Enzyme kinetics substrate effects

Enzyme reaction kinetics were modelled on the basis of rapid equilibrium assumption. Rapid equilibrium condition (also known as quasi-equilibrium) assumes that only the early components of the reaction are at equilibrium.8-10 In rapid equilibrium conditions, the enzyme (E), substrate (S) and enzyme-substrate (ES), the central complex equilibrate rapidly compared with the dissociation rate of ES into E and product (P ). The combined inhibition effects by 2-ethoxyethanol as a non-competitive inhibitor and (S)-ibuprofen ester as an uncompetitive inhibition resulted in an overall mechanism, shown in Figure 5.20. 

Fibrinolytics. Figure 3 Plasminogen activation (a) Kinetics of plasminogen activation by uPA (urokinase-type) and tPA (tissue-type) plasminogen activators. Effect of fibrin (b) Ternary complex formation between enzyme (tPA), substrate (Pg) and cofactor (F) Abbreviations plasmin (P), fibrin (F), plasminogen (Pg). Plasmin, formed in time, is expressed in arbitrary units. 

To refer to the kinetics of allosteric inhibition as competitive or noncompetitive with substrate carries misleading mechanistic implications. We refer instead to two classes of regulated enzymes K-series and V-se-ries enzymes. For K-series allosteric enzymes, the substrate saturation kinetics are competitive in the sense that is raised without an effect on V. For V-series allosteric enzymes, the allosteric inhibitor lowers... 

Two other general ways of treating micellar kinetic data should be noted. Piszkiewicz (1977) used equations similar to the Hill equation of enzyme kinetics to fit variations of rate constants and surfactant concentration. This treatment differs from that of Menger and Portnoy (1967) in that it emphasizes cooperative effects due to substrate-micelle interactions. These interactions are probably very important at surfactant concentrations close to the cmc because solutes may promote micellization or bind to submicellar aggregates. Thus, eqn (1) and others like it do not fit the data for dilute surfactant, especially when reactants are hydrophobic and can promote micellization. 

The expression for the effectiveness factor q in the case of zero-order kinetics, described by the Michaelis-Menten equation (Eq. 8) at high substrate concentration, can also be analytically solved. Two solutions were combined by Kobayashi et al. to give an approximate empirical expression for the effectiveness factor q [9]. A more detailed discussion on the effects of internal and external mass transfer resistance on the enzyme kinetics of a Michaelis-Menten type can be found elsewhere [10,11]. 

Using the various simplifications above, we have arrived at a model for reaction 11.9 in which only one step, the chemical conversion occurring at the active site of the enzyme characterized by the rate constant k3, exhibits the kinetic isotope effect Hk3. From Equations 11.29 and 11.30, however, it is apparent that the observed isotope effects, HV and H(V/K), are not directly equal to this kinetic isotope effect, Hk3, which is called the intrinsic kinetic isotope effect. The complexity of the reaction may cause part or all of Hk3 to be masked by an amount depending on the ratios k3/ks and k3/k2. The first ratio, k3/k3, compares the intrinsic rate to the rate of product dissociation, and is called the ratio of catalysis, r(=k3/ks). The second, k3/k2, compares the intrinsic rate to the rate of the substrate dissociation and is called forward commitment to catalysis, Cf(=k3/k2), or in short, commitment. The term partitioning factor is sometimes used in the literature for this ratio of rate constants. 

The haloalkane dehalogenase DhlA mechanism takes place in two consecutive Sn2 steps. In the first, the carboxylate moiety of the aspartate Aspl24, acting as a nucleophile on the carbon atom of DCE, displaces chloride anion which leads to formation of the enzyme-substrate intermediate (Equation 11.86). That intermediate is hydrolyzed by water in the subsequent step. The experimentally determined chlorine kinetic isotope effect for 1-chlorobutane, the slow substrate, is k(35Cl)/k(37Cl) = 1.0066 0.0004 and should correspond to the intrinsic isotope effect for the dehalogenation step. While the reported experimental value for DCE hydrolysis is smaller, it becomes practically the same when corrected for the intramolecular chlorine kinetic isotope effect (a consequence of the two identical chlorine labels in DCE). 

There are, however, many specific and anomalous kinetic salt effects, especially at higher salt concentrations, the origin of which lies in the effects on nonelectrolyte reactant activity coefficients. This is often the most interesting effect for enzymes, because the charge on the substrate is frequently zero, making the product ZiZ also zero. The exact charge on the enzyme molecules can be difficult to determine if one is working at a pH removed from the isoelectric point of the enzyme. 

Abstract Neuroscientists may wish to quantify an enzyme activity for one of many reasons. In order to do so, the researcher must be able to set up an assay appropriately, and this requires some understanding of the kinetic behavior of the enzyme toward the substrate used. Furthermore, such an understanding is vital if the inhibitory effects of a drug are to be assessed appropriately. This chapter outlines key principles that must be adhered to, and describes basic approaches by which rather complex kinetic data might be obtained, in order that enzyme kinetics and inhibitor kinetics might be studied successfully by the nonexpert. 

Human type II inosine monophosphate dehydrogenase catalyses NAD-dependent conversion of inosine monophosphate (IMP) into xanthosine monophosphate (XMP) measurements of the primary kinetic isotope effect using [ H]IMP suggest that both substrates (IMP and NAD) can dissociate from the enzyme-substrate complex therefore, the kinetic mechanism is not ordered. NMR studies indicate hydride transfer to the B or pro-S face of the nicotinamide ring of NAD, while kinetic studies suggest... 

This zinc metalloenzyme [EC 1.1.1.1 and EC 1.1.1.2] catalyzes the reversible oxidation of a broad spectrum of alcohol substrates and reduction of aldehyde substrates, usually with NAD+ as a coenzyme. The yeast and horse liver enzymes are probably the most extensively characterized oxidoreductases with respect to the reaction mechanism. Only one of two zinc ions is catalytically important, and the general mechanistic properties of the yeast and liver enzymes are similar, but not identical. Alcohol dehydrogenase can be regarded as a model enzyme system for the exploration of hydrogen kinetic isotope effects. 

Selected entries from Methods in Enzymology [vol, page(s)] Dilution of enzyme samples, 63, 10 lipolysis substrate effect, 64, 361, 362 dilution jump kinetic assay, 74, 14-19, 28 dilution method [for dissociation equilibria, 61, 65-96 continuous dilution cuvette, 61, 78-96 data analysis, 61, 74, 75 equations, 61, 70-74 errors, 61, 76-78 experimental procedures, 61, 69, 70 merits, 61, 75, 76 theory, 61, 68, 69... 

Such considerations raise the concept of the intrinsic kinetic isotope effect—the effect of isotopic substitution on a specific step in an enzyme-catalyzed reaction. The magnitude of an intrinsic isotope effect may not equal the magnitude of an isotope effect on collective rate parameters such as Vmax or Emax/ m, unless the isotopi-cally sensitive step is the rate-limiting or rate-contributing step. To tackle this problem, Northrop extended the kinetic theory for primary isotope effects in enzyme-catalyzed reactions. His approach can be illustrated with the following example of a one-substrate/two-intermedi-ate enzyme-catalyzed reaction ... 

For example, Bachelard used [Mgtotai]/[ATPtotai ] = 1 in his rate studies, and he obtained a slightly sigmoidal plot of initial velocity versus substrate ATP concentration. This culminated in the erroneous proposal that brain hexokinase was allosterically activated by magnesium ions and by magnesium ion-adenosine triphosphate complex. Purich and Fromm demonstrated that failure to achieve adequate experimental control over the free magnesium ion concentration can wreak havoc on the examination of enzyme kinetic behavior. Indeed, these investigators were able to account fully for the effects obtained in the previous hexokinase study. ... 

A enzyme kinetic technique, introduced by Britton and co-workers "", that permits one to measure the equilibrium distribution of enzyme-bound substrate(s), inter-mediate(s), and product(s). In this procedure, radiolabeled substrate or product is initially permitted to react with enzyme for sufficient time to equilibrate. At thermodynamic equilibrium, all the different enzyme-bound species will be present at concentrations reflecting their stability relative to each other. One can then add a large excess of unlabeled substrate. Under this condition, any unbound or newly released radiolabel will mix with the large unlabeled pool of substrate or product, where it will undergo substantial reduction in its radiospecific activity. This dilution effectively reduces or eliminates any significant recycling of released radiolabel. One can then... 

The contributions of hydrogen bond donors to catalysis can be estimated by site-directed mutagenesis studies in cases where the hydrogen bond donor is located in the amino acid side chain. Deletion of the main chain NH is only possible by substituting the amino acid with a proUne. In all cases, the effects of the substitution to key enzyme kinetic parameters, and K, should be checked. Typically, the oxyanion hole residues contribute only Uttle to the binding of substrate [19-21]. This is reflected in the values, which typically remain very similar... 

When substrate activities are used instead of substrate concentrations in studies of enzyme kinetics in organic media, solvent effects due to substrate solvation disappear. Remaining solvent effects should be due to direct interactions between the enzyme and the solvent. In a study of lipase-catalyzed esterification reactions, it was found that Km values based on activities were indeed more similar tban those based on concentrations in different solvents, but still some differences remained [49]. 

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