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Park JH, Kim JK, Song BS. Comparison of gamma irradiation and heating treatment on cytotoxicity, insulinotropic activity, and molecular structure change of mistletoe viscothionin. Food Sci Biotechnol 2020; 29:1531-1539. [PMID: 33088602 DOI: 10.1007/s10068-020-00804-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 11/25/2022] Open
Abstract
Mistletoe offers health-promoting effects; however, it has toxicity, requiring careful application. Viscothionin is a polypeptide of mistletoe that while contributing to toxicity also demonstrates anti-cancer and anti-diabetic activities. The aim of this study was to evaluate whether gamma irradiation or heating treatment could selectively reduce viscothionin-mediated cytotoxicity. Gamma irradiation effectively inhibited viscothionin-induced cytotoxicity to RIN5mF cells, but heating treatment did not affect its cytotoxicity. Both heating and gamma irradiation further increased the insulinotropic activity of viscothionin, whereas the effect of gamma irradiation was dose-dependent and diminished above 20 kGy. Structural analysis showed that gamma irradiation significantly altered the ordered structure of viscothionin, unlike heating treatment, resulting in a change of its molecular properties, which could be linked to the observed changes in the cytotoxicity and insulinotropic activity of the polypeptide. These results suggest gamma irradiation as an alternative method for minimizing viscothionin toxicity without interfering with anti-diabetic effect.
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Affiliation(s)
- Jong-Heum Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Beom-Seok Song
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk-do 56212 Republic of Korea
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Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies. J Mol Model 2016; 22:146. [PMID: 27259531 PMCID: PMC4893064 DOI: 10.1007/s00894-016-3020-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023]
Abstract
Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.
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Li M, Diao L, Liao X, Kou L, Lu W. DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Minjie Li
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Ling Diao
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xiaofei Liao
- School of Information Science and Technology; Donghua University; Shanghai 201620 China
| | - Li Kou
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Wencong Lu
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
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Ostakhov SS, Sultanbaev MV, Khursan SL, Shishlov NM, Lebedev YA, Kinzyabulatov RR. Photophysics and photochemistry of crystalline 5-fluorouracil. HIGH ENERGY CHEMISTRY 2014. [DOI: 10.1134/s0018143914050117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tachikawa H, Fukuzumi T. Ionization dynamics of aminopyridine dimer: a direct ab initio molecular dynamics (MD) study. Phys Chem Chem Phys 2011; 13:5881-7. [DOI: 10.1039/c0cp01542c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Cheng Q, Gu J, Compaan KR, Schaefer HF. Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes. Chemistry 2010; 16:11848-58. [DOI: 10.1002/chem.201001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Jiande Gu
- Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203 (P. R. China)
| | - Katherine R. Compaan
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
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Pauwels E, De Cooman H, Waroquier M, Hole EO, Sagstuen E. On the identity of the radiation-induced stable alanine radical. Phys Chem Chem Phys 2010; 12:8733-6. [DOI: 10.1039/c004380j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pauwels E, De Cooman H, Vanhaelewyn G, Sagstuen E, Callens F, Waroquier M. Radiation-induced radicals in glucose-1-phosphate. II. DFT analysis of structures and possible formation mechanisms. J Phys Chem B 2009; 112:15054-63. [PMID: 18973365 DOI: 10.1021/jp804287c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1-R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.
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Affiliation(s)
- Ewald Pauwels
- Center for Molecular Modeling, Ghent University, Gent, Belgium.
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Bose A, Basu S. Laser Flash Photolysis and Magnetic Field Effect Studies on the Interaction of Uracil and Its Derivatives with Menadione and 9,10-Anthraquinone. J Phys Chem A 2008; 112:12045-53. [DOI: 10.1021/jp805632j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adity Bose
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata−700 064, India
| | - Samita Basu
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata−700 064, India
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Pauwels E, Declerck R, Speybroeck VV, Waroquier M. Evidence for a Grotthuss-Like Mechanism in the Formation of the Rhamnose Alkoxy Radical Based on Periodic DFT Calculations. Radiat Res 2008; 169:8-18. [DOI: 10.1667/rr1039.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 09/04/2007] [Indexed: 11/03/2022]
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Wang W, Jin L, Wang W, Lu J, Yang J. Theoretical study on the multi-channel reaction of OH radical with 5-methylcytosine. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim S, Meehan T, Schaefer HF. Hydrogen-Atom Abstraction from the Adenine−Uracil Base Pair†. J Phys Chem A 2007; 111:6806-12. [PMID: 17388361 DOI: 10.1021/jp070225x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.
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Affiliation(s)
- Sunghwan Kim
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
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von Sonntag C. Free-Radical-Induced DNA Damage as Approached by Quantum-Mechanical and Monte Carlo Calculations: An Overview from the Standpoint of an Experimentalist. ADVANCES IN QUANTUM CHEMISTRY 2007. [DOI: 10.1016/s0065-3276(06)52002-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Tureček F. Computational Studies of Radicals Relevant to Nucleic Acid Damage. ADVANCES IN QUANTUM CHEMISTRY 2007. [DOI: 10.1016/s0065-3276(06)52005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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Purkayastha S, Milligan JR, Bernhard WA. The role of hydration in the distribution of free radical trapping in directly ionized DNA. Radiat Res 2006; 166:1-8. [PMID: 16808596 PMCID: PMC1847792 DOI: 10.1667/rr3585.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The purpose of this study was to elucidate the role of hydration (Gamma) in the distribution of free radical trapping in directly ionized DNA. Solid-state films of pUC18 (2686 bp) plasmids were hydrated to Gamma in the range 2.5 < or = Gamma < or = 22.5 mol water/mol nucleotide. Free radical yields, G(Sigmafr), measured by EPR at 4 K are seen to increase from 0.28 +/- 0.01 micromol/J at Gamma = 2.5 to 0.63 +/- 0.01 micromol/J at Gamma= 22.5, respectively. Based on a semi-empirical model of the free radical trapping events that follow the initial ionizations of the DNA components, we conclude that two-thirds of the holes formed on the inner solvation shell (Gamma < 10) transfer to the sugar-phosphate backbone. Likewise, of the holes produced by direct ionization of the sugar-phosphate, about one-third are trapped by deprotonation as neutral sugar-phosphate radical species, while the remaining two-thirds are found to transfer to the bases. This analysis provides the best measure to date for the probability of hole transfer (approximately 67%) into the base stack. It can thus be predicted that the distribution of holes formed in fully hydrated DNA at 4 K will be 78% on the bases and 22% on the sugar-phosphate. Adding the radicals due to electron attachment (confined to the pyrimidine bases), the distribution of all trapped radicals will be 89% on the bases and 11% on the sugar-phosphate backbone. This prediction is supported by partitioning results obtained from the high dose-response curves fitted to the two-component model. These results not only add to our understanding of how the holes redistribute after ionization but are also central to predicting the yield and location of strand breaks in DNA exposed to the direct effects of ionizing radiation.
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Affiliation(s)
- Shubhadeep Purkayastha
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, 14642
| | - Jamie R. Milligan
- Department of Radiology, University of California at San Diego, La Jolla, California 92093-0610
| | - William A. Bernhard
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, 14642
- Address for correspondence: Department of Biochemistry & Biophysics, 575 Elmwood Ave., Rochester, NY 14642; e-mail:
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Zhang JD, Xie Y, Schaefer HF, Luo Q, Li QS. Addition of hydrogen atom/hydride anion to the double bonds of cytosine tautomers: radical and anion structures and energetics. Mol Phys 2006. [DOI: 10.1080/00268970600653209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sagstuen E, Close DM, Vågane R, Hole EO, Nelson WH. Electron Transfer in Amino Acid·Nucleic Acid Base Complexes: EPR, ENDOR, and DFT Study of X-Irradiated N-Formylglycine·Cytosine Complex Crystals. J Phys Chem A 2006; 110:8653-62. [PMID: 16836426 DOI: 10.1021/jp0610822] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single crystals of the 1:1 complex of the nucleic acid base cytosine and the dipeptide N-formylglycine (C.NFG) have been irradiated at 10 and 273 K to doses of about 70 kGy and studied at temperatures between 10 and 293 K using 24 GHz (K-band) and 9.5 GHz (X-band) electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) spectroscopy. In this complex, the cytosine base is hydrogen bonded at positions N3 and N4 to the carboxylic group of the dipeptide, and the N3 position of cytosine has become protonated by the carboxylic group. At 10 K, two major radicals were characterized and identified. One of these (R1) is ascribed to the decarboxylated N-formylglycine one-electron oxidized species. The other (R2) is the N3-protonated cytosine one-electron reduced species. A third minority species (R3) appears to be a different conformation or protonation state of the one-electron reduced cytosine radical. Upon warming, the R2 and R3 radicals decay at about 100 K, and at 295 K, the only cytosine-centered radicals present are the C5 and C6 H-addition radicals (R5, R6). The R1 radical decays at about 150 K, and a glycine backbone radical (R4) grows in slowly. Thus, in the complex, a complete separation of initial oxidation and reduction events occurs, with oxidation localized at the dipeptide moiety, whereas reduction occurs at the nucleic acid base moiety. DFT calculations indicate that this separation is driven by large differences in electron affinities and ionization potentials between the two constituents of the complex. Once the initial oxidation and reduction products are trapped, no further electron transfer between the two constituents of the complex takes place.
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Affiliation(s)
- Einar Sagstuen
- Department of Physics, University of Oslo, P.O. Box 1048 Blindern, N-0316 Oslo, Norway.
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Wu Y, Mundy CJ, Colvin ME, Car R. On the Mechanisms of OH Radical Induced DNA-Base Damage: A Comparative Quantum Chemical and Car−Parrinello Molecular Dynamics Study†. J Phys Chem A 2004. [DOI: 10.1021/jp0363592] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tureček F, Yao C. Hydrogen Atom Addition to Cytosine, 1-Methylcytosine, and Cytosine−Water Complexes. A Computational Study of a Mechanistic Dichotomy. J Phys Chem A 2003. [DOI: 10.1021/jp030698d] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Chunxiang Yao
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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Mundy CJ, Colvin ME, Quong AA. Irradiated Guanine: A Car-Parrinello Molecular Dynamics Study of Dehydrogenation in the Presence of an OH Radical. J Phys Chem A 2002. [DOI: 10.1021/jp0212904] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Mundy
- Chemistry and Materials Science, Lawrence Livermore National Laboratory, Livermore, California 94550, and Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Michael E. Colvin
- Chemistry and Materials Science, Lawrence Livermore National Laboratory, Livermore, California 94550, and Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Andrew A. Quong
- Chemistry and Materials Science, Lawrence Livermore National Laboratory, Livermore, California 94550, and Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550
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