Two different ways that hydrogen ions are involved in the thermodynamics and rapid-equilibrium kinetics of the enzymatic catalysis of S=P and S+H2O=P

Hydrogen ions are involved in two different ways in the thermodynamics and rapid-equilibrium kinetics of enzyme-catalyzed reactions. The two ways are through pKs and through the production or consumption of hydrogen ions in the mechanism. These ways are examined for the catalyzed reactions S=P and S+H2O=P. Since the apparent equilibrium constant K' can be calculated from the kinetic parameters by use of the Haldane equation, the treatment of the effects of pH must be consistent in thermodynamics and kinetics. This leads to a new kind of Haldane equation that involves 10(pH) or 10(-pH) in addition to the kinetic parameters when hydrogen ions are produced or consumed. These concepts are applicable to more complicated reactions and rate equations. Derivations of equations for calculating these two types of pH effects are discussed in thermodynamics and rapid-equilibrium kinetics. A computer program is used to make four plots of apparent equilibrium constants and changes in the binding of hydrogen ions in the catalyzed reaction.     

Rapid-equilibrium rate equations for the enzymatic catalysis of A+B=P+Q over a range of pH

This article shows how pKs for the enzymatic site and enzyme-substrate complexes can be obtained from kinetic experiments on the reaction A+B=P+Q, with and without the consumption of hydrogen ions. The rapid-equilibrium rate equation makes it possible to obtain the pKs and chemical equilibrium constants involved in the mechanism, the apparent equilibrium constant K' for the catalyzed reaction, and the number of hydrogen ions consumed in the rate-determining reaction. Experimentally-determined Michaelis constants can be adjusted for the pKs of the substrates A, B, P, and Q so that it is easier to obtain the pKs of E, EA, EB, EAB, EQ, and EPQ, and the chemical equilibrium constants. Reaction rates are discussed for the forward reaction ordered A+B=ordered P+Q with zero, one, or two hydrogen ions consumed in the rate-determining reaction and for random A+B=ordered P+Q with zero, one, or two hydrogen ions consumed in the rate-determining reaction. When hydrogen ions are consumed in the rate-determining reaction, there is a new factor 10(n)(pH) in the rate equation, where n is the number of hydrogen ions consumed in the rate-determining reaction for the forward reaction. The integer n can be obtained from rate measurements over a range of pH, but it cannot be determined from thermodynamic measurements.     

Kinetic studies of the urokinase-catalysed conversion of NH2-terminal glutamic acid plasminogen to plasmin.

Initial velocities for the urokinase (EC 3.4.99.26)-catalysed conversion of glutamic acid plasminogen to plasmin (EC 3.4.21.7) have been determined at various urokinase and glutamic acid plasminogen concentrations. As has been found for the corresponding reaction with lysine plasminogen this conversion obeys the Michaelis rate equation. The apparent Michaelis constants are of the same order of magnitude for lysine and glutamic acid plasminogens. The difference in conversion rates for the reactions has been shown to be connected with their having different catalytic constants. The data were analysed according to two reaction schemes, in one of which only one peptide bond is split during the glutamic acid plasminogen-plasmin conversion and in the other of which the cleavage of two peptide bonds with the obligatory formation of an intermediate plasminogen is assumed. The results favour the former.     

15-Hydroxyprostaglandin dehydrogenase from human placenta, II. Steady state kinetics and influence of prostaglandin F2alpha analogues (author's transl)]

A complete initial rate analysis of the forward reaction catalyzed by 15-hydroxyprostaglandin dehydrogenase from human term placenta was carried out at pH 7.4 (100mM triethanolamine) with the substrates NAD, and the prostaglandins E1, E2 and F2alpha. The limiting Michaelis constants, the dissociation constants, and the limiting maximum velocities for these substrates were calculated by fitting the obtained data by weighted linear regression analysis to the complete rate equation. The product inhibition of the reaction by NADH and 15-oxoprostaglandin was studied and the inhibition constants were graphically determined. The initial rate and inhibition patterns obtained indicate that the reaction follows kinetically an ordered Bi Bi mechanism. The prostaglandin F2alpha analogues ICI 81,008 and ICI 79,939 were not utilized by the enzyme. With ICI 81,008 a slight inhibition of the enzymatic reaction with prostaglandin F2alpha was observed, whereas ICI 79,939 showed no effect. The results are discussed with respect to their possible biological significance.     

Thermodynamic properties of nucleotide reductase reactions

Recent thermodynamic measurements have made it possible to calculate the apparent equilibrium constants of the ribonucleoside diphosphate reductase reaction and the ribonucleoside triphosphate reductase reaction with various reducing agents. Third law heat capacity measurements on crystals of d-ribose and other calorimetric measurements make it possible to calculate Delta(f)G degrees for D-ribose and two species of D-ribose 5-phosphate. The experimental value of the apparent equilibrium constant K' for the deoxyribose-phosphate aldolase reaction makes it possible to calculate the standard Gibbs energies of formation Delta(f)G degrees for two protonation states of 2'-deoxy-D-ribose 5-phosphate. This shows that Delta(f)G degrees (2'-deoxy-D-ribose 5-phosphate(2)(-)) - Delta(f)G degrees (D-ribose 5-phosphate(2)(-)) = 147.86 kJ mol(-1) at 298.15 K and zero ionic strength in dilute aqueous solutions. This difference between reduced and oxidized forms is expected to apply to D-ribose, D-ribose 1-phosphate, ribonucleosides, and ribonucleotides in general. This expectation is supported by two other enzyme-catalyzed reactions for which apparent equilibrium constants have been determined. The availability of Delta(f)G degrees values for the species of 2'-deoxy-D-ribose and its derivatives makes it possible to calculate standard transformed Gibbs energies of formation of these reactants, apparent equilibrium constants for their reactions, changes in the binding of hydrogen ions in these reactions, and standard apparent reduction potentials of the half reactions involved as a function of pH and ionic strength at 298.15 K. The apparent equilibrium constant for ADP + thioredoxin(red) = 2'-deoxyADP + H(2)O + thioredoxin(ox) is 1.4 x 10(11) at 298.15 K, pH 7, and 0.25 M ionic strength.     

Characteristics of the interaction of adrenal lipoamide dehydrogenase with physiological and quinone electron acceptors

Lipoamide dehydrogenase (EC 1.6.4.3) from the ketoglutarate dehydrogenase complex of adrenals catalyzes the oxidation of NADH by lipoamide and quinone compounds according to the "ping-pong" scheme. The catalytic constants of these reactions are equal to 220 and 24 s-1, respectively (pH 7.0). The maximal quinone reductase activity is observed at pH 5.6, whereas the lipoamide reductase activity changes insignificantly at pH 7.5-5.5. The maximal dihydrolipoamide-NAD+ reductase activity is observed at pH 7.8. The oxidative constants of quinone electron acceptors vary from 6 X 10(6) to 4 X 10(2) M-1 s-1 and increase with their redox potential. The patterns of NAD+ inhibition in the quinone reductase reaction differ from that of lipoamide reductase reaction. The quinones are reduced by lipoamide dehydrogenase in the one-electron mechanism.     

The halide complexes of myeloperoxidase and the mechanism of the halogenation reactions

The spectral changes caused by the addition of halides to myeloperoxidase (donor:hydrogen-peroxide oxidoreductase, EC 1.11.1.7) have been investigated and the dissociation constants of the enzyme-halide complexes have been determined. The pH dependence of the dissociation constants suggests that halide binding is associated with a protonation step in myeloperoxidase. Myeloperoxidase catalyzes the peroxidative chlorination and bromination of monochlorodimedone. It is shown that at low pH, chloride acts as a competitive inhibitor with respect to H2O2, whereas at higher pH, H2O2 inhibits the chlorination reaction. The dissociation constant (Kd) of the spectroscopically detectable complex and the Km for chloride are considerably smaller than the inhibition constant (Ki) for chloride. These halogenation reactions are strongly pH dependent, the logarithm of the Km for chloride varies linearly with pH. The position of the pH optimum of the chlorination and bromination reaction is a linear function of the logarithm of the [halide]/[H2O2] ratio. A mechanism of the chlorination and bromination reaction is suggested with substrate inhibition for both hydrogen peroxide and the halide.     

The characterization of two reduced nicotinamide–adenine dinucleotide phosphate-linked aldehyde reductases from pig brain

1. NADPH-linked aldehyde reductase from pig, ox and rat brain exhibits non-linear reciprocal plots when partially purified enzyme preparations are studied. 2. In pig brain this non-linearity is due to the presence of two distinct aldehyde reductases, which can be separated by DEAE-cellulose chromatography. 3. These two enzymes can be distinguished by several criteria, including pH optima, Michaelis constants for substrates and their inhibitor sensitivity. 4. The probable role of these enzymes in the metabolism of the aldehydes derived from the biogenic amines is discussed.     

Thermodynamics of the reactions of carbamoyl phosphate

Two measurements of equilibrium constants by Marshall and Cohen make it possible to calculate standard Gibbs energies of formation of the species of carbamate and carbamoyl phosphate. Carbamate formation from carbon dioxide and ammonia does not require an enzyme, and the equilibrium concentrations of carbamate in ammonium bicarbonate are calculated. Knowing the values of standard Gibbs energies of formation of species of carbamate and carbamoyl phosphate make it possible to calculate the dependencies of the standard transformed Gibbs energies of formation of these reactants on pH and ionic strength and to calculate apparent equilibrium constants for several enzyme-catalyzed reactions and several chemical reactions. These calculations are sufficiently complicated that computer programs in Mathematica are used to make tables and plots. The dependences of apparent equilibrium constants on pH are consequences of the production or consumption of hydrogen ions, which are shown in plots. As usual the increase in the number of enzyme-catalyzed reactions for which apparent equilibrium constants can be calculated is larger than the number of reactions required to obtain the thermodynamic properties of the species involved.     

The role of water in the thermodynamics of dilute aqueous solutions

Water plays a role in the thermodynamics of dilute aqueous solutions that is unusual in two ways. First, knowledge of hydration equilibrium constants of species is not required in calculations of thermodynamic properties of biochemical reactants and reactions at specified pH. Second, since solvent provides an essentially infinite source of oxygen atoms in a reaction system where water is a reactant, oxygen atoms are not conserved in the reaction system in dilute aqueous solutions. This is related to the fact that H₂O is omitted in equilibrium expressions for dilute aqueous solutions. Calculations of the standard transformed Gibbs energies of formation of total carbon dioxide and total ammonia at specified pH are discussed, and the average bindings of hydrogen ions by these reactants are calculated by differentiation. Since both of these reactants are involved in the urease reaction, the apparent equilibrium constants and changes in the numbers of hydrogen ions bound are calculated for this reaction as functions of pH.     

Lysine-ketoglutarate reductase in human tissues.

Lysine-ketoglutarate reductase (saccharopine dehydrogenase (NADP+, lysine-forming) EC 1.5.1.8) from human liver has been partially purified and characterized. A spectrophotometric assay is described. The Michaelis constants have been determined for lysine (1.5-10-3 M), alpha-ketoglutarate (1-10-3 M) and NADPH (8-10-5 M). The pH optimum is 7.8. The enzyme is product inhibited. The specificity of the enzyme, response to inhibitors, pH and thermal stability are reported. Lysine-ketoglutarate reductase is present in high concentration in liver and heart, to a lesser degree in kidney and skin and in trace amounts in several other tissues. Saccharopine dehydrogenase (saccharopine dehydrogenase (NAD+, L-glutamate-forming) EC 1.5.1.9) was demonstrable only in liver and kidney. Lysine-ketoglutarate reductase reacts effectively with delta-hydroxylysine.     

A kinetic study of the reactions between H2O2 and Cu,Zn superoxide dismutase; evidence for an electrostatic control of the reaction rate

H2O2 was shown to reduce the copper ion of native bovine Cu,Zn superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) (ECu2+) and to oxidize the reduced enzyme (ECu+). The time-course of these processes was monitored by NMR measurement of the longitudinal relaxation rate of the water protons. A steady-state characterized by the same ratio [ECu2+]/[( EC2+] + [ECu+]) was obtained either by starting from the oxidized or the reduced enzyme. The kinetics of these processes appear to be quite complex, since different reactions between H2O2, or its reaction products, and the enzyme-bound copper control the reaction rate. The solution of the differential equations describing the kinetic processes showed that the oxidation and the reduction of the copper ion by H2O2 are first-order with respect to the copper ion itself only when these processes approach the steady-state. The rate constants of the reduction and oxidation reactions were calculated according to these equations and were found to have comparable values which are in the range 5-80 and 5-45 M-1.min-1, respectively, changing the pH from 5.6 to 7 at 0.21 M ionic strength. This result, together with the dependence of the reaction rates on pH and ionic strength, points to HO2- as the reactive species in both processes, and indicates that the electrostatic control of the access of the peroxide to the active site is the rate-determining step of the two redox reactions.     

Adenylate kinase of plants. Properties of adenylate kinase of pea leaves]

The properties of adenylate kinase in 2 ADP in equilibrium ATP + AMP reaction have been studied. The dependence of the enzyme activity on medium pH, protein concentration, substrates, Mg++ ions, AMP, adenine and adenosine has been also investigated. pH optimum is found to be 8.5 for forward reaction and 8-9--for the reverse one. The Michaelis constants are as follows: for ADP--1.17-10(-4) M, for ATP--3.33-10(-4) M at 24 degrees C, in 50 mM tris-HCl pH 7.6. The optimal ratio, Mg++ ions/substrates (ADP, ATP + AMP), is 1:2. The chelates of adenine nucleotides with Mg++ ions are proved to be "true" reaction substrates. Unlike adenine and adenosine, the product of AMP reaction inhibits adenylate kinase activity. It is concluded that the properties of adenylate kinase in plants are similar to those of animals and humans (moikinase).     

Bull sperm adenylate cyclase: localization and partial characterization.

A purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1) from bovine thyroid tissue has been purified 670-fold utilizing the techniques of ammonium sulfate precipitation, ion-exchange and molecular-exclusion chromatography, and polyacrylamide-gel electrophoresis. The protein has an apparent molecular weight of 90,000, a single isoelectric point at 5.6, and a Michaelis constant of 0.028 mm for inosine. Double-reciprocal plots of the reaction rate for the phosphorylase-catalyzed reaction versus phosphate or arsenate concentration display a downward trend at high substrate concentrations. Two apparent Michaelis constants of 0.38 and 1.49 mm were determined for phosphate.     

The purification and characterization of acetoacetyl-coenzyme A reductase from Azotobacter beijerinckii

A soluble acetoacetyl-CoA reductase (EC 1.1.1.36) was purified 54-fold from Azotobacter beijerinckii N.C.I.B. 9067 and the reaction product identified as d(-)-beta-hydroxybutyryl-CoA. The Michaelis constants for acetoacetyl-CoA, NADPH and NADH were determined and the reaction rate was found to be some fivefold greater with NADPH than with NADH. At neutral pH the equilibrium greatly favours the formation of the reduced product. Substrate specificity was in the order: acetoacetyl-CoA>acetoacetylpantetheine>acetoacetyl-(acyl-carrier protein). The enzyme possesses a functional thiol group, suffers inactivation by oxygen and is inhibited by thiol-blocking reagents. Inhibition by p-chloromercuribenzoate is reversed by excess of dithiothreitol, which also protects the enzyme from inactivation by oxygen.     

Studies on the biosynthesis of cytochrome P-450 in rat liver--a probe with phenobarbital.

The reaction of NAD(P)H:flavin oxidoreductase (flavin reductase) from Photobacterium fischeri is proposed to follow a ping-pong bisubstrate-biproduct mechanism. This is based on a steady-state kinetic analysis of initial velocities and patterns of inhibition by NAD⁺ and AMP. The double reciprocal plots of initial velocities versus concentrations of FMN or NADH show, in both cases, a series of parallel lines. The Michaelis constants for NADH (FMN saturating) and FMN (NADH saturating) are 2.2 and 1.2 × 10^?4m, respectively. The product NAD⁺ has been found to be an inhibitor competitive with FMN but non-competitive with NADH. Using AMP as an inhibitor, noncompetitive inhibition patterns were observed with respect to both NADH and FMN as the varied substrate. In addition, the reductase was not inactivated by treatment with N-ethylmaleimide either alone or in the presence of FMN, but the enzyme was inactivated by N-ethylmaleimide in the presence of NADH. These findings suggest that flavin reductase shuttles between disulfide- and sulfhydryl-containing forms during catalysis.     

Redox intermediates in the catalase cycle of catalase-peroxidases from Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis

Monofunctional catalases (EC 1.11.1.6) and catalase-peroxidases (KatGs, EC 1.11.1.7) have neither sequence nor structural homology, but both catalyze the dismutation of hydrogen peroxide (2H2O2 --> 2H2O + O2). In monofunctional catalases, the catalatic mechanism is well-characterized with conventional compound I [oxoiron(IV) porphyrin pi-cation radical intermediate] being responsible for hydrogen peroxide oxidation. The reaction pathway in KatGs is not as clearly defined, and a comprehensive rapid kinetic and spectral analysis of the reactions of KatGs from three different sources (Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis) with peroxoacetic acid and hydrogen peroxide has focused on the pathway. Independent of KatG, but dependent on pH, two low-spin forms dominated in the catalase cycle with absorbance maxima at 415, 545, and 580 nm at low pH and 418 and 520 nm at high pH. By contrast, oxidation of KatGs with peroxoacetic acid resulted in intermediates with different spectral features that also differed among the three KatGs. Following the rate of H2O2 degradation by stopped-flow allowed the linking of reaction intermediate species with substrate availability to confirm which species were actually present during the catalase cycle. Possible reaction intermediates involved in H2O2 dismutation by KatG are discussed.     

The kinetic properties and reaction mechanism of histamine methyltransferase from human skin.

The substrate kinetic properties of histamine methyltransferase from human skin were studied at limiting concentrations of both histamine and S-adenosylmethionine. Substrate inhibition by histamine was observed at concentrations above 10 microM. Primary plots showed evidence of a sequential reaction mechanism. The Michaelis constants were derived from secondary plots of slopes from the primary plots ([S]/v versus [S]) versus reciprocal of the second substrate concentration. The mean Km values for histamine and S-adenosylmethionine were 4.2 and 1.8 microM respectively. Histamine in concentrations of 25-100 microM inhibited enzyme activity uncompetitively with respect to S-adenosylmethionine. No substrate inhibition was observed with S-adenosylmethionine. To elucidate the reaction mechanism further, inhibition by the two products, S-adenosylhomocysteine and 1-methylhistamine, was studied. S-Adenosylhomocysteine inhibited non-competitively with respect to histamine and competitively with respect to S-adenosylmethionine. 1-Methylhistamine inhibited non-competitively with respect to histamine and to S-adenosylmethionine. These results are interpreted as providing evidence for an ordered sequential Bi Bi reaction mechanism, with the methyl-group donor S-adenosylmethionine as the first substrate that adds to the enzyme and histamine as the second substrate. 1-Methylhistamine is the first product to leave the enzyme and S-adenosylhomocysteine is the second. The results are discussed in terms of the possible role that this enzyme could play in the modulation of histamine-mediated reactions in skin.     

Reaction of phenylaminoethyl selenides with peroxynitrite and hydrogen peroxide

Peroxynitrite, a reactive cytotoxic species generated by the reaction of superoxide with nitric oxide, rapidly oxidizes phenylaminoethyl selenide (PAESe) and its para-substituted derivatives with second-order rate constants ranging from 900 to 3000 M(-1) s(-1) at neutral pH (pH 7.0) and 25 degrees C. These values are approximately 3 x 10(4) times greater than the corresponding rate constants for the reactions of selenides with hydrogen peroxide. The peroxynitrite reaction was also studied at alkaline pH. HPLC analysis confirms that both the peroxynitrite and hydrogen peroxide reactions produced the corresponding phenylaminoethyl selenoxide (PAESeO) as the sole selenium-containing product, with a stoichiometry of 1 mol of PAESe oxidized per 1 mol of PAESeO formed per 1 mol of oxidant reacted. The influence of para-substituents on the rate constants was investigated using Hammett plots; in both cases the data are consistent with an S(N)2-type mechanism, wherein the selenium atom acts as the nucleophile. Our results provide further evidence that organoselenium compounds may play a protective role in the defense against the many reactive oxidizing species produced in cellular metabolism.