Telomere length kinetics assay (TELKA) sorts the telomere length maintenance (tlm) mutants into functional groups.

Genome-wide systematic screens in yeast have uncovered a large gene network (the telomere length maintenance network or TLM), encompassing more than 400 genes, which acts coordinatively to maintain telomere length. Identifying the genes was an important first stage; the next challenge is to decipher their mechanism of action and to organize then into functional groups or pathways. Here we present a new telomere-length measuring program, TelQuant, and a novel assay, telomere length kinetics assay, and use them to organize tlm mutants into functional classes. Our results show that a mutant defective for the relatively unknown MET7 gene has the same telomeric kinetics as mutants defective for the ribonucleotide reductase subunit Rnr1, in charge of the limiting step in dNTP synthesis, or for the Ku heterodimer, a well-established telomere complex. We confirm the epistatic relationship between the mutants and show that physical interactions exist between Rnr1 and Met7. We also show that Met7 and the Ku heterodimer affect dNTP formation, and play a role in non-homologous end joining. Thus, our telomere kinetics assay uncovers new functional groups, as well as complex genetic interactions between tlm mutants.

Uracil-containing DNA in Drosophila: stability, stage-specific accumulation, and developmental involvement.

Base-excision repair and control of nucleotide pools safe-guard against permanent uracil accumulation in DNA relying on two key enzymes: uracil-DNA glycosylase and dUTPase. Lack of the major uracil-DNA glycosylase UNG gene from the fruit fly genome and dUTPase from fruit fly larvae prompted the hypotheses that i) uracil may accumulate in Drosophila genomic DNA where it may be well tolerated, and ii) this accumulation may affect development. Here we show that i) Drosophila melanogaster tolerates high levels of uracil in DNA; ii) such DNA is correctly interpreted in cell culture and embryo; and iii) under physiological spatio-temporal control, DNA from fruit fly larvae, pupae, and imago contain greatly elevated levels of uracil (200-2,000 uracil/million bases, quantified using a novel real-time PCR-based assay). Uracil is accumulated in genomic DNA of larval tissues during larval development, whereas DNA from imaginal tissues contains much less uracil. Upon pupation and metamorphosis, uracil content in DNA is significantly decreased. We propose that the observed developmental pattern of uracil-DNA is due to the lack of the key repair enzyme UNG from the Drosophila genome together with down-regulation of dUTPase in larval tissues. In agreement, we show that dUTPase silencing increases the uracil content in DNA of imaginal tissues and induces strong lethality at the early pupal stages, indicating that tolerance of highly uracil-substituted DNA is also stage-specific. Silencing of dUTPase perturbs the physiological pattern of uracil-DNA accumulation in Drosophila and leads to a strongly lethal phenotype in early pupal stages. These findings suggest a novel role of uracil-containing DNA in Drosophila development and metamorphosis and present a novel example for developmental effects of dUTPase silencing in multicellular eukaryotes. Importantly, we also show lack of the UNG gene in all available genomes of other Holometabola insects, indicating a potentially general tolerance and developmental role of uracil-DNA in this evolutionary clade.

The reaction of ozone with the hydroxide ion: mechanistic considerations based on thermokinetic and quantum chemical calculations and the role of HO4- in superoxide dismutation.

The reaction of OH(-) with O(3) eventually leads to the formation of *OH radicals. In the original mechanistic concept (J. Staehelin, J. Hoigné, Environ. Sci. Technol. 1982, 16, 676-681), it was suggested that the first step occurred by O transfer: OH(-)+O(3)-->HO(2)(-)+O(2) and that *OH was generated in the subsequent reaction(s) of HO(2)(-) with O(3) (the peroxone process). This mechanistic concept has now been revised on the basis of thermokinetic and quantum chemical calculations. A one-step O transfer such as that mentioned above would require the release of O(2) in its excited singlet state ((1)O(2), O(2)((1)Delta(g))); this state lies 95.5 kJ mol(-1) above the triplet ground state ((3)O(2), O(2)((3)Sigma(g)(-))). The low experimental rate constant of 70 M(-1) s(-1) is not incompatible with such a reaction. However, according to our calculations, the reaction of OH(-) with O(3) to form an adduct (OH(-)+O(3)-->HO(4)(-); DeltaG=3.5 kJ mol(-1)) is a much better candidate for the rate-determining step as compared with the significantly more endergonic O transfer (DeltaG=26.7 kJ mol(-1)). Hence, we favor this reaction; all the more so as numerous precedents of similar ozone adduct formation are known in the literature. Three potential decay routes of the adduct HO(4)(-) have been probed: HO(4)(-)-->HO(2)(-)+(1)O(2) is spin allowed, but markedly endergonic (DeltaG=23.2 kJ mol(-1)). HO(4)(-)-->HO(2)(-)+(3)O(2) is spin forbidden (DeltaG=-73.3 kJ mol(-1)). The decay into radicals, HO(4)(-)-->HO(2)*+O(2)(*-), is spin allowed and less endergonic (DeltaG=14.8 kJ mol(-1)) than HO(4)(-)-->HO(2)(-)+(1)O(2). It is thus HO(4)(-)-->HO(2)*+O(2)(*-) by which HO(4)(-) decays. It is noted that a large contribution of the reverse of this reaction, HO(2)*+O(2)(*-)-->HO(4)(-), followed by HO(4)(-)-->HO(2)(-)+(3)O(2), now explains why the measured rate of the bimolecular decay of HO(2)* and O(2)(*-) into HO(2)(-)+O(2) (k=1 x 10(8) M(-1) s(-1)) is below diffusion controlled. Because k for the process HO(4)(-)-->HO(2)*+O(2)(*-) is much larger than k for the reverse of OH(-)+O(3)-->HO(4)(-), the forward reaction OH(-)+O(3)-->HO(4)(-) is practically irreversible.

Carbon dioxide-catalyzed peroxynitrite reactivity - The resilience of the radical mechanism after two decades of research.

Peroxynitrite, ONOO-, formed in tissues that are simultaneously generating NO• and O2•-, is widely regarded as a major contributor to oxidative stress. Many of the reactions involved are catalyzed by CO2 via formation of an unstable adduct, ONOOC(O)O-, that undergoes O-O bond homolysis to produce NO2• and CO3•- radicals, whose yields are equal at about 0.33 with respect to the ONOO- reactant. Since its inception two decades ago, this radical-based mechanism has been frequently but unsuccessfully challenged. The most recent among these [Serrano-Luginbuehl et al. Chem. Res. Toxicol.31:721-730; 2018] claims that ONOOC(O)O- is stable, predicts a yield of NO2•/CO3•- of less than 0.01 under physiological conditions and, contrary to widely accepted viewpoints, suggests that radical generation is inconsequential to peroxynitrite-induced oxidative damage. Here we review the experimental and theoretical evidence that support the radical model and show this recently proposed alternative mechanism to be incorrect.

The chemistry of peroxynitrite: implications for biological activity.

In biological systems, nitric oxide (NO) combines rapidly with superoxide (O2-) to form peroxynitrite ion (ONOO-), a substance that has been implicated as a culprit in many diseases. Peroxynitrite ion is essentially stable, but its protonated form (ONOOH, pKa = 6.5 to 6.8) decomposes rapidly via homolysis of the O-O bond to form about 28% free NO2 and OH radicals. At physiological pH and in the presence of large amounts of bicarbonate, ONOO- reacts with CO2 to produce about 33% NO2 and carbonate ion radicals (CO3-) in the bulk of the solution. The quantitative role of OH/CO3(-) and NO2 radicals during the decomposition of peroxynitrite (ONOOH/ONOO-) under physiological conditions is described in detail. Specifically, the effect of the peroxynitrite dosage rate on the yield and distribution of the final products is demonstrated. By way of an example, the detailed mechanism of nitration of tyrosine, a vital aromatic amino acid, is delineated, showing the difference in the nitration yield between the addition of authentic peroxynitrite and its continuous generation by NO and O2- radicals.

Kinetics of the reaction between nitroxide and thiyl radicals: nitroxides as antioxidants in the presence of thiols.

Cyclic nitroxides effectively protect cells, tissues, isolated organs, and laboratory animals from radical-induced damage. The present study focuses on the kinetics and mechanisms of the reactions of piperidine and pyrrolidine nitroxides with thiyl radicals, which are involved in free radical "repair" equilibria, but being strong oxidants can also produce cell damage. Thiyl radicals derived from glutathione, cysteine, and penicillamine were generated in water by pulse radiolysis, and the rate constants of their reactions with 2,2,6,6-tetramethylpiperidine-1-oxyl (TPO), 4-OH-TPO, and 3-carbamoyl-proxyl were determined to be (5-7) x 10 (8) M (-1) s (-1) at pH 5-7, independent of the structure of the nitroxide and the thiyl radical. It is suggested that the reaction of nitroxide (>NO (*)) with thiyl radical (RS (*)) yields an unstable adduct (>NOSR). The deprotonated form of this adduct decomposes via heterolysis of the N-O bond, yielding the respective amine (>NH) and sulfinic acid (RS(O)OH). The protonated form of the adduct decomposes via homolysis of the N-O bond, forming the aminium radical (>NH (*+)) and sulfinyl radical (RSO (*)), which by subsequent reactions involving thiol and nitroxide produce the respective amine and sulfonic acid (RS(O) 2OH). Nitroxides that are oxidized to the respective oxoammonium cations (>N (+)O) are recovered in the presence of NADH but not in the presence of thiols. This suggests that the reaction of >N (+)O with thiols yields the respective amine. Two alternative mechanisms are suggested, where >N (+)O reacts with thiolate (RS (-)) directly generating the adduct >NOSR or indirectly forming >NO (*) and RS (*), which subsequently together yield the adduct >NOSR. Under physiological conditions the adduct is mainly deprotonated, and therefore nitroxides can detoxify thiyl radicals. The proposed mechanism can account for the protective effect of nitroxides against reactive oxygen- and nitrogen-derived species in the presence of thiols.

Trading in cooperativity for specificity to maintain uracil-free DNA.

Members of the dUTPase superfamily play an important role in the maintenance of the pyrimidine nucleotide balance and of genome integrity. dCTP deaminases and the bifunctional dCTP deaminase-dUTPases are cooperatively regulated by dTTP. However, the manifestation of allosteric behavior within the same trimeric protein architecture of dUTPases, the third member of the superfamily, has been a question of debate for decades. Therefore, we designed hybrid dUTPase trimers to access conformational states potentially mimicking the ones observed in the cooperative relatives. We studied how the interruption of different steps of the enzyme cycle affects the active site cross talk. We found that subunits work independently in dUTPase. The experimental results combined with a comparative structural analysis of dUTPase superfamily enzymes revealed that subtile structural differences within the allosteric loop and the central channel in these enzymes give rise to their dramatically different cooperative behavior. We demonstrate that the lack of allosteric regulation in dUTPase is related to the functional adaptation to more efficient dUTP hydrolysis which is advantageous in uracil-DNA prevention.

Dynamic niche-specific adaptations in Neisseria meningitidis during infection.

Neisseria meningitidis is an opportunistic human pathogen that usually colonizes the nasopharyngeal mucosa asymptomatically. Upon invasion into the blood and central nervous system, this bacterium triggers a fulminant inflammatory reaction with the manifestations of septicemia and meningitis, causing high morbidity and mortality. To reveal the bacterial adaptations to specific and dynamic host environments, we performed a comprehensive proteomic survey of N. meningitidis isolated from the nasal mucosa, CSF and blood of a mouse disease model. We could identify 51 proteins whose expression pattern has been changed during infection, many of which have not yet been characterized. The abundance of proteins was markedly lower in the bacteria isolated from the nasal mucosa compared to the bacteria from the blood and CSF, indicating that initiating adhesion is the harshest challenge for meningococci. The high abundance of the glutamate dehydrogenase (GdhA) and Opa1800 proteins in all bacterial isolates suggests their essential role in bacterial survival in vivo. To evaluate the biological relevance of our proteomic findings, four candidate proteins from representative functional groups, such as the bacterial chaperone GroEL, IMP dehydrogenase GuaB, and membrane proteins PilQ and NMC0101, were selected and their impact on bacterial fitness was investigated by mutagenesis assays. This study provides an integrated picture of bacterial niche-specific adaptations during consecutive infection processes.

S phase block following MEC1ATR inactivation occurs without severe dNTP depletion.

Inactivation of Mec1, the budding yeast ATR, results in a permanent S phase arrest followed by chromosome breakage and cell death during G2/M. The S phase arrest is proposed to stem from a defect in Mec1-mediated degradation of Sml1, a conserved inhibitor of ribonucleotide reductase (RNR), causing a severe depletion in cellular dNTP pools. Here, the casual link between the S phase arrest, Sml1, and dNTP-levels is examined using a temperature sensitive mec1 mutant. In addition to S phase arrest, thermal inactivation of Mec1 leads to constitutively high levels of Sml1 and an S phase arrest. Expression of a novel suppressor, GIS2, a conserved mRNA binding zinc finger protein, rescues the arrest without down-regulating Sml1 levels. The dNTP pool in mec1 is reduced by ∼17% and GIS2 expression restores it, but only partially, to ∼93% of a control. We infer that the permanent S phase block following Mec1 inactivation can be uncoupled from its role in Sml1 down-regulation. Furthermore, unexpectedly modest effects of mec1 and GIS2 on dNTP levels suggest that the S phase arrest is unlikely to result from a severe depletion of dNTP pool as assumed, but a heightened sensitivity to small changes in its availability.

Mechanism of Decomposition of Peroxynitric Ion (O(2)NOO(-)): Evidence for the Formation of O(2)(*-) and (*)NO(2) Radicals.

The rate constant of the self-decomposition of O(2)NOO(-) was determined to be 1.35 +/- 0.03 s(-)(1) at 25 degrees C. The decomposition rate constant of O(2)NOO(-) in the presence of C(NO(2))(4), CuSO(4), SOD, and Fe(CN)(6)(4)(-) was found to be 2.4 +/- 0.2 s(-)(1), independent of the concentration of these substrates. The oxidation yields of C(NO(2))(3)(-) and ferricyanide were measured to be 47 +/- 5 and 83 +/- 9% of added peroxynitrate, respectively, where the latter decreased to 54 +/- 6% in the presence of SOD. We therefore suggest that ca. 50% of O(2)NOO(-) homolyses into O(2)(*)(-) and (*)NO(2) (k = 1.05 +/- 0.23 s(-)(1)). The equilibrium constant of the homolysis of O(2)NOO(-) into (*)NO(2) and O(2)(*)(-) and the reduction potential of the couple O(2)NOOH,H(+)/NO(3)(-) were calculated to be 2.3 x 10(-)(10) M and 1.83 V, respectively.

Calpain-catalyzed proteolysis of human dUTPase specifically removes the nuclear localization signal peptide.

BACKGROUND: Calpain proteases drive intracellular signal transduction via specific proteolysis of multiple substrates upon Ca(2+)-induced activation. Recently, dUTPase, an enzyme essential to maintain genomic integrity, was identified as a physiological calpain substrate in Drosophila cells. Here we investigate the potential structural/functional significance of calpain-activated proteolysis of human dUTPase. METHODOLOGY/PRINCIPAL FINDINGS: Limited proteolysis of human dUTPase by mammalian m-calpain was investigated in the presence and absence of cognate ligands of either calpain or dUTPase. Significant proteolysis was observed only in the presence of Ca(II) ions, inducing calpain action. The presence or absence of the dUTP-analogue α,ß-imido-dUTP did not show any effect on Ca(2+)-calpain-induced cleavage of human dUTPase. The catalytic rate constant of dUTPase was unaffected by calpain cleavage. Gel electrophoretic analysis showed that Ca(2+)-calpain-induced cleavage of human dUTPase resulted in several distinctly observable dUTPase fragments. Mass spectrometric identification of the calpain-cleaved fragments identified three calpain cleavage sites (between residues (4)SE(5); (7)TP(8); and (31)LS(32)). The cleavage between the (31)LS(32) peptide bond specifically removes the flexible N-terminal nuclear localization signal, indispensable for cognate localization. CONCLUSIONS/SIGNIFICANCE: Results argue for a mechanism where Ca(2+)-calpain may regulate nuclear availability and degradation of dUTPase.

Cellular response to efficient dUTPase RNAi silencing in stable HeLa cell lines perturbs expression levels of genes involved in thymidylate metabolism.

dUTPase is involved in preserving DNA integrity in cells. We report an efficient dUTPase silencing by RNAi-based system in stable human cell line. Repression of dUTPase induced specific expression level increments for thymidylate kinase and thymidine kinase, and also an increased sensitization to 5-fluoro-2'-deoxyuridine and 5-fluoro-uracil. The catalytic mechanism of dUTPase was investigated for 5-fluoro-dUTP. The 5F-substitution on the uracil ring of the substrate did not change the kinetic mechanism of dUTP hydrolysis by dUTPase. Results indicate that RNAi silencing of dUTPase induces a complex cellular response wherein sensitivity towards fluoropyrimidines and gene expression levels of related enzymes are both modulated.

Reaction of ozone with hydrogen peroxide (peroxone process): a revision of current mechanistic concepts based on thermokinetic and quantum-chemical considerations.

The reaction of ozone with the anion of H(2)O(2) (peroxone process) gives rise to (*)OH radicals (Staehelin, J.; Hoigne, J. Environ. Sci. Technol. 1982, 16, 676-681). Thermokinetic considerations now suggest that the electron transfer originally assumed as the first step has to be replaced by the formation of an adduct, HO(2)(-) + O(3) --> HO(5)(-) (DeltaG degrees = -39.8 kJ mol(-1)). This decomposes into HO(2)(*) and O(3)(*-) (DeltaG(0) = 13.2 kJ mol(-1)). HO(2)(*) is in equilibrium with O(2)(*-) + H(+), and O(2)(*-) undergoes electron transfer to O(3) giving rise to further O(3)(*-). The decay of O(3)(*-) into (*)OH is now discussed on the basis of the equilibria O(3)(*-) right arrow over left arrow O(2) + O(*-) and O(*-) + H(2)O right arrow over left arrow (*)OH + OH(-), excluding HO(3)(*) as the intermediate originally assumed. To account for the observation of the peroxone process being only 50% efficient, the decay of HO(5)(-) into 2 O(2) + OH(-) (DeltaG(0) = -197 kJ mol(-1)) is proposed to compete with the decay into HO(2)(*) and O(3)(*-).

Drosophila proteins involved in metabolism of uracil-DNA possess different types of nuclear localization signals.

Adequate transport of large proteins that function in the nucleus is indispensable for cognate molecular events within this organelle. Selective protein import into the nucleus requires nuclear localization signals (NLS) that are recognized by importin receptors in the cytoplasm. Here we investigated the sequence requirements for nuclear targeting of Drosophila proteins involved in the metabolism of uracil-substituted DNA: the recently identified uracil-DNA degrading factor, dUTPase, and the two uracil-DNA glycosylases present in Drosophila. For the uracil-DNA degrading factor, NLS prediction identified two putative NLS sequences [PEKRKQE(320-326) and PKRKKKR(347-353)]. Truncation and site-directed mutagenesis using YFP reporter constructs showed that only one of these basic stretches is critically required for efficient nuclear localization in insect cells. This segment corresponds to the well-known prototypic NLS of SV40 T-antigen. An almost identical NLS segment is also present in the Drosophila thymine-DNA glycosylase, but no NLS elements were predicted in the single-strand-specific monofunctional uracil-DNA glycosylase homolog protein. This latter protein has a molecular mass of 31 kDa, which may allow NLS-independent transport. For Drosophila dUTPase, two isoforms with distinct features regarding molecular mass and subcellular distribution were recently described. In this study, we characterized the basic PAAKKMKID(10-18) segment of dUTPase, which has been predicted to be a putative NLS by in silico analysis. Deletion studies, using YFP reporter constructs expressed in insect cells, revealed the importance of the PAA(10-12) tripeptide and the ID(17-18) dipeptide, as well as the role of the PAAK(10-13) segment in nuclear localization of dUTPase. We constructed a structural model that shows the molecular basis of such recognition in three dimensions.

Kinetic and thermodynamic properties of the aminoxyl (NH2O*) radical.

The product of one-electron oxidation of (or H-atom abstraction from) hydroxylamine is the H2NO* radical. H2NO* is a weak acid and deprotonates to form HNO-*; the pKa(H2NO*) value is 12.6+/-0.3. Irrespective of the protonation state, the second-order recombination of the aminoxyl radical yields N2 as the sole nitrogen-containing product. The following rate constants were determined: kr(2H2NO*)=1.4x10(8) M-1 s-1, kr(H2NO*+HNO-*)=2.5x10(9) M-1 s-1, and kr(2HNO-*)=4.5x10(8) M-1 s-1. The HNO-* radical reacts with O2 in an electron-transfer reaction to yield nitroxyl (HNO) and superoxide (O2-*), with a rate constant of ke(HNO-*+O2-->HNO+O2-*)=2.2x10(8) M-1 s-1. Both O2 and O2-* seem to react with deprotonated hydroxylamine (H2NO-) to set up an autoxidative chain reaction. However, closer analysis indicates that these reactions might not occur directly but are probably mediated by transition-metal ions, even in the presence of chelators, such as ethylenediamine tetraacetic acid (EDTA) or diethylenetriamine pentaacetic acid (DTPA). The following standard aqueous reduction potentials were derived: E degrees (H2NO*,2H+/H3NOH+)=1.25+/-0.01 V; E degrees (H2NO*,H+/H2NOH)=0.90+/-0.01 V; and E degrees (H2NO*/H2NO-)=0.09+/-0.01 V. In addition, we estimate the following: E degrees (H2NOH+*/H2NOH)=1.3+/-0.1 V, E degrees (HNO, H+/H2NO*)=0.52+/-0.05 V, and E degrees (HNO/HNO-*)=-0.22+/-0.05 V. From the data, we also estimate the gaseous O-H and N-H bond dissociation enthalpy (BDE) values in H2NOH, with BDE(H2NO-H)=75-77 kcal/mol and BDE(H-NHOH)=81-82 kcal/mol. These values are in good agreement with quantum chemical computations.

Structure-activity relationship of cyclic nitroxides as SOD mimics and scavengers of nitrogen dioxide and carbonate radicals.

Synthetic nitroxide antioxidants attenuate oxidative damage in various experimental models. Their protective effect reportedly depends on ring size and ring substituents and is greater for nitroxides having lower oxidation potential. The present study focuses on the kinetics and mechanisms of the reactions of piperidine, pyrrolidine and oxazolidine nitroxides with HO2*/O2*-, *NO2 and CO3*- radicals, which are key intermediates in many inflammatory and degenerative diseases. It is demonstrated that nitroxides are the most efficient scavengers of *NO2 at physiological pH (k = (3-9) x 10(8) M(-1) s(-1)) and among the most effective metal-independent scavengers of CO3*- radicals (k = (2 - 6) x 10(8) M(-1) s(-1)). Their reactivity toward HO2*, though not toward *NO2 and CO3*-, depends on the nature of the ring side-chain and particularly on the ring-size. All nitroxide derivatives react slowly with O2*- and are relatively inefficient SOD mimics at physiological pH. Even piperidine nitroxides, having the highest SOD-like activity, demonstrate a catalytic activity of about 1000-fold lower than that of native SOD at pH 7.4. The present results do not indicate any correlation between the kinetics of HO2*/O2*-, *NO2 and CO3*- removal by nitroxides and their protective activity against biological oxidative stress and emphasize the importance of target-oriented nitroxides, i.e., interaction between the biological target and specific nitroxides.

Kinetic effects of hydrogen bonds on proton-coupled electron transfer from phenols.

The kinetics and mechanism of proton-coupled electron transfer (PCET) from a series of phenols to a laser flash generated [Ru(bpy)(3)](3+) oxidant in aqueous solution was investigated. The reaction followed a concerted electron-proton transfer mechanism (CEP), both for the substituted phenols with an intramolecular hydrogen bond to a carboxylate group and for those where the proton was directly transferred to water. Without internal hydrogen bonds the concerted mechanism gave a characteristic pH-dependent rate for the phenol form that followed a Marcus free energy dependence, first reported for an intramolecular PCET in Sjödin, M. et al. J. Am. Chem. Soc. 2000, 122, 3932-3962 and now demonstrated also for a bimolecular oxidation of unsubstituted phenol. With internal hydrogen bonds instead, the rate was no longer pH-dependent, because the proton was transferred to the carboxylate base. The results suggest that while a concerted reaction has a relatively high reorganization energy (lambda), this may be significantly reduced by the hydrogen bonds, allowing for a lower barrier reaction path. It is further suggested that this is a general mechanism by which proton-coupled electron transfer in radical enzymes and model complexes may be promoted by hydrogen bonding. This is different from, and possibly in addition to, the generally suggested effect of hydrogen bonds on PCET in enhancing the proton vibrational wave function overlap between the reactant and donor states. In addition we demonstrate how the mechanism for phenol oxidation changes from a stepwise electron transfer-proton transfer with a stronger oxidant to a CEP with a weaker oxidant, for the same series of phenols. The hydrogen bonded CEP reaction may thus allow for a low energy barrier path that can operate efficiently at low driving forces, which is ideal for PCET reactions in biological systems.

Kinetics and mechanism of *NO2 reacting with various oxidation states of myoglobin.

Nitrogen dioxide ((*)NO(2)) participates in a variety of biological reactions. Of great interest are the reactions of (*)NO(2) with oxymyoglobin and oxyhemoglobin, which are the predominant hemeproteins in biological systems. Although these reactions occur rapidly during the nitrite-catalyzed autoxidation of hemeproteins, their roles in systems producing (*)NO(2) in the presence of these hemeproteins have been greatly underestimated. In the present study, we employed pulse radiolysis to study directly the kinetics and mechanism of the reaction of oxymyoglobin (MbFe(II)O(2)) with (*)NO(2). The rate constant of this reaction was determined to be (4.5 +/- 0.3) x 10(7) M(-1)s(-1), and is among the highest rate constants measured for (*)NO(2) with any biomolecule at pH 7.4. The interconversion among the various oxidation states of myoglobin that is prompted by nitrogen oxide species is remarkable. The reaction of MbFe(II)O(2) with (*)NO(2) forms MbFe(III)OONO(2), which undergoes rapid heterolysis along the O-O bond to yield MbFe(V)=O and NO(3-). The perferryl-myoglobin (MbFe(V)=O) transforms rapidly into the ferryl species that has a radical site on the globin ((*)MbFe(IV)=O). The latter oxidizes another oxymyoglobin (10(4) M(-1)s(-1) < k(17) < 10(7) M(-1)s(-1)) and generates equal amounts of ferrylmyoglobin and metmyoglobin. At much longer times, the ferrylmyoglobin disappears through a relatively slow comproportionation with oxymyoglobin (k(18) = 21.3 +/- 5.3 M(-1)s(-1)). Eventually, each (*)NO(2) radical converts three oxymyoglobin molecules into metmyoglobin. The same intermediate, namely MbFe(III)OONO(2), is also formed via the reaction peroxynitrate (O(2)NOO(-)/O(2)NOOH) with metmyoglobin (k(19) = (4.6 +/- 0.3) x 10(4) M(-1)s(-1)). The reaction of (*)NO(2) with ferrylmyoglobin (k(20) = (1.2 +/- 0.2) x 10(7) M(-1)s(-1)) yields MbFe(III)ONO(2), which in turn dissociates (k(21) = 190 +/- 20 s(-1)) into metmyoglobin and NO(3-). This rate constant was found to be the same as that measured for the decay of the intermediate formed in the reaction of MbFe(II)O(2) with (*)NO, which suggests that MbFe(III)ONO(2) is the intermediate observed in both processes. This conclusion is supported by thermokinetic arguments. The present results suggest that hemeproteins may detoxify (*)NO(2) and thus preempt deleterious processes, such as nitration of proteins. Such a possibility is substantiated by the observation that the reactions of (*)NO(2) with the various oxidation states of myoglobin lead to the formation of metmyoglobin, which, though not functional in the gas transport, is nevertheless nontoxic at physiological pH.

Reactions of nitric oxide, peroxynitrite, and carbonate radicals with nitroxides and their corresponding oxoammonium cations.

Cyclic nitroxides effectively protect biological systems against radical-induced damage. However, the mechanism of the reactions of nitroxides with nitrogen-derived reactive species and carbonate radicals is far from being elucidated. In the present study, the reactions of several representative piperidine- and pyrrolidine-based nitroxides with *NO, peroxynitrite, and CO3*- were investigated, and the results are as follows: (i) There is no evidence for any direct reaction between the nitroxides and the *NO. In the presence of oxygen, the nitroxides are readily oxidized by *NO2, which is formed as an intermediate during autoxidation of *NO. (ii) *NO reacts with the oxoammonium cations to form nitrite and the corresponding nitroxides with k1 = (9.8 +/- 0.2) x 10(3) and (3.7 +/- 0.1) x 10(5) M(-1) s(-1) for the oxoammonium cations derived from 2,2,6,6-tetramethylpiperidine-1-oxyl (TPO) and 3-carbamoyl-proxyl (3-CP), respectively. (iii) CO3*- oxidizes all nitroxides tested to their oxoammonium cations with similar rate constants of (4.0 +/- 0.5) x 10(8) M(-1) s(-1), which are about 3-4 times higher than those determined for H-abstraction from the corresponding hydroxylamines TPO-H and 4-OH-TPO-H. (iv) Peroxynitrite ion does not react directly with the nitroxides but rather with their oxoammonium cations with k(10) = (6.0 +/- 0.9) x 10(6) and (2.7 +/- 0.9) x 10(6) M(-1) s(-1) for TPO+ and 3-CP+, respectively. These results provide a better insight into the complex mechanism of the reaction of peroxynitrite with nitroxides, which has been a controversial subject. The small effect of relatively low concentrations of nitroxides on the decomposition rate of peroxynitrite is attributed to their ability to scavenge efficiently *NO2 radicals, which are formed during the decomposition of peroxynitrite in the absence and in the presence of CO2. The oxoammonium cations, thus formed, are readily reduced back to the nitroxides by ONOO-, while forming *NO and O2. Hence, nitroxides act as true catalysts in diverting peroxynitrite decomposition from forming nitrating species to producing nitrosating ones.

The rate of homolysis of adducts of peroxynitrite to the C=O double bond.

Nucleophilic addition of the peroxynitrite anion, ONOO(-), to the two prototypical carbonyl compounds, acetaldehyde and acetone, was investigated in the pH interval 7.4-14. The process is initiated by fast equilibration between the reactants and the corresponding tetrahedral adduct anion, the equilibrium being strongly shifted to the reactant side. The adduct anion also undergoes fast protonation by water and added buffers. Consequently, the rate of the bimolecular reaction between ONOO(-) and the carbonyl is strongly dependent on the pH and on the concentration of the buffer. The pK(a) of the carbonyl-ONOO adduct was estimated to be approximately 11.8 and approximately 12.3 for acetone and acetaldehyde, respectively. It is shown that both the anionic and the neutral adducts suffer fast homolysis along the weak O-O bond to yield free alkoxyl and nitrogen dioxide radicals. The yield of free radicals was determined to be about 15% with both carbonyl compounds at low and high pH, while the remainder collapses to molecular products in the solvent cage. The rate constants for the homolysis of the adducts vary from ca. 3 x 10(5) to ca. 5 x 10(6) s(-1), suggesting that they cannot act as oxidants in biological systems. This small variation around a mean value of about 10(6) s(-1) suggests that the O-O bond in the adduct is rather insensitive to its protonation state and to the nature of its carbonyl precursor. An overall reaction scheme was proposed, and all the corresponding rate constants were evaluated. Finally, thermokinetic considerations were employed to argue that the formation of dioxirane as an intermediate in the reaction of ONOO(-) with acetone is an unlikely process.