The enzymatic mechanism of glucuronidation catalyzed by two purified rat liver steroid UDP-glucuronosyltransferases

A kinetic analysis of two homogeneous rat liver steroid (3 alpha-hydroxysteroid and 17 beta-hydroxysteroid) UDP-glucuronosyltransferases was conducted using bisubstrate kinetic analysis, product inhibition studies, and dead-end competitive inhibition studies. Double reciprocal plots of initial velocity versus substrate concentration, using bisubstrate kinetic analysis, gave a sequential mechanism. Product inhibition studies were compatible with either a rapid equilibrium, random-order kinetic mechanism or an ordered Theorell-Chance mechanism. Results of dead-end competitive inhibition studies excluded an ordered Theorell-Chance mechanism. The cumulative results are consistent with a rapid equilibrium random-order sequential kinetic mechanism for the glucuronidation of testosterone by purified 17 beta-hydroxysteroid UDP-glucuronosyltransferase and of androsterone by purified 3 alpha-hydroxysteroid UDP-glucuronosyltransferase.     

Diagnosis of enzyme inhibition based on the degree of inhibition

In this work, a method for the diagnosis of kinetic inhibition, based on the dependence of the degree of inhibition (epsilon(i)) on the inhibitor concentration [I] and on the substrate concentration [S], is presented. Because the degree of inhibition is a ratio between rates, kinetic data are normalized by the introduction of an internal control-the rate of the uninhibited reaction. Therefore, the error associated with the kinetic measurements decreases and less experimental measurements are necessary to achieve the diagnosis. The process described, which uses graphical and/or non-linear fitting procedures, allows distinguishing between 20 different kinds of inhibition, including not only linear and hyperbolic, but also parabolic and rational 2,2 inhibitions. Rational 2,2 indicates a new type of inhibition corresponding to an incomplete parabolic inhibition, i.e. mechanistically it corresponds to an inhibitor that binds to two inhibition sites producing enzymatic complexes that are still active. In spite of its comprehensiveness, the diagnosis process is greatly facilitated by the division of the diagnosis of the inhibition in a step-by-step procedure, where only two rival models are evaluated in each step. In the non-linear fittings, the choice between rival models uses a test based on information statistics theory, the Akaike information criterion test, in order to penalize complex models that tend to be favoured in fittings. Finally, equations that allow the determination of inhibition kinetic constants were also deduced. The formalism presented was tested by examining inhibition of acid phosphatase by phosphate (a linear competitive inhibitor).     

Evaluating kinetics of enzymatic saccharification of lignocellulose by fractal kinetic analysis

The effects of impacting factors, including cellulase loading, operation temperature, product glucose inhibition, and high solid pretreated biomass loading were examined systemically on the enzymatic saccharification of lignocellulose (dilute acid pretreated corn stover) in the presence and absence of tri-block copolymer L64 (also referred to polymeric nonionic surfactant). The complex kinetics of enzymatic saccharification of cellulose were subjected to fractal kinetic analysis based on a fractal kinetic model, which is described with fractal kinetic parameters of the rate constant and fractal exponent. The results indicate that glucose inhibition including high lignocellulose loading is indexed by decreasing rate constant while lignin inhibition and high operation temperature is indexed by increasing fractal exponent. The effect of a nonionic surfactant on the enzymatic saccharification of lignocellulose mainly contributed to the elimination of lignin inhibition by decreasing the corresponding fractal exponent. However, the effect of the nonionic surfactant on cellulase activity and stability was very limited.     

Substrate inhibition mode of omega-transaminase from Vibrio fluvialis JS17 is dependent on the chirality of substrate

Substrate inhibition is a common phenomenon in enzyme chemistry, which is observed only with a fast-reacting substrate enantiomer. We report here for the first time substrate inhibition of an enantioselective enzyme by both substrate enantiomers. The enantioselective substrate inhibition, i.e., different mode of inhibition by each substrate enantiomer, of (S)-specific omega-transaminase was found with various chiral amines. A kinetic model based on ping-pong bi-bi mechanism has been developed and kinetic parameters were measured. The kinetic model reveals that the inhibition by (R)-amine results from formation of Michaelis complex with enzyme-pyridoxal 5'-phosphate, whereas the inhibition by (S)-amine results from the formation of the complex with enzyme-pyridoxamine 5'-phosphate. Substrate inhibition constants (K(SI)) of each (S)-enantiomer of four chiral amines showed a linear correlation with those of cognate (R)-amines. Such a correlation was also found between the K(SI) values and Michaelis constants of (S)-amines. These correlations indicate that recognition mechanisms and active site structures of both enzyme-pyridoxal 5'-phosphate, enzyme-pyridoxamine 5'-phosphate are similar. Taken together with the results, high propensity for non-productive substrate binding strongly suggests that binding pockets of the omega-transaminase is loosely defined, which accounts for the enantioselective substrate inhibition.     

Kinetic evidence for the presence of two forms of M2-type pyruvate kinase in rat small intestine

Some kinetic properties of pyruvate kinase from rat small intestine have been investigated. The relative insensitivity of the enzyme to ATP inhibition and the amino acid inhibition pattern allows the conclusion that intestinal pyruvate kinase belongs to the M₂-type. The pyruvate kinase activity as a function of the phosphoenol pyruvate concentration is characterized by two different n values. The activity correlating with the low n value is stimulated by Fru-1,6-P₂, whereas the activity at higher phosphoenol pyruvate concentrations is not influenced by this glycolytic intermediate. These results, together with the partial relief of the amino acid inhibition by Fru-1,6-P₂, show that two forms of the enzyme are present with different kinetic properties. The metabolic implication of the kinetic properties of pyruvate kinase for rat small intestine is discussed.     

Mechanism of the inhibition of milk xanthine oxidase activity by metal ions: a transient kinetic study

The nature and mechanism of the inhibition of the oxidoreductase activity of milk xanthine oxidase (XO) by Cu(2+), Hg(2+) and Ag(+) ions has been studied by steady state and stopped flow transient kinetic measurements. The results show that the nature of the inhibition is noncompetitive. The inhibition constants for Cu(2+) and Hg(2+) are in the micromolar and that for Ag(+) is in the nanomolar range. This suggests that the metal ions have strong affinity towards XO. pH dependence studies of the inhibition indicate that at least two ionisable groups of XO are involved in the binding of these metal ions. The effect of the interaction of the metal ions on the reductive and oxidative half reactions of XO has been investigated, and it is observed that the kinetic parameters of the reductive half reaction are not affected by these metal ions. However, the interaction of these metal ions with XO significantly affects the kinetic parameters of the oxidative half reaction. It is suggested that this may be the main cause for the inhibition of XO activity by the metal ions.     

Glucose-6-phosphate dehydrogenase from Dicentrarchus labrax liver: kinetic mechanism and kinetics of NADPH inhibition

The kinetic mechanism of the reaction catalyzed by glucose-6-phosphate dehydrogenase (EC 1.1.1.49) from Dicentrarchus labrax liver was examined using initial velocity studies, NADPH and glucosamine 6-phosphate inhibition and alternate coenzyme experiments. The results are consistent with a steady-state ordered sequential mechanism in which NADP+ binds first to the enzyme and NADPH is released last. Replots of NADPH inhibition show an uncommon parabolic pattern for this enzyme that has not been previously described. A kinetic model is proposed in agreement with our kinetic results and with previously published structural studies (Bautista et al. (1988) Biochem. Soc. Trans. 16, 903-904). The kinetic mechanism presented provides a possible explanation for the regulation of the enzyme by the [NADPH]/[NADP+] ratio.     

Polyphenol interactions: astringency and the loss of astringency in ripening fruit

The inhibition of the enzyme β-glucosidase by natural polyphenolic substrates is described. The kinetic data suggest that the pattern of inhibition w     

Time-dependent slowly-reversible inhibition of monoamine oxidase A by N-substituted 1,2,3,6-tetrahydropyridines

A novel class of N-substituted tetrahydropyridine derivatives was found to have multiple kinetic mechanisms of monoamine oxidase A inhibition. Eleven structurally similar tetrahydropyridine derivatives were synthesized and evaluated as inhibitors of MAO-A and MAO-B. The most potent MAO-A inhibitor in the series, 2,4-dichlorophenoxypropyl analog 12, displayed time-dependent mixed noncompetitive inhibition. The inhibition was reversed by dialysis, indicating reversible enzyme inhibition. Evidence that the slow-binding inhibition of MAO-A with 12 involves a covalent bond was gained from stabilizing a covalent reversible intermediate product by reduction with sodium borohydride. The reduced enzyme complex was not reversible by dialysis. The results are consistent with slowly reversible, mechanism-based inhibition. Two tetrahydropyridine analogs that selectively inhibited MAO-A were characterized by kinetic mechanisms differing from the kinetic mechanism of 12. As reversible inhibitors of MAO-A, tetrahydropyridine analogs are at low risk of having an adverse effect of tyramine-induced hypertension.     

Kinetic Formulations for the Reduction of Ketomalonate by Lactate Dehydrogenase

Abstract

Initial rate kinetic studies of lactate dehydrogenase with ketomalonate and NADH as substrates suggest that this enzymatic system is adapted to a rapid equilibrium ordered bi-bi ternary complex mechanism. The application of the reaction product inhibition method reveals the existence of the enzyme-NADH-hydroxy-malonate and enzyme-NAD⁺-ketomalonate abortive complexes. This kinetic behaviour is confirmed by the differential inhibition induced by several alternate products on the pyruvate-lactate dehydrogenase-NADH and ketomalonate-lactate dehydrogenase-NADH systems.     

Kinetic characterization of dopamine as a suicide substrate of tyrosinase

A kinetic study of the inactivation of frog epidermis tyrosinase by a suicide substrate dopamine hydrochloride is described. The kinetic parameters and constants which characterize this reaction have been determined and the effects of pH and the stoichiometric inhibition by chloride have been considered.     

Kinetic mechanism of catalytic subunits (c3) of E. coli aspartate transcarbamylase at pH 7.0

In contrast to holo-enzyme (c6r6), catalytic subunits (c3) of Escherichia coli aspartate transcarbamylase (carbamoyl-phosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2) do not exhibit allosteric interactions or inhibition effects that complicate kinetic investigations of substrate binding order. Equilibrium isotope-exchange kinetic probes of c3 at pH 7.0 and 30 degrees C produced kinetic saturation patterns consistent with a strongly preferred order random kinetic mechanism, in which carbamoyl phosphate binds prior to aspartate and carbamoyl aspartate is released before Pi. Weak substrate inhibition effects observed with c6r6 did not occur with c3, possibly due to decreased affinity for ligands at the dianion inhibition site.     

Studies of the ammonia-dependent reaction of beef pancreatic asparagine synthetase

We have studied the asparagine synthetase reaction with regard to the ammonia-dependent production of asparagine. Hydroxylamine was shown to be an alternate substrate for the asparagine synthetase reaction, and some of its kinetic properties were examined. The ammonia-dependent reaction was examined with regard to inhibition by asparagine. It was found that asparagine inhibition was partial competitive with respect to ammonia, regardless of the concentration of aspartate. However, when MgATP was not saturating, the inhibition by asparagine became linear competitive. These results were interpreted to be consistent with a kinetic mechanism for asparagine synthetase where ammonia is bound to the enzyme followed by MgATP causing asparagine release.     

Transient phase calibration of tyrosinase-based carbaryl biosensor

The inhibition of tyrosinase, used as a selective compound in amperometric biosensor for the detection of carbaryl and the possibilities of calibration of carbaryl biosensor have been studied. The kinetic analysis of biosensor data was based on the application of the biosensor dynamic model, allowing a quick calculation of independent on each other kinetic and steady-state parameters. It was found that carbaryl acts as an inhibiting substrate of tyrosinase and at low concentrations accelerates the tyrosinase-catalyzed oxidation of tyrosine by dissolved oxygen. The reaction mechanism is analogous to that usually considered for uncompetitive inhibition and the plot of kinetic parameter as a function of carbaryl concentration has a flat asymmetric maximum. Consequently, the kinetic parameter alone is not sufficient for the calibration of carbaryl biosensor and simultaneous application of other carbaryl-dependent parameters, like steady-state parameter, is essential.     

A unique adenosine diphosphoglucose pyrophosphorylase associated with maize embryo tissue

A comparison of heat stabilities and various kinetic properties between the adenosine diphosphoglucose pyrophosphorylases isolated from endosperm and embryo tissues from starchy maize seeds indicates that the adenosine diphosphoglucose pyrophosphorylase associated with the embryo is distinct from the enzyme isolated from the endosperm. The embryo enzyme is more stable to incubation for 5 minutes at 60 C while the endosperm enzyme is labile to this treatment. Both enzymes are activated by glycerate-3-P. The embryo enzyme is more sensitive to inhibition by phosphate than is the endosperm enzyme. Glycerate-3-P, which reverses the inhibition of the endosperm enzyme by phosphate, has little effect on the phosphate inhibition of the embryo enzyme. Other kinetic studies distinguish the two enzymes.     

Glucose-6-phosphate dehydrogenase from Dicentrarchus labrax liver: kinetic mechanism and kinetics of NADPH inhibition

The kinetic mechanism of the reaction catalyzed by glucose-6-phosphate dehydrogenase (EC 1.1.1.49) from Dicentrarchus labrax liver was examined using initial velocity studies,NADPH and glucosamine 6-phosphate inhibition and alternate coenzyme experiments. The results are consistent with a steady-state ordered sequential mechanism in which NADP⁺ binds first to the enzyme and NADPH is released last. Replots of NADPH inhibition show an uncommon parabolic pattern for this enzyme that has not been previously described. A kinetic model is proposed in agreement with our kinetic results and with previously published structural studies (Bautista et al. (1988) Biochem. Soc. Trans. 16, 903–904). The kinetic mechanism presented provides a possible explanation for the regulation of the enzyme by the [NADPH]/[NADP⁺] ratio.     

Kinetic studies on beta-site amyloid precursor protein-cleaving enzyme (BACE). Confirmation of an iso mechanism

The steady-state kinetic mechanism of beta-amyloid precursor protein-cleaving enzyme (BACE)-catalyzed proteolytic cleavage was evaluated using product and statine- (Stat(V)) or hydroxyethylene-containing (OM99-2) peptide inhibition data, solvent kinetic isotope effects, and proton NMR spectroscopy. The noncompetitive inhibition pattern observed for both cleavage products, together with the independence of Stat(V) inhibition on substrate concentration, suggests a uni-bi-iso kinetic mechanism. According to this mechanism, the enzyme undergoes multiple conformation changes during the catalytic cycle. If any of these steps are rate-limiting to turnover, an enzyme form preceding the rate-limiting conformational change should accumulate. An insignificant solvent kinetic isotope effect (SKIE) on k(cat)/K(m), a large inverse solvent kinetic isotope effect on k(cat), and the absence of any SKIE on the inhibition onset by Stat(V) during catalysis together indicate that the rate-limiting iso-step occurs after formation of a tetrahedral intermediate. A moderately short and strong hydrogen bond (at delta 13.0 ppm and phi of 0.6) has been observed by NMR spectroscopy in the enzyme-hydroxyethylene peptide (OM99-2) complex that presumably mimics the tetrahedral intermediate of catalysis. Collapse of this intermediate, involving multiple steps and interconversion of enzyme forms, has been suggested to impose a rate limitation, which is manifested in a significant SKIE on k(cat). Multiple enzyme forms and their distribution during catalysis were evaluated by measuring the SKIE on the noncompetitive (mixed) inhibition constants for the C-terminal reaction product. Large, normal SKIE values were observed for these inhibition constants, suggesting that both kinetic and thermodynamic components contribute to the K(ii) and K(is) expressions, as has been suggested for other iso-mechanism featuring enzymes. We propose that a conformational change related to the reprotonation of aspartates during or after the bond-breaking event is the rate-limiting segment in the catalytic reaction of beta-amyloid precursor protein-cleaving enzyme, and ligands binding to other than the ground-state forms of the enzyme might provide inhibitors of greater pharmacological relevance.     

Steady state analysis of the enhancement in ethanol productivity of a continuous fermentation process employing a protein-phospholipid complex as a protecting agent

A continuous cascade fermentation process comprising eight tanks in series, employing a protein-phopholipid complex as a protective agent (PA) was performed for ethanol production from glucose. An increase of 58.4% in fermenter productivity was obtained due to the addition of PA. A kinetic model including product and substrate inhibition effects is proposed. Parameters appearing in the kinetic model were estimated by using the method of least squares. It is found that the product inhibition effect dominates over the substrate inhibition effect for the range of concentrations studied in our fermentation system. Upon addition of PA, both inhibitory effects are reduced to as little as about one quarter of that without PA. It was also found that the use of PA primarily protected the cells against ethanol inhibition rather than substrate inhibition. A steady state criterion is also discussed.     

A general solution for the steady-state kinetics of immobilized enzyme systems

A power series solution is presented which describes the steady-state concentration profiles for substrate and product molecules in immobilized enzyme systems. Diffusional effects and product inhibition are incorporated into this model. The kinetic consequences of diffusion limitation and product inhibition for immobilized enzymes are discussed and are compared to kinetic behavior characteristic of other types of effects, such as substrate inhibition and substrate activation.     

Human deoxycytidine kinase: kinetic mechanism and end product regulation

The kinetic properties of the monomeric deoxycytidine kinase (EC 2.7.1.74) from leukemic human T-lymphoblasts have been investigated. The results of steady-state initial-rate kinetic analysis and product inhibition studies at pH 7.5 and 37 degrees C indicate that substrate binding follows an ordered sequential pathway, with the magnesium salt of ATP being the first substrate to bind and dCMP the last product to dissociate. At subsaturating substrate concentrations, dCMP produced competitive inhibition against ATP, while against varied deoxycytidine concentrations dCMP exhibited mixed-type inhibition. ADP produced noncompetitive inhibition against either substrate. The limiting Km values for deoxycytidine and MgATP were 0.94 and 30 microM, respectively. The end product inhibitor dCTP exhibited competitive inhibition against varied ATP concentration, with a dissociation constant estimated to be 0.7 microM when extrapolated to zero ATP concentration. dCTP was purely noncompetitive against varied deoxycytidine concentration. On the basis of these kinetic results, and on the strong and specific inhibition by dCTP, it is proposed that this end product functions as a multisubstrate analogue, with its triphosphate group binding to the phosphate donor site of the enzyme and its deoxycytidine moiety overlapping and binding to the deoxynucleoside site in a highly specific manner.