Effectiveness, in enzyme reactions

Solvent Kinetic Isotope Effects in Enzyme Reactions (See Also Section 11.4)... 

Solvent Kinetic Isotope Effects in Enzyme Reactions... 

Kinetic Isotope Effects in Enzymic Reactions J. H. Richards... 

Northrop DB. Steady-state analysis of kinetic isotope effects in enzymic reactions. Biochemistry 1975 14 2644-2651. 

The interiors of proteins are more densely packed than liquids [181], and so the participation of the atoms of the protein surrounding the reactive system in an enzyme-catalysed reaction is likely to be at least as important as for a reaction in solution. There is experimental evidence which indicates that protein dynamics may modulate barriers to reaction in enzymes [10,11]. Ultimately, therefore, the effects of the dynamics of the bulk protein and solvent should be included in calculations on enzyme-catalysed reactions. Dynamic effects in enzyme reactions have been studied in empirical valence bond simulations Neria and Karplus [180] calculated a transmission coefficient of 0.4 for proton transfer in triosephosphate isomerase, a value fairly close to unity, and representing a small dynamical correction. Warshel has argued, based on EVB simulations of reactions in enzymes and in solution, that dynamical effects are similar in both, and therefore that they do not contribute to catalysis [39]. 

Hwang et al.131 were the first to calculate the contribution of tunneling and other nuclear quantum effects to enzyme catalysis. Since then, and in particular in the past few years, there has been a significant increase in simulations of QM-nuclear effects in enzyme reactions. The approaches used range from the quantized classical path (QCP) (e.g., Refs. 4,57,136), the centroid path integral approach,137,138 and vibrational TS theory,139 to the molecular dynamics with quantum transition (MDQT) surface hopping method.140 Most studies did not yet examine the reference water reaction, and thus could only evaluate the QM contribution to the enzyme rate constant, rather than the corresponding catalytic effect. However, studies that explored the actual catalytic contributions (e.g., Refs. 4,57,136) concluded that the QM contributions are similar for the reaction in the enzyme and in solution, and thus, do not contribute to catalysis. 

The entropic hypothesis seems at first sight to gain strong support from experiments with model compounds of the type listed in Table 9.1. These compounds show a huge rate acceleration when the number of degrees of freedom (i.e., rotation around different bonds) is restricted. Such model compounds have been used repeatedly in attempts to estimate entropic effects in enzyme catalysis. Unfortunately, the information from the available model compounds is not directly transferable to the relevant enzymatic reaction since the observed changes in rate constant reflect interrelated factors (e.g., strain and entropy), which cannot be separated in a unique way by simple experiments. Apparently, model compounds do provide very useful means for verification and calibration of reaction-potential surfaces... 

The importance of hydrophobic binding interactions in facilitating catalysis in enzyme reactions is well known. The impact of this phenomenon in the action of synthetic polymer catalysts for reactions such as described above is significant. A full investigation of a variety of monomeric and polymeric catalysts with nucleophilic sites is currently underway. They are being used to study the effect of polymer structure and morphology on catalytic activity in transacylation and other reactions. 

Inhibition Effects in Enzyme Catalyzed Reactions. Enzyme catalyzed reactions are often retarded or inhibited by the presence of species that do not participate in the reaction in question as well as by the products of the reaction. In some cases the reactants themselves can act as inhibitors. Inhibition usually results from the formation of various enzyme-inhibitor complexes, a situation that decreases the amount of enzyme available for the normal reaction sequence. The study of inhibition is important in the investigation of enzyme action. By determining what compounds behave as inhibitors and what type of kinetic patterns are followed, it may be possible to draw important conclusions about the mechanism of an enzyme s action or the nature of its active site. 

Ionic dissociation of carbon-carbon a-bonds in hydrocarbons and the formation of authentic hydrocarbon salts, 30, 173 Ionization potentials, 4, 31 Ion-pairing effects in carbanion reactions, 15, 153 Ions, organic, charge density-NMR chemical shift correlations, 11, 125 Isomerization, permutational, of pentavalent phosphorus compounds, 9, 25 Isotope effects and quantum tunneling in enzyme-catalyzed hydrogen transfer. 

W. W. Cleland, M. H. O Leary and D. B. Northrup (Eds.), Isotope Effects in Enzyme-catalyzed Reactions, University Park Press, Baltimore, 1977. 

Abstract This chapter introduces the basic principles used in applying isotope effects to studies of the kinetics and mechanisms of enzyme catalyzed reactions. Following the introduction of algebraic equations typically used for kinetic analysis of enzyme reactions and a brief discussion of aqueous solvent isotope effects (because enzyme reactions universally occur in aqueous solutions), practical examples illustrating methods and techniques for studying enzyme isotope effects are presented. Finally, computer modeling of enzyme catalysis is briefly discussed. 

In the following year, Cleland and his coworkers reported further and more emphatic examples of the phenomenon of exaltation of the a-secondary isotope effects in enzymic hydride-transfer reactions. The cases shown in Table 1 for their studies of yeast alcohol dehydrogenase and horse-liver alcohol dehydrogenase would have been expected on traditional grounds to show kinetic isotope effects between 1.00 and 1.13 but in fact values of 1.38 and 1.50 were found. Even more impressively, the oxidation of formate by NAD was expected to exhibit an isotope effect between 1.00 and 1/1.13 = 0.89 - an inverse isotope effect because NAD" was being converted to NADH. The observed value was 1.22, normal rather than inverse. Again the model of coupled motion, with a citation to Kurz and Frieden, was invoked to interpret the findings. 

Cook, P.F., Oppenheimer, N.J. and Cleland, W.W. (1981). Secondary deuterium and nitrogen-15 isotope effects in enzyme-catalyzed reactions. Chemical mechanism of liver alcohol dehydrogenase. Biochemistry 20, 1817-1825... 

Klinman, J.P. (1991). Hydrogen tunneling and coupled motion in enzyme reactions. In Enzyme Mechanism from Isotope Effects, Cook, P.F. (ed.), pp. 127-148. CRC Press, Boca Raton... 

Klinman, J.P. (1989). Quantum mechanical effects in enzyme-catalysed hydrogen transfer reactions. Trends Biochem. Sci 14, 368-373... 

In order to understand the mechanisms of the enzymatic process and also predict the reaction characteristics, one needs to understand the kinetics of the reaction. The important factor that effects the enzyme reaction is the availability and concentration of the substrates. An important model that gives a mathematical relationship is the Michaelis-Menten and Hill equation. The equation is denoted as... 

This mechanism involves the ordered addition of inhibitors, such that X must bind before Y can. As a result, the following are essential properties (a) the presence of only X along with substrate S has no effect of enzyme reaction rate, because X does not affect substrate binding or the rate of ES breakdown (b) the presence of only Y along with S is without effect, because Y cannot bind in the absence of X and (c) inhibition will take place only when X and Y are both present, thereby allowing inactive EXY complex to accumulate. 

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 ... 

A term used in the study of isotope effects in enzyme-catalyzed reactions, namely (equivalent to... 

In enzymic reactions the central ES<= EP transformation is very fast, and the value of kcat is very high. In addition to correctly oriented binding of the substrate at the active center of the enzyme, an effective decrease in activation energy of this reaction step might also be provided by stabilization of the transition state of the substrate molecule in the ES complex. 

A major source of acceleration in enzymic reactions is approximation, that is to say, the bringing together of two or more reactants in the active site. Once the reagents are in contact, the subsequent reaction is intra- rather than intermolecular. Comparisons of the rates of intermolecular and intramolecular reactions are, however, difficult because the rate constants for bimolecular reactions have the units of M "1 s-1, whereas rate constants for unimolecular reactions have the units of s l. The best one can do in comparing them is to state the molarity at which the reactants would have to be present in the bimolecular reaction to achieve the rate of the unimolecular process when the effective molarity is large-say 1000 M or more-one has some measure of the power of approximation to accelerate chemical reaction. 

In the catalyst reoxidation step, contrary to the electron-transfer step, the polymer ligand should shrink because of the formation of the Cu(II) complex. Therefore, the polymer chain may partially repeat are expansion and contraction occurring during the catalytic cycle. When one has a view of the polymer-Cu catalyst as a whole, each part of the polymer catalyst domain, which is drifted in solution, is seen to be fluctuating during the catalytic process [Fig. 32(b)]. The fluctuating shape of biopolymers in enzymic reactions has been pointed out, and the dynamically conformational change of a flexible polymer chain is considered to be one of the effects of the polymer catalyst. 

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