pH-dependent intermediate plateaux in the kinetics of the reaction catalyzed by "biosynthetic" L-threonine dehydratase of Escherichia coli K-12

Characterization of aminoacrylate intermediates of pyridoxal-5'-phosphate dependent enzymes

Pyridoxal-5'-phosphate (PLP) Schiff's bases of 2-aminoacrylate are intermediates in β-elimination and β-substitution reaction of PLP-dependent enzymes. These enzymes are found in two major families, the α-, or aminotransferase, superfamily, and the β-family. While the α-family enzymes primarily catalyze β-eliminations, the β-family enzymes catalyze both β-elimination and β-substitution reactions. Tyrosine phenol-lyase (TPL), which catalyzes the reversible elimination of phenol from l-tyrosine, is an example of an α-family enzyme. Tryptophan synthase catalyzes the irreversible formation of l-tryptophan from l-serine and indole, and is an example of a β-family enzyme. The identification and characterization of aminoacrylate intermediates in the reactions of both of these enzymes is discussed. The use of UV-visible absorption and fluorescence spectroscopy, X-ray and neutron crystallography, and NMR spectroscopy to identify aminoacrylate intermediates in these and other PLP enzymes is presented.

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.

Nucleotide vesicular transporter of bovine chromaffin granules. Evidence for a mnemonic regulation

The nucleotide vesicular transport has been studied with the fluorescent substrate analogues, the (1,N6-ethenoadenosine) nucleotides. The transport experiments were carried out with granular preparations from bovine adrenal medulla, and epsilon-ATP, epsilon-ADP, and epsilon-AMP were quantified after separation by high performance liquid chromatography. The granular concentration increase of all three nucleotides was time-dependent. The concentration dependence of epsilon-nucleotide transport to chromaffin granules did not follow the Michaelis-Menten kinetics and presented a similar three-step curve with cooperativity. This shape can be considered to be the result of the addition of three sigmoidal curves with their corresponding kinetic parameters. epsilon-ATP exhibited K values of 0.25, 1, and 3 mM and Vmax values of 0.02, 0.04 and 0.19 nmol.min-1.mg of protein-1, for the first, second, and third curves for each step, respectively. epsilon-ADP exhibited K values of 0.15, 0.9, and 3.6 mM and Vmax values of 0.025, 0.035, and 0.3 nmol.min-1.mg of protein-1, respectively for the first, second, and third curves. epsilon-AMP exhibited K values of 0.2, 1.2, and 3.2 mM, and Vmax values of 0.01, 0.04, and 0.055 nmol.min-1.mg of protein-1, also for the first to third steps. The Hill numbers for epsilon-ATP, epsilon-ADP, and epsilon-AMP were not constant but a function of the transport saturation. The nonhydrolyzable ATP analogues AMPPNP, ATP gamma S, and ADP beta S were activators of epsilon-nucleotide transport at concentrations under 1 mM and inhibitors at higher concentrations. Atractyloside and N-ethylmaleimide partially inhibited the nucleotide granular transport. High extragranular ATP concentrations specifically induced the exit of the previously transporter granular epsilon-ATP.

Kinetic and binding properties of the oxoglutarate translocator of rat-heart mitochondria

The kinetic study of the oxoglutarateout/malatein exchange through the inner mitochondrial membrane of rat-heart mitochondria has been compelted and extended to higher external-oxoglutarate and to lower internal-malate concentrations. It has been found that the external oxoglutarate inhibits the exchange at high concentration. This excess-substrate inhibition is preceded by four jumps. The kinetic-saturation curve by the internal malate presents an apparent positive cooperativity that may be interpreted in different ways. The independence of the effects of the two substrates on the initial rate has been observed again and supports the conclusions reached in previous work. A method for the determination of oxoglutarate binding to the external face of the inner membrane is described. The binding curve shows four intermediary plateau regions that reflect significant apparent K-effects, alternatively negative and positive. For external-oxoglutarate concentrations below the region of excess-substrate inhibition, the binding-saturation curve and the kinetic-saturation curve are similar, demonstrating that K-effects are predominant. A particularly wide intermediary plateau that seems to correspond to half saturation of the active sites is common to both saturation curves. A clear lack of proportionality between the two curves at low oxoglutarate concentrations seems to indicate that more than one catalytic-rate constant is implied in the exchange kinetics. Two models of the oxoglutarate carrier are presented. Both lead to a minimum degree of 10:10 for the equation of the binding of oxoglutarate to the catalytic sites. In the first model this corresponds to ten subunits associated into a single oligomer while in the second model this results from a mixture of monomeric, dimeric, trimeric and tetrameric associations.

Steady-state kinetics of smooth muscle myosin

The kinetic properties of purified smooth muscle myosin, free of actin, have been examined. Analysis of the steady-state kinetic data revealed an intermediary plateau region on the substrate saturation curves. In addition, these data, when analyzed by Hill and Lineweaver and Burk plots, indicate both positive and negative cooperativity, suggesting at least four substrate binding sites. The plateau region was abolished when the kinetic measurements were made at pH 5.5 and 9.0. Both positive and negative cooperative effects were absent at pH 9.0 and hyperbolic kinetics was observed. In contrast, at pH 5.5, although the plateau region was abolished, the enzyme exhibited positive cooperativity of substrate binding. When either heated or urea treated enzyme was used for kinetic measurements: (i) the plateau region shifted toward higher substrate concentration range; (ii) the cooperativity of binding sites was lost at low substrate concentrations but was instead seen at higher concentrations; and (iii) the Vmax was doubled. These data have been interpreted as due to ligand-induced conformational changes in the enzyme according to J. Teipel and D. E. Koshland, Jr. (1969).

Dose any enzyme follow the Michaelis-Menten equation?

A literature search has been conducted to see to what extent steady-state kinetics studies in the period 1965-1976 have revealed deviations from Michaelis-Menten kinetics. It was found that over 800 enzymes have been reported as giving complex curves for a variety of reasons and a group by group classification of all these enzymes has been carried out listing all the types of variations reported and the authors' explanations. In addition, for highly complex curves, we have determined the minimum degree of the rate equation. There were very few determined attempts to demonstrate adherence to the Michaelis-Menten equation over a wide variety of experimental conditions and substrate concentration and almost invariably detailed experimental work revealed unsuspected complexities. For these reasons, it is concluded that the assumption that most enzymes follow the Michaelis-Menten equation can not be supported by an appeal to the literature.

Studies of homogeneous "biosynthetic" L-threonine dehydratase from Escherichia coli K-12. Some kinetic properties and molecular multiplicity

"Biosynthetic" L-threonine dehydratase (EC 4.2.1.16) was purified to a homogeneous state with 29% yield of total activity from Escherichia coli K-12. The homogeneity of the enzyme was shown by polyacrylamide gel disc electrophoresis in the presence of dodecyl sulphate. The enzyme consisted of equal subunits having a molecular weight of about 57 000. The polyacrylamide gel disc electrophoresis has shown that the native enzyme consisted of a set of oligomeric forms. The multiplicity of molecular organization of the enzyme was reflected in complicated kinetic behaviour: at pH greater than 9 on the plots of initial reaction rate (v) versus initial substrate concentration ([S]o) there were four inflexion points (two intermediate plateaux), the position and deepness of which depended on enzyme concentration. At pH 8.3 on the v versus [S]o plots appeared two inflexion points (one intermediate plateu), the position of which practically did not depend on enzyme concentration in the reaction mixture, but strongly depended on the enzyme concentration in the stock solution. Repeated polyacrylamide gel disc electrophoresis of several oligomeric forms, isolated by the first electrophoresis, has shown that the oligomeric forms underwent a slow polymerization. It was suggested that "biosynthetic" L-threonine dehydratase from E. coli K-12 is a set of multiple oligomeric forms, having different kinetic parameters. Probably, each form of the enzyme has a "simple" kinetics characterized by hyperbolic or sigmoidal shape of v versus [S]o plots. The rate of equilibrium installation between the oligomeric forms was small in comparison with the enzyme reaction velocity, that lead to the complex kinetic curves, appearing as a result of summing up of the kinetics inherent to theindividual forms.

Evidence for cooperative effects in the exchange reaction catalysed by the oxoglutarate translocator of rat-heart mitochondria

The initial rates of the exchange external oxoglutarate/internal malate through the inner membrane of rat-heart mitochondria, for various concentrations of the two substrates, have been reinvestigated for an extended range of concentrations of the external oxoglutarate. This has been made possible by use of the inhibitor-stop technique that allows 100 times smaller incubation times than the centrifugation-stop technique used previously. Under the experimental conditions the uptake of the external-labelled oxoglutarate into the mitochondrial-matrix space is mediated by the oxoglutarate translocator performing a ono-to-one exchange of the anions oxoglutarate (external) and malate (internal). Two intermediary-plateau regions are observed in the kinetic saturation curve of the translocator by the external oxoglutarate, revealing a complex rate equation which is found to be the product of two one-substrate functions. Analysing these features it is shown that the model, proposed earlier, of a "double carrier" as catalyst in a rapid-equilibrium random bi-bi mechanism, is still applicable but that several external binding sites have to be considered. As already noticed the external and the internal substrates bind to their respective sites independently of each other. Furthermore, some additional requirements imposed by the observed kinetics suggest that the exchange reaction is performed by only one translocator species made of identical interacting subunits. The anion exchange is tentatively viewed as a rotation of a subunit around an axis situated in the plane of the membrane after two independent local configuration changes induced by the binding of the two substrates on this subunit.

Evaluation of Hill slopes and Hill coefficients when the saturation binding or velocity is not known

1. The Hill coefficient (nH), an often-used measure of deviations from hyperbolic behaviour (nonhyperbolicity) in kinetic and binding systems, is usually estimated from the maximum or minimum slope of the Hill plot. The method depends strongly on the assumed magnitude of the asymptotic velocity (V) or binding (P) whose evaluation may be difficult in nonlinear/co-operative systems. Therefore, alternative procedures were devised for the estimation nH which do not require the prior knowledge of V or P. 2. When pairs of velocity/binding readings (v and w) are obtained at concentrations of c and alpha c, respectively (where alpha is a fixed constant), then the relation between w and v is described by a hyperbola, provided that Hill's equation is valid. In this case, linearizing plots, v/w versus v, w versus, w/v, and 1/w versus 1/v, can be used for estimation of the degree of the equation. However, if the Hill expression is applicable, these methods are not efficient and traditional procedures, particularly nonlinear regression, should be used. 3. The 'linearizing' plots of the Hill equation can be applied advantageously for the evaluation of the Hill slope and of nH also in the general case, when the Hill expression is actually not valid, provided that deviations from hyperbolic behaviour are positive. Appropriately extrapolated intercepts of the first two plots estimate alphanH. Furthermore, the slope of the third plot yields, similarly to the method of Kurganov et al., a continuous measure of the Hill slope (including its maximum) at all concentrations. The agreement is, at positive nonhyperbolicities, excellent theoretical values of Hill slopes and coefficients and those estimated by the proposed methods. 4. A coefficient of nonhyperbolicity (theta) is defined for 2nd-degree rate equations which provides a quantitative measure of positive or negative deviation from first-degree, hyperbolic characteristics. It is closely related to the Hill coefficient.