Studies on succinate dehydrogenase. IV. Kinetics of the overall reaction catalysed by preparations of the purified enzyme

Computationally modeling mammalian succinate dehydrogenase kinetics identifies the origins and primary determinants of ROS production

Succinate dehydrogenase (SDH) is an inner mitochondrial membrane protein complex that links the Krebs cycle to the electron transport system. It can produce significant amounts of superoxide ([Formula: see text]) and hydrogen peroxide (H₂O₂); however, the precise mechanisms are unknown. This fact hinders the development of next-generation antioxidant therapies targeting mitochondria. To help address this problem, we developed a computational model to analyze and identify the kinetic mechanism of [Formula: see text] and H₂O₂ production by SDH. Our model includes the major redox centers in the complex, namely FAD, three iron-sulfur clusters, and a transiently bound semiquinone. Oxidation state transitions involve a one- or two-electron redox reaction, each being thermodynamically constrained. Model parameters were simultaneously fit to many data sets using a variety of succinate oxidation and free radical production data. In the absence of respiratory chain inhibitors, model analysis revealed the 3Fe-4S iron-sulfur cluster as the primary [Formula: see text] source. However, when the quinone reductase site is inhibited or the quinone pool is highly reduced, [Formula: see text] is generated primarily by the FAD. In addition, H₂O₂ production is only significant when the enzyme is fully reduced, and fumarate is absent. Our simulations also reveal that the redox state of the quinone pool is the primary determinant of free radical production by SDH. In this study, we showed the importance of analyzing enzyme kinetics and associated side reactions in a consistent, quantitative, and biophysically detailed manner using a diverse set of experimental data to interpret and explain experimental observations from a unified perspective.

Toxicity evaluation of silver nanoparticles synthesized by chemical and green route in different experimental models

With the increased exposure of silver nanoparticles (AgNPs) to human beings, the risk and safety should be considered. In this study, nephro-toxicity of AgNPs prepared by chemical and green route (aqueous extract of Desmodium gangeticum root) in rat, proximal epithelial cell lines and renal mitochondria was evaluated. AgNPs (100 mg/kg) were administered orally to the wistar rats. After 15 d, we observed significant changes in the renal architecture of both AgNPs, supported by the urine and blood chemistry data. Further, exposure towards renal epithelial cells and renal mitochondria also confirm the toxic similarities between the AgNPs synthesized from two routes.

Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase

The E. coli protein WrbA is an FMN-dependent NAD(P)H:quinone oxidoreductase that has been implicated in oxidative defense. Three subunits of the tetrameric enzyme contribute to each of four identical, cavernous active sites that appear to accommodate NAD(P)H or various quinones, but not simultaneously, suggesting an obligate tetramer with a ping-pong mechanism in which NAD departs before oxidized quinone binds. The present work was undertaken to evaluate these suggestions and to characterize the kinetic behavior of WrbA. Steady-state kinetics results reveal that WrbA conforms to a ping-pong mechanism with respect to the constancy of the apparent Vmax to Km ratio with substrate concentration. However, the competitive/non-competitive patterns of product inhibition, though consistent with the general class of bi-substrate reactions, do not exclude a minor contribution from additional forms of the enzyme. NMR results support the presence of additional enzyme forms. Docking and energy calculations find that electron-transfer-competent binding sites for NADH and benzoquinone present severe steric overlap, consistent with the ping-pong mechanism. Unexpectedly, plots of initial velocity as a function of either NADH or benzoquinone concentration present one or two Michaelis-Menten phases depending on the temperature at which the enzyme is held prior to assay. The effect of temperature is reversible, suggesting an intramolecular conformational process. WrbA shares these and other details of its kinetic behavior with mammalian DT-diaphorase, an FAD-dependent NAD(P)H:quinone oxidoreductase. An extensive literature review reveals several other enzymes with two-plateau kinetic plots, but in no case has a molecular explanation been elucidated. Preliminary sedimentation velocity analysis of WrbA indicates a large shift in size of the multimer with temperature, suggesting that subunit assembly coupled to substrate binding may underlie the two-plateau behavior. An additional aim of this report is to bring under wider attention the apparently widespread phenomenon of two-plateau Michaelis-Menten plots.

Fumarate reductase activity of bovine heart succinate-ubiquinone reductase. New assay system and overall properties of the reaction

A simple system for aerobic assay of the quinol-fumarate reductase reaction catalyzed by purified soluble bovine heart succinate-ubiquinone reductase in the presence of NADH, NAD(P)H-quinone reductase (DT-diaphorase) and an appropriate quinone is described. The reaction is inhibited by carboxin, suggesting that the same quinone/quinol binding site is involved in electron transfer from succinate to ubiquinone and from ubiquinol to fumarate. The kinetic properties of the reaction in both directions and comparative affinities of the substrate binding sites of the enzyme to substrates (products) and competitive inhibitors are reported. Considerable difference in affinity of the substrates binding site to oxaloacetate was demonstrated when the enzyme was assayed in the direct and reverse directions. These results were taken to indicate that the oxidized dicarboxylate-free enzyme is an intermediate during the steady-state succinate-ubiquinone reductase reaction, whereas the reduced dicarboxylate-free enzyme is an intermediate of the steady-state ubiquinol-fumarate reductase reaction. No difference in the reactivity of the substrate-protected cysteine and arginine residues was found when the pseudo-first-order rate constants for N-ethylmaleimide and phenylglyoxal inhibition were determined for oxidized and quinol-reduced enzyme. Quinol-fumarate reductase activity was reconstituted from the soluble succinate dehydrogenase and low-molecular-mass ubiquinone reactivity conferring protein(s). No reduction of cytochrome b was observed in the presence of quinol generating system, whereas S-3 low temperature EPR-detectable iron-sulfur center was completely reduced by quinol under equilibrium (without fumarate) or steady-state (in the presence of fumarate). No significant reduction of ferredoxin type iron-sulfur centers was detected during the steady-state quinol-fumarate oxidoreductase reaction. The data obtained eliminate participation of cytochrome b in the quinol-fumarate reductase reaction and show that the rate limiting step of the overall reaction lies between iron-sulfur center S-3 and lower midpoint potential redox components of the enzyme.

Simulation of the purine nucleotide cycle as an anaplerotic process in skeletal muscle

A computer model of purine nucleotide and citric acid cycles joined through fumarate is given. Steady-state equations corresponding to metabolic enzymes are written based on the information from the literature about their kinetic behavior. Numerical integration of this set of equations is performed and in order to maintain an overall stabilization between the two cycles, enzymatic activities, in the form of V, have been calculated. Sensitivity coefficients for enzymes indicate that the control is exerted, depending upon the intermediate concentrations, and furthermore, it is demonstrated that AMP concentration in muscle should be very low. From stabilization, simulation of exercise conditions has been performed by diminishing [ATP] and increasing accordingly [ADP] and [AMP]. In such conditions the operation of purine nucleotide cycle leads to a considerable increase in the level of citric acid cycle intermediates. Disruption of purine nucleotide cycle by altering some of the three enzymatic steps leads to a lesser increase of these intermediates. The set of results presented seems to confirm the hypothesis that purine nucleotide cycle acts as an anaplerotic process in muscle, as the experimental results of Aragon and Lowenstein (Aragon, J.J., and Lowenstein, J.M. (1980) Eur. J. Biochem. 110, 371-377) suggest.

Kinetic behaviour of succinate dehydrogenase of three fibre types in skeletal muscle. I. Effects of temperature and a competitive inhibitor

The kinetic behaviour of succinate dehydrogenase [EC 1.3.99.1] in three fibre types of rat gastrocnemius was examined by a quantitative histochemical method without disruption of the cellular structure. 2-(2-Benzothiazolyl)-3-(4-phthalhydrazidyl)-5-styryl-t etrazolium chloride (BPST) and phenazine methosulphate were used as electron acceptors. On measurement of the absorbance value at 530 nm of BPST formazan, produced by the succinate dehydrogenase reaction in sections, it was found that the staining intensity of succinate dehydrogenase was linearly proportional to both the incubation time and the thickness of the slice therefore, the initial velocity of the staining could be calculated. By Michaelis-Menten (1913) treatment of the dependence of the initial velocity on the substrate concentration in the absence and the presence of a competitive inhibitor, malonate, the Km and Vmax values for succinate and the Ki value for malonate were obtained. The Km and Ki values of the three fibre types were similar. The ration of the Vmax values of type A, B and C fibres was 1.0:2.0:3.3. The temperature dependence of the kinetic parameters was very similar in the three fibre types. These findings confirm that the differences in the staining intensity of the three fibre types reflect differences in the amounts, but not the properties, of succinate dehydrogenase.

Interaction of the membrane-bound succinate dehydrogenase with substrate and competitive inhibitors

The protective effect of dicarboxylates on the active-site-directed inhibition of the membrane-bound succinate dehydrogenase by N-ethylmaleimide, steady-state kinetics methods for Ki and Ks determinations, and equilibrium studies were employed to quantitate the relative affinities of succinate, fumarate, malonate and oxaloacetate to the reduced and oxidized species of the enzyme. A more than 10-fold difference in the relative affinities of the reduced and oxidized succinate dehydrogenase to succinate, fumarate and oxaloacetate is found, whereas the reactivity of the active-site sulphydryl group does not depend on the redox state of the enzyme. The redox-state-dependent changes in the affinity of the membrane-bound succinate dehydrogenase to oxaloacetate can be quantitatively accounted for by a 10-fold increase in the rate of dissociation of the enzyme-inhibitor complex which occurs upon reduction of the enzyme. The data obtained give no support for either the existence of a sulphydryl group other than the active-site one important for the catalysis or for the presence of a separate dicarboxylate-specific regulatory site in the succinate dehydrogenase molecule.

Sulphate ion-induced slow transformation of succinate dehydrogenase

A new type of slow change of succinate dehydrogenase (EC 1.3.99), activity which is induced by sulphate ion is described. After preincubation of submitochondrial particles or soluble succinate dehydrogenase with sulphate both preparations catalyze succinate:phenazine methosulphate reductase reaction with a significant lag. When added to the assay medium sulphate ion induces biphasic time-dependent competitive inhibition of the enzyme. The sulphate-induced inhibition is apparently due to a rapid interaction of the anion with an active site of the enzyme which is followed by a slow pH-dependent (pKa = 7.2) transformation of the enzyme-inhibitor complex. pH profiles of the overall succinate dehydrogenase reaction and of equilibrium between fast and slow enzyme-sulphate complexes suggest that the same protolytic equilibrium step is involved in the formation of an active intermediate and an inactive enzyme-sulphate complex.

Studies on the succinate dehydrogenating system. I. Kinetics of the succinate dehydrogenase interaction with a semiquindiimine radical of N,N,N',N'-tetramethyl-p-phenylenediamine

1. The activities of the soluble reconstitutively active succinate dehydrogenase (EC 1.3.99.1) measured with three artificial electron acceptors, e.g. ferricyanide, phenazine methosulfate and free radical of N,N,N',N'-tetramethyl-p-phenylenediamine (WB), have been compared. The values estimated by extrapolation to infinite acceptor concentration using double reciprocal plots 1/v versus 1/[acceptor] are nearly the same for ferricyanide and phenazine methosulfate and about twice as high for the WB. 2. The double reciprocal plots 1/v versus 1/[succinate] in the presence of malonate at various concentrations of WB give a series of straight lines intercepting in the third quadrant. The data support the mechanism of the overall reaction, in which the reduced enzyme is oxidized by WB before dissociation of the enzyme-product complex. 3. The dependence of the rate of the overall reaction on WB concentration shows that only one kinetically significant redox site of the soluble succinate dehydrogenase is involved in the reduction of WB. 4. Studies of the change of V and Km values during aerobic inactivation of the soluble enzyme suggest that only 'the low Km ferricyanide reactive site' (Vinogradov, A.D., Gavrikova, E.V. and Goloveshkina, V.G. (1975) Biochem. Biophys, Res. Commun. 65, 1264--1269) is involved in reoxidation of the reduced enzyme by WB. 5. The pH dependence of V for the succinate-WB reductase reaction shows that the group of the enzyme with the pKa value of 6.7 at 22 degrees C is responsible for the reduction of dehydrogenase in the enzyme-substrate complex. 6. When WB interacts with the succinate-ubiquinone region of the respiratory chain, the double reciprocal plot 1/v versus 1/[WB] gives a straight line. The thenoyltrifluoroacetone inhibition of succinate-ubiquinone reductase or extraction of ubiquinone alter the 1/v versus 1/[WB] plots for the curves with a positive initial slope intercepting the ordinate at the same V as in the native particles. The data support the mechanism of succinate-ubiquinone reduction, in which no positive modulation of succinate dehydrogenase by ubiquinone exist in the membrane.

The composition and biosynthesis of the glycoproteins and glycolipids of the rabbit small-intestinal brush border

1. The glycoprotein and glycolipid composition of isolated rabbit small-intestinal brush borders has been studied. 2. The total glycoprotein fraction contains an average 95 microgram carbohydrate per mg protein, composed of mannose, galactose, fucose, N-acetylglucosamine and N-acetylgalactosamine. Glucose is also present but sialic acid is absent. 3. The isolated glycolipids include ceramide lactoside, ceramide trihexoside and two N-acetylglucosamine-containing glycolipids. Sialic acid containing glycolipid (gangliosides) is present only in trace quantities. 4. The biosynthesis of the brush border-bound glycoproteins and glycolipids has been studied following intraperitoneal injection with D-[1-14C]glucosamine and isolation of the brush borders at intervals between 3 and 24 h. 5. The total glycoprotein fraction labels maximally 7.5 h after injection and subsequently exhibits an exponential loss of radioactivity with a half-life of 11.2 h. The labelling kinetics of one of the glucosamine-containing glycolipids is similar to that of the glycoproteins in that it labels maximally between 7.5 and 12 h, but the second glucosamine-containing glycolipid labels later at approximately 18 h. These results indicate that the glycoproteins and glycolipids are actively synthesized and degraded within the mature small intestinal enterocyte and that individual glycolipids turn over independently.

The mechanism of C-20 hydroxylation of alpha-ecdysone in the desert locust, Schistocerca gregaria

1. The C-20 hydroxylation of alpha-ecdysone to produce beta-ecdysone was investigated in the desert locust, Schistocerca gregaria. 2. alpha-Ecdysone C-20 hydroxylase activity was located primarily in the fat-body and Malpighian tubules. The properties of the hydroxylation system from Malpighian tubules investigated further. 3. The enzyme system was mitochondrial, had a pH optimum of 6.5, an apparent Km of 12.5 micron and required O2 and NADPH. 4. The activity of the hydroxylation system showed developmental variation within the fifth instar, the maximum activity corresponding to the maximum tire of endogenous moulting hormone. The significance of these results is assessed in relation to the control of the endogenous titre of beta-ecdysone. 5. The mechanism of the hydroxylation system was investigated by using known inhibitors of hydroxylation reactions such as CO, metyrapone and cyanide. 6. The CO difference spectrum of the reduced mitochondrial preparation indicated the presence of cytochrome P-450 in the preparation. 7. It concluded that the alpha-ecdysone C-20 hydroxylase system is a cytochrome P-450-deendent mono-oxygenase.

Reactivity of the sulfhydryl groups of soluble succinate dehydrogenase

Soluble succinate dehydrogenase prepared by butanol extraction reacts with N-ethylmaleimide according to first-order kinetics with respect to both remaining active enzyme and the inhibitor concentration. Binding of the sulfhydryl groups of the enzyme prevents its alkylation by N-ethylmaleimide and inhibition by oxaloacetate. A kinetic analysis of the inactivation of alkylating reagent in the presence of succinate or malonate suggests that N-ethylmaleimide acts as a site-directed inhibitor. The apparent first-order rate constant of alkylation increases between pH 5.8 and 7.8 indicating a pKa value for the enzyme sulfhydryl group equal to 7.0 at 22 degrees C in 50 mM Tris-sufate buffer. Certain anions (phosphate, citrate, maleate and acetate) decrease the reactivity of the enzyme towards the alkylating reagent. Succinate/phenazine methosulfate reductase activity measured in the presence of a saturating concentration of succinate shows the same pH-dependence as the alkylation rate by N-ethylmaleimide. The mechanism of the first step of succinate oxidation, including a nucleophilic attack of substrate by the active-site sulfhydryl group, is discussed.

Correlation of the effects of citric acid cycle metabolites on succinate oxidation by rat liver mitochondria and submitochondrial particles

1. Succinate dehydrogenase is inhibited by citrate and beta-hydroxy-butyrate in a complex manner, both in mitochondria and submitochondrial particles. Kinetics of inhibition in the particles points to a competitive component in the mechanism involved. 2. Pyruvate, alpha-ketoglutarate, malate, and glutamate stimulate oxidation of succinate by mitochondria. 3. Stimulation by alpha-ketoglutarate and glutamate is not influenced by the presence of rotenone. 4. Stimulation by pyruvate is higher in the absence of rotenone and increases significantly in the presence of K+ and valinomycin. Pyruvate supplies in mitochondria reducing equivalents for malate dehydrogenase operating in the reverse direction-reduction of oxaloacetate to malate. 5. Stimulation by malate is higher in the presence of rotenone.

Characterization of the membrane-bound succinic dehydrogenase of Micrococcus lysodeikticus

The occurrence of succinic dehydrogenase [succinic:(acceptor) oxidoreductase, EC 1.3.99.1] in membrane fractions of Micrococcus lysodeikticus was investigated. The enzyme could be purified 10-fold, by deoxycholate treatment. Butanol extraction of membranes yielded an active fraction, nonsedimentable at 130,000 x g for 2 hr and altered in its phospholipid content relative to membranes. The activity of the enzyme in particulate preparations was decreased in the presence of competitive inhibitors and by compounds known to react with iron, sulfhydryl groups, and flavine. In this respect, the bacterial succinic dehydrogenase is similar to the enzyme derived from yeast and mammalian sources. In certain membrane fractions, Ca(2+) and Mg(2+) exhibited inhibitory effects whereas Triton X-100 caused activation. The enzyme could also be activated by substrate. In the phenazine reductase assay, incomplete reduction of electron acceptor was observed upon addition of divalent cations and iron binding agents.

Mammalian D-2-hydroxy acid dehydrogenase. Effect of inhibitors and reaction sequence

1. The reaction of d-2-hydroxy acid dehydrogenase with d-lactate and 2,6-dichlorophenol-indophenol (DCIP) at pH8.6 yields reciprocal plots of 1/rate versus 1/[d-lactate], at different DCIP concentrations, which appear to be parallel. However, at pH7.55, or in the presence of the competitive inhibitor oxalate at pH8.6, the plots are convergent. This is inconsistent with the mechanism previously proposed for this enzyme. 2. The pattern of inhibition by the product, pyruvate, is consistent with either an Ordered mechanism or an Iso Theorell-Chance mechanism. 3. The observation that the enzyme forms a complex with d-lactate favours the Ordered reaction. In this, first d-lactate and then DCIP bind to the enzyme to form a ternary complex, from which pyruvate and reduced DCIP dissociate in that order.