Kinetics alternative substrates

Occasionally, one can increase the Ae by utilizing alternative substrates. For example, 3-acetyl-NAD or thio-NAD can often be used with NAD -dependent dehydrogenases. Note however that an alternative substrate may change the kinetic mechanism, as compared to that observed with the naturally occurring substrate. Alternative substrates are of particular value when the normal substrate(s) and product(s) do not efficiently absorb UV or visible light. For example, many p-nitroaniline or p-nitrophenyl derivatives have proved to be quite useful in enzyme assays because they exhibit intense absorption around 410 nm. 

MULTISUBSTRATE SYSTEMS. Wong and Hanes were probably among the first to suggest that alternative substrates may be useful in mechanistic studies. Fromm s laboratory was the first to use and extend the theory of alternative substrate inhibition to address specific questions about multisubstrate enzyme kinetic mechanisms. Huang demonstrated the advantages of a constant ratio approach when dealing with alternative substrate kinetics. 

There are three basic methods for carrying out alternative substrate inhibition studies. In the first, the investigator seeks to observe numerical changes in the coefficients of the double-reciprocal form of the enzyme rate expression in the presence and absence of the alternative substrate. For some mechanisms, only certain coefficients will be altered. This method requires extremely accurate estimates of the magnitudes of the coefficients and should always be supplemented with other kinetic probes . 

While requiring the availability of competitive inhibitors for each of the substrates, Fromm s use of competitive inhibitors to distinguish multisubstrate enzyme kinetic pathways represents the most powerful initial rate method. See Alternative Substrate Inhibition... 

Hexokinase provides another example of the stereochemical inferences that can be drawn on the basis of kinetic studies with alternative substrates and competi-... 

If a noncompetitive or an uncompetitive inhibitor were present with the substrate at constant ratio, then graphical analysis would suggest that the phenomenon of substrate inhibition is present. If an investigator analyzed the apparent substrate inhibition via a Marmasse plot, wrong estimates of both the K a and K s values would be reported and the investigator would be mislead with respect to the kinetic mechanism. If partial inhibitors or alternative substrates are present in constant ratio, depending on the relative sizes of the Ymax and values,... 

ALTERNATIVE PRODUCT INHIBITION ABORTIVE COMPLEXES ALTERNATIVE SUBSTRATES COMPETITIVE INHIBITOR ABORTIVE COMPLEXES MAPPING SUBSTRATE INTERACTIONS USING KINETIC DATA MEMBRANE TRANSPORT ENERGY OF ACTIVATION Old... 

These were differently affected by different procedures. For example, when the enzyme was activated at 55°, the increment in ki was slight, but k2 increased 3.5-fold. Similarly, in the presence of EDTA, fc, and k2 values decreased independently, suggesting that the sites for both activities were different. Center and Behai (5) found that with the P. mirabilis enzyme, cyclic 2, 3 -UMP competitively inhibited the hydrolysis of bis(p-nitrophenyl) phosphate. The Ki was 40 pAf very close to the Km for the cyclic nucleotide (Km, 75 yM) which indicated that the two compounds could serve as alternate substrates being hydrolyzed at the same active site. In contrast, 3 -AMP was a mixed inhibitor of cyclic 2, 3 -UMP and bis(p-nitrophenyl) phosphate hydrolysis. Adenosine was a mixed inhibitor of bis(p-nitrophenyl) phosphate hydrolysis but a competitive inhibitor of 3 -AMP hydrolysis. From such kinetic studies Center and Behai (5) suggested that two separate and adjacent sites A and B are involved in the hydrolysis of the diester and phos-phomonoester substrates. Site A serves as a binding site for hydrolysis of ribonucleoside 2, 3 -cyclic phosphates and together with site B catalyzes the hydrolysis of the diester bond. During this reaction 3 -... 

Measurement of the in vitro efficacy of compounds as substrates is usually deduced by comparison of their k JK ratios where is the first-order rate constant for product formation and is the Michaelis equilibrium constant [38]. For those compounds which are classical, reversible inhibitors, K, the dissociation (or inhibition) equilibrium constant, and (kassoc) the rate constant for enzyme inhibition, are the most commonly reported kinetic values. These values may be measured while using either a high-molecular-weight natural substrate or a low-molecular-weight synthetic substrate. For alternate-substrate inhibitors, that is, compounds which form a stable complex (an acyl-enzyme ) that dissociates to enzyme and intact inhibitor or to enzyme and an altered form of the inhibitor, the usually reported value is K, the apparent K. For compounds which irreversibly inactivate the enzyme, the kinetics are usually measured under conditions such that the initial enzyme concentration [E] is much lower than the inhibitor concentration [I] which in turn is much lower than the Ky Under these conditions the commonly reported value is obs/[I]> the apparent... 

Any fast reaction that follows a slow reaction will occur at the rate of the slow reaction. Consider the formation of an enzyme intermediate according to Scheme XVIII. This enzyme-bound intermediate (E l) will be invisible kinetically and thermodynamically if A3 ki and k-2 A 3. Thus, one can only define the kinetically significant intermediates or conformational states. Transition states or extremely reactive intermediates cannot be directly observed their presence can only be inferred by knowledge of the chemistry of the reaction. Alternatively, the use of alternate substrates or analogs has provided evidence for an intermediate by slowing the rate of the second step. For example, in studies on chymo-... 

Initial rate measurements, especially with alternative substrates and with a product or substrate analog as inhibitor, and measurements of the rate of isotope exchange at equilibrium, can give a great deal of information about mechanism, and in some cases allow estimates of individual velocity constants and dissociation constants. The results of such studies, which require little enzyme, are an essential basis for the proper interpretation, in relation to the overall catalytic reaction, of pre-steady-state studies and kinetic and thermodynamic studies of enzyme-coenzyme reactions in isolation. 

Comparisons of the kinetic coefficients in Eq. (1) obtained from initial rate measurements with alternative substrates have given a considerable amount of information about reaction pathways as well as indications of the molecular basis of specificity (60). This approach, much used for proteolytic enzymes, has been exploited particularly with the alcohol dehydrogenases, which catalyze the oxidation of a variety of primary and secondary alcohols (61). While several other dehydrogenases have been studied in this way, most of the results have been reported only as apparent maximum rates and apparent Km values for the alternative substrate, which restricts the amount of information that can be derived. 

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