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International Journal of Molecular... Jun 2021In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based ("on-lattice") model to simulate water radiolysis....
In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based ("on-lattice") model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume ("mesh"), which is divided into sub-volumes (or "voxels"). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME ("hRDME"). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step ("SBS") Brownian dynamics model and the compartment-based model ("SBS-RDME model") for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy.
Topics: Algorithms; Computer Simulation; DNA; Diffusion; Linear Energy Transfer; Models, Chemical; Models, Molecular; Monte Carlo Method; Pulse Radiolysis; Water
PubMed: 34199598
DOI: 10.3390/ijms22116023 -
Biomolecules Oct 2023We examined the reaction of hydroxyl radicals (HO) and sulfate radical anions (SO), which is generated by ionizing radiation in aqueous solutions under anoxic...
We examined the reaction of hydroxyl radicals (HO) and sulfate radical anions (SO), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO to the G:C pair moiety, affording the [8-HO-G:C] detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H):C] after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G], in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C] detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
Topics: Oligonucleotides; Hydroxyl Radical; Electrons; Free Radicals; Oxidation-Reduction; Oligodeoxyribonucleotides
PubMed: 37892175
DOI: 10.3390/biom13101493 -
International Journal of Molecular... Jun 2019Retinoids are present in human tissues exposed to light and under increased risk of oxidative stress, such as the retina and skin. Retinoid cation radicals can be formed...
Retinoids are present in human tissues exposed to light and under increased risk of oxidative stress, such as the retina and skin. Retinoid cation radicals can be formed as a result of the interaction between retinoids and other radicals or photoexcitation with light. It has been shown that such semi-oxidized retinoids can oxidize certain amino acids and proteins, and that α-tocopherol can scavenge the cation radicals of retinol and retinoic acid. The aim of this study was to determine (i) whether β-, γ-, and δ-tocopherols can also scavenge these radicals, and (ii) whether tocopherols can scavenge the cation radicals of another form of vitamin A-retinal. The retinoid cation radicals were generated by the pulse radiolysis of benzene or aqueous solution in the presence of a selected retinoid under oxidizing conditions, and the kinetics of retinoid cation radical decays were measured in the absence and presence of different tocopherols, Trolox or urate. The bimolecular rate constants are the highest for the scavenging of cation radicals of retinal, (7 to 8) × 10 M·s, followed by retinoic acid, (0.03 to 5.6) × 10 M·s, and retinol, (0.08 to 1.6) × 10 M·s. Delta-tocopherol is the least effective scavenger of semi-oxidized retinol and retinoic acid. The hydrophilic analogue of α-tocopherol, Trolox, is substantially less efficient at scavenging retinoid cation radicals than α-tocopherol and urate, but it is more efficient at scavenging the cation radicals of retinoic acid and retinol than δ-tocopherol. The scavenging rate constants indicate that tocopherols can effectively compete with amino acids and proteins for retinoid cation radicals, thereby protecting these important biomolecules from oxidation. Our results provide another mechanism by which tocopherols can diminish the oxidative damage to the skin and retina and thereby protect from skin photosensitivity and the development and/or progression of changes in blinding retinal diseases such as Stargardt's disease and age-related macular degeneration (AMD).
Topics: Cations; Chromans; Free Radical Scavengers; Retinoids; Tocopherols; Uric Acid
PubMed: 31181693
DOI: 10.3390/ijms20112799 -
Zeitschrift Fur Naturforschung. C,... 1990Hydroxyl radicals were generated radiolytically in N2O- and N2O/O2(4:1)-saturated aqueous solutions of hyaluronic acid. The hydroxyl radicals react rapidly with...
Hydroxyl radicals were generated radiolytically in N2O- and N2O/O2(4:1)-saturated aqueous solutions of hyaluronic acid. The hydroxyl radicals react rapidly with hyaluronic acid mainly by abstracting carbon-bound H atoms. As a consequence of subsequent free-radical reactions, chain breakage occurs the kinetics of which has been followed using the pulse radiolysis technique. In the absence of oxygen, strand breakage was followed by the change in conductivity induced by the release of cationic counterions condensed at the surface of hyaluronic acid which is a polyanion consisting of subunits of glucuronic acid alternating with N-acetyl-glucosamine. It appears that strand breakage is not due to one single first-order process, however, the contributions of the different components cannot be adequately resolved. At pH 7 the overall half-life is 1.4 ms, in both acid and basic solutions the rate of free-radical induced strand breakage is accelerated (at pH 4.8, t1/2 = 0.6 ms; at pH 10, t1/2 = 0.18 ms). In the absence of oxygen there is no effect of dose rate on the kinetics of strand breakage. In the presence of oxygen in addition to conductometric detection, strand breakage was also followed by changes in low-angle laser light-scattering. These two techniques are complementary in that in this system the conductometry requires high doses per pulse while the light-scattering technique is best operated in the low-dose range. In the presence of oxygen a pronounced dose-rate effect is observed, e.g. at pH 9.7 after a dose of 9.4 Gy the overall half-time is approx. 0.5 s, while after a dose of 6.6 Gy the half-time is approx. 0.23 s. Both the yield and the rate of strand breakage increase with increasing pH, e.g. at pH 7 G(strand breaks) = 0.7 x 10(-7) mol J-1 and at pH 10.4, 4.8 x 10(-7) mol J-7. The radiolytic yields of CO2, H2O2, organic hydroperoxides, O2.- and oxygen consumption have been determined in gamma-irradiated N2O/O2(4:1)-saturated solutions of both hyaluronic acid and beta-cyclodextrin.
Topics: Carbohydrate Sequence; Electrochemistry; Free Radicals; Hyaluronic Acid; Hydrolysis; Hydroxides; Hydroxyl Radical; Kinetics; Lasers; Molecular Sequence Data; Scattering, Radiation
PubMed: 1963301
DOI: 10.1515/znc-1990-9-1016 -
The FEBS Journal Sep 2011Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the... (Comparative Study)
Comparative Study
Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the fungus Trametes hirsuta and the lacquer tree Rhus vernicifera, using the pulse radiolysis method. The rate constant at 298 K and the enthalpy and entropy of activation were 25 ± 1 s(-1), 39.7 ± 5.0 kJ·mol(-1) and -87 ± 9 J·mol(-1) ·K(-1) for the fungal enzyme and 1.1 ± 0.1 s(-1), 9.8 ± 0.2 kJ·mol(-1) and -211 ± 3 J·mol(-1) ·K(-1) for the tree enzyme. The initial reduction of the T1 site by pulse radiolytically produced radicals was direct in the case of T. hirsuta laccase, but occured indirectly via a disulfide radical in R. vernicifera. The equilibrium constant that characterizes the electron transfer from T1 to T3 copper ions was 0.4 for T. hirsuta laccase and 1.5 for R. vernicifera laccase, leading to full reduction of the T1 site occurring at 2.9 ± 0.2 electron equivalents for T. hirsuta and 4 electron equivalents for R. vernicifera laccase. These results were compared with each other and with those for the same process in other multicopper oxidases, ascorbate oxidase and Streptomyces coelicolor laccase, using available structural information and electron transfer theory.
Topics: Biocatalysis; Carbon Dioxide; Catalytic Domain; Copper; Databases, Protein; Electron Transport; Entropy; Free Radicals; Fungal Proteins; Kinetics; Laccase; Models, Molecular; Oxidation-Reduction; Plant Proteins; Pulse Radiolysis; Rhus; Trametes
PubMed: 21790996
DOI: 10.1111/j.1742-4658.2011.08268.x -
Journal of Radiation Research Jun 2004Poly(vinylbenzyltrimethylammonium chloride) (PVBT) has been synthesized by radiation-induced polymerization of Vinylbenzyltrimethylammonium chloride (VBT). The viscosity... (Comparative Study)
Comparative Study
Poly(vinylbenzyltrimethylammonium chloride) (PVBT) has been synthesized by radiation-induced polymerization of Vinylbenzyltrimethylammonium chloride (VBT). The viscosity average molecular weight of synthesized polymer was estimated to be approximately 10(5) by viscosity measurements. The radiation-induced affects on PVBT have been investigated by steady-state and pulse radiolysis (PR) techniques. The reactions of primary radicals (*)OH, e(aq)(-), and H(*) generated by the radiolysis of water with PVBT were studied. The reactions of some other species such as N(3)(*), Cl(2)(*-), Br(2)(*-), SO(4)(*-), and CO(2)(*-) with PVBT were also investigated. The results indicate that the reactivity of these species toward PVBT is lower then that with the monomer VBT. The rate constants for the reactions of OH radical and H atom with PVBT were evaluated both by competition kinetics and by direct observation of the buildup of transient species. The difference in the rate constant values evaluated by the two methods indicated that (*)OH and H(*) react with PVBT to give more than one species. It was observed that the OH radical and H atom react with PVBT in different manners. Near neutral pH, the OH radicals react to form an adduct and to generate a radical by abstracting methylenic H atom. The H atom, however, also abstracts the H atom from the PVBT backbone. The rate constant value for the reaction of hydrated electron with PVBT was found to be 3.1 currency 10(9) dm(3) mol(-1) s(-1). Steady-state irradiation studies of the aqueous PVBT solution indicated that PVBT predominantly undergoes cross-linking on irradiation. Cross-linking is a function of dose rate, concentration, and ambient of irradiation. At concentrations < 2%, only intramolecular cross-linking takes place, whereas beyond this concentration, the intermolecular cross-linking of polymer chains takes place to form a soft gel. The gel dose (D(gel)) is a function of the ambient of irradiation.
Topics: Biocompatible Materials; Dose-Response Relationship, Radiation; Materials Testing; Molecular Conformation; Polystyrenes; Quaternary Ammonium Compounds; Radiation Dosage; Solutions; Water
PubMed: 15304973
DOI: 10.1269/jrr.45.291 -
Free Radical Biology & Medicine Aug 2014The pharmacological effects of hydroxamic acids are partially attributed to their ability to serve as HNO and/or NO donors under oxidative stress. Previously, it was...
The pharmacological effects of hydroxamic acids are partially attributed to their ability to serve as HNO and/or NO donors under oxidative stress. Previously, it was concluded that oxidation of the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) by the metmyoglobin/H2O2 reaction system releases NO, which was based on spin trapping of NO and accumulation of nitrite. Reinvestigation of this system demonstrates the accumulation of N2O, which is a marker of HNO formation, at similar rates under normoxia and anoxia. In addition, the yields of nitrite that accumulated in the absence and the presence of O2 did not differ, implying that the source of nitrite is other than autoxidation of NO. In this system metmyoglobin is instantaneously and continuously converted into compound II, leading to one-electron oxidation of SAHA to its respective transient nitroxide radical. Studies using pulse radiolysis show that one-electron oxidation of SAHA (pKa=9.56 ± 0.04) yields the respective nitroxide radical (pKa=9.1 ± 0.2), which under all experimental conditions decomposes bimolecularly to yield HNO. The proposed mechanism suggests that compound I oxidizes SAHA to the respective nitroxide radical, which decomposes bimolecularly in competition with its oxidation by compound II to form HNO. Compound II also oxidizes HNO to NO and NO to nitrite. Given that NO, but not HNO, is an efficient hypoxic cell radiosensitizer, we hypothesized that under an oxidizing environment SAHA might act as a NO donor and radiosensitize hypoxic cells. Preincubation of A549 and HT29 cells with 2.5 μM SAHA for 24h resulted in a sensitizer enhancement ratio at 0.01 survival levels (SER0.01) of 1.33 and 1.59, respectively. Preincubation of A549 cells with oxidized SAHA had hardly any effect and, with 2mM valproic acid, which lacks the hydroxamate group, resulted in SER0.01=1.17. Preincubation of HT29 cells with SAHA and Tempol, which readily oxidizes HNO to NO, enhanced the radiosensitizing effect of SAHA. Pretreatment with SAHA blocked A549 cells at the G1 stage of the cell cycle and upregulated γ-H2AX after irradiation. Overall, we conclude that SAHA enhances tumor radioresponse by multiple mechanisms that might also involve its ability to serve as a NO donor under oxidizing environments.
Topics: Antioxidants; Cell Hypoxia; Cell Line, Tumor; Cyclic N-Oxides; Enzyme Inhibitors; G1 Phase Cell Cycle Checkpoints; HT29 Cells; Histones; Humans; Hydrogen Peroxide; Hydroxamic Acids; Metmyoglobin; Neoplasms; Nitric Oxide; Nitrogen Oxides; Oxidation-Reduction; Oxidative Stress; Radiation-Sensitizing Agents; Spin Labels; Valproic Acid; Vorinostat
PubMed: 24880052
DOI: 10.1016/j.freeradbiomed.2014.05.019 -
Acta Biochimica Et Biophysica Sinica Jul 2010Silybin (SLB) and similar analogues, namely, hesperetin (HESP), naringenin (NAN) and naringin (NAR), are believed to be active constituents of natural flavonoids that...
Silybin (SLB) and similar analogues, namely, hesperetin (HESP), naringenin (NAN) and naringin (NAR), are believed to be active constituents of natural flavonoids that have been reported as chemopreventive agents for certain cancers. Moreover, SLB and analogues have been determined to fast repair DNA bases from oxidative damage by pulse radiolysis techniques. The present study was designed to evaluate the protective effects of SLB and analogues on soft X-ray-induced damage to plasmid DNA in vitro. The DNA damage was determined by agarose gel electrophoresis. SLB and analogues were found to protect DNA from radiation damage at micromolar concentrations. Among the compounds tested, HESP and SLB were the most effective in preventing X-ray-induced formation of DNA single-strand breaks (SSB). A comparison of these results with other experiments showed that the ability of SLB and analogues to inhibit DNA damage in vitro correlated with the ability of the compounds to scavenge free radicals. Our work revealed that natural flavonoids, SLB and analogues may be used as potent radioprotectors against radiation damage.
Topics: Antioxidants; DNA; DNA Breaks, Single-Stranded; DNA Damage; Dose-Response Relationship, Radiation; Electrophoresis, Agar Gel; Flavanones; Hesperidin; Models, Chemical; Molecular Structure; Plasmids; Silybin; Silymarin
PubMed: 20705588
DOI: 10.1093/abbs/gmq045 -
The Journal of Biological Chemistry Jul 1996The depletion of superoxide catalyzed by human manganese superoxide dismutase (MnSOD) was observed spectrophotometrically by measuring the absorbance of superoxide at...
The depletion of superoxide catalyzed by human manganese superoxide dismutase (MnSOD) was observed spectrophotometrically by measuring the absorbance of superoxide at 250-280 nm following pulse radiolysis and by stopped-flow spectrophotometry. Catalysis showed an initial burst of activity lasting approximately 1 ms followed by the rapid emergence of a greatly inhibited catalysis of zero-order rate. These catalytic properties of human MnSOD are qualitatively similar to those reported for MnSOD from Thermus thermophilus (Bull, C., Niederhoffer, E. C., Yoshida, T., and Fee, J. A.(1991) J. Am. Chem. Soc. 113, 4069-4076). However, there are significant quantitative differences; the emergence of the inhibited form is approximately 30-fold more rapid for human MnSOD. The turnover number for human MnSOD at pH 9.4 and 20 degrees C was kcat = 4 x 10(4) s-1 and kcat/Km = 8 x 10(8) M-1 s-1, determined by a simulated fit of the model of Bull et al. (1991) to the pulse radiolysis data. We also report that the maximum of the visible absorption spectrum of human MnSOD (epsilon480 = 525 M-1 cm-1) showed a strong dependence on pH that could be described by an ionization of pKa 9.4 +/- 0.1 with a maximum at low pH.
Topics: Base Sequence; Catalysis; Enzyme Inhibitors; Escherichia coli; Humans; Hydrogen-Ion Concentration; Kinetics; Models, Chemical; Molecular Sequence Data; Pulse Radiolysis; Recombinant Proteins; Spectrophotometry; Superoxide Dismutase; Superoxides
PubMed: 8663465
DOI: 10.1074/jbc.271.30.17687 -
The Journal of Biological Chemistry Dec 2017Cytochrome P450cam (CYP101Fe) regioselectively hydroxylates camphor. Possible hydroxylating intermediates in the catalytic cycle of this well-characterized enzyme have...
Cytochrome P450cam (CYP101Fe) regioselectively hydroxylates camphor. Possible hydroxylating intermediates in the catalytic cycle of this well-characterized enzyme have been proposed on the basis of experiments carried out at very low temperatures and shunt reactions, but their presence has not yet been validated at temperatures above 0 °C during a normal catalytic cycle. Here, we demonstrate that it is possible to mimic the natural catalytic cycle of CYP101Fe by using pulse radiolysis to rapidly supply the second electron of the catalytic cycle to camphor-bound CYP101[FeO] Judging by the appearance of an absorbance maximum at 440 nm, we conclude that CYP101[FeOOH] (compound 0) accumulates within 5 μs and decays rapidly to CYP101Fe, with a of 9.6 × 10 s All processes are complete within 40 μs at 4 °C. Importantly, no transient absorbance bands could be assigned to CYP101[FeOpor] (compound 1) or CYP101[FeO] (compound 2). However, indirect evidence for the involvement of compound 1 was obtained from the kinetics of formation and decay of a tyrosyl radical. 5-Hydroxycamphor was formed quantitatively, and the catalytic activity of the enzyme was not impaired by exposure to radiation during the pulse radiolysis experiment. The rapid decay of compound 0 enabled calculation of the limits for the Gibbs activation energies for the conversions of compound 0 → compound 1 → compound 2 → CYP101Fe, yielding a Δ of 45, 39, and 39 kJ/mol, respectively. At 37 °C, the steps from compound 0 to the iron(III) state would take only 4 μs. Our kinetics studies at 4 °C complement the canonical mechanism by adding the dimension of time.
Topics: Binding Sites; Camphor 5-Monooxygenase; Catalysis; Cytochrome P-450 Enzyme System; Electron Transport; Electrons; Ferric Compounds; Kinetics; Models, Molecular; Oxidation-Reduction
PubMed: 29109145
DOI: 10.1074/jbc.M117.813683