Models of allosteric activity

See also Oxygen Binding by Myoglobin, Oxygen Binding by Hemoglobin, Models of Allosteric Activity, Histidine... 

See also Models of Allosteric Activity, Hemoglobin Allostery... 

Glycogen phosphorylase conforms to the Monod-Wyman-Changeux model of allosteric transitions, with the active form of the enzyme designated the R state and the inactive form denoted as the T state (Figure 15.17). Thus, AMP promotes the conversion to the active R state, whereas ATP, glucose-6-P, and caffeine favor conversion to the inactive T state. 

Figure 2 Representation of a "cubic ternary complex" model of allosteric interaction R, the inactive state of the receptor R, the active state of the receptor A, ligand X, allosteric agent. (From Ref. 14.)...

When binding of a substrate molecule at an enzyme active site promotes substrate binding at other sites, this is called positive homotropic behavior (one of the allosteric interactions). When this co-operative phenomenon is caused by a compound other than the substrate, the behavior is designated as a positive heterotropic response. Equation (6) explains some of the profile of rate constant vs. detergent concentration. Thus, Piszkiewicz claims that micelle-catalyzed reactions can be conceived as models of allosteric enzymes. A major factor which causes the different kinetic behavior [i.e. (4) vs. (5)] will be the hydrophobic nature of substrate. If a substrate molecule does not perturb the micellar structure extensively, the classical formulation of (4) is derived. On the other hand, the allosteric kinetics of (5) will be found if a hydrophobic substrate molecule can induce micellization. 

Fig. 2.1L Model of allosteric and covalent activation of glycogen phosphorylase of muscle. The R-form of the subunits are represented by circles, the T-form by squares. The active state of glycogen phosphorylase (GP) is characterized by a high affinity, the inactive state by low affinity for the substrate PI.

The symmetry model is useful even if it does oversimplify the situation, because it provides a conceptual framework for discussing the relationships between conformational transitions and the effects of allosteric activators and inhibitors. In the following sections we consider three oligomeric enzymes that are under metabolic control and see that substrates and allosteric effectors do tend to stabilize each of these enzymes in one or the other of two distinctly different conformations. 

Phosphofructokinase was one of the first enzymes to which Monod and his colleagues applied the symmetry model of allosteric transitions. It contains four identical subunits, each of which has both an active site and an allosteric site. The cooperativity of the kinetics suggests that the enzyme can adopt two different conformations (T and R) that have similar affinities for ATP but differ in their affinity for fructose-6-phosphate. The binding for fructose-6-phosphate is calculated to be about 2,000 times tighter in the R conformation than in T. When fructose-6-phosphate binds to any one of the subunits, it appears to cause all four subunits to flip from the T conformation to the R conformation, just as the symmetry model specifies. The allosteric effectors ADP, GDP, and phosphoenolpyruvate do not alter the maximum rate of the reaction but change the dependence of the rate on the fructose-6-phosphate concentration in a manner suggesting that they change the equilibrium constant (L) between the T and R conformations. 

Figure 3.12. The allosteric model of receptor activation, inhibition and partial agonism. The receptor itself is characterized by an intrinsic conformational equilibrium that favours the inactive state. Agonists bind exclusively to the active state, with a characteristic dissociation constant and thus increase the over-...

For information on BlueShift Isocyte. www.blueshiftbiotech.com. Rodriguez A, Williams R, Jones C, Niswender C, Meng X, Lindsley CW, Conn PJ. Novel positive allosteric modulators of mGluR5 discovered in HTS have in vivo activity in rat behavioral models of antipsychotic activity. Nat. Chem. Bio. In press. Dorwald FZ. Organic Synthesis on Solid Phase. 2000. Wiley-VCH, Weinheim. 

According to the concerted model, an allosteric activator shifts the conformational equilibrium of all subunits toward the R state, whereas an allosteric inhibitor shifts it toward the T state. Thus, ATP (an allosteric activator) shifted the equilibrium to the R form, resulting in an absorption change similar to that obtained when substrate is bound. CTP had a different effect. Hence, this allosteric inhibitor shifted the equilibrium to theT form. Thus, the concerted model accounts for the ATP-induced and CTP-induced (heterotropic), as well as for the substrate-induced (homotropic), allosteric interactions of ATGase. 

An analysis of the influence of enzyme cooperativity in the mathematical model of product activated oscillatory glycolysis reaction was made by Goldbetter and Venieratos (1980). They established the relationship between the instabilities and the value of the Hill coefficient in the allosteric model for phosphofructokinase. 

FIGURE 15.12 71 versus [S] curves for an allosteric V system. The V system fits the model of Moiiod, Wyman, and Chaiigeux, given the following conditions (1) R and T have the affinity for the substrate, S. (2) The effectors A and I have different affinities for R and T and thus can shift the relative T/R distribution. (That is, A and I change the apparent value of L.) Assume as before that A binds only to the R state and I binds only to the T state. (3) R and T differ in their catalytic ability. Assume that R is the enzymatically active form, whereas T is inactive. Because A perturbs the T/R equilibrium in favor of more R, A increases the apparent Vmax- I favors transition to the inactive T state. 

In the Monod-Wyman-Changeux model for allosteric regulation, what values of L and relative affinities of R and T for A will lead activator A to exhibit positive homotropic effects (That is, under what conditions will the binding of A enhance further A-binding, in the same manner that S-binding shows positive coop-... 

Rational design, 148-149, 152 Real-time assays, 83, 88 Receptor(s). See also Drug receptors affinity for, 6, 63 allosteric model of, 143 Clark s work, 3 classical model of, 44-45 concept of, 2-4 conformations, 13-14, 13 Of conservation equation for, 76 constitutive activity of, 49-51 coupling of, 27 definition of, 2 desensitization of, 34 efficacy for, 6... 

One current model of G-protein receptor activation is the allosteric ternary complex model of Lefkowitz and Costa. The agonist, receptor and G-protein must combine to... 

Vistoli, G., Pedretti, A., Cattaneo, M., Aldini, G., Testa B. Homology modeling of human serum carnosinase, a potential medicinal target, and MD simulations of its allosteric activation by citrate. J. Med. Chem. 2006, 49, 3259-3277. 

The MWC model says that in the R state, all the active sites are the same and all have higher substrate affinity than in the T state. If one site is in the R state, all are. In any one protein molecule at any one time, all subunits are supposed to have identical affinities for substrate. Because the transition between the R and the T states happens at the same time to all subunits, the MWC model has been called file concerted model for allosterism and cooperativity. The MWC model invokes this symmetry principle because the modelers saw no compelling reason to think that one of the chemically identical subunits of a protein would have a conformation that was different from the others. Alternative models exist that suggest that each subunit can have a different conformation and different affinities for substrate. Experimentally, examples are known that follow each model. 

Figure 11. Allosteric regulation A conformational change of the active site of an enzyme induced by reversible binding of an effector molecule (A). The model of Monod, Wyman, and Changeux (B) Cooperativity in the MWC is induced by a shift of the equilibrium between the T and R state upon binding of the receptor. Note that the sequential dissociation constants Kr and KR do not change. The T and R states of the enzyme differ in their catalytic properties for substrates. Both plots are adapted from Ref. 140. See color insert.

For the irreversible reactions, we assume Michaelis Menten kinetics, giving rise to 15 saturation parameters O1. C [0, 1] for substrates and products, respectively. In addition, the triosephospate translocator is modeled with four saturation parameters, corresponding to the model of Petterson and Ryde-Petterson [113]. Furthermore, allosteric regulation gives rise to 10 additional parameters 7 parameters 9" e [0, — n for inhibitory interactions and 3 parameters 0" [0, n] for the activation of starch synthesis by the metabolites PGA, F6P, and FBP. We assume n = 4 as an upper bound for the Hill coefficient. 

---