Comparative study of the reaction kinetics of cytochrome P-450 reduction by NADPH-cytochrome P-450 reductase and dithionite

The reactions of NADPH- or dithionite-dependent reduction of cytochrome P-450 were studied using a stopped flow technique. It was found that the kinetic curves for both reactions may be fitted by a sum of the two exponents. The arrhenius plots for the fast phase rate constants are linear for both reactions. On the contrary, the breaks on the corresponding plots for the slow phase rate constants are observed at 22 and 33 degrees C for cytochrome P-450 reduction by dithionite and at 31 degrees C for NADPH-dependent reduction of cytochrome P-450. The coincidence of the values of the rate constants and activation energy (56 +/- 5 kJ/mol) for the fast phase of NADPH-dependent reduction of cytochrome P-450 with values of catalytic constants and activation energy for demethylation of tertiary amines suggests that the first electron transfer process from NADPH-cytochrome P-450 reductase to cytochrome P-450 may be the rate-limiting step. A diverse character of the kinetic parameters for the two cytochrome P-450 reduction reactions is indicative of different nature of biphasity of these processes.     

Metabolic Fluxes Between [14C]2-Deoxy-D-Glucose and [14C]2-Deoxy-D-Glucose-6-Phosphate in Brain In Vivo

The rates of the phosphorylation and dephosphorylation of 2-deoxyglucose were measured in rat brain in vivo using tracer kinetic techniques. The rate constant for each reaction was estimated from two separate experiments with different protocols for tracer administration. Tracer amounts of [1-14C]2-deoxyglucose (1 microCi) were injected through the internal carotid artery (intraarterial experiment), or through the atrium (intravenous experiment). Brains were sampled by freeze-blowing at various times after the injection. In the intraarterial experiment, the rate constant for the forward reaction from 2-deoxyglucose to 2-deoxyglucose phosphate was calculated by dividing the initial rate of 2-deoxyglucose phosphate production by the 2-deoxyglucose content in brain. The rate constant for the reverse reaction from 2-deoxyglucose phosphate to 2-deoxyglucose was calculated from the decay constant of 2-deoxyglucose phosphate. The rate constants estimated were 10.1 +/- 1.4%/min (SD) and 3.00 +/- 0.01%/min (SD), respectively, for the forward and reverse reactions. In the intravenous experiment, rate constants for both reactions were estimated by compartmental analysis. By fitting data to program SAAM-27, the rate constants for the forward and reverse reactions were estimated as 11.4 +/- 0.4%/min (SD) and 5.1 +/- 0.4%/min (SD), respectively. The rate constants determined were compared to those for the reactions between glucose and glucose-6-phosphate, estimated previously from labeled glucoses. It is concluded that the rate of glucose utilization measured by the 2-deoxyglucose method reflects the rate of the hexokinase reaction and not the rate of glucose utilization or brain energy utilization.     

The apparent inhibition of superoxide dismutase activity by quinones

It has been demonstrated that several quinones can modify the activity of bovine copper superoxide dismutase by undergoing equilibrium reactions with superoxide radicals. The extent of this apparent inhibition correlates with the one electron reduction potentials of the quinones and the equilibrium constants of the semiquinone radical/superoxide radical reactions. Various rate constants have been estimated including those for the reactions of semiquinone radicals with cytochrome c and with superoxide dismtuase. Semiquinone radicals cannot be dismutated by superoxide dismutase.     

Oxidation and reduction of cytochrome c bound to the phosphoprotein phosvitin

The oxidation-reduction reactions and structural characteristics of phosvitin-bound cytochrome c were examined at various ratios of cytochrome c to phosvitin. At binding ratios below half the maximum, the rate constants for the oxidation reactions with cytochrome c oxidase and ferricyanide and the rate constants for the reduction reactions with cytochrome b2 and ascorbate were low, but at higher ratios these rate constants gradually increased to that of free cytochrome c and, in particular, the rate constant for oxidation by cytochrome c oxidase was raised to two to three times that of the free form. This binding-ratio dependence of the rate constants for the oxidation and reduction reactions was different from that of the net charge of the cytochrome c-phosvitin complex, implying that the negative charges of phosvitin are unlikely to modulate the rates. In contrast, the broadening of the NMR signals for the heme and methionine-80 methyl groups and the conformational transition in the vicinity of the heme moiety on change from the native to the cyanide-bound or urea-denatured form of cytochrome c showed a similar binding-ratio dependence to the rate constants for the oxidation and reduction reactions. Since the conformation and electronic structure in the heme environment of ferric and ferrous cytochromes c were not changed significantly by binding to phosvitin, and since the binding strength of cytochrome c to phosvitin at binding ratios below half the maximum is different from that at higher ratios, these findings suggest that a difference in the movement of cytochrome c in its complex with phosvitin may modulate its oxidation-reduction reactions.     

Application of Marcus theory of electron transfer for the reactions between HRP compound I and II and 2,4-disubstituted phenols

Reactions between horseradish peroxidase (HRP) compound I and II and some natural phenolic antioxidants were studied at pH 7. The bimolecular rate constants for these reactions were determined using a sequential mixing stopped-flow spectrometer. The rate constants for the reactions of compound I were found to be two orders of magnitude higher than those for compound II. The phenols under study showed a significant difference in their one-electron reduction potential values. As the rate constants also changed systematically with their one-electron potentials, the Marcus theory of electron transfer was applied to the above determined rate constants and the thermodynamic driving force (deltaG(o)), from which the reorganization energy (lambda) for the electron transfer from phenols to both compound I and II was estimated.     

The temperature dependences of some types of gaseous ionic reactions of astrochemical interest.

The rate constants of ion-molecule reactions which are of potential significance in astrochemical systems are found to exhibit significant, and in many cases, negative temperature dependences. The rate constants of fast ion-polar molecule reactions (e.g., XH+ + B leads to BH+ + X) may increase by a factor of 5-10 between 1000 and 10D. Slow reactions that proceed via reaction complexes (e.g., H- transfer and association reactions) often exhibit temperature dependences of the form k = AT-n, n = 1-5. Both transition state theory considerations and the coupled-oscillator RRK-type model are seen to be able to account qualitatively for the behavior of slow ion-molecule reactions.     

An evolutionary approach to enzyme kinetics: Optimization of ordered mechanisms

A theoretical investigation is presented which allows the calculation of rate constants and phenomenological parameters in states of maximal reaction rates for unbranched enzymic reactions. The analysis is based on the assumption that an increase in reaction rates was an important characteristic of the evolution of the kinetic properties of enzymes. The corresponding nonlinear optimization problem is solved taking into account the constraint that the rate constants of the elementary processes do not exceed certain upper limits. One-substrate-one-product reactions with two, three and four steps are treated in detail. Generalizations concern ordered uni-uni-reactions involving an arbitrary number of elementary steps. It could be shown that depending on the substrate and product concentrations different types of solutions can be found which are classified according to the number of rate constants assuming in the optimal state submaximal values. A general rule is derived concerning the number of possible solutions of the given optimization problem. For high values of the equilibrium constant one solution always applies to a very large range of the concentrations of the reactants. This solution is characterized by maximal values of the rate constants of all forward reactions and by non-maximal values of the rate constants of all backward reactions. Optimal kinetic parameters of ordered enzymic mechanisms with two substrates and one product (bi-uni-mechanisms) are calculated for the first time. Depending on the substrate and product concentrations a complete set of solutions is found. In all cases studied the model predicts a matching of the concentrations of the reactants and the corresponding Michaelis constants, which is in good accordance with the experimental data. It is discussed how the model can be applied to the calculation of the optimal kinetic design of real enzymes.     

Determination of relative rate constants for in vitro RNA processing reactions by internal competition

Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.     

State-dependent Accessibility and Electrostatic Potential in the Channel of the Acetylcholine Receptor : Inferences from Rates of Reaction of Thiosulfonates with Substituted Cysteines in the M2 Segment of the α Subunit

Ion channel function depends on the chemical and physical properties and spatial arrangement of the residues that line the channel lumen and on the electrostatic potential within the lumen. We have used small, sulfhydryl-specific thiosulfonate reagents, both positively charged and neutral, to probe the environment within the acetylcholine (ACh) receptor channel. Rate constants were determined for their reactions with cysteines substituted for nine exposed residues in the second membrane-spanning segment (M2) of the α subunit. The largest rate constants, both in the presence and absence of ACh, were for the reactions with the cysteine substituted for αThr244, near the intracellular end of the channel. In the open state of the channel, but not in the closed state, the rate constants for the reactions of the charged reagents with several substituted cysteines depended on the transmembrane electrostatic potential, and the electrical distance of these cysteines increased from the extracellular to the intracellular end of M2. Even at zero transmembrane potential, the ratios of the rate constants for the reactions of three positively charged reagents with αT244C, αL251C, and αL258C to the rate constant for the reaction of an uncharged reagent were much greater in the open than in the closed state. This dependence of the rate constants on reagent charge is consistent with an intrinsic electrostatic potential in the channel that is considerably more negative in the open state than in the closed state. The effects of ACh on the rate constants for the reactions of substituted Cys along the length of αM2, on the dependence of the rate constants on the transmembrane potential, and on the intrinsic potential support a location of a gate more intracellular than αThr244.     

The rate constants of the reaction of hydroxyl radicals (*OH) with alcohol dehydrogenase and Glyceraldehyde-3-phosphate dehydrogenase

The rate constants of the reactions of alcohol dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase with hydroxyl radicals were determined using the method of steady-state competitive reactions. Ethanol was used as a scavenger of hydroxyl radicals. The rate constants of the reactions of hydroxyl radicals with alcohol dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase were found to be 2.8 x 10(12) dm(3) mol(-1) s(-1), and 1.6 x 10(12) dm(3) mol(-1) s(-1), respectively.     

Sensitivity to values of the rate constants in a neurochemical metabolic model

Equations were derived for the instantaneous relative sensitivities of reaction rates (controllability indices) and metabolite concentrations (response indices) to perturbations in the values of rate constants and were used to analyze the behavior of a model of in vivo glutamate metabolism in rat brain. Controllabilities of reversible reactions were found to increase as the values of the corresponding rate constants (i.e., the rate of approach to equilibrium) increased. Response indices generally declined with the metabolic distance between the metabolite and the rate constant, but they were unexpectedly high for reversible reactions with high controllabilities. The transient response of a given metabolite is most sensitive to reactions involving metabolites which are changing most rapidly relative to their respective pool sizes. Rapidly reversible reactions are most important for communication between metabolite pools.     

Kinetics of conformational change of troponin-C induced by proton binding or removal in the absence of calcium ions.

The kinetics of the conformational change of troponin-C induced by binding or removal of protons was studied by a stopped-flow pH-jump spectrofluorometric method. In the pH-down experiment (to investigate the kinetics of conformational change from the deprotonated state to the protonated state), a single first-order reaction with a rate constant and amplitude of 1.75-2.4 sec-1 and around 10% respectively, was observed. On the other hand, two first-order reactions with rate constants of 0.84-1.6 sec-1 and 0.08-0.4 sec-1 were observed in the pH-up experiment, the total amplitudes of these reactions being around 10-20%. The pH dependences of the rate constants of these reactions were analyzed in terms of a three-species mechanism.     

Calculating reaction rate constants and estimating the efficacy of selective enzyme inhibitors

The dynamic steady state of a pair of forward and backward enzymatic reactions is dependent on the balance between the enzymes catalyzing the reactions. By selectively inhibiting one or more of the enzymes involved, this balance is shifted into a new steady state, making it possible to calculate the reaction rate constants after measurement of the reactants. Ideally, the inhibitors should completely eliminate either reaction, but this is often not the case. Here we present and discuss a method for calculating the reaction rate constants and, thus, for evaluating the efficacy of one or more inhibitors when introduced to a forward-backward pair of enzymatic reactions.     

Quantitative correlations relating the interaction of Zn(II)-tetraphenylporphine and horseradish peroxidase with amines

Reactions of nucleophilic substitution and enzymatic processes involving metalloporphirins (MP) are considered in terms of coordination of zinc(II)tetraphenylporphine (Zn-TPhP) with corresponding ligands/nucleophiles/substrates/bases. Linear correlations are performed between kinetic parameters of the Zn-TPhP coordination processes in chloroform (stability constants) and reactions of nucleophilic substitution both in aqueous and organic solvents involving pyridines, pyridine N-oxides, anilines, primary amines, as well as in reactions of oxidation of anilines with horseradish peroxidase in aqueous media (rate constants). Thermodynamic parameters of the complex formation and nucleophilic substitution linearly correlate with each other in the case of pyridines, anilines, and primary amines.     

Exchange and shuttling of electrons by nitroxide spin labels

The ability of nitroxide spin labels to act as oxidizers of reduced nitroxides (hydroxylamines) in biological and model systems was demonstrated. All of the nitroxides tested were able to act as oxidizing agents with respect to hydroxylamine derivatives of nitroxides. The rates of these reactions were first order with respect to nitroxide concentration and with respect to hydroxylamine concentration, making the reaction second order overall. The second-order rate constants are reported for a number of these reactions. These reactions proceeded to an equilibrium state and the equilibrium constants for several combinations of reactants are presented. Both the rate constants and the equilibrium constants were found to be dependent on the ring structure of the nitroxide and hydroxylamine, with piperidines being reduced more easily and pyrrolidines and oxazolidines being oxidized more easily. All of the hydroxylamine derivatives were oxidized by air to their respective nitroxides, with the rate of this oxidation greater for pyrrolidines than for piperidines. Furthermore, hydroxylamines that are permeable to lipid bilayers were able to act as shuttles of reducing equivalents to liposome-encapsulated nitroxides that were otherwise inaccessible to reducing agents. This mechanism of shuttling of electrons was able to explain the relatively rapid reduction by cells of a nonpermeable nitroxide in the presence of a permeable nitroxide.     

The effects of thioureylene compounds (goitrogens) on lactoperoxidase activity.

The rates of oxidation of several goitrogens by lactoperoxidase and the rates of inactivation of lactoperoxidase by the same goitrogens have been measured. The influence of iodide on both reactions has also been evaluated. It has been shown by us that iodide acts catalytically in regulating lactoperoxidase activity at pH 8.8. The rate data have been analyzed by a computer program which solves the differential equations for the above mentioned reactions. From this computer analysis we have been able to obtain binding constants of the goitrogens and inactivation rate constants of lactoperoxidase. Iodide was shown to inhibit goitrogenic activity either by increasing the rate of drug oxidation or by reducing the rate of enzyme inactivation, or both, depending on the particular drug. Iodide had little or no effect on the goitrogen-binding constants. We have also shown that the relative rates of enzyme inactivation can be correlated with the potency of the goitrogen as an antithyroid drug.     

Oxidations of p-alkoxyacylanilides catalyzed by human cytochrome P450 1A2: structure-activity relationships and simulation of rate constants of individual steps in catalysis

Human cytochrome P450 (P450) 1A2 is involved in the oxidation of many important drugs and carcinogens. The prototype substrate phenacetin is oxidized to an acetol as well as the O-dealkylation product [Yun, C.-H., Miller, G. P., and Guengerich, F. P. (2000) Biochemistry 39, 11319-11329]. In an effort to improve rates of catalysis of P450 1A2 enzymes, we considered a set of p-alkoxyacylanilide analogues of phenacetin and found that variations in the O-alkyl and N-acyl substituents altered the rates of the two oxidation reactions and the ratio of acetol/phenol products. Moving one methylene group of phenacetin from the O-alkyl group to the N-acyl moiety increased rates of both oxidations approximately 5-fold and improved the coupling efficiency (oxidation products formed/NADPH consumed) from 6% to 38%. Noncompetitive kinetic deuterium isotope effects of 2-3 were measured for all O-dealkylation reactions examined with wild-type P450 1A2 and the E225I mutant, which has 6-fold higher activity. A trend of decreasing kinetic deuterium isotope effect for E225I > wild-type > mutant D320A was observed for O-demethylation of p-methoxyacetanilide, which follows the trend for k(cat). The set of O-dealkylation and acetol formation results for wild-type P450 1A2 and the E225I mutant with several of the protiated and deuterated substrates were fit to a model developed for the basic catalytic cycle and a set of microscopic rate constants in which the only variable was the rate of product formation (substrate oxygenation, including hydrogen abstraction). In this model, k(cat) is considerably less than any of the microscopic rate constants and is affected by several individual rate constants, including the rate of formation of the oxygenating species, the rate of substrate oxidation by the oxygenating species, and the rates of generation of reduced oxygen species (H(2)O(2), H(2)O). This analysis of the effects of the individual rate constants provides a framework for consideration of other P450 reactions and rate-limiting steps.     

Steady-state parameters of an enzyme from n.m.r. spin transfer with thermal variation.

N.m.r. spin-exchange analysis of enzymic reactions at chemical equilibrium is akin to radioactive-tracer-exchange analysis; unidirectional flux rates are obtained for the overall reaction. These data, by themselves, are not sufficient to define the values of all the individual rate constants or steady-state parameters. However, it is shown that, by measuring the dependence of the exchange rate constants on solute concentration and temperature, the individual rate constants, and hence the steady-state parameters, can be obtained for a simple enzyme system.     

Mechanism of reaction of nitrogen dioxide radical with hydroxycinnamic acid derivatives: A pulse radiolysis study

Nitrogen dioxide radical (NO^·₂) is known as a toxic agent produced in the metabolism of nitrates and nitrites. By the use of the pulse radiolysis technique, the mechanism of the reaction of NO^·₂ radical with hydroxycinnamic acid derivatives (HCA) was studied and the rate constants have been measured. The rate constants were found to be 7.4 × 10⁸, 7.2 × 10⁸, 8.6 × 10⁸ dm³ mol^-1s^-1 for ferulic acid, sinapic acid and caffeic acid, respectively. The reactions produce the corresponding phenoxyl radical.