Enzyme-catalyzed reactions comparison

A Comparison of Enzyme-Catalyzed Reactions and Their Uncatalyzed Counterparts... 

The optical purities were determined solely from the optical rotations of the (/ -cyanohydrins thus obtained. Only for (/ )-a-hydroxybcnzeneacetonitrile, available from benzaldehyde, was an optical purity determined by comparison with the natural product. Variation of the reaction conditions (pH, temperature, concentration) in water/ethanol led to no appreciable improvementsl4. The use of organic solvents that are not miscible with water, but in which the enzyme-catalyzed reaction can still take place, resulted in suppression of the spontaneous addition to a significant extent, whereas the enzyme-catalyzed formation of cyanohydrins was only slightly slower (Figure l)13. 

What about reactions of the type A + B — C This is a second-order reaction, and the second-order rate constant has units of M min-1. The enzyme-catalyzed reaction is even more complicated than the very simple one shown earlier. We obviously want to use a second-order rate constant for the comparison, but which one There are several options, and all types of comparisons are often made (or avoided). For enzyme-catalyzed reactions with two substrates, there are two Km values, one for each substrate. That means that there are two kcJKm values, one for each substrate. The kcJKA5 in this case describes the second-order rate constant for the reaction of substrate A with whatever form of the enzyme exists at a saturating level B. Cryptic enough The form of the enzyme that is present at a saturating level of B depends on whether or not B can bind to the enzyme in the absence of A.6 If B can bind to E in the absence of A, then kcJKA will describe the second-order reaction of A with the EB complex. This would be a reasonably valid comparison to show the effect of the enzyme on the reaction. But if B can t bind to the enzyme in the absence of A, kcat/KA will describe the second-order reaction of A with the enzyme (not the EB complex). This might not be quite so good a comparison. 

From bisubstrate, kinetic analysis with a transferase from hen oviduct that, under the conditions of the assay, formed only GlcNAc-PP-Dol, it followed that both dolichol phosphate and UDP-GlcNAe have to he bound to the enzyme before release of the product occurs.52 However, the fact that only partially purified preparations have thus far been obtained (the preparations may also still be contaminated with substrates and product), together with experimental difficulties in handling both the substrate dolichol phosphate (which, furthermore, is not one compound, see the earlier discussion) and the unstable enzyme (enveloped in micelles of detergent), make difficult a sensible interpretation and comparison of the kinetic parameters detenuined for the different enzvme-preparations. The solubilized enzymes catalyzing reactions 1,2, and 3 have in common their alkaline pH optima and dependence on Mg2+ or Mn2+ ions. The latter fact makes (ethylenedinitrilo)tetraacetic acid (EDTA) a reversible inhibitor of enzyme activity and an important experimental tool. 

This reaction rearranges the carbonyl and hydroxyl groups on carbons 1 and 2. However, more than 80% of the enzymatic rate acceleration has been traced to enzyme-substrate interactions involving the phosphate group on carbon 3 of the substrate. This was determined by a careful comparison of the enzyme-catalyzed reactions with glyceraldehyde 3-phosphate and with glyceraldehyde (no phosphate group at position 3) as substrate. 

The accurate prediction of enzyme kinetics from first principles is one of the central goals of theoretical biochemistry. Currently, there is considerable debate about the applicability of TST to compute rate constants of enzyme-catalyzed reactions. Classical TST is known to be insufficient in some cases, but corrections for dynamical recrossing and quantum mechanical tunneling can be included. Many effects go beyond the framework of TST, as those previously discussed, and the overall importance of these effects for the effective reaction rate is difficult (if not impossible) to determine experimentally. Efforts are presently oriented to compute the quasi-thermodynamic free energy of activation with chemical accuracy (i.e., 1 kcal mol-1), as a way to discern the importance of other effects from the comparison with the effective measured free energy of activation. 

Table 10.1 gives values of rate constants, activation energies, and frequency factors for three enzyme-catalyzed reactions. For comparison, the values for other catalysts are included. Note that molecule for molecule, the enzymes are much more effective catalysts than the nonbiological catalysts. In urease and catalase this higher effectiveness is related to a much smaller activation energy, which is true for a number of other enzyme systems. Enzymes evidently exert their action by allowing the process to occur by a much more favorable reaction path. 

The observed changes both in the rates of formation and in the extent of accumulation of reaction intermediates at the )3 active site of the o R179L mutant have been shown to be predominantly due to changes in the affinity of ligands for the a active site. Comparison of the dependence of the rate of E(Q3) formation, as followed by the increase in absorbance at 476 nm, on the concentration of IGP between the wild-type and q R179L enzyme-catalyzed reactions (data not shown) reveal that the binding affinity... 

The Michaelis-Menten mechanism of enzyme activity models the enzyme with one active site that, weakly and reversibly, binds a substrate in homogeneous solution. It is a three-step mechanism. The first and second steps are the reversible formation of the enzyme-substrate complex (ES). The third step is the decay of the complex into the product. The steady-state approximation is applied to the concentration of the intermediate (ES) and its use simplifies the derivation of the final rate expression. However, the justification for the use of the approximation with this mechanism is suspect, in that both rate constants for the reversible steps may not be as large, in comparison to the rate constant for the decay to products, as they need to be for the approximation to be valid. The simplest form of the mechanism applies only when A h 2> k. Neverthele.ss, the form of the rate equation obtained does seem to match the principal experimental features of enzyme-catalyzed reactions it explains why there is a maximum in the reaction rate and provides a mechanistic understanding of the turnover number. The model may be expanded to include multisubstrate reaction rate and provides a mechanistic understanding of the turnover number. The model may be expanded to include multisubstrate reactions and inhibition. 

In the measurement of enzyme activity, a high substrate concentration that is greatly in excess of the Km value is always used, and the enzyme sample to be investigated is correspondingly diluted vmder the conditions, the rate of the enzyme-catalyzed reaction depends only on the enzyme concentration, i.e., it is a zero order reaction. Even under conditions of substrate saturation, the measured catalytic activities are influenced by slight differences in reaction conditions, such as the temperature, composition and concentration of the buffer, pH value, nature of the substrate and its concentration, coenzymes, and protein content in the sample. Therefore, the results of measurement of the catalytic activity of an enzyme are in principle method dependent direct comparison of the results between laboratories is made difficult by the use of different methods in different laboratories. 

As a first comparison of a chemocatalytic reaction with an analogous enzyme-catalyzed reaction, we discuss the hydrolysis of CO2 by H2O to give HCO3 by the enzyme carbonic anhydrase. The reaction steps involved in the enzyme catalyzed mechanism will be compared with the chemocatalytic steps involved in the hydrolysis of acetonitrile by a Zn + containing zeolite as discussed on page 186 in Chapter 4. Similarly to the zeolite, the interior of the enzyme is hydrophobic except for the region close to the Zn + center. Its structure is shown in Fig. 7.6. 

For a direct comparison of the temporary silicon tethered strategy to enzyme catalyzed reaction, see Xin, Y.C., Mallet, J.-M., and Sinay, P. (1993) J. Chem. Soc., Chem. Commun., 864-865. 

U Bolz, K Stephan, P Stylos, A Riek, M Rizzi, M Reuss. Comparison of enzymic catalyzed reactions in organic solvents and in supercritical fluids. Biochem Eng —Stuttgart, [Proc. Int. Symp.], 2nd Meeting Date 1990, 82-5. Edited by Reuss, Matthias. Fischer Stuttgart, Fed. Rep. Ger., 1991. 

Acyloins (a-hydroxy ketones) are formed enzymatically by a mechanism similar to the classical benzoin condensation. The enzymes that can catalyze reactions of this type arc thiamine dependent. In this sense, the cofactor thiamine pyrophosphate may be regarded as a natural- equivalent of the cyanide catalyst needed for the umpolung step in benzoin condensations. Thus, a suitable carbonyl compound (a -synthon) reacts with thiamine pyrophosphate to form an enzyme-substrate complex that subsequently cleaves to the corresponding a-carbanion (d1-synthon). The latter adds to a carbonyl group resulting in an a-hydroxy ketone after elimination of thiamine pyrophosphate. Stereoselectivity of the addition step (i.e., addition to the Stand Re-face of the carbonyl group, respectively) is achieved by adjustment of a preferred active center conformation. A detailed discussion of the mechanisms involved in thiamine-dependent enzymes, as well as a comparison of the structural similarities, is found in references 1 -4. 

To impress you, enzymologists often tell you how much faster their enzyme is than the uncatalyzed reaction. These comparisons are tricky. Here s the problem Suppose we know that the reaction S — P has a first-order rate constant of 1 X 10 3 min 1 (a half-life of 693 min). When an enzyme catalyzes transformation of S to P, we have more than one reaction ... 

The practical usefulness of Equations 11.46 through 11.53 has been demonstrated for the malic enzyme catalyzed conversion of L-malate to pyruvate (Equation 11.72). Table 11.1 lists experimentally determined isotope effects for this reaction. Comparison of carbon kinetic isotope effects for protio and deutero-malate substituted at position 2 (the carbon that undergoes sp3 to sp2 transition) rules out the possibility that the hydride transfer and the decarboxylation events are concerted. This conclusion follows from Equation 11.48 which, for a concerted reaction, predicts that 13(V/K) should be smaller than 13(V/K)D, which is opposite to the order observed experimentally. 

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