, Coskun E, Jaruga P. Measurement of oxidatively induced DNA damage and its repair, by mass spectrometric techniques. Free Radic Res 2015; 49:525-48. [PMID: 25812590 DOI: 10.3109/10715762.2015.1014814] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidatively induced damage caused by free radicals and other DNA-damaging agents generate a plethora of products in the DNA of living organisms. There is mounting evidence for the involvement of this type of damage in the etiology of numerous diseases including carcinogenesis. For a thorough understanding of the mechanisms, cellular repair, and biological consequences of DNA damage, accurate measurement of resulting products must be achieved. There are various analytical techniques, with their own advantages and drawbacks, which can be used for this purpose. Mass spectrometric techniques with isotope dilution, which include gas chromatography (GC) and liquid chromatography (LC), provide structural elucidation of products and ascertain accurate quantification, which are absolutely necessary for reliable measurement. Both gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS), in single or tandem versions, have been used for the measurement of numerous DNA products such as sugar and base lesions, 8,5'-cyclopurine-2'-deoxynucleosides, base-base tandem lesions, and DNA-protein crosslinks, in vitro and in vivo. This article reviews these techniques and their applications in the measurement of oxidatively induced DNA damage and its repair.
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Affiliation(s)
- M Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, MD , USA
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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