Enzymatic reactions, isotope effects

The introduction of deuterium in place of proton in water, and its consequent exchange into some positions of enzymes and substrates, produces solvent isotope effect on the kinetic and equilihrium constants associated with the enzymatic reactions. These effects, usually expressed as ratios of the appropriate constants in two isotopic solvents HOH and DOD, are useful in the study of reaction mechanisms (Candour Schowen, 1978 Cook, 1991 Quinn Sutton, 1991). 

PROTON TRANSFER IN ENZYMATIC HYDROLYSIS REACTIONS. ISOTOPE EFFECT... 

Today a good understanding of transition state structure can be obtained through a combination of experimental measurements of kinetic isotope effects (KIE) and computational chemistry methods (Schramm, 1998). The basis for the KIE approach is that incorporation of a heavy isotope, at a specific atom in a substrate molecule, will affect the enzymatic reaction rate to an extent that is correlated with the change in bond vibrational environment for that atom, in going from the ground state to the... 

Because solvent viscosity experiments indicated that the rate-determining step in the PLCBc reaction was likely to be a chemical one, deuterium isotope effects were measured to probe whether proton transfer might be occurring in this step. Toward this end, the kinetic parameters for the PLCBc catalyzed hydrolysis of the soluble substrate C6PC were determined in D20, and a normal primary deuterium isotope effect of 1.9 on kcat/Km was observed for the reaction [34]. A primary isotope effect of magnitude of 1.9 is commonly seen in enzymatic reactions in which proton transfer is rate-limiting, although effects of up to 4.0 have been recorded [107-110]. 

Korzekwa KR, Trager WF, Gillette JR. Theory for the observed isotope effects from enzymatic systems that form multiple products via branched reaction pathways cytochrome P-450. Biochemistry 1989 28(23) 9012-9018. 

Recently, this view of secondary a-deuterium KIEs has had to be modified in the light of results obtained from several different theoretical calculations which showed that the Ca—H(D) stretching vibration contribution to the isotope effect was much more important than previously thought. The first indication that the original description of secondary a-deuterium KIEs was incorrect was published by Williams (1984), who used the degenerate displacement of methylammonium ion by ammonia (equation (4)) to model the compression effects in enzymatic methyl transfer (SN2) reactions. 

Interpretation of KIEs on enzymatic processes (see Chapter 11) has been frequently based on the assumption that the intrinsic value of the kinetic isotope effect is known. Chemical reactions have long been used as models for catalytic events occurring in enzyme active sites and in some cases this analogy has worked quite well. One example is the decarboxylation of 4-pyridylacetic acid presented in Fig. 10.9. Depending on the solvent, either the zwitterionic or the neutral form dominates in the solution. Since the reaction rates in D20/H20 solvent mixtures are the same (see Section 11.4 for a discussion of aqueous D/H solvent isotope effects), as are the carbon KIEs for the carboxylic carbon, it is safe to assume that this is a single step reaction. The isotope effects on pKa are expected to be close to the value of 1.0014 determined for benzoic acid. This in mind, changes in the isotope effects have been attributed to changes in solvation. 

If the overall reaction rate is controlled by step three (k3) (i.e. if that is the rate limiting step), then the observed isotope effect is close to the intrinsic value. On the other hand, if the rate of chemical conversion (step three) is about the same or faster than processes described by ks and k2, partitioning factors will be large, and the observed isotope effects will be smaller or much smaller than the intrinsic isotope effect. The usual goal of isotope studies on enzymatic reactions is to unravel the kinetic scheme and deduce the intrinsic kinetic isotope effect in order to elucidate the nature of the transition state corresponding to the chemical conversion at the active site of an enzyme. Methods of achieving this goal will be discussed later in this chapter. 

In the remaining part of our presentation of the formal kinetics of enzyme isotope effects a few more complicated examples will be discussed. The methods developed here should be also useful for unraveling other complicated enzyme reactions, and in reading and understanding the modern literature on isotope effects on enzymatic processes. 

The principal goal of most studies of kinetic isotope effects on enzymatic reactions is to deduce intrinsic rate constants, which, in turn, can be correlated with the geometric features, that is the structure, of the corresponding transition states. Formal kinetics provides several options for reaching this goal. For example, as we have seen above, changes in concentration can diminish the commitment to the point where the KIE experimental value corresponds directly to the intrinsic kinetic... 

An S Ar (nucleophilic substitution at aromatic carbon atom) mechanism has been proposed for these reactions. Both nonenzymatic and enzymatic reactions that proceed via this mechanism typically exhibit inverse solvent kinetic isotope effects. This observation is in agreement with the example above since the thiolate form of glutathione plays the role of the nucleophile role in dehalogenation reactions. Thus values of solvent kinetic isotope effects obtained for the C13S mutant, which catalyzes only the initial steps of these reactions, do not agree with this mechanism. Rather, the observed normal solvent isotope effect supports a mechanism in which step(s) that have either no solvent kinetic isotope effect at all, or an inverse effect, and which occur after the elimination step, are kinetically significant and diminish the observed solvent kinetic isotope effect. 

For heavy atom isotope effects tunneling is relatively unimportant and the TST model suffices. As an example the dehalogenation of 1,2-dichloroethane (DCE) to 2-chloroethanol catalyzed by haloalkane dehalogenase DhlA is discussed below. This example has been chosen because the chlorine kinetic isotope effect for this reaction has been computed using three different schemes, and this system is among the most thoroughly studied examples of heavy atom isotope effects in enzymatic reactions. 

Kinetic complexity definition, 43 Klinman s approach, 46 Kinetic isotope effects, 28 for 2,4,6-collidine, 31 a-secondary, 35 and coupled motion, 35, 40 in enzyme-catalyzed reactions, 35 as indicators of quantum tunneling, 70 in multistep enzymatic reactions, 44-45 normal temperature dependence, 37 Northrop notation, 45 Northrop s method of calculation, 55 rule of geometric mean, 36 secondary effects and transition state, 37 semiclassical treatment for hydrogen transfer,... 

Carbon isotope fractionation effects of individual compounds were observed in living organisms and also as a result of enzymatic isotope effects and reaction kinetics in biological systems. Such fractionation effects have to be examined by isotope ratio mass spectrometry in order to understand specific processes in life sciences or in environment.75... 

A change in isotopic mass, especially from H to 2H or 3H, often produces a strong effect on reaction rates and the study of kinetic isotope effects has provided many insights into the mechanisms of enzymatically catalyzed reactions. Isotopes have permitted a detailed understanding of the stereo-... 

These result from bond cleavage between atoms adjacent to the isotopically substituted atom. Secondary isotope effects are caused by a change in the electronic hybridization of the bond linking the isotope, rather than by cleavage of the bond. One example of this in enzymatic reactions is the substitution... 

R and S isomers of HDT]acetic acid were synthesized by chemical and enzymatic methods that yield products of known stereochemistry.1819 The two isomers were then distinguished by using the following ingenious enzymatic assays. The acetic acid was first converted to acetyl-coenzyme A (by a reaction of the carboxyl group—and not the methyl—of acetic acid). The acetyl-coenzyme A was then condensed with glyoxylate to form malate in an essentially irreversible reaction catalyzed by malate synthase (equation 8.27). The crucial feature of this reaction is that it is subject to a normal kinetic isotope effect, so that more H than D... 

Solvent isotope effects are a useful diagnostic tool in simple chemical reactions, although they can be variable. For example, it is found that general-base-catalyzed reactions such as equation 2.84 have a kH/kD of about 2, whereas the nucleophilic attack on an ester has a kH/kD of about 1. The isotope effects in enzymatic reactions are more difficult to analyze because the protein has so many protons that may exchange with deuterons from D20.61 Also there may be slight changes in the structure of the protein on the change of solvent. 

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