Multisubstrate enzymes

Hydrolases represent a significant class of therapeutic enzymes [Enzyme Commission (EC) 3.1—3.11] (14) (Table 1). Another group of enzymes with pharmacological uses has budt-ia cofactors, eg, in the form of pyridoxal phosphate, flavin nucleotides, or zinc (15). The synthases, and other multisubstrate enzymes that require high energy phosphates, are seldom available for use as dmgs because the required co-substrates are either absent from the extracellular space or are present ia prohibitively low coaceatratioas. 

While many enzymes have a single substrate, many others have two—and sometimes more than two—substrates and products. The fundamental principles discussed above, while illustrated for single-substrate enzymes, apply also to multisubstrate enzymes. The mathematical expressions used to evaluate multisubstrate reactions are, however, complex. While detailed kinetic analysis of multisubstrate reactions exceeds the scope of this chapter, two-substrate, two-product reactions (termed Bi-Bi reactions) are considered below. 

Symbols for substrates and products, respectively, in multisubstrate enzyme-catalyzed reactions. In all ordered reaction mechanisms, A represents the first substrate to bind, B is the second, eta, whereas P denotes the first product to be released, Q represents the second, eta See Cleland Nomenclature... 

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. 

Whenever using alternative substrate inhibition procedures, the investigator must demonstrate that initial rate conditions remain valid throughout the course of the experiment. This is particularly true of the other sub-strate(s) in multisubstrate enzymes. Because both the substrate under study and its analog are present in the reaction mixtures, the other cosubstrates will be depleted faster. This should always be a consideration in the design of the experiment. 

A noncovalent complex between two molecules. Binary complex often refers to an enzyme-substrate complex, designated ES in single-substrate reactions or as EA or EB in certain multisubstrate enzyme-catalyzed reactions. See Michaelis Complex... 

Fromm first demonstrated how competitive inhibitors can be employed to distinguish the order of substrate binding for multisubstrate enzyme mechanisms. Each competitive inhibitor, with respect to one substrate, displays distinctive pattern(s) relative to the other substrate (s) . ... 

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... 

DERIVATION OF MORE COMPLICATED RATE EQUATIONS. So far, the rate equations that describe one-substrate enzyme systems have been fairly simple, and the usual algebraic manipulations of substitution and/or addition of simultaneous equations have permitted us to obtain the pertinent rate law. When the number of steps increases and especially when there are branched pathways involved, these manual methods become cumbersome, and more systematic procedures are required. The next two sections should allow the reader to develop a working knowledge of effective methods for obtaining multisubstrate enzyme rate expressions. 

Efforts should be made to stabilize an enzyme s activity. Certain agents (such as glycerol, ammonium ions, boric acid, polyethylene glycol, and even talcum powder or bentonite clay) have proven widely to be effective enzyme stabilizers. For multisubstrate enzymes, inclusion of one particular substrate with the enzyme (in the absence of other substrates or cofactors) often stabilizes an enzyme s catalytic activity. Such a substrate may also assist in unlocking the enzyme from a particularly inactive conformational form. In addition to substrates, other ligands and effectors (including reaction products. 

Fromm and Cleland provide valuable discussions of the utility of Haldane relations in excluding certain kinetic reaction mechanisms based on a numerical evaluation of the constants on each side of the equal sign in the Haldane relation. If the equality is maintained, the candidate mechanism is consistent with the observed rate parameter data. Obviously, one must be concerned about the quality of experimentally derived estimates of rate parameters, because chemists have frequently observed that thermodynamic data (such as equilibrium constants) are often more accurate and precise than kinetically derived parameters. See Haldane Relations for Multisubstrate Enzymes... 

Rose and co-workers first demonstrated that a proteo-lyzed form of hexokinase forms a sticky (or sluggishly dissociable) complex with glucose. The generalized application of this approach to the kinetic characterization of multisubstrate enzymes has been treated in detail. See also Partition Coefficient Radiospecific Activity Stickiness... 

In the Briggs-Haldane steady-state treatment of a one-substrate enzyme system, the Michaelis constant, usually symbolized by, is ( 2 + k3)/ki. For more complex reactions (e.g., with several substrates and/or isomerization steps), the Michaelis constant for a given substrate is a more complex collection of rate constants. For a multisubstrate enzyme having substrates A and B, the Michaelis constants are usually symbolized by and, by and, or by and, respectively. 

The reduction in enzymatic activity that results from the formation of nonproductive enzyme complexes at high substrate concentration. The most straightforward explanation for substrate inhibition is that a second set of lower affinity binding sites exists for a substrate, and occupancy of these sites ties up the enzyme in nonproductive or catalytically inefficient forms. Other explanations include (a) the removal of an essential active site metal ion or other cofactor from the enzyme by high concentrations of substrate, (b) an excess of unchelated substrate (such as ATP" , relative to the metal ion-substrate complex (such as CaATP or MgATP ) which is the true substrate and (c) the binding of a second molecule of substrate at a subsite of the normally occupied substrate binding pocket, such that neither substrate molecule can attain the catalytically active conformation". For multisubstrate enzymes, nonproductive dead-end complexes can also result in substrate inhibition in the presence of one of the reaction... 

A substrate analog will frequently inhibit only one of the two forms of a multisubstrate enzyme with a ping-pong mechanism.1 72 Reciprocal plots made for various inhibitor concentrations consist of a family of parallel lines reminiscent of uncompetitive inhibition. Observation of such parallel line plots can support a ping-pong mechanism for an enzyme but cannot prove it because in some cases parallel lines are observed for inhibition of enzymes acting by an ordered sequential mechanism. The following question arises naturally for any ordered bimolecular reaction (Eq. 9-43) Of the... 

Multidrug resistance protein 417 Multilamellar vesicles (liposomes) 392 Multiple attack concept 606 Multisubstrate enzymes, kinetics of 464 Muramic acid (Mur) 165s Murein 170,428,429s. See also Peptidoglycan Musci 29 Muscle(s)... 

Second order reactions 458 Secondary kinetic isotope effect 592, 600 on fumarate hydratase 684 Secondary plots for kinetics of multisubstrate enzymes 465 Secondary structure 63... 

Fiqtire 3.5 (a) Competitive inhibition inhibitor and substrate compete for the same binding site. For example, indole, phenol, and benzene bind in the binding pocket of chymotrypsin and inhibit the hydrolysis of derivatives of tryptophan, tyrosine, and / phenylalanine, (b) Noncompetitive inhibition inhibitor and substrate bind simultaneously to the enzyme. An example is the inhibition of fructose 1,6-diphosphatase by AMP. This type of inhibition is very common with multisubstrate enzymes. A rare example of / uncompetitive inhibition of a single-substrate enzyme is the inhibition of alkaline phosphatase by L-phenylalanine. This enzyme is composed of two identical subunitjs, so presumably the phenylalanine binds at one site and the substrate at the other. [From N. K. Ghosh and W. H. Fishman, J. Biol. Chem. 241, 2516 (1966) see also M. Caswell and M. Caplow, Biochemistry 19, 2907 (1980). 

While such a study might have been carried out with conventional methods, the use of HPLC facilitated the work considerably by allowing all reactants and products to be measured in one analysis. Clearly, the HPLC assay method should be considered when the kinetics of a multisubstrate enzyme reaction are to be studied. 

It should also be noted that a multisubstrate enzyme also allows the application of substrate trapping methods to estimate the rates of dissociation of the first substrate to bind to the enzyme. These methods will be described in Section IV,F,2. 

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