Allosteric effector

The two states have the same affinity for ATP but differ with respect to their affinity for the substrate F6P, the allosteric effector ADP and the inhibitor PEP. Because of these differences in affinity, ligand binding can shift the equilibrium between the R and T states to favor one or the other state depending on which ligand is bound. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Some of the procaryotic DNA-binding proteins are activated by the binding of an allosteric effector molecule. This event changes the conformation of the dimeric protein, causing the helix-tum-helix motifs to move so that they are 34 A apart and able to bind to the major groove. The dimeric repressor for purine biosynthesis, PurR, induces a sharp bend in DNA upon binding caused by insertion of a helices in the minor groove between the two... 

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

Muscle glycogen phosphorylase is a dimer of two identical subunits (842 residues, 97.44 kD). Each subunit contains a pyridoxal phosphate cofactor, covalently linked as a Schiff base to Lys °. Each subunit contains an active site (at the center of the subunit) and an allosteric effector site near the subunit interface (Eigure 15.15). In addition, a regulatory phosphorylation site is located at Ser on each subunit. A glycogen-binding site on each subunit facilitates prior association of glycogen phosphorylase with its substrate and also exerts regulatory control on the enzymatic reaction. 

FIGURE 15.15 (a) The structure of a glycogen phosphorylase monomer, showing the locations of the catalytic site, the PLP cofactor site, the allosteric effector site, the glycogen storage site, the tower helix (residnes 262 throngh 278), and the snbnnit interface. 

FIGURE 15.36 The structure, in ionic form, of BPG or 2,3-bisphosphoglycerate, an important allosteric effector for hemoglobin. 

Acetyl-CoA is a potent allosteric effector of glycolysis and gluconeogenesis. It allosterically inhibits pyruvate kinase (as noted in Chapter 19) and activates pyruvate carboxylase. Because it also allosterically inhibits pyruvate dehydrogenase (the enzymatic link between glycolysis and the TCA cycle), the cellular fate of pyruvate is strongly dependent on acetyl-CoA levels. A rise in... 

Johnson, L. N., 1992. Glycogen phosphorylase Control by phosphorylation and allosteric effectors. FASEB Journal 6 2274-2282. 

The most potent positive allosteric effector of phospho-ffuctokinase-1 and inhibitor of fructose-1,6-bisphos-phatase in liver is fructose 2,6-bisphosphate. It relieves inhibition of phosphofructokinase-1 by ATP and increases affinity for fructose 6-phosphate. It inhibits fructose-1,6-bisphosphatase by increasing the for fructose 1,6-bisphosphate. Its concentration is under both substrate (allosteric) and hormonal control (covalent modification) (Figure 19-3). 

The separation between allosteric effectors and cooperativity lies in the molecule doing the affecting. If the effector molecule acts at another site and the effector is not the substrate, the effect is deemed allosteric and heterotropic. If the effector molecule is the substrate itself, the effect is called cooperative and/or homotropic. 

ALLOSTERIC EFFECTORS bind specifically to either the T or the R states. 

Similar to generalized mass-action models, lin-log kinetics provide a concise description of biochemical networks and are amenable to an analytic solution, albeit without sacrificing the interpretability of parameters. Note that lin-log kinetics are already written in term of a reference state v° and S°. To obtain an approximate kinetic model, it is thus sometimes suggested to choose the reference elasticities according to simple heuristic principles [85, 89]. For example, Visser et al. [85] report acceptable result also for the power-law formalism when setting the elasticities (kinetic orders) equal to the stoichiometric coefficients and fitting the values for allosteric effectors to experimental data. 

When parameterizing the Jacobian, obviously, redundancies should be avoided. In particular, if a metabolite affects a reaction as a substrate, as well as an allosteric effector, the interaction should be coded into one parameter, rather than a sum of two parameters. Unfortunately, to detect and avoid higher order redundancies is no easy task and we are not aware of any straightforward solution. 

A. Pi/ erard, Control of the activity of Escherichia coli carbamoyl phosphate synthetase by antagonistic allosteric effectors. Science 154, 1572 1573 (1966). 

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