The computation of hyperbolic dependences in enzyme kinetics.

A computer program aimed at analysing results following Michaelis-Menten kinetics can be used unmodified in the treatment of other kinetic results provided that the kinetic equations in these cases can be written in the form of the Michaelis-Menten equation. A list is presented of the parameters to be set instead of substrate concentration and reaction rate, and of constants replacing Km and V, if such a program is applied in analysing enzyme inhibitions, activations and pH-dependences.     

On true and apparent Michaelis constants in enzymology. III. Is it linear dependence between apparent michaelis constant and limiting rate and is it possible to determine the substrate constant value using this dependence?

The Slater-Bonner method which is used for graphic determination of substrate constant (Ks) by linear dependence of apparent Michaelis constant (Km(app)) on the limiting rate (V(app)) of enzyme-catalysed reactions with activator participation has been critically analysed. It has been shown that although it is possible to record the mechanisms of such reactions as a scheme similar to Michaelis-Menten model which allow to find correlation Km(app) and V(app) as equation Km(app) = Ks + V(app)/k1[E]0 ([E]0 is a total enzyme concentration, k1 is a rate constant of enzyme-substrate complex formation from free enzyme and substrate) in order to calculate Ks and individual rate constants (k1, k(-1)), but this approach for investigation of all reactions with activator participation ought not to be used. The above equation is not obeyed in general, it may be true for some mechanisms only or under certain ratios of kinetic parameters of enzyme-catalysed reactions.     

Assays for mechanistic investigations of protein/histone acetyltransferases

Protein/histone acetyltransferases (PATs/HATs) have been implicated in a number of cellular functions including gene regulation, DNA synthesis, and repair. This paper reviews methods that can be used to quantitatively determine the activity and ultimately the catalytic/kinetic mechanism of PAT/HATs in vitro. Two methods will be described in detail. The first method is a filter-binding assay that measures the transfer of radiolabeled acetate from acetyl-CoA to protein. The second method is a continuous, spectroscopic, enzyme-coupled assay that links the PAT/HAT reaction to the reduction of NAD+ by pyruvate or alpha-ketoglutarate dehydrogenase. Both methods are highly applicable in determining steady-state reaction rates, and obtaining the kinetic constants Vmax, Km, and V/K from substrate saturation curves. We describe a new application of the filter-binding assay to determine the kinetic parameters for HATs using low concentrations of nucleosomal substrates.     

Phosphorylation reaction of vertebrate smooth muscle myosin: an enzyme kinetic analysis

Phosphorylation of vertebrate smooth muscle myosin or its isolated 20 000-dalton light chains by myosin light-chain kinase (MLCK) was found to follow first-order kinetics not only at low ([M] much less than Km) but also at high ([M] greater than or equal to Km) substrate concentration. This observation can most simply be explained by a product inhibition for which the Michaelis constants (Km) of the enzyme for the substrate (dephosphorylated myosin) and for the product (phosphorylated myosin) are approximately the same. For such a case, integration of the kinetic velocity equation gives an exponential formula similar to that of a true first-order reaction, the only difference being that its rate constant (k) depends additionally on the initial substrate concentration ([M]0). The standard kinetic constants (k, Km, Vmax) have been calculated by using this pseudo-first-order relationship. Independent evidence for the validity of the derived kinetic relationship was obtained from binding studies with myosin and MLCK. These showed that MLCK binds to phosphorylated and dephosphorylated myosin with approximately equal affinity (Ks = 30 X 10(-9) M). The possible applicability of the same kinetic relationship to other enzyme systems is discussed.     

Two-hydronic-reactive states of acetylcholinesterase, mechanistically relevant acid-base catalyst of pKa 6.5 and a modulatory group of pKa 5.5

Variation of experimentally observed pKa values in pH-dependent kinetic studies using acetylcholinesterase (AcChE) is rationalized by proposal of two-hydronic-reactive states, EH and EH2, of the free AcChE molecule. Two kinetically influential ionizations with pKa 6.5 for the general acid-base catalyst, possibly the imidazole group of histidine, and a modulatory group with pKa 5.5 residing at the juxtaposal modulatory site, provided fundamental bases for the observed variation in pK(app) values. Appropriate equations applicable to the proposed kinetic model in conjunction with pKa values (pKI 5.5, pKII 6.5) and relative varied values of the pH-independent rate constants, k'cat/K'm and kcat/Km, of the reactive states were used to generate computer simulation error-free pH-rate profiles. A series of theoretical apparently simple sigmoidal pH-rate profiles with characterizing parameters pK(app) varying between 5.5-6.5 were obtained. Ionization of a modulatory group with pKa 5.5 alone modifies the reaction mechanism of AcChE, and binding of substrates and inhibitors at this site provides modulation of catalysis/binding at the active center. Analysis of the relative magnitudes of pH-independent rate constants for the two reactive states revealed that in terms of the overall catalysis, the EH state shows favorable reactivity towards the cationic reagents with reactivity 1.0, as compared to the EH2 state with reactivities 0.25-0.55. Neutral reagents, in general, make use of the EH2 state more than cationic reagents, with reactivities 1.0 for the EH state and 0.3-1.0 for the EH2 state. Further analysis showed that this discrimination between the two reactive states, by both types of reagents, occurs predominantly through the difference in binding constants K'm and Km. Relative binding of a given cationic reagent to the respective reactive states ranges from K'm = 1.8 X Km to 4.0 X Km, and from K'm = 1.0 X Km to 2.0 X Km for the neutral reagents.     

Changes in Regional Blood–Brain Transfer of l-Leucine Elicited by Arginine-Vasopressin

Arginine-vasopressin (AVP), injected into the carotid artery in physiological concentration together with L-leucine, changed kinetic constants of the blood-brain barrier (BBB) transport of this neutral amino acid without changing the cerebral blood flow (CBF). The maximum velocity of transport (Vmax), the half-saturation constant (Km), the nonsaturable transport constant (KD), and CBF were estimated in nine brain regions of male Wistar rats anesthetized with ether. In cerebral hemisphere, Vmax decreased from 21 nmol . min-1 . g-1 (control) to 7.6 nmol . min-1 . g-1 (AVP). Km decreased from 0.11 to 0.029 mM. Regional differences of the kinetic constants were found in controls as well as in AVP-treated animals. In all regions, the calculated constants Vmax and Km of animals coinjected with AVP were significantly decreased when compared to controls. A direct or indirect interaction of AVP with the transport system of large neutral amino acids is suggested.     

Initial reaction kinetics of succinate dehydrogenase in mouse liver studied with a real-time image analyser system.

The initial reaction kinetics of succinate dehydrogenase in situ were investigated in sections of mouse unfixed liver using an ARGUS-100 image analyser system. The sections were incubated on substrate-containing agarose gel films. Images of a section, illuminated with monochromatic light (584 nm), were captured with the image analyser in real time at intervals of 10 s during the incubation. The absorbances of selected hepatocytes in the successive images were determined as a function of time. In every cell, the absorbance increased nonlinearly after the first minute of incubation. The initial velocity of the dehydrogenase was calculated from the linear activities during the first 20 s of incubation. Hanes plots of the initial velocities and succinate concentration yielded the following mean kinetic constants. For periportal hepatocytes, the apparent Km = 1.2 +/- 0.8 mM and Vmax = 29 +/- 2 mumol hydrogen equivalents formed/cm3 hepatocyte cytoplasm per min. For pericentral hepatocytes, Km = 1.4 +/- 1.0 mM and Vmax = 21 +/- 2 mumol hydrogen equivalents/cm3 per min. The Km values are very similar to those determined previously from biochemical assays. These results, and the observed dependence of the initial velocity on the enzyme concentration, suggest that the technique reported here is valid for the histochemical assay of succinate dehydrogenase.     

Kinetics of Neutral Amino Acid Transport Across the Blood-Brain Barrier

Neutral amino acid (NAA) transport across the blood-brain barrier was examined in pentobarbital-anesthetized rats with an in situ brain perfusion technique. Fourteen of 16 plasma NAAs showed measurable affinity for the cerebrovascular NAA transport system. Values of the transport constants (Vmax, Km, KD) were determined for seven large NAAs from saturation studies, whereas Km values for five small NAAs were estimated from inhibition studies. These data, together with our previous work, provide a complete set of constants for prediction of NAA influx from plasma. Among the NAAs, Vmax varied at least fivefold and Km varied approximately 700 fold. The apparent affinity (1/Km) of each NAA was related linearly (r = 0.910) to the octanol/water partition coefficient, a measure of NAA side-chain hydrophobicity. Predicted influx values from transport constants and average plasma concentrations agree well with values measured using plasma perfusate. These results provide accurate new estimates of the kinetic constants that determine NAA transport across the blood-brain barrier. Furthermore, they suggest that affinity of a L-alpha-amino acid for the transport system is determined primarily by side-chain hydrophobicity.     

Glutamine transaminase from brain tissue. Further studies on kinetic properties and specificity of the enzyme.

Glutamine transaminase, highly purified from rat brain, was studied. In the first series of experiments, the kinetics of the transamination reaction between 2-oxoglutaramate and phenylalanine were examined in order to determine the type of reaction mechanism. This proved to be of the ping-pont type, as can be expected for a transamination. The specificity of the enzyme for various amino acids and 2-oxo acids was then studied in detail. The most active substrates were glutamine, methionine and ethionine as amino-group donors, and phenylpyruvate, glyoxalate and 2-oxo-4-methiobutyrate as amino-group acceptors. For these and several other substrates, the kinetic constants, V and Km, were determined.     

The steady-state rate equation for cytochrome c oxidase based on a minimal kinetic scheme

A minimal catalytic cycle for cytochrome c oxidase has been suggested, and the steady-state kinetic equation for this mechanism has been derived. This equation has been used to simulate experimental data for the pH dependence of the steady-state kinetic parameters, kcat and Km. In the simulations the rate constants for binding and dissociation of cytochrome c and for two internal electron-transfer steps have been allowed to vary, whereas fixed experimental values (for pH 7.4) have been used for the other rate constants. The results show that the dissociation of the product, ferricytochrome c, cannot be rate-limiting under all conditions, but that intramolecular electron-transfer steps also limit the rate. They also demonstrate that Km can differ considerably from the dissociation constant for the cytochrome c-oxidase complex. Published values for the rate constant for the dissociation of ferricytochrome c are too small to account for the steady-state rates. It is suggested that, at high concentrations, ferryocytochrome c transfers an electron to a cytochrome c molecule which remains bound to the oxidase. This can also explain the nonhyperbolic kinetics, which is observed at low substrate concentrations.     

Kinetics of enzymatic hydrolysis of quaternary aminoalkyl esters of aromatic mono- and dicarboxylic acids by butyrylcholinesterase from horse serum]

Enzymatic hydrolysis kinetics of benzoylcholine (BzCh), phehylpropionic acid choline ester (PK-157), suberic acid dicholine ester (D-6) and p-phenylenediacetic (PK-139), p-phenylenedipropionic (PK-154 and PK-155), p-phenylenediacryc (PK-150 and PK-151) and phtalic (PK-105) acids diaminoalkyl esters by horse blood serum butyrylcholinesterase (BuChE) was studied. Hydrolysis constants Km, V and Kss were estimated by means of different graphic methods. PK-157 ester turned to be highly specific selective substrate for BuChE, its V being 20 times as high and Km -- 20 times as low as those for acetylcholine (ACh). The highest V value was found for D-6 in the case of diesters. Hydrolysis of aromatic dicarbonic acids diesters was characterized with significantly lower V values (0.6-10.% of V for ACh) and extremely low Km values (approximately 10(-5) -- 10(-6) M). Substrate inhibition was observed under the hydrolysis of BzCh, PK-157, D-6 and all aromatic dicarbonic acids esters by BuChE. Formal kinetic analysis revealed that inactive complex, which formed in this case, corresponded to ES2 composition. The appearance of substrate inhibition for BuChE and its increasing are supposed to be due to the increase in the size and in the rigidity of the acyl part of the molecule in the number of substrates studied.     

Kinetic properties of highly purified luciferase from fireflies Luciola mingrelica.]

Luciferase of the fireflies Luciola mingrelica was isolated from dried lanterns of fireflies and purified by chromatography on DEAE-Sephadex. The homogeneity of the preparation was determined by polyacrylamide gel disc electrophoresis. The molecular weight of the enzyme equal to 45000 was determined by disc electrophoresis in the presence of sodium dodecyl sulfate. The kinetic properties of the enzyme (V and Km for luciferin and ATP) within the pH-range of 7,0--8,5 were studied. The kinetic curves of the pH-dependences of log V and log Km for both substrates are bell-shaped, with a slope equal to 2. At pH optimum (7,7--7,9) the Km values for luciferin and ATP are 6,6 mkM and 0,3 mM, respectively. The properties of luciferase L. m. were compared to those of luciferase from fireflies Phophinus pyralis previously described in literature.     

General base catalysis in a glutamine for histidine mutant at position 51 of human liver alcohol dehydrogenase

On the basis of the three-dimensional structure of horse liver alcohol dehydrogenase determined by X-ray crystallography, His 51 has been proposed to act as a general base during catalysis by abstracting a proton from the alcohol substrate. A hydrogen-bonding system (proton relay system) connecting the alcohol substrate and His 51 has been proposed to mediate proton transfer. We have mutated His 51 to Gln in the homologous human liver beta 1 beta 1 alcohol dehydrogenase isoenzyme which is expected to have a similar proton relay system. The mutation resulted in an about 6-fold drop in V/Kb (Vmax for ethanol oxidation divided by Km for ethanol) at pH 7.0 and a 12-fold drop at pH 6.5. V/Kb could be restored completely or partially by the presence of high concentrations of glycylglycine, glycine, and phosphate buffers. A Br?nsted plot of the effect on V/Kb versus the pKa of these bases plus H2O and OH- was linear. Only secondary or tertiary amine buffers differed from linearity, presumably due to steric hindrance. These results suggest that His 51 acts as a general base catalyst during alcohol oxidation in the wild-type enzyme and can be functionally replaced in the mutant enzyme by general base catalysts present in the solvent. Steady-state kinetic constants for NAD+ and the trifluoroethanol inhibition patterns were similar between the wild-type and the mutant enzyme. Differences in the inhibition constants (Ki) of caprate and trifluoroethanol below pH 7.8 and in the pH dependence of Ki can be explained by the substitution of neutral Gln for positively charged His.     

The regulation of glycogen metabolism. Phosphorylation of inhibitor-1 from rabbit skeletal muscle, and its interaction with protein phosphatases-III and -II.

Inhibitor-1 from rabbit skeletal muscle was phosphorylated by protein kinase dependent on adenosine 3' :5'-monophosphate (cyclic AMP), but not by phosphorylase kinase or by glycogen synthetase kinase-2. Protein phosphatase-III, isolated and stored in the presence of manganese ions to keep it stable, was in a form which catalysed a rapid dephosphorylation and inactivation of inhibitor-1. The kinetic constants for the dephosphorylation of inhibitor-1 [Km = 0.7 micron, V(rel) = 40] were comparable to those for the dephosphorylation of phosphorylase kinase [Km =1.1 micron, V (rel) = 62] and phosphorylase [Km = 5.0 micron, V (rel) = 100]. The dephosphorylation of inhibitor -1 was inhibited by inhibitor-2, indicating that it was catalysed by protein phosphatase-III, and not by another enzyme that might be contaminating the preparation. When protein phosphatase-III was diluted into buffers containing excess EDTA, it lost activity initially, but after 90 min, the activity reached a plateau that remained stable for at least 20h. The initial loss in activity varied with the substrate that was tested; it was 20-30% with phosphorylase a, 50-60% with phosphorylase kinase and greater than or equal to 95% with inhibitor-1. This form of protein phosphatase-III was inhibited by inhibitor-1 in a noncompetitive manner, and the Ki for inhibitor-1 was 1.6 +/- 0.3 nM. The phosphorylase phosphatase, phosphorylase kinase phosphatase and glycogen synthetase phosphatase activities of protein phosphatase-III were inhibited in an identical manner by inhibitor-1. This result emphasizes the potential importance of inhibitor-1 in the regulation of glycogen metabolism, since it can influence the state of phosphorylation of three different enzymes. The formation of the inactive complex between inhibitor-1 and protein phosphatase-III was reversed by incubation with trypsin (which destroyed inhibitor-1, but not protein phosphatase-III) or by dilution of the inactive complex. Kinetic studies, using the form of protein phosphatase-III which dephosphorylated inhibitor-1 very rapidly, demonstrated three unusual features of the system: (a) inhibitor-1 was still as powerful and inhibitor of the dephosphorylation of phosphorylase a and phosphorylase kinase a even under conditions where it was being rapidly dephosphorylated; (b) inhibitor-1 was not an inhibitor of its own dephosphorylation; (c) phosphorylase a did not effect the rate of dephosphorylation of inhibitor-1 even when it was present in a 50-fold molar excess over inhibitor-1. The result of these three properties is that inhibitor-1 is preferentially dephosphorylated by protein phosphatase-III even in the presence of a large excess of other phosphoprotein substrates. Inhibitor-1 was also dephosphorylated by protein phosphatase-II. The kinetic constants for the dephosphorylation of inhibitor-1 [Km = 2.8 micron, V (rel) = 200] and the alpha-subunit of phosphorylase kinase [Km = 3.7 micron, V (rel) = 100]were comparable...     

Malate oxidation by mitochondrial succinate:ubiquinone-reductase

Succinate:ubiquinone reductase was shown to catalyze the oxidation of L- and D-stereoisomers of malate by artificial electron acceptors and ubiquinone. The rate of malate oxidation by succinate:ubiquinone reductase is by two orders of magnitude lower than that for the natural substrate--succinate. The values of kinetic constants for the oxidation of D- and L-stereoisomers of malate are equal to: V infinity = 0.1 mumol/min/mg protein, Km = 2 mM and V infinity = 0.05 mumol/min/mg protein, Km = 2 mM, respectively. The malate dehydrogenase activity is fully inhibited by the inhibitors of the dicarboxylate-binding site of the enzyme, i.e., N-ethylmaleimide and malonate and is practically insensitive to carboxin, a specific inhibitor of the ubiquinone-binding center. The enol form of oxaloacetate was shown to be the product of malate oxidation by succinate:ubiquinone reductase. The kinetics of inhibition of the enzyme activity by the ketone and enol forms of oxaloacetate was studied. Both forms of oxaloacetate effectively inhibit the succinate:ubiquinone reductase reaction.     

Mammalian adenylosuccinate lyase. Participation in the conversion of 2'-dIMP and beta-D-arabinosyl-IMP to adenine nucleotides.

Adenylosuccinate synthetase (EC 6.3.4.4) from rabbit muscle efficiently catalyzes the formation of 2'-deoxyadenylosuccinate and beta-D-arabinosylade-nylosuccinate from 2'-dIMP and beta-D-arabinosylIMP (Spector, T. and Miller, RL. (1976) Biochim. Biophys. Acta 445, 509-517). These novel analogs of adenylosuccinate were synthesized with this enzyme and their kinetic constants were determined with adenylosuccinate lyase purified from Ehrlich ascites cells. 2'-Deoxyadenylosuccinate and beta-D-arabinosyladenylosuccinate were readily cleaved to 2'-dAMP and beta-D-arabinosylAMP, respectively. Their Km values were similar to that of adenylosuccinate (3-6 micronM) and their substrate efficiencies (V/Km) were 120 for 2-deoxyadenylosuccinate and 32 for beta-D-arabinosyl-adenylosuccinate, compared to a value of 100 for adenylosuccinate. The products of the reactions, 2'-dAMP and beta-D-arabinosylAMP, were competitive inhibitors with Ki values of 5 and 87 micronM, respectively. ATP and ADP were considerably weaker competitive inhibitors with Ki values of 200-300 micronM. IMP, GMP, xanthosine 5'-monophosphate, 6-thioIMP and 6-thioGMP had Ki values greater than 200 micronM.     

Kinetics of trypsin from rainbow trout are not influenced by level of feeding

1. Specific activity and kinetic constants of trypsin from the pyloric caeca of rainbow trout (Salmo gairdneri) were measured. 2. Although one group was fed more than twice as much as the other (1.8 compared to 0.7% body weight per day), there were no significant differences in the weight of the pyloric caeca, specific activity of trypsin, or kinetic constants (apparent Km or Vmax) between the two groups. 3. The caecum of trout contains enough trypsin to digest all of the protein in a typical meal in less than 5 hr.     

Prostaglandin-E2 9-ketoreductase from human uterine decidua vera

Prostaglandin-E2 9-ketoreductase, the enzyme which catalyzes the reaction from prostaglandin E2 (PGE2) to prostaglandin F2 alpha (PGF2 alpha), has been purified 232-fold from human uterine decidua vera. The molecular mass of the enzyme, as estimated by fast protein liquid chromatography, was 29 kDa. Sodium dodecyl sulfate disc gel electrophoresis of the denatured enzyme revealed a molecular mass of 31 kDa. These data suggest that the enzyme consists of a single polypeptide chain. The rate equation of the enzyme reaction for two substrates was used for the determination of five kinetic constants. The equilibrium constant with respect to PGE2 was 83 microM, the Michaelis constant, Km, for PGE2 was 93 microM. For NADPH, the equilibrium constant was 1.0 microM and Km was 1.6 microM. The maximal velocity for the forward reaction was V1 = 217 pmol/min. The inhibition constants for the analgesic agents indomethacin and fentiazac were Ki = 850 microM and Ki = 450 microM and for the steroid progesterone Ki = 1.5 mM, respectively. Prostaglandin-E2 9-ketoreductase might be responsible for the control of the PGE2/PGF2 alpha ratio in human decidua vera. The enzyme, therefore, might be an important factor in the cascade of events leading to uterine contractions and parturition.     

Mechanistic studies with solubilized rat liver steroid 5 alpha-reductase: elucidation of the kinetic mechanism

A solubilized preparation of steroid 5 alpha-reductase (EC 1.3.1.30) from rat liver has been used in studies focused toward an understanding of the kinetic mechanism associated with enzyme catalysis. From the results of analyses with product and dead-end inhibitors, a preferentially ordered binding of substrates and release of products from the surface of the enzyme is proposed. The observations from these experiments were identical with those using the steroid 5 alpha-reductase activity associated with rat liver microsomes. The primary isotope effects on steady-state kinetic parameters when [4S-2H]NADPH was used also were consistent with an ordered kinetic mechanism. Normal isotope effects were observed for all three kinetic parameters (Vm/Km for both testosterone and NADPH and Vm) at all substrate concentrations used experimentally. Upon extrapolation to infinite concentration of testosterone, the isotope effect on Vm/Km for NADPH approached unity, indicating that the nicotinamide dinucleotide phosphate is the first substrate binding to and the second product released from the enzyme. The isotope effects on Vm/Km for testosterone at infinite concentration of cofactor and on Vm were 3.8 +/- 0.5 and 3.3 +/- 0.4, respectively. Data from the pH profiles of these three steady-state parameters and the inhibition constants (1/Ki) of competitive inhibitors versus both substrates indicate that the binding of nicotinamide dinucleotide phosphate involves coordination of its anionic 2'-phosphate to a protonated enzyme-associated base with an apparent pK near 8.0. From these results, relative limits have been placed on several of the internal rate constants used to describe the ordered mechanism of the rat liver steroid 5 alpha-reductase.     

Phosphorylation of synthetic peptides by skeletal muscle myosin light chain kinases

Substrate determinants for rabbit and chicken skeletal muscle myosin light chain kinases were examined with synthetic peptides. Both skeletal muscle myosin light chain kinases had similar phosphorylation kinetics with synthetic peptide substrates. Average kinetic constants for skeletal muscle myosin light chain heptadecapeptide, (formula; see text) where S(P) is phosphoserine, were Km, 2.3 microM and Vmax, 0.9 mumol/min/mg of enzyme. Km values were 122 and 162 microM for skeletal muscle peptides containing A-A for basic residues at positions 2-3 and 6-7, respectively. Average kinetic constants for smooth muscle myosin light chain peptide, (formula; see text), were Km, 1.4 microM and Vmax 27 mumol/min/mg of enzyme. Average Km values for the smooth muscle peptide, residues 11-23, were 10 microM which increased 6- and 11-fold with substitutions of alanine at residues 12 and 13, respectively. Vmax values decreased and Km values increased markedly by substitution of residue 16 with glutamate in the 11-23 smooth muscle tridecapeptide. Basic residues located 3 and 6-7 residues toward the NH2 terminus from phosphoserine in smooth muscle myosin light chain and 6-8 and 10-11 residues toward the NH2 terminus from phosphoserine in skeletal muscle myosin light chain appear to be important substrate determinants for skeletal muscle myosin light chain kinases. These properties are different from myosin light chain kinase from smooth muscle.