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Huang Y, Kumar S, Lee J, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. Nat Struct Mol Biol 2024:10.1038/s41594-024-01316-4. [PMID: 38773335 DOI: 10.1038/s41594-024-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species.
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Affiliation(s)
- Yihe Huang
- Van Andel Institute, Grand Rapids, MI, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Junuk Lee
- Van Andel Institute, Grand Rapids, MI, USA
| | - Wei Lü
- Van Andel Institute, Grand Rapids, MI, USA.
| | - Juan Du
- Van Andel Institute, Grand Rapids, MI, USA.
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2
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Huang Y, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533055. [PMID: 36993210 PMCID: PMC10055075 DOI: 10.1101/2023.03.16.533055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The canonical ion channels gated by chemical ligands use the free energy of agonist binding to open the channel pore, returning to a closed state upon agonist departure. A unique class of ion channels, known as channel-enzymes (chanzymes), possess additional enzymatic activity that is directly or indirectly linked to their channel function. Here we investigated a TRPM2 chanzyme from choanoflagellates, an evolutionary ancestor of all metazoan TRPM channels, which integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP ribose (ADPR) with high open probability and an enzyme module (NUDT9-H domain) consuming ADPR at a remarkably slow rate. Using time-resolved cryo- electron microscopy (cryo-EM), we captured a complete series of structural snapshots of the gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. Our results showed that the slow kinetics of the NUDT9-H enzyme module confers a novel self-regulatory mechanism, whereby the enzyme module modulates channel gating in a binary manner. Binding of ADPR to NUDT9-H first triggers tetramerization of the enzyme modules, promoting channel opening, while the subsequent hydrolysis reaction reduces local ADPR availability, inducing channel closure. This coupling enables the ion-conducting pore to alternate rapidly between open and closed states, avoiding Mg 2+ and Ca 2+ overload. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADPR hydrolase module in early species TRPM2 to a fully integrated component of a gating ring essential for channel activation in advanced species TRPM2. Our study demonstrated an example of how organisms can adapt to their environments at the molecular level.
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Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010089. [PMID: 36615284 PMCID: PMC9822328 DOI: 10.3390/molecules28010089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Breast cancer, a heterogeneous disease, is among the most frequently diagnosed diseases and is the second leading cause of death due to cancer among women after lung cancer. Phytoactives (plant-based derivatives) and their derivatives are safer than synthetic compounds in combating chemoresistance. In the current work, a template-based design of the coumarin derivative was designed to target the ADP-sugar pyrophosphatase protein. The novel coumarin derivative (2R)-2-((S)-sec-butyl)-5-oxo-4-(2-oxochroman-4-yl)-2,5-dihydro-1H-pyrrol-3-olate was designed. Molecular docking studies provided a docking score of -6.574 kcal/mol and an MM-GBSA value of -29.15 kcal/mol. Molecular dynamics simulation studies were carried out for 500 ns, providing better insights into the interaction. An RMSD change of 2.4 Å proved that there was a stable interaction and that there was no conformational change induced to the receptor. Metadynamics studies were performed to calculate the unbinding energy of the principal compound with NUDT5, which was found to be -75.171 kcal/mol. In vitro validation via a cytotoxicity assay (MTT assay) of the principal compound was carried out with quercetin as a positive control in the MCF7 cell line and with an IC50 value of 55.57 (+/-) 0.7 μg/mL. This work promoted the research of novel natural derivatives to discover their anticancer activity.
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4
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Qi H, Grace Wright RH, Beato M, Price BD. The ADP-ribose hydrolase NUDT5 is important for DNA repair. Cell Rep 2022; 41:111866. [PMID: 36543120 DOI: 10.1016/j.celrep.2022.111866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage leads to rapid synthesis of poly(ADP-ribose) (pADPr), which is important for damage signaling and repair. pADPr chains are removed by poly(ADP-ribose) glycohydrolase (PARG), releasing free mono(ADP-ribose) (mADPr). Here, we show that the NUDIX hydrolase NUDT5, which can hydrolyze mADPr to ribose-5-phosphate and either AMP or ATP, is recruited to damage sites through interaction with PARG. NUDT5 does not regulate PARP or PARG activity. Instead, loss of NUDT5 reduces basal cellular ATP levels and exacerbates the decrease in cellular ATP that occurs during DNA repair. Further, loss of NUDT5 activity impairs RAD51 recruitment, attenuates the phosphorylation of key DNA-repair proteins, and reduces both H2A.Z exchange at damage sites and repair by homologous recombination. The ability of NUDT5 to hydrolyze mADPr, and/or regulate cellular ATP, may therefore be important for efficient DNA repair. Targeting NUDT5 to disrupt PAR/mADPr and energy metabolism may be an effective anti-cancer strategy.
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Affiliation(s)
- Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA
| | - Roni Helene Grace Wright
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Miguel Beato
- Centro de Regulación Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA.
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5
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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Janssens GE, Grevendonk L, Perez RZ, Schomakers BV, de Vogel-van den Bosch J, Geurts JMW, van Weeghel M, Schrauwen P, Houtkooper RH, Hoeks J. Healthy aging and muscle function are positively associated with NAD + abundance in humans. NATURE AGING 2022; 2:254-263. [PMID: 37118369 DOI: 10.1038/s43587-022-00174-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/12/2022] [Indexed: 04/30/2023]
Abstract
Skeletal muscle is greatly affected by aging, resulting in a loss of metabolic and physical function. However, the underlying molecular processes and how (lack of) physical activity is involved in age-related metabolic decline in muscle function in humans is largely unknown. Here, we compared, in a cross-sectional study, the muscle metabolome from young to older adults, whereby the older adults were exercise trained, had normal physical activity levels or were physically impaired. Nicotinamide adenine dinucleotide (NAD+) was one of the most prominent metabolites that was lower in older adults, in line with preclinical models. This lower level was even more pronounced in impaired older individuals, and conversely, exercise-trained older individuals had NAD+ levels that were more similar to those found in younger individuals. NAD+ abundance positively correlated with average number of steps per day and mitochondrial and muscle functioning. Our work suggests that a clear association exists between NAD+ and health status in human aging.
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Affiliation(s)
- Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Lotte Grevendonk
- Department of Nutrition and Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Ruben Zapata Perez
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Bauke V Schomakers
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | | | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Patrick Schrauwen
- Department of Nutrition and Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
| | - Joris Hoeks
- Department of Nutrition and Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands.
- TI Food and Nutrition, Wageningen, the Netherlands.
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7
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Zhong Z, Xu P, Wen J, Li X, Zhang X. Enriched Environment Regulates Dendritic Cells to Alleviate Inflammation in Cerebral Infarction Lesions. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:1574109. [PMID: 34976103 PMCID: PMC8719993 DOI: 10.1155/2021/1574109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The aim was to investigate the role that enriched environment (EE) plays in the regulation of inflammation in cerebral infarction (CI) lesions and further explore the relationship between this regulation and dendritic cells (DCs). METHODS 72 Sprague-Dawley rats were randomly divided into sham operation group (CON group, n = 24) and CI model group (n = 48). On completion of the establishment of CI rat models by Longa's method, rats in the models group were further assigned to standard environment group (NC group, n = 24) and EE group (n = 24). HE staining was utilized for evaluation of neuronal injury in the lesions. The number of CD74- and integrin αE-positive cells was detected by immunofluorescence. The expression of the IL-1β, IL-6, and TNF-α in the brain tissue and serum of rats was measured by immunohistochemistry and ELISA, respectively. RESULTS In comparison with the CON group, the NC and EE groups showed significant increases in neuronal injury, CD74- and Integrin αE-positive cells, DC content, as well as IL-1β, IL-6, and TNF-α expression in brain tissue and serum. According to the further comparison between the NC group and EE group, the latter showed decreases in each indicator, and these decreases were in a time-dependent manner. CONCLUSION EE avoids the accumulation of DCs in the lesions and reduces the contents of IL-1β, IL-6, and TNF-α, consequently promoting the recovery of CI. And better recovery results can be obtained through increasing the time to stay in EE.
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Affiliation(s)
- Zhenzhen Zhong
- Department of Neurology, The First People's Hospital of Changde City, Changde, Hunan, China 415000
| | - Ping Xu
- Department of Neurology, The First People's Hospital of Changde City, Changde, Hunan, China 415000
| | - Jun Wen
- Department of Neurology, The First People's Hospital of Changde City, Changde, Hunan, China 415000
| | - Xiangdong Li
- Department of Neurology, The First People's Hospital of Changde City, Changde, Hunan, China 415000
| | - Xiaobo Zhang
- Department of Neurology, The First People's Hospital of Changde City, Changde, Hunan, China 415000
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8
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Wright RHG, Beato M. Role of the NUDT Enzymes in Breast Cancer. Int J Mol Sci 2021; 22:2267. [PMID: 33668737 PMCID: PMC7956304 DOI: 10.3390/ijms22052267] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Despite global research efforts, breast cancer remains the leading cause of cancer death in women worldwide. The majority of these deaths are due to metastasis occurring years after the initial treatment of the primary tumor and occurs at a higher frequency in hormone receptor-positive (Estrogen and Progesterone; HR+) breast cancers. We have previously described the role of NUDT5 (Nudix-linked to moiety X-5) in HR+ breast cancer progression, specifically with regards to the growth of breast cancer stem cells (BCSCs). BCSCs are known to be the initiators of epithelial-to-mesenchyme transition (EMT), metastatic colonization, and growth. Therefore, a greater understanding of the proteins and signaling pathways involved in the metastatic process may open the door for therapeutic opportunities. In this review, we discuss the role of NUDT5 and other members of the NUDT family of enzymes in breast and other cancer types. We highlight the use of global omics data based on our recent phosphoproteomic analysis of progestin signaling pathways in breast cancer cells and how this experimental approach provides insight into novel crosstalk mechanisms for stratification and drug discovery projects aiming to treat patients with aggressive cancer.
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Affiliation(s)
- Roni H. G. Wright
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08003 Barcelona, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Life Science, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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9
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Sultana R, Islam M, Haque M, Evamoni FZ, Imran ZM, Khanom J, Munim M. Molecular docking based virtual screening of the breast cancer target NUDT5. Bioinformation 2019; 15:784-789. [PMID: 31902977 PMCID: PMC6936656 DOI: 10.6026/97320630015784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer affects one in eight women in Bangladesh and is the most common cancer among women in South Asia next to skin cancer. NUDT5 are nucleotide-metabolizing enzymes (NUDIX hydrolases) linked with the ADP ribose and 8-oxo-guanine metabolism. It is known to be associated with the hormone dependent gene regulation and proliferation in breast cancer cells. It blocks progestin-dependent, PAR-derived nuclear ATP synthesis and subsequent chromatin remodeling, gene regulation and proliferation in this context. We describe the structure based binding features of a lead compound (7-[[5-(3, 4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8piperazin-1yl-purine-2,6-dione-C20H20Cl2N8O3) with NUDT5 for further in vitro and in vivo validation. It is a promising inhibitor for blocking NUDT5 activity. Thus, structure based virtual screening is used to identify a potential therapeutic inhibitor for NUDT5.
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Affiliation(s)
- Razia Sultana
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
- Equal contribution
| | - Monjia Islam
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
- Equal contribution
| | - Md.Azizul Haque
- Department of Applied Chemistry and Chemical Engineering, Faculty
of Engineering and Technology, Noakhali Science and Technology University, Noakhali-3814
| | - Fatematuz Zuhura Evamoni
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
| | - Zahid Mohammad Imran
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
| | - Jabunnesa Khanom
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
| | - Md.Adnan Munim
- Department of Biotechnology and Genetic Engineering, Faculty of
Science, Noakhali Science and Technology University, Noakhali-3814
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PARP1 and Poly(ADP-ribosyl)ation Signaling during Autophagy in Response to Nutrient Deprivation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2641712. [PMID: 31281570 PMCID: PMC6590576 DOI: 10.1155/2019/2641712] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/28/2019] [Accepted: 05/07/2019] [Indexed: 12/28/2022]
Abstract
Autophagy is considered to be the primary degradative pathway that takes place in all eukaryotic cells. Morphologically, the autophagy pathway refers to a process by which cytoplasmic portions are delivered to double-membrane organelles, called autophagosomes, to fuse with lysosomes for bulk degradation. Autophagy, as a prosurvival mechanism, can be stimulated by different types of cellular stress such as nutrient deprivation, hypoxia, ROS, pH, DNA damage, or ER stress, promoting adaptation of the cell to the changing and hostile environment. The functional relevance of autophagy in many diseases such as cancer or neurodegenerative diseases remains controversial, preserving organelle function and detoxification and promoting cell growth, although in other contexts, autophagy could suppress cell expansion. Poly(ADP-ribosyl)ation (PARylation) is a covalent and reversible posttranslational modification (PTM) of proteins mediated by Poly(ADP-ribose) polymerases (PARPs) with well-described functions in DNA repair, replication, genome integrity, cell cycle, and metabolism. Herein, we review the current state of PARP1 activation and PARylation in starvation-induced autophagy.
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11
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Iordanov I, Tóth B, Szollosi A, Csanády L. Enzyme activity and selectivity filter stability of ancient TRPM2 channels were simultaneously lost in early vertebrates. eLife 2019; 8:44556. [PMID: 30938679 PMCID: PMC6461439 DOI: 10.7554/elife.44556] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
Transient Receptor Potential Melastatin 2 (TRPM2) is a cation channel important for the immune response, insulin secretion, and body temperature regulation. It is activated by cytosolic ADP ribose (ADPR) and contains a nudix-type motif 9 (NUDT9)-homology (NUDT9-H) domain homologous to ADPR phosphohydrolases (ADPRases). Human TRPM2 (hsTRPM2) is catalytically inactive due to mutations in the conserved Nudix box sequence. Here, we show that TRPM2 Nudix motifs are canonical in all invertebrates but vestigial in vertebrates. Correspondingly, TRPM2 of the cnidarian Nematostella vectensis (nvTRPM2) and the choanoflagellate Salpingoeca rosetta (srTRPM2) are active ADPRases. Disruption of ADPRase activity fails to affect nvTRPM2 channel currents, reporting a catalytic cycle uncoupled from gating. Furthermore, pore sequence substitutions responsible for inactivation of hsTRPM2 also appeared in vertebrates. Correspondingly, zebrafish (Danio rerio) TRPM2 (drTRPM2) and hsTRPM2 channels inactivate, but srTRPM2 and nvTRPM2 currents are stable. Thus, catalysis and pore stability were lost simultaneously in vertebrate TRPM2 channels.
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Affiliation(s)
- Iordan Iordanov
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - Balázs Tóth
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - Andras Szollosi
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
| | - László Csanády
- Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,MTA-SE Lendület Ion Channel Research Group, Semmelweis University, Budapest, Hungary
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12
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Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells. Nat Commun 2018; 9:250. [PMID: 29343827 PMCID: PMC5772648 DOI: 10.1038/s41467-017-02293-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/17/2017] [Indexed: 11/08/2022] Open
Abstract
With a diverse network of substrates, NUDIX hydrolases have emerged as a key family of nucleotide-metabolizing enzymes. NUDT5 (also called NUDIX5) has been implicated in ADP-ribose and 8-oxo-guanine metabolism and was recently identified as a rheostat of hormone-dependent gene regulation and proliferation in breast cancer cells. Here, we further elucidate the physiological relevance of known NUDT5 substrates and underscore the biological requirement for NUDT5 in gene regulation and proliferation of breast cancer cells. We confirm the involvement of NUDT5 in ADP-ribose metabolism and dissociate a relationship to oxidized nucleotide sanitation. Furthermore, we identify potent NUDT5 inhibitors, which are optimized to promote maximal NUDT5 cellular target engagement by CETSA. Lead compound, TH5427, blocks progestin-dependent, PAR-derived nuclear ATP synthesis and subsequent chromatin remodeling, gene regulation and proliferation in breast cancer cells. We herein present TH5427 as a promising, targeted inhibitor that can be used to further study NUDT5 activity and ADP-ribose metabolism.
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13
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Long A, Klimova N, Kristian T. Mitochondrial NUDIX hydrolases: A metabolic link between NAD catabolism, GTP and mitochondrial dynamics. Neurochem Int 2017; 109:193-201. [PMID: 28302504 DOI: 10.1016/j.neuint.2017.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/28/2017] [Accepted: 03/09/2017] [Indexed: 12/19/2022]
Abstract
NAD+ catabolism and mitochondrial dynamics are important parts of normal mitochondrial function and are both reported to be disrupted in aging, neurodegenerative diseases, and acute brain injury. While both processes have been extensively studied there has been little reported on how the mechanisms of these two processes are linked. This review focuses on how downstream NAD+ catabolism via NUDIX hydrolases affects mitochondrial dynamics under pathologic conditions. Additionally, several potential targets in mitochondrial dysfunction and fragmentation are discussed, including the roles of mitochondrial poly(ADP-ribose) polymerase 1(mtPARP1), AMPK, AMP, and intra-mitochondrial GTP metabolism. Mitochondrial and cytosolic NUDIX hydrolases (NUDT9α and NUDT9β) can affect mitochondrial and cellular AMP levels by hydrolyzing ADP- ribose (ADPr) and subsequently altering the levels of GTP and ATP. Poly (ADP-ribose) polymerase 1 (PARP1) is activated after DNA damage, which depletes NAD+ pools and results in the PARylation of nuclear and mitochondrial proteins. In the mitochondria, ADP-ribosyl hydrolase-3 (ARH3) hydrolyzes PAR to ADPr, while NUDT9α metabolizes ADPr to AMP. Elevated AMP levels have been reported to reduce mitochondrial ATP production by inhibiting the adenine nucleotide translocase (ANT), allosterically activating AMPK by altering the cellular AMP: ATP ratio, and by depleting mitochondrial GTP pools by being phosphorylated by adenylate kinase 3 (AK3), which uses GTP as a phosphate donor. Recently, activated AMPK was reported to phosphorylate mitochondria fission factor (MFF), which increases Drp1 localization to the mitochondria and promotes mitochondrial fission. Moreover, the increased AK3 activity could deplete mitochondrial GTP pools and possibly inhibit normal activity of GTP-dependent fusion enzymes, thus altering mitochondrial dynamics.
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Affiliation(s)
- Aaron Long
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States
| | - Nina Klimova
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States; Department of Anesthesiology and the Center for Shock, Trauma, and Anesthesiology Research (S.T.A.R.), United States; Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, United States
| | - Tibor Kristian
- Veterans Affairs Maryland Health Center System, 10 North Greene Street, Baltimore, MD 21201, United States; Department of Anesthesiology and the Center for Shock, Trauma, and Anesthesiology Research (S.T.A.R.), United States.
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14
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Wang Y, Wan F, Chang K, Lu X, Dai B, Ye D. NUDT expression is predictive of prognosis in patients with clear cell renal cell carcinoma. Oncol Lett 2017; 14:6121-6128. [PMID: 29113256 DOI: 10.3892/ol.2017.6997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/27/2017] [Indexed: 01/20/2023] Open
Abstract
The nudix hydroxylase (NUDT) family of genes may have notable roles in cancer growth and metastasis. The present study aimed to determine the prognostic ability of NUDT genes in clear cell renal cell carcinoma (ccRCC). Data from 509 patients with ccRCC was obtained from The Cancer Genome Atlas (TCGA) database and 192 patient samples from Fudan University Shanghai Cancer Center (FUSCC) were analyzed in the present study. The expression profile of NUDT gene family members in the TCGA cohort was obtained from the TCGA RNA sequencing database. Pathological characteristics, including age, sex, tumor size, tumor grade, stage, laterality and overall survival were collected. Cox proportional hazards regression model and Kaplan-Meier survival analysis were performed to assess the associations between pathological characteristics and expression levels of NUDT family genes. NUDT family genes that exhibited associations with overall survival (OS) were further validated in the FUSCC cohort. In the TCGA cohort, Cox proportional hazards analysis found that NUDT5 [hazards ratio (HR)=1.676; 95% confidence interval (CI), 1.097-2.559] and NUDT17 (HR=1.375; 95% CI, 1.092-1.732) were predictive of ccRCC prognosis. Further analysis revealed that low NUDT5 (P<0.0001) and NUDT17 (P<0.0001) expression were associated with poorer OS rates in the TCGA cohort. In the FUSCC cohort, low NUDT5 expression was also associated with poor OS rates (P=0.0116), and tumor grade was a factor that influenced the expression level of NUDT5 (P=0.016).
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Affiliation(s)
- Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Xiaolin Lu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
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15
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Wright RHG, Fernandez-Fuentes N, Oliva B, Beato M. Insight into the machinery that oils chromatin dynamics. Nucleus 2016; 7:532-539. [PMID: 27893319 DOI: 10.1080/19491034.2016.1255392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The packaging of genetic information in form of chromatin within the nucleus provides cells with the ability to store and protect massive amounts of information within a compact space. Storing information within chromatin allows selective access to specific DNA sequences by regulating the various levels of chromatin structure from nucleosomes, to chromatin fibers, loops and topological associating domains (TADs) using mechanisms that are being progressively unravelled. However, a relatively unexplored aspect is the energetic cost of changing the chromatin configuration to gain access to DNA information. Among the enzymes responsible for regulating chromatin access are the ATP-dependent chromatin remodellers that act on nucleosomes and use the energy of ATP hydrolysis to make chromatin DNA more accessible. It is assumed that the ATP used by these enzymes is provided by the mitochondria or by cytoplasmic glycolysis. We hypothesize that though this may be the case for cells in steady state, when gene expression has to be globally reprogramed in response to externals signals or stress conditions, the cell directs energy production to the cell nucleus, where rapid chromatin reorganization is needed for cell survival. We discovered that in response to hormones a nuclear ATP synthesis mechanism is activated that utilizing ADP-ribose and pyrophosphate as substrates. 1 This extra view aims to put this process within its historical context, to describe the enzymatic steps in detail, to propose a possible structure of the ATP synthesising enzyme, and to shed light on how this may link to other reactions within the cell providing a perspective for future lines of investigation.
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Affiliation(s)
- Roni H G Wright
- a Gene Regulation Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Barcelona , Spain.,b University Pompeu Fabra (UPF) , Barcelona , Spain
| | - Narcis Fernandez-Fuentes
- c Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University , Aberystwyth , United Kingdom
| | | | - Miguel Beato
- a Gene Regulation Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Barcelona , Spain.,b University Pompeu Fabra (UPF) , Barcelona , Spain
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16
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Furuike Y, Akita Y, Miyahara I, Kamiya N. ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors. Biochemistry 2016; 55:1801-12. [PMID: 26979298 DOI: 10.1021/acs.biochem.5b00886] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn(2+), Zn(2+), or Mg(2+) as cofactors. Here, we report the reaction pathway observed in the catalytic center of TtADPRase, based on cryo-trapping X-ray crystallography at atomic resolutions around 1.0 Å using Mn(2+) as the reaction trigger, which was soaked into TtADPRase-ADPR binary complex crystals. Integrating 11 structures along the reaction timeline, five reaction states of TtADPRase were assigned, which were ADPRase alone (E), the ADPRase-ADPR binary complex (ES), two ADPRase-ADPR-Mn(2+) reaction intermediates (ESM, ESMM), and the postreaction state (E'). Two Mn(2+) ions were inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states. The ADPR-hydrolysis reaction was characterized by electrostatic, proximity, and orientation effects, and by preferential binding for the transition state. A new reaction mechanism is proposed, which differs from previous ones suggested from structure analyses with nonhydrolyzable substrate analogues or point-mutated ADPRases.
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Affiliation(s)
- Yoshihiko Furuike
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Yuka Akita
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Ikuko Miyahara
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Nobuo Kamiya
- Graduate School of Science, Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
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17
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Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 2016; 34:184-191. [PMID: 26780180 PMCID: PMC4744125 DOI: 10.1038/nbt.3437] [Citation(s) in RCA: 2559] [Impact Index Per Article: 319.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/19/2015] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), one can reprogram Cas9 to target different sites in the genome with relative ease, but the on-target activity and off-target effects of individual sgRNAs can vary widely. Here, we use recently devised sgRNA design rules to create human and mouse genome-wide libraries, perform positive and negative selection screens and observe that the use of these rules produced improved results. Additionally, we profile the off-target activity of thousands of sgRNAs and develop a metric to predict off-target sites. We incorporate these findings from large-scale, empirical data to improve our computational design rules and create optimized sgRNA libraries that maximize on-target activity and minimize off-target effects to enable more effective and efficient genetic screens and genome engineering.
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Affiliation(s)
- John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicolo Fusi
- Microsoft Research New England, Cambridge, Massachusetts, USA
| | - Meagan Sullender
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Emma W Vaimberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Ian Smith
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zuzana Tothova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana Farber Cancer Institute, Division of Hematologic Malignancies, Boston, Massachusetts, USA
| | - Craig Wilen
- Washington University School of Medicine, Department of Pathology and Immunology, St. Louis, Missouri, USA
| | - Robert Orchard
- Washington University School of Medicine, Department of Pathology and Immunology, St. Louis, Missouri, USA
| | - Herbert W Virgin
- Washington University School of Medicine, Department of Pathology and Immunology, St. Louis, Missouri, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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18
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Rampazzo C, Tozzi MG, Dumontet C, Jordheim LP. The druggability of intracellular nucleotide-degrading enzymes. Cancer Chemother Pharmacol 2015; 77:883-93. [PMID: 26614508 DOI: 10.1007/s00280-015-2921-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 01/24/2023]
Abstract
Nucleotide metabolism is the target of a large number of anticancer drugs including antimetabolites and specific enzyme inhibitors. We review scientific findings that over the last 10-15 years have allowed the identification of several intracellular nucleotide-degrading enzymes as cancer drug targets, and discuss further potential therapeutic applications for Rcl, SAMHD1, MTH1 and cN-II. We believe that enzymes involved in nucleotide metabolism represent potent alternatives to conventional cancer chemotherapy targets.
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Affiliation(s)
- Chiara Rampazzo
- Department of Biology, University of Padova, 35131, Padua, Italy
| | - Maria Grazia Tozzi
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
| | - Charles Dumontet
- Université de Lyon, 69000, Lyon, France.,Université de Lyon 1, 69622, Lyon, France.,Université de Lyon 1, 69000, Lyon, France.,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,Centre Léon Bérard, 69008, Lyon, France.,Hospices Civils de Lyon, 69000, Lyon, France
| | - Lars Petter Jordheim
- Université de Lyon, 69000, Lyon, France. .,Université de Lyon 1, 69622, Lyon, France. .,Université de Lyon 1, 69000, Lyon, France. .,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,Centre Léon Bérard, 69008, Lyon, France. .,Equipe Anticorps-Anticancer, INSERM U1052 - CNRS UMR 5286, Faculté Rockefeller, Centre de Recherche en Cancérologie de Lyon, 8 avenue Rockefeller, 69008, Lyon, France.
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19
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Palazzo L, Thomas B, Jemth AS, Colby T, Leidecker O, Feijs K, Zaja R, Loseva O, Puigvert JC, Matic I, Helleday T, Ahel I. Processing of protein ADP-ribosylation by Nudix hydrolases. Biochem J 2015; 468:293-301. [PMID: 25789582 PMCID: PMC6057610 DOI: 10.1042/bj20141554] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
ADP-ribosylation is a post-translational modification (PTM) of proteins found in organisms from all kingdoms of life which regulates many important biological functions including DNA repair, chromatin structure, unfolded protein response and apoptosis. Several cellular enzymes, such as macrodomain containing proteins PARG [poly(ADP-ribose) glycohydrolase] and TARG1 [terminal ADP-ribose (ADPr) protein glycohydrolase], reverse protein ADP-ribosylation. In the present study, we show that human Nudix (nucleoside diphosphate-linked moiety X)-type motif 16 (hNUDT16) represents a new enzyme class that can process protein ADP-ribosylation in vitro, converting it into ribose-5'-phosphate (R5P) tags covalently attached to the modified proteins. Furthermore, our data show that hNUDT16 enzymatic activity can be used to trim ADP-ribosylation on proteins in order to facilitate analysis of ADP-ribosylation sites on proteins by MS.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
| | - Benjamin Thomas
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Street 9b, D-50931 Köln/Cologne, Germany
| | - Orsolya Leidecker
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Street 9b, D-50931 Köln/Cologne, Germany
| | - Karla Feijs
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
| | - Roko Zaja
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
| | - Olga Loseva
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Jordi Carreras Puigvert
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Street 9b, D-50931 Köln/Cologne, Germany
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, United Kingdom
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20
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Gruber M, Greisen P, Junker CM, Hélix-Nielsen C. Phosphorus Binding Sites in Proteins: Structural Preorganization and Coordination. J Phys Chem B 2014; 118:1207-15. [DOI: 10.1021/jp408689x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mathias Gruber
- The Biomimetic Membrane Group,
Department of Physics, Technical University of Denmark, DK 2800 Kongens Lyngby Denmark
| | - Per Greisen
- The Biomimetic Membrane Group,
Department of Physics, Technical University of Denmark, DK 2800 Kongens Lyngby Denmark
| | - Caroline M. Junker
- The Biomimetic Membrane Group,
Department of Physics, Technical University of Denmark, DK 2800 Kongens Lyngby Denmark
| | - Claus Hélix-Nielsen
- The Biomimetic Membrane Group,
Department of Physics, Technical University of Denmark, DK 2800 Kongens Lyngby Denmark
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21
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Moreau C, Kirchberger T, Swarbrick JM, Bartlett SJ, Fliegert R, Yorgan T, Bauche A, Harneit A, Guse AH, Potter BVL. Structure-activity relationship of adenosine 5'-diphosphoribose at the transient receptor potential melastatin 2 (TRPM2) channel: rational design of antagonists. J Med Chem 2013; 56:10079-102. [PMID: 24304219 PMCID: PMC3873810 DOI: 10.1021/jm401497a] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Adenosine
5′-diphosphoribose (ADPR) activates TRPM2, a Ca2+, Na+, and K+ permeable cation channel.
Activation is induced by ADPR binding to the cytosolic C-terminal
NudT9-homology domain. To generate the first structure–activity
relationship, systematically modified ADPR analogues were designed,
synthesized, and evaluated as antagonists using patch-clamp experiments
in HEK293 cells overexpressing human TRPM2. Compounds with a purine C8 substituent show antagonist activity, and an 8-phenyl
substitution (8-Ph-ADPR, 5) is very effective. Modification
of the terminal ribose results in a weak antagonist, whereas its removal
abolishes activity. An antagonist based upon a hybrid structure, 8-phenyl-2′-deoxy-ADPR
(86, IC50 = 3 μM), is more potent than
8-Ph-ADPR (5). Initial bioisosteric replacement of the
pyrophosphate linkage abolishes activity, but replacement of the pyrophosphate
and the terminal ribose by a sulfamate-based group leads to a weak
antagonist, a lead to more drug-like analogues. 8-Ph-ADPR (5) inhibits Ca2+ signalling and chemotaxis in human neutrophils,
illustrating the potential for pharmacological intervention at TRPM2.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath , Claverton Down, Bath BA2 7AY, United Kingdom
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22
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Posavec M, Timinszky G, Buschbeck M. Macro domains as metabolite sensors on chromatin. Cell Mol Life Sci 2013; 70:1509-24. [PMID: 23455074 PMCID: PMC11113152 DOI: 10.1007/s00018-013-1294-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/30/2022]
Abstract
How metabolism and epigenetics are molecularly linked and regulate each other is poorly understood. In this review, we will discuss the role of direct metabolite-binding to chromatin components and modifiers as a possible regulatory mechanism. We will focus on globular macro domains, which are evolutionarily highly conserved protein folds that can recognize NAD(+)-derived metabolites. Macro domains are found in histone variants, histone modifiers, and a chromatin remodeler among other proteins. Here we summarize the macro domain-containing chromatin proteins and the enzymes that generate relevant metabolites. Focusing on the histone variant macroH2A, we further discuss possible implications of metabolite binding for chromatin function.
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Affiliation(s)
- Melanija Posavec
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
| | - Gyula Timinszky
- Butenandt Institute of Physiological Chemistry, Ludwig Maximilian University of Munich, Butenandtstrasse 5, 81377 Munich, Germany
| | - Marcus Buschbeck
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
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23
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Takagi Y, Setoyama D, Ito R, Kamiya H, Yamagata Y, Sekiguchi M. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J Biol Chem 2012; 287:21541-9. [PMID: 22556419 PMCID: PMC3375575 DOI: 10.1074/jbc.m112.363010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/25/2012] [Indexed: 01/25/2023] Open
Abstract
Most of the proteins carrying the 23-residue MutT-related sequence are capable of hydrolyzing compounds with a general structure of nucleoside diphosphate linked to another moiety X and are called the Nudix hydrolases. Among the 22 human Nudix proteins (identified by the sequence signature), some remain uncharacterized as enzymes without a defined substrate. Here, we reveal that the NUDT18 protein, whose substrate was unknown, can degrade 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing nucleoside diphosphates to the monophosphates. Because this enzyme is closely related to MTH1 (NUDT1) and MTH2 (NUDT15), we propose that it should be named MTH3. Although these three human proteins resemble each other in their sequences, their substrate specificities differ considerably. MTH1 cleaves 8-oxo-dGTP but not 8-oxo-dGDP, whereas MTH2 can degrade both 8-oxo-dGTP and 8-oxo-dGDP, although the intrinsic enzyme activity of MTH2 is considerably lower than that of MTH1. On the other hand, MTH3 is specifically active against 8-oxo-dGDP and hardly cleaves 8-oxo-dGTP. Other types of oxidized nucleoside diphosphates, 2-hydroxy-dADP and 8-hydroxy-dADP, were also hydrolyzed by MTH3. Another notable feature of the MTH3 enzyme is its action toward the ribonucleotide counterpart. MTH3 can degrade 8-oxo-GDP as efficiently as 8-oxo-dGDP, which is in contrast to the finding that MTH1 and MTH2 show a limited activity against the ribonucleotide counterpart, 8-oxo-GTP. These three enzymes may function together to help maintain the high fidelity of DNA replication and transcription under oxidative stress.
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Affiliation(s)
| | | | - Riyoko Ito
- From the Fukuoka Dental College, Fukuoka 814-0193
| | - Hiroyuki Kamiya
- the Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, and
| | - Yuriko Yamagata
- the Graduate School of Pharmaceutical Science, Kumamoto University, Kumamoto 862-0973, Japan
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24
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Boto AN, Xu W, Jakoncic J, Pannuri A, Romeo T, Bessman MJ, Gabelli SB, Amzel LM. Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition. Proteins 2011; 79:2455-66. [PMID: 21638333 PMCID: PMC3164844 DOI: 10.1002/prot.23069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/05/2011] [Accepted: 04/19/2011] [Indexed: 01/02/2023]
Abstract
The Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX(5)EX(7)REUXEEXGU (where U is I, L, or V), is a well-studied family in which relations have been established between primary sequence and substrate specificity for many members. For example, enzymes that hydrolyze the diphosphate linkage of ADP-ribose are characterized by having a proline 15 amino acids C-terminal of the Nudix signature sequence. GDPMK is a Nudix enzyme that conserves this characteristic proline but uses GDP-mannose as the preferred substrate. By investigating the structure of the GDPMK alone, bound to magnesium, and bound to substrate, the structural basis for this divergent substrate specificity and a new rule was identified by which ADP-ribose pyrophosphatases can be distinguished from purine-DP-mannose pyrophosphatases from primary sequence alone. Kinetic and mutagenesis studies showed that GDPMK hydrolysis does not rely on a single glutamate as the catalytic base. Instead, catalysis is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. GDPMK was thought to play a role in biofilm formation because of its upregulation in response to RcsC signaling; however, GDPMK knockout strains show no defect in their capacity of forming biofilms.
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Affiliation(s)
- Agedi N. Boto
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Wenlian Xu
- Department of Biology. School of Arts and Sciences. Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jean Jakoncic
- Brookhaven National Laboratory, National Synchrotron Light Source, Building 725, Upton, NY 11973, USA
| | - Archana Pannuri
- Department of Microbiology and Cell Science. University of Florida. Gainesville, FL 32611-0700, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science. University of Florida. Gainesville, FL 32611-0700, USA
| | - Maurice J. Bessman
- Department of Biology. School of Arts and Sciences. Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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25
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Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y. Diverse substrate recognition and hydrolysis mechanisms of human NUDT5. Nucleic Acids Res 2011; 39:8972-83. [PMID: 21768126 PMCID: PMC3203587 DOI: 10.1093/nar/gkr575] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Human NUDT5 (hNUDT5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dGDP, 8-oxo-dADP and ADP-ribose (ADPR). However, the structural basis of the broad substrate specificity remains unknown. Here, we report the crystal structures of hNUDT5 complexed with 8-oxo-dGDP and 8-oxo-dADP. These structures reveal an unusually different substrate-binding mode. In particular, the positions of two phosphates (α and β phosphates) of substrate in the 8-oxo-dGDP and 8-oxo-dADP complexes are completely inverted compared with those in the previously reported hNUDT5–ADPR complex structure. This result suggests that the nucleophilic substitution sites of the substrates involved in hydrolysis reactions differ despite the similarities in the chemical structures of the substrates and products. To clarify this hypothesis, we employed the isotope-labeling method and revealed that 8-oxo-dGDP is attacked by nucleophilic water at Pβ, whereas ADPR is attacked at Pα. This observation reveals that the broad substrate specificity of hNUDT5 is achieved by a diversity of not only substrate recognition, but also hydrolysis mechanisms and leads to a novel aspect that enzymes do not always catalyze the reaction of substrates with similar chemical structures by using the chemically equivalent reaction site.
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Affiliation(s)
- Takao Arimori
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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Nakayama S, Kajiya H, Okabe K, Ikebe T. Effects of oxidative stress on the expression of 8-oxoguanine and its eliminating enzymes in human keratinocytes and squamous carcinoma cells. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1348-8643(11)00004-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Ito R, Sekiguchi M, Setoyama D, Nakatsu Y, Yamagata Y, Hayakawa H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J Biochem 2011; 149:731-8. [PMID: 21389046 DOI: 10.1093/jb/mvr028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MutT-related proteins, including Escherichia coli MutT and the human MTH1 (NUDT1), degrade 8-oxo-7, 8-dihydrodeoxyguanosine triphosphate (8-oxo-dGTP) to 8-oxo-dGMP and thereby prevent mutations caused by the misincorporation of 8-oxoguanine into DNA. The human NUDT5, which has an intrinsic activity to cleave ADP sugars to AMP and sugar phosphate, possesses the ability to degrade 8-oxo-dGDP to the monophosphate. Since 8-oxo-dGDP and 8-oxo-dGTP are interconvertible by cellular enzymes, NUDT5 has the potential to prevent errors during DNA replication. The two activities associated with NUDT5 exhibit different pH dependencies; the optimum for the cleavage of ADP ribose is pH 7-9, while that for 8-oxo-dGDPase is around pH 10. The kinetic parameters for the two types of reactions indicated that ADP ribose is a better substrate for NUDT5 compared with oxidized guanine nucleotides. The 8-oxo-dGDP cleavage was competitively inhibited by ADP ribose and its reaction product, AMP, and in reverse, the cleavage of ADP ribose was inhibited by 8-oxo-dGDP. These results imply that the two types of substrates may share the same binding site for catalysis.
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Affiliation(s)
- Riyoko Ito
- Department of Functional Bioscience and Advanced Science Research Center, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka, Japan.
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28
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Nakamura T, Meshitsuka S, Kitagawa S, Abe N, Yamada J, Ishino T, Nakano H, Tsuzuki T, Doi T, Kobayashi Y, Fujii S, Sekiguchi M, Yamagata Y. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. J Biol Chem 2010; 285:444-52. [PMID: 19864691 PMCID: PMC2804192 DOI: 10.1074/jbc.m109.066373] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/14/2009] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in DNA. Of the several enzymes that recognize 8-oxoguanine, MutT exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. The crystal structures of MutT in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dGMP and 8-oxo-dGMP plus Mn(2+), respectively, were determined. MutT strictly recognizes the overall conformation of 8-oxo-dGMP through a number of hydrogen bonds. This recognition mode revealed that 8-oxoguanine nucleotides are discriminated from guanine nucleotides by not only the hydrogen bond between the N7-H and Odelta (N119) atoms but also by the syn glycosidic conformation that 8-oxoguanine nucleotides prefer. Nevertheless, these discrimination factors cannot by themselves explain the roughly 34,000-fold difference between the affinity of MutT for 8-oxo-dGMP and dGMP. When the binary complex of MutT with 8-oxo-dGMP is compared with the ligand-free form, ordering and considerable movement of the flexible loops surrounding 8-oxo-dGMP in the binary complex are observed. These results indicate that MutT specifically recognizes 8-oxoguanine nucleotides by the ligand-induced conformational change.
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Affiliation(s)
- Teruya Nakamura
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Sachiko Meshitsuka
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Seiju Kitagawa
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Nanase Abe
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Junichi Yamada
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Tetsuya Ishino
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Hiroaki Nakano
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Teruhisa Tsuzuki
- the Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582
| | - Takefumi Doi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Yuji Kobayashi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Satoshi Fujii
- the School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, and
| | | | - Yuriko Yamagata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
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Przybylski JL, Wetmore SD. Designing an Appropriate Computational Model for DNA Nucleoside Hydrolysis: A Case Study of 2′-Deoxyuridine. J Phys Chem B 2009; 113:6533-42. [DOI: 10.1021/jp810472q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Przybylski
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge Alberta T1K 3M4 Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge Alberta T1K 3M4 Canada
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