Analysis of slow-binding enzyme inhibitors at elevated enzyme concentrations

The improvement in the characterization of slow-binding inhibitors achieved by performing experiments at elevated enzyme concentrations is presented. In particular, the characterization of slow-binding inhibitors conforming to a two-step mode of inhibition with a steady-state dissociation constant that is much lower than the initial dissociation constant with enzyme is discussed. For these systems, inhibition is rapid and low steady-state product concentrations are produced at saturating inhibitor concentrations. By working at elevated enzyme concentrations, improved signal-to-noise ratios are achieved and data may be collected at saturating inhibitor levels. Numerical simulations confirmed that improved parameter estimates are obtained and useful data to discern the mechanism of slow-binding inhibition are produced by working at elevated enzyme concentrations. The saturation kinetics that were unobservable in two previous studies of an enzyme inhibitor system were measured by performing experiments at an elevated enzyme concentration. These results indicate that consideration of the quality of the data acquired using a particular assay is an important factor when selecting the enzyme concentration at which to perform experiments used to characterize the class of enzyme inhibitors examined herein.     

Inhibitory effects of salts on the nicotinamide adenine dinucleotide specific isocitrate dehydrogenase from Blastocladiella emersonii.

The effect of different salts on the NAD-specific isocitrate dehydrogenase from Blastocladiella emersonii has been studied. The results show that the salt inhibition depends on the size of the anions and that the ionic strength is of minor importance.The salts inhibit the enzyme in a competitive manner with regard to isocitrate. The isocitrate concentration giving half saturation increased by the same factor whether or not the activator AMP was present. The finding that higher salt concentrations are needed to inhibit the enzyme in the presence of AMP is due to the fact that in this case isocitrate is more tightly bound.Stopped-flow experiments demonstrated that when the enzyme was incubated with isocitrate and metal ions prior to initiation of the reaction by addition of NAD, the salt inhibition needed several seconds to be fully expressed. Moreover, a lag occurred before NADH was formed when the enzyme was mixed with its substrates and cofactor. The data suggest that the hysteretic properties of the enzyme are due to isomerization of the enzyme molecules, and that specific binding sites are involved in the salt inhibition.     

Purine nucleoside phosphorylase of rabbit liver. Mechanism of catalysis.

Initial velocity studies and product inhibition patterns for purine nucleoside phosphorylase from rabbit liver were examined in order to determine the predominant catalytic mechanism for the synthetic (forward) and phosphorolytic (reverse) reactions of the enzyme. Initial velocity studies in the absence of products gave intersecting or converging linear double reciprocal plots of the kinetic data for both the synthetic and phosphorolytic reactions of the enzyme. The observed kinetic pattern was consistent with a sequential mechanism, requiring that both substrates add to the enzyme before products may be released. The product inhibition patterns showed mutual competitive inhibition between guanine and guanosine as variable substrates and inhibitors. Ribose 1-phosphate and inorganic orthophosphate were also mutually competitive toward each other. Other combinations of substrates and products gave noncompetitive inhibition. Apparent inhibition constants calculated for guanine as competitive inhibitor and for ribose 1-phosphate as noncompetitive inhibitor of the enzyme, with guanosine as variable substrate, did not vary significantly with increasing concentrations of inorganic orthophosphate as fixed substrate. These results suggest that the mechanism was order and that substrates add to the enzyme in an obligatory order. Dead end inhibition studies carried out in the presence of the products guanine and ribose 1-phosphate, respectively, showed that the kinetically significant abortive ternary complexes of enzyme-guanine-inorganic orthophosphate (EQB) and enzyme-guanose-ribose 1-phosphate (EAP) are formed. The results of dead end inhibition studies are consistent with an obligatory order of substrate addition to the enzyme. The nucleoside or purine is probably the first substrate to form a binary complex with the enzyme, and with which inorganic orthophosphate or ribose 1-phosphate may interact as secondary substrates. The evidences presented in this investigation support an Ordered Theorell-Chance mechanism for the enzyme.     

Modeling substrate inhibition of microbial growth

This article presents a general equation for substrate inhibition of microbial growth using a statistical thermodynamic approach. Existing empirical models adapted from enzyme kinetics, for example, the Haldane-Andrews equation, often criticized for not being physically based for microbial growth, are shown to derive from the general equation in this article, and their empirical parameters are shown to be well defined physically. Three sets of experimental data from the literature are used to test the modeling abilities of the general equation to represent experimental data. The results are compared with those obtained by fitting the same data set to a widely used empirical model existing in the literature. The general equation is found to represent all three experimental data sets better than the alternative model tested. In addition, a graphical method existing in enzyme kinetics is successfully adapted and further developed to determine the number of inhibition sites of a basic functional unit of a bacterial cell. (c) 1996 John Wiley & Sons, Inc.     

Inhibition of the catecholase and cresolase activity of mushroom tyrosinase by azide

The inhibition of mushroom tyrosinase by azide is examined as a function of the concentrations of l-tyrosine, l-3,4-dihydroxyphenylalanine (l-Dopa), and oxygen at pH 5.6 and 7.0. Mixed inhibition is observed with respect to l-tyrosine, l-Dopa, and oxygen. The data are interpreted in terms of azide combining with both the oxidized and reduced forms of the enzyme. A scheme is presented for the catecholase and cresolase reactions which explains the results of azide inhibition and also the effect of other inhibitors which complex with the copper of tyrosinase. Double-reciprocal plots of oxygen variation with l-tyrosine as the fixed substrate are nonlinear above about 500 μm oxygen. When l-Dopa is the fixed substrate, no curvature is observed. These results could be explained in terms of negative cooperativity or the presence of two kinetically distinct enzyme forms having different K_m values for oxygen. Although the kinetic data do not permit a choice between the two possibilities, the occurrence in all tyrosinase preparations of two forms, resting, bicupric enzyme and “intrinsic oxytyrosinase,” lends support to the latter suggestion.     

Substrate inhibition of the mitochondrial and cytoplasmic malate dehydrogenases.

The mechanism that leads to an inhibition of enzyme activity in the presence of high concentrations of substrate was investigated with the two malate dehydrogenase isoenzymes obtained from pig heart. The inhibition is promoted by an abortive binary complex formed by the enzymes and the enol form of of oxalacelate. Neither the oxidized coenzyme nor the reduced coenzyme appears to be involved in the formation of this complex. These results suggest that the mechanism of substrate inhibition that occurs with the pig heart malate dehydrogenases is different from that observed with the lactate dehydrogenases from chicken hearts. The inhibition constants for oxalacetate are 2.0 mM with the mitochondrial enzyme and 4.5 mM with the cytoplasmic enzyme. Since the in vivo concentration of oxalacetate is reported to be about 10 micrometer, these data suggest that the substrate inhibition that is exhibited by the malate dehydrogenases may not be of any significance in vivo.     

Hill coefficients of dietary polyphenolic enzyme inhibitiors: can beneficial health effects of dietary polyphenols be explained by allosteric enzyme denaturing?

Inspired by a recent article by Prinz, suggesting that Hill coefficients, obtained from four parameter logistic fits to dose–response curves, represent a parameter allowing distinction between a general allosteric denaturing process and real single site enzyme inhibition, Hill coefficients of a number of selected dietary polyphenol enzyme inhibitions were compiled from the available literature. From available literature data, it is apparent that the majority of polyphenol enzyme interactions reported lead to enzyme inhibition via allosteric denaturing rather than single site inhibition as judged by their reported Hill coefficients. The results of these searches are presented and their implications discussed leading to the suggestion of a novel hypothesis for polyphenol biological activity termed the insect swarm hypothesis.     

General theory of determining intraparticle active immobilized enzyme distribution and rate parameters

A general theory is presented in this article for determining the intrinsic rate constants for the main reaction and deactivation reaction, the effective diffusivity of the substrate, and the active enzyme distribution within porous solid supports from deactivation study of a continuous stirred-basket reactor (CSBR). For the parallel deactivation five reaction kinetics are considered: (a) Michaelis-Menten, (b) substrate inhibition, (c) product inhibition (competitive), (d) product inhibition (anticompetitive), and (e) zero-order kinetics. The experimental results of the system of hydrogen-peroxide-immobilized catalase on controlled-pore glass particles are analyzed to demonstrate the application of the theory developed for parallel deactivation of active immobilized enzyme (IME). For series deactivation only first-order kinetics is treated, and a numerical procedure is proposed to deter mine the rate parameters and the internal active enzyme distribution. The experimental data of the system of glucose-immobilized glucose oxidase on silica-alumina and controlled-pore glass particles are used to verify the theory.     

Inhibitory kinetics of mercuric ion on the activity of beta-N-acetyl-D-glucosaminidase from green crab (Scylla serrata)

Chemical modification of p-chloromercuribenzoate (PCMB) on beta-N-acetyl-d-glucosaminidase (NAGase, EC 3.2.1.52) from green crab (Scylla serrata) has been studied. The results show that sulfhydryl group is essential for the activity of the enzyme. Inhibitory kinetics of the enzyme by mercuric chloride (HgCl2) has been studied using the kinetic method of the substrate reaction during inhibitor of enzyme. The kinetic results show that the inhibition of the enzyme by mercuric ion (Hg2+) at lower than 1.0 microM is a reversible reaction with residual activity and the inhibition belongs to be competitive. The inhibition kinetics model of Hg2+ on the enzyme was set up and the microscopic rate constants were determined and the data obtained were well fitted with the model. It was also turned out that only one molecule of HgCl2 binds to the enzyme molecule to lead the enzyme lose its activity. The above results suggest that the cysteine residue is essential for activity and is situated at the active site of the enzyme.     

Mechanism of activation by anions of phosphoglycolate phosphatases from spinach and human red blood cells

Phosphoglycolate phosphatases from spinach and human red blood cells show a number of common features not often found in enzymes. Both enzymes are activated more than 50-fold by millimolar concentrations of Cl-. Other inorganic anions and a number of carboxylic acids also activate. Each enzyme has limited substrate specificity yet each hydrolyzes P-glycolate and ethyl-P with the same maximal velocity. L-P-lactate is only a good substrate for the red cell enzyme. With both enzymes initial rate data obtained by varying both the P-glycolate and Cl- give parallel line double reciprocal plots. Similar experiments with ethyl-P as substrate give intersecting lines with both enzymes. The likelihood that both classes of substrates are acting at the same site is strengthened by the results of inhibition studies with alternative substrates and the constancy of inhibition constants for glycolate with all substrates for a given enzyme. For each substrate the experimentally observed variation in V/Km with different activators is small, suggesting that the enzyme has an ordered mechanism with the phosphorylated substrate reacting first. A mechanism that is consistent with all of the data is presented.     

Pyrimidine nucleoside monophosphate kinase from rat bone marrow cells: a kinetic analysis of the reaction mechanism

A kinetic analysis of the reaction mechanism of pyrimidine nucleoside monophosphate kinase was carried out with a highly purified enzyme preparation from rat bone marrow cells. The results of initial rate and product inhibition studies provided insight into the mode of action of the enzyme. The data support the views that the reaction mechanism is sequential and nonequilibrium in nature. Substrates bind to the enzyme in a random order. Substrate binding is cooperative. That is, the binding of the first substrate facilitates the binding of the second substrate. UMP can bind to the purine site on the enzyme, resulting in substrate inhibition. Product inhibition can result from the binding of UDP to either the pyrimidine or purine site, or from the binding of ADP to the purine site.     

Slow- and tight-binding inhibition of aspartate aminotransferase by L-hydrazinosuccinate

The inhibition of aspartate aminotransferase (L-aspartate: 2-oxoglutarate aminotransferase, EC 2.6.1.1) by L-hydrazinosuccinate has been studied. The velocity of the enzyme reaction decreased with time when the reaction was initiated by the addition of enzyme to a mixture of the assay components and L-hydrazinosuccinate, while it increased slowly from a low level when a preincubated mixture of the enzyme and the inhibitor was added to the reaction mixture to initiate the reaction. Nearly 50% decrease in the initial reaction velocity was produced by a prolonged preincubation of the enzyme with the inhibitor, both at low concentrations of about 2 nM. These findings indicate that the inhibition is of the slow- and tight-binding type. The time-course of the reaction of the enzyme and the inhibitor, examined by the change in activity, was not in accord with single-step mechanisms, but rather appeared to follow biphasic kinetics. The inhibition could be fully reversed only in the presence of L-cysteine sulfinate or large excess of L-aspartate to convert the regenerated enzyme to its pyridoxamine form. The time-course of the reversal followed pseudo-first-order kinetics. Quantitative analysis of the experimental data has shown that the results are consistent with a mechanism of enzyme-inhibitor interaction which involves a reaction of two consecutive, reversible steps. The overall inhibition constant for L-hydrazinosuccinate was calculated to be approx. 0.2 nM.     

Effects of paraoxon and ethylparathion on choline oxidase from Alcaligenes species: inhibition and denaturation

The kinetics and thermodynamics of the effects of paraoxon (POX) and ethylparathion (EPA) on choline oxidase (ChOx) were studied. Lineweaver–Burk plots of initial velocity data showed a parallel pattern indicating uncompetitive inhibition versus choline. The inhibition constant (K_I) obtained from the secondary plots for POX and EPA were 0.14 ± 0.01 and 0.48 ± 0.05 mM, respectively, suggesting that POX is a more potent inhibitor of ChOx than EPA. UV absorption was used to monitor the denaturation of ChOx by POX and EPA. A decrease in FAD fluorescence associated with the interaction of POX and EPA with ChOx suggested a tertiary structural change. Interaction of the enzyme molecule with POX or EPA resulted in inhibition and subsequently denaturation of the enzyme. The results indicate that inhibition and denaturation of the enzyme by POX and EPA are linked, but not parallel events, with inhibition occurring at lower concentrations with respect to denaturation. This suggests that the loss of initial velocity of the enzyme is an active site specific effect and not due to global conformational changes induced by the inhibitors.     

Mechanistic and kinetic studies of inhibition of enzymes

A graphical method for analyzing enzyme data to obtain kinetic parameters, and to identify the types of inhibition and the enzyme mechanisms, is described. The method consists of plotting experimental data as nu/(V0 - nu) vs 1/(I) at different substrate concentrations. I is the inhibitor concentration; V0 and nu are the rates of enzyme reaction attained by the system in the presence of a fixed amount of substrate, and in the absence and presence of inhibitor, respectively. Complete inhibition gives straight lines that go through the origin; partial inhibition gives straight lines that converge on the 1-I axis, at a point away from the origin. For competitive inhibition, the slopes of the lines increase with increasing-substrate concentration; with noncompetitive inhibition, the slopes are independent of substrate concentration; with uncompetitive inhibition, the slopes of the lines decrease with increasing substrate concentrations. The kinetic parameters, Km, Ki, Ki', and beta (degree of partiality) can best be determined from respective secondary plots of slope and intercept vs substrate concentration, for competitive and noncompetitive inhibition mechanism or slope and intercept vs reciprocal substrate concentration for uncompetitive inhibition mechanism. Functional consequencs of these analyses are represented in terms of specific enzyme-inhibitor systems.     

Inhibition of vanadium chloroperoxidase from the fungus Curvularia inaequalis by hydroxylamine, hydrazine and azide and inactivation by phosphate

The first detailed inhibition study of recombinant vanadium chloroperoxidase (rVCPO) using hydroxylamine, hydrazine and azide has been carried out. Hydroxylamine inhibits rVCPO both competitively and uncompetitively. The competitive inhibition constant K(ic) and the uncompetitive inhibition constant K(iu) see are 40 and 80 microM, respectively. The kinetic data suggest that rVCPO may form a hydroxylamido complex, hydroxylamine also seems to react with the peroxovanadate complex during turnover. The kinetic data show that the type of inhibition for hydrazine and azide is uncompetitive with the uncompetitive inhibition constant K(iu) of 350 microM and 50 nM, respectively, showing that in particular azide is a very potent inhibitor of this enzyme. Substitution of vanadate in the active site by phosphate also leads to inactivation of vanadium chloroperoxidase. However, the presence of H(2)O(2) clearly prevents the inactivation of the enzyme by phosphate. This shows that pervanadate is bound much more strongly to the enzyme than vanadate.     

Mechanism of palmityl coenzyme A inhibition of liver glycogen synthase.

Palmityl-CoA inhibits free liver glycogen synthase; the concentration required for half-maximum inhibition is 3 to 4 micrometer. Almost complete inhibition was observed at 50 micrometer. Palmityl-CoA inhibition is associated with dissociation of the tetrameric enzyme into monomers, and binding of palmityl-CoA to the monomers. Glycogen-bound enzyme is also inhibited by palmityl-CoA, resulting in dissociation of the enzyme into monomers and concomitant release of the enzyme from the primer glycogen. Palmityl-CoA inhibition of the enzyme is partially reversed by the glycogen synthase activator, glucose-6-P, whereas sodium lauryl sulfate-inhibited enzyme is not reactivated by glucose-6-P. Sodium lauryl sulfate inhibition results in the dissociation of the tetramer into the monomers. Bovine serum albumin and cyclodextrin can prevent palmityl-CoA inhibition only when they are added prior to palmityl-CoA addition. The possible physiological role of palmityl-CoA in glucose homeostasis is discussed.     

Kinetic properties of normal human erythrocyte glucose-6-phosphate dehydrogenase dimers.

The steady-state kinetics of normal human erythrocyte glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP+ oxidoreductase, EC 1.1.1.49) dimers were studied as a function of pH and temperature. Inhibition studies using glucosamine 6-phosphate, NADPH and p-hydroxymercuribenzoate (P-OHMB) were also carried out at pH 8.0. The existence of two binding sites on the enzyme with a transition from low to high affinity for NADP+ when NADP+ concentration is increased is indicated by the nonlinear Lineweaver-Burk plots and sigmoid kinetic patterns. NADPH inhibition was found to be competitive with respect to NADP+ and non-competitive with respect to glucose-6-phosphate. Logarithmic plot of Vmax against pH and inactivation by P-OHMB indicate the participation in the reaction mechanism of imidazolium group of histidine and sulhydryl groups. The initial velocity and product inhibition data gave results which are consistent with the dimeric enzyme following an ordered sequential mechanism. A possible random mechanism is ruled out by the inhibition results of glucosamine 6-phosphate.     

Characterisation of phosphate binding to mitochondrial and bacterial membrane-bound ATP synthase by studies of inhibition with 4-chloro-7-nitrobenzofurazan

The effect of phosphate on the inhibition by 4-chloro-7-nitrobenzofurazan of the ATPase activity of the proton-translocating ATP synthase in heart submitochondrial particles was investigated. Binding of phosphate protected strongly against the inhibition. A dissociation constant of 0.2 mM was determined for the enzyme X Pi complex and shown to be independent of pH in the range 7.0-8.0. The protective effect of phosphate was mimicked by arsenate but not by sulphate or malonate. Similar results were obtained for the enzyme from Paracoccus denitrificans. 2,4-Dinitrophenol enhanced phosphate binding to the mitochondrial enzyme since the protective effect of phosphate was increased. The data are compatible with protection arising from binding of phosphate to a catalytic site.     

Influential factor contributing to the isoform-specific inhibition by ATP of human mitochondrial NAD(P)+-dependent malic enzyme: functional roles of the nucleotide binding site Lys346

Human mitochondrial NAD(P)(+)-dependent malic enzyme (m-NAD-ME) is a malic enzyme isoform with dual cofactor specificity, ATP inhibition and substrate cooperativity. The determinant of ATP inhibition in malic enzyme isoforms has not yet been identified. Sequence alignment of nucleotide-binding sites of ME isoforms revealed that Lys346 is conserved uniquely in m-NAD-ME. In other ME isoforms, this residue is serine. As the inhibitory effect of ATP is more pronounced on m-NAD-ME than on other ME isoforms, we have examined the possible role of Lys346 by replacing it to alanine, serine or arginine. Our kinetic data indicate that the K346S mutant enzyme displays a shift in its cofactor preference from NAD(+) to NADP(+) upon increasing k(cat,NADP) and decreasing K(m,NADP). Furthermore, the cooperative binding of malate becomes less significant in human m-NAD-ME after mutation of Lys346. The h value for the wild-type is close to 2, but those of the K346 mutants are approximately 1.5. The K346 mutants can also be activated by fumarate and the cooperative effect can be abolished by fumarate, suggesting that the allosteric property is retained in these mutants. Our data strongly suggest that Lys346 in human m-NAD-ME is required for ATP inhibition. Mutation of Lys346 to Ser or Ala causes the enzyme to be much less sensitive to ATP, similar to cytosolic NADP-dependent malic enzyme. Substitution of Lys to Arg did not change the isoform-specific inhibition of the enzyme by ATP. The inhibition constants of ATP are increased for K346S and K346A, but are similar to those of the wild-type for K346R, suggesting that the positive charge rather than group specificity is required for binding affinity of ATP. Thus, ATP inhibition is proposed to be determined by the electrostatic potential involving the positive charge on the side chain of Lys346.