Pulse radiolysis of aqueous solutions of sodium azide: Reactions of azide radical with tryptophan and tyrosine

Radical-Mediated Covalent Azidylation of Hydrophobic Microdomains in Water-Soluble Proteins

Hydrophobic microdomains, also known as hydrophobic patches, are essential for many important biological functions of water-soluble proteins. These include ligand or substrate binding, protein-protein interactions, proper folding after translation, and aggregation during denaturation. Unlike transmembrane domains, which are easily recognized from stretches of contiguous hydrophobic sidechains in amino acids via primary protein sequence, these three-dimensional hydrophobic patches cannot be easily predicted. The lack of experimental strategies for directly determining their locations hinders further understanding of their structure and function. Here, we posit that the small triatomic anion N3- (azide) is attracted to these patches and, in the presence of an oxidant, forms a radical that covalently modifies C-H bonds of nearby amino acids. Using two model proteins (BSA and lysozyme) and a cell-free lysate from the model higher plant Arabidopsis thaliana, we find that radical-mediated covalent azidylation occurs within buried catalytic active sites and ligand binding sites and exhibits similar behavior to established hydrophobic probes. The results herein suggest a model in which the azido radical is acting as an "affinity reagent" for nonaqueous three-dimensional protein microenvironments and is consistent with both the nonlocalized electron density of the azide moiety and the known high reactivity of azido radicals widely used in organic chemistry syntheses. We propose that the azido radical is a facile means of identifying hydrophobic microenvironments in soluble proteins and, in addition, provides a simple new method for attaching chemical handles to proteins without the need for genetic manipulation or specialized reagents.

Photoredox-HAT Catalysis for Primary Amine α-C-H Alkylation: Mechanistic Insight with Transient Absorption Spectroscopy

The synergistic use of (organo)photoredox catalysts with hydrogen-atom transfer (HAT) cocatalysts has emerged as a powerful strategy for innate C(sp³)-H bond functionalization, particularly for C-H bonds α- to nitrogen. Azide ion (N₃^-) was recently identified as an effective HAT catalyst for the challenging α-C-H alkylation of unprotected, primary alkylamines, in combination with dicyanoarene photocatalysts such as 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN). Here, time-resolved transient absorption spectroscopy over sub-picosecond to microsecond timescales provides kinetic and mechanistic details of the photoredox catalytic cycle in acetonitrile solution. Direct observation of the electron transfer from N₃^- to photoexcited 4CzIPN reveals the participation of the S₁ excited electronic state of the organic photocatalyst as an electron acceptor, but the N₃^• radical product of this reaction is not observed. Instead, both time-resolved infrared and UV-visible spectroscopic measurements implicate rapid association of N₃^• with N₃^- (a favorable process in acetonitrile) to form the N₆^•- radical anion. Electronic structure calculations indicate that N₃^• is the active participant in the HAT reaction, suggesting a role for N₆^•- as a reservoir that regulates the concentration of N₃^•.

Oxidation of Silver Cyanide Ag(CN)2- by the OH Radical: From Ab Initio Calculation to Molecular Simulation and to Experiment

We investigate the oxidation of silver cyanide AgI(CN)2- in water by the OH radical in order to compare this complex with the free cation Ag⁺ and to measure the influence of the ligands. High-level ab initio calculations of the model species AgII(CN)2· enable the calibration of molecular simulations and the prediction of the oxidized species: AgII(CN)2(H2O)2· and its absorption spectrum, with an intense band at 292 nm and a weaker one at 390 nm. Pulse radiolysis measurements of the oxidation of AgI(CN)2- by the OH radical in water yields a transient species with a broad, intense band at 290 nm and a weaker band at 410 nm at short times after the pulse and a blue shift of the spectrum at longer times. The prediction of the simulations, that the oxidized complex AgII(CN)2(H2O)2· is formed, is confirmed by thermochemistry. Our calculations also suggest that the formation of the OH-adduct is possible only in very basic solution and that the blue shift observed at long times after the pulse is due to disproportionation of the oxidized complex. We also perform molecular simulations of the oxidation of free Ag⁺ cations by the OH radical. The results are compared to that of the literature and to the results obtained with the AgI(CN)2- complex.

Contribution of the Excited Triplet State of Humic Acid and Superoxide Radical Anion to Generation and Elimination of Phenoxyl Radical

Contributions of excited triplet state of humic acid (³HA*) and superoxide radical anion (O₂^•-), which is mainly generated via the reaction of O₂ with HA-derived reducing intermediates (HA^•-), to phenol transformation were revealed using acetaminophen, 2,4,6-trimethylphenol and tyrosine as probe molecules. Phenol transformation was initiated by ³HA*, leading to the formation of the phenoxyl radical (PhO•), but the distribution of transformation intermediates was codetermined by ³HA* and HA^•-. The influence of HA^•- essentially resulted from the production of O₂^•-, which affected the fate of PhO•. PhO• could undergo dimerization, or react with O₂^•-, leading to either phenol peroxide formation (radical addition) or phenol regeneration (electron transfer). In addition, PhO• could bind to HA or react with HA radicals, particularly in the absence of O₂ and O₂^•-. These PhO• reactions were dependent on the reduction potential and structure of PhO•. This study also proved that the reaction of phenol with ¹O₂ and the reaction of PhO• with O₂^•- lead to the same oxidation product. The contributions of ³HA* and its generated ¹O₂, HA^•- and its generated O₂^•- to phenol transformation were pH-dependent.

Self-radiolysis of tritiated water. 4. The scavenging effect of azide ions (N3−) on the molecular hydrogen yield in the radiolysis of water by 60Co γ-rays and tritium β-particles at room temperature

The effect of the azide ion N₃⁻ on the yield of molecular hydrogen in water irradiated with ⁶⁰Co γ-rays (∼1 MeV Compton electrons) and tritium β-electrons (mean electron energy of ∼7.8 keV) at 25 °C is investigated using Monte Carlo track chemistry simulations in conjunction with available experimental data. N₃⁻ is shown to interfere with the formation of H₂ through its high reactivity towards hydrogen atoms and, but to a lesser extent, hydrated electrons, the two major radiolytic precursors of the H₂ yield in the diffusing radiation tracks. Chemical changes are observed in the H₂ scavengeability depending on the particular type of radiation considered. These changes can readily be explained on the basis of differences in the initial spatial distribution of primary radiolytic species (i.e., the structure of the electron tracks). In the “short-track” geometry of the higher “linear energy transfer” (LET) tritium β-electrons (mean LET ∼5.9 eV nm⁻¹), radicals are formed locally in much higher initial concentration than in the isolated “spurs” of the energetic Compton electrons (LET ∼0.3 eV nm⁻¹) generated by the cobalt-60 γ-rays. As a result, the short-track geometry favors radical–radical reactions involving hydrated electrons and hydrogen atoms, leading to a clear increase in the yield of H₂ for tritium β-electrons compared to ⁶⁰Co γ-rays. These changes in the scavengeability of H₂ in passing from tritium β-radiolysis to γ-radiolysis are in good agreement with experimental data, lending strong support to the picture of tritium β-radiolysis mainly driven by the chemical action of short tracks of high local LET. At high N₃⁻ concentrations (>1 M), our H₂ yield results for ⁶⁰Co γ-radiolysis are also consistent with previous Monte Carlo simulations that suggested the necessity of including the capture of the precursors to the hydrated electrons (i.e., the short-lived “dry” electrons prior to hydration) by N₃⁻. These processes tend to reduce significantly the yields of H₂, as is observed experimentally. However, this dry electron scavenging at high azide concentrations is not seen in the higher-LET ³H β-radiolysis, leading us to conclude that the increased amount of intra-track chemistry intervening at early time under these conditions favors the recombination of these electrons with their parent water cations at the expense of their scavenging by N₃⁻.

The effect of the azide ion on the yield of molecular hydrogen in water irradiated with ⁶⁰Co γ-rays and tritium β-electrons at 25 °C is investigated using Monte Carlo track chemistry simulations.

Fast repair of protein radicals by urate

The repair of tryptophan and tyrosine radicals in proteins by urate was studied by pulse radiolysis. In chymotrypsin, urate repairs tryptophan radicals efficiently with a rate constant of 2.7 × 10(8)M(-1)s(-1), ca. 14 times higher than the rate constant derived for N-acetyltryptophan amide, 1.9 × 10(7)M(-1)s(-1). In contrast, no repair of tryptophan radicals was observed in pepsin, which indicates a rate constant smaller than 6 × 10(7)M(-1)s(-1). Urate repairs tyrosine radicals in pepsin with a rate constant of 3 × 10(8)M(-1)s(-1)-ca. 12 times smaller than the rate constant reported for free tyrosine-but not in chymotrypsin, which implies an upper limit of 1 × 10(6)M(-1)s(-1) for the corresponding rate constant. Intra- and intermolecular electron transfer from tyrosine residues to tryptophan radicals is observed in both proteins, however, to different extents and with different rate constants. Urate inhibits electron transfer in chymotrypsin but not in pepsin. Our results suggest that urate repairs the first step on the long path to protein modification and prevents damage in vivo. It may prove to be a very important repair agent in tissue compartments where its concentration is higher than that of ascorbate. The product of such repair, the urate radical, can be reduced by ascorbate. Loss of ascorbate is then expected to be the net result, whereas urate is conserved.

Proposed mechanism for the photodynamic generation of 8-oxo-7,8-dihydro-2'-deoxyguanosine produced in cultured cells by exposure to lomefloxacin

In this study, lomefloxacin (LMX), a widely used quinolone antibiotic with a high frequency of clinical phototoxicity, was investigated by measuring the effects of several antioxidants on its ability to form of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in cultured adult rat liver cells after exposure to UVA. In the current study the observed DNA damage, reflected by the formation of 8-oxo-dG, was almost completely inhibited by co-incubation of LMX and cultured cells with sodium azide (NaN3) that specifically quenches singlet oxygen. Vitamin E (alpha-tocopherol), known to quench both superoxide and singlet oxygen, inhibited 8-oxo-dG formation by approximately 54%. Mannitol, a hydroxyl radical scavenger, inhibited 8-oxo-dG formation by 64%. Butylated hydroxyanisole (BHA), a scavenger of hydroxyl, peroxy and alkoxy radicals, showed no inhibition of 8-oxo-dG formation but in fact enhanced levels of 8-oxo-dG by 169%. The results of this study suggest that the mechanism for the photodynamic generation of 8-oxo-dG by LMX is mediated, at least in part, by both singlet oxygen and hydroxyl radical and involves both type I and type II photosensitization.

Potentiation of oxidative damage to proteins by ultraviolet-A and protection by antioxidants

We have studied the damage of alcohol dehydrogenase (ADH) and glyceraldehyde 3-phosphate dehydrogenase (GAPD) induced by Fe++/EDTA + H2O2 in combination with UV-A (main output at 365 nm). Enzyme inactivation, formation of hydroxyl radicals (measured in the absence of enzymes), increase in protein carbonyls, oxidation of sulfhydryl (SH) groups, loss of native protein fluorescence, and enhanced protease degradation were used to determine protein damage. Hydroxyl radical production was greatly enhanced by the combination of UV-A with Fe++/EDTA + H2O2. The combined treatment increased protein carbonyls but decreased native protein fluorescence and SH groups. The combined treatment caused turbidity in GAPD but not in ADH, whereas trypsin susceptibility was increased more in ADH than in GAPD. These measurements of protein oxidation correlated well with enzyme activities. Glyceraldehyde 3-phosphate dehydrogenase and dithiothreitol were most protective against such damage, while hydroxyl radical and singlet oxygen scavengers were partially effective. Superoxide dismutase had no effect. Thus, UV-A potentiation of protein damage induced by FE++/EDTA + H2O2 appeared to involve hydroxyl radicals and perhaps singlet oxygen but not superoxide radicals. The damage to proteins induced by combination of UV-A with physiological oxidants, iron ions and H2O2 may be relevant to UV-A-induced skin and tissue damage.

The effect of oxygen, antioxidants, and superoxide radical on tyrosine phenoxyl radical dimerization

Dimerization of tyrosine phenoxyl radical yields bityrosine (BT) which can easily be monitored by its characteristic fluorescence at 400 nm. The reactivity of tyrosine phenoxyl radical with O2 was examined by a variety of techniques. BT fluorescence was measured as a function of O2 concentration. Over a range of pH values (4-12) there was no effect of oxygen on BT production ([O2] less than or equal to 0.72 mM). In addition, oxygen uptake by the phenoxyl radical was measured directly with an oxygen electrode. It was determined by this technique that oxygen does not react with the phenoxyl radical with a rate constant greater than 10(3) M-1 s-1. Tyrosine phenoxyl radical "repair" by superoxide and physiological antioxidants was examined by BT fluorescence quenching as well as pulse radiolysis. Implications of these results as to the fate of tyrosine phenoxyl radicals produced in biological systems is discussed.

The importance of free radicals and catalytic metal ions in human diseases

The study of free radical reactions is not an isolated and esoteric branch of science. A knowledge of free radical chemistry and biochemistry is relevant to an understanding of all diseases and the mode of action of all toxins, if only because diseased or damaged tissues undergo radical reactions more readily than do normal tissues. However it does not follow that because radical reactions can be demonstrated, they are important in any particular instance. We hope that the careful techniques needed to assess the biological role of free radicals will become more widely used.

Effect of gamma radiation on E. coli ribosomes, tRNA and aminoacyl-tRNA synthetases

Gamma-irradiated E coli ribosomes and tRNA, in aerated solutions, were inactivated with D37 doses of 144 and 77 Gy, respectively. Aminoacyl-tRNA-synthetases were only slightly inactivated under comparable conditions. Effects of additives to ribosome and tRNA solutions suggest that hydroxyl radicals were the major damaging species, that superoxide anions were not damaging and that radiolytically-formed hydrogen peroxide was also unimportant. Part of the damage by hydroxyl radicals is expressed through secondary radicals produced from additives and buffers. Results obtained with three different buffers suggest that (1) acetate ions provide protection by competing for hydroxyl radicals, (2) chloride ions are without effect and (3) inactivation of ribosomes and aminoacyl-tRNA-synthetases in Tris-HCl/MgCl2 and phosphate/MgCl2 buffered solutions was similar but the tRNA inactivation was lower in Tris-HCl/MgCl2 buffer.