Kinetics bisubstrate

With the exception of a recent bisubstrate kinetic analysis of bilirubin UDP-glucuronyltransferase (P5), saturation with either one of the substrates was investigated at some rather arbitrarily fixed concentration of the other substrate. The results, therefore, have to be interpreted with caution. 

In determining enzyme activities, it is usually assumed that at a fixed set of so-called saturating substrate concentrations a sufficiently accurate value of F, ax is obtained. Bisubstrate kinetic analyses of UDP-glucu-ronyltransferase [assayed with bilirubin (P5) and p-nitrophenol (V6), respectively] indicate that a true measure of the amount of enzyme can be obtained only by suitable extrapolation procedures. This restriction applies in particular to bilirubin (A2, HIO, T8) and other aglycons (M15, V6) because of substrate inhibition. UDP-glucuronic acid was inhibitory at concentrations only about 10-fold higher than the apparent Km value (HIO) this was most pronounced at relatively short incubation times. Mg was noninhibitory at concentrations equal to 20 times the apparent Km values (F3, HIO). 

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. 

Seltzer WK, McCabe ER (1984) Human and rat adrenal glycerol kinase subcellular distribution and bisubstrate kinetics. Mol Cell Biochem 62 43-50... 

In this chapter we described the thermodynamics of enzyme-inhibitor interactions and defined three potential modes of reversible binding of inhibitors to enzyme molecules. Competitive inhibitors bind to the free enzyme form in direct competition with substrate molecules. Noncompetitive inhibitors bind to both the free enzyme and to the ES complex or subsequent enzyme forms that are populated during catalysis. Uncompetitive inhibitors bind exclusively to the ES complex or to subsequent enzyme forms. We saw that one can distinguish among these inhibition modes by their effects on the apparent values of the steady state kinetic parameters Umax, Km, and VmdX/KM. We further saw that for bisubstrate reactions, the inhibition modality depends on the reaction mechanism used by the enzyme. Finally, we described how one may use the dissociation constant for inhibition (Kh o.K or both) to best evaluate the relative affinity of different inhibitors for ones target enzyme, and thus drive compound optimization through medicinal chemistry efforts. 

The determination of bisubstrate reaction mechanism is based on a combination of steady state and, possibly, pre-steady state kinetic studies. This can include determination of apparent substrate cooperativity, as described in Chapter 2, study of product and dead-end inhibiton patterns (Chapter 2), and attempts to identify... 

Let us now examine the behavior of enzymes operating by way of ordered and random kinetic bisubstrate mechanisms ... 

Fromm and Rudolph have discussed the practical limitations on interpreting product inhibition experiments. The table below illustrates the distinctive kinetic patterns observed with bisubstrate enzymes in the absence or presence of abortive complex formation. It should also be noted that the random mechanisms in this table (and in similar tables in other texts) are usually for rapid equilibrium random mechanism schemes. Steady-state random mechanisms will contain squared terms in the product concentrations in the overall rate expression. The presence of these terms would predict nonhnearity in product inhibition studies. This nonlin-earity might not be obvious under standard initial rate protocols, but products that would be competitive in rapid equilibrium systems might appear to be noncompetitive in steady-state random schemes , depending on the relative magnitude of those squared terms. See Abortive Complex... 

We have introduced kinetics as the primary method for studying the steps in an enzymatic reaction, and we have also outlined the limitations of the most common kinetic parameters in providing such information. The two most important experimental parameters obtained from steady-state kinetics are kcat and kcat/Km. Variation in kcat and kcat/Km with changes in pH or temperature can provide additional information about steps in a reaction pathway. In the case of bisubstrate reactions, steady-state kinetics can help determine whether a ternary complex is formed during the reaction (Fig. 6-14). A more complete picture generally requires more sophisticated kinetic methods that go beyond the scope of an introductory text. Here, we briefly introduce one of the most important kinetic approaches for studying reaction mechanisms, pre-steady state kinetics. 

FIGURE 6-14 Steady-state kinetic analysis of bisubstrate reactions. 

In practice, uncompetitive and mixed inhibition are observed only for enzymes with two or more substrates—say, Sj and S2—and are very important in the experimental analysis of such enzymes. If an inhibitor binds to the site normally occupied by it may act as a competitive inhibitor in experiments in which [SJ is varied. If an inhibitor binds to the site normally occupied by S2, it may act as a mixed or uncompetitive inhibitor of Si. The actual inhibition patterns observed depend on whether the and S2-binding events are ordered or random, and thus the order in which substrates bind and products leave the active site can be determined. Use of one of the reaction products as an inhibitor is often particularly informative. If only one of two reaction products is present, no reverse reaction can take place. However, a product generally binds to some part of the active site, thus serving as an inhibitor. Enzymologists can use elaborate kinetic studies involving different combinations and amounts of products and inhibitors to develop a detailed picture of the mechanism of a bisubstrate reaction. 

The general rule for writing the rate equation according to the quasi-equilibrium treatment of enzyme kinetics can be exemplified for the random bisubstrate reaction with substrates A and B forming products P and Q (Figure 7.1), where KaKab = KbKba and KpKpq = KqKqp. 

Nazari K, Mahmoudi A, Khosraneh M et al (2009) Kinetic analysis for suicide-substrate inactivation of microperoxidase-11 a modified model for bisubstrate enzymes in the presence of reversible inhibitors. J Mol Catal B Enzym 56 61-69... 

While almost all synthetically useful catalytic reactions involve two reactants it will be best to first illustrate this graphical approach using a unimolecular process and the way it can be affected by inhibitors. After this some different types of bisubstrate reactions will be discussed. More detailed analyses of the kinetics of multisubstrate systems have been published in texts 13 and... 

Typically, the kinetics of bisubstrate reactions are studied by measuring the initial reaction rates over a range of concentrations of one substrate. A, while holding the concentration of the second substrate, B, constant and doing this for several fixed values of [B]. If specific concentrations of A are used for all of the reaction series, these same rates can also be used to examine changes in reaction rate when [B] is varied at fixed concentrations of A for several values of [A]. 

When one of the substrates is water (i.e., when the process is one of hydrolysis), with the reaction taking place in aqueous solution, only a fraction of the total number of water molecules present participates in the reaction. The small change in the concentration of water has no effect on the rate of reaction and these pseudo-one substrate reactions are described by one-substi ate kinetics. More generally the concentrations of both substrates may be variable, and both may affect the rate of reaction. Among the bisubstrate reactions important in clinical enzymology are the reactions catalyzed by dehydrogenases, in which the second substrate is a specific coenzyme, such as the oxidized or reduced forms of nicotinamide adenine dinucleotide, (NADH), or nicotinamide adenine dinucleotide phosphate, (NADPH), and the amino-group transfers catalyzed by the aminotransferases. 

Most enzymatic reactions involving two-substrate reactions show more complex kinetics than do one-substrate reactions. Examples are catalyzed by dehydrogenases and aminotransferases. Hydrolytic reactions are bisubstrate reactions in which water is one of the substrates. The change in water concentration is negligible and has no effect on the rate of reaction. A two-suhstrate reaction can be written as... 

For a sequential bisubstrate enzyme, the rate of dissociation of the hrst substrate can be estimated by substrate trapping methods. The rationale for this experimental approach is shown in Scheme XXII. The enzyme is first preincubated with radiolabeled substrate A and is then mixed with an excess of unlabeled substrate A and substrate B to initiate the reaction. The recovery of radio-labeled product is a function of the kinetic partitioning of the enzyme-bound substrate between dissociation to yield free S and forward reaction with substrate B to yield product P. 

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