Structure allosteric

FIGURE 7.1 Enzyme ortho- and allosterism as presented by Koshland [2], Steric hindrance whereby the competing molecules physically interfered with each other as they bound to the substrate site was differentiated from a direct interaction where only portions of the competing molecules interfered with each other. If no direct physical interaction between the molecules occurred, then the effects were solely due to effects transmitted through the protein structure (allosteric). 

H NMR findings that two-structure allosteric models are not sufficient to describe the cooperative oxygenation of Hb A. In this section, we shall summarize some of these results. 

Sixth, the extensive thermodynamic and kinetic studies on dimer-tetramer assembly using various hybrid and mutant hemoglobins carried out by Ackers and co-workers clearly indicate that there are at least three molecular functional states for Hb A during the transition from the deoxy to the oxy state (Smith and Ackers, 1985 Ackers and Smith, 1987 Smith et al., 1987 Daugherty et al., 1991 Ackers et al., 1992). These results are not consistent with a two-structure allosteric description for the oxygenation of Hb A. 

The regulation of enzymes by metabolites leads to the concept of allostenc regulation. Allosteric means other structure. Allosteric modulators can bind at a site other than the active site in question and cause activation or inhibition. These modulators can include the substrate itself, which binds at another active site in a multi-subunit enzyme. In fact, allosterically modulated enzymes almost always have a complex quaternary structure (multiple subunits) and exhibit non-Michaelis-Menten kinetics. 

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

Steitz, T.A., et al. High resolution x-ray structure of yeast hexokinase, an allosteric protein exhibiting a non-symmetric arrangement of subunits. 

For many years hemoglobin was the only allosteric protein whose stereochemical mechanism was understood in detail. However, more recently detailed structural information has been obtained for both the R and the T states of several enzymes as well as one genetic repressor system, the trp-repressor, described in Chapter 8. We will here examine the structural differences between the R and the T states of a key enzyme in the glycolytic pathway, phosphofructokinase. 

Figure 6.24 The function of the enzyme phosphofructokinase. (a) Phosphofructokinase is a key enzyme in the gycolytic pathway, the breakdown of glucose to pyruvate. One of the end products in this pathway, phosphoenolpyruvate, is an allosteric feedback inhibitor to this enzyme and ADP is an activator, (b) Phosphofructokinase catalyzes the phosphorylation by ATP of fructose-6-phosphate to give fructose-1,6-bisphosphate. (c) Phosphoglycolate, which has a structure similar to phosphoenolpyruvate, is also an inhibitor of the enzyme.

The group of Phil Evans, MRC Laboratory of Molecular Biology, Cambridge, UK, has determined x-ray structures of bacterial PFK both in the R and the T states. These studies have confirmed the above conclusions and given insight into how an allosteric enzyme accomplishes its complex behavior. 

The basic kinetic properties of this allosteric enzyme are clearly explained by combining Monod s theory and these structural results. The tetrameric enzyme exists in equilibrium between a catalytically active R state and an inactive T state. There is a difference in the tertiary structure of the subunits in these two states, which is closely linked to a difference in the quaternary structure of the molecule. The substrate F6P binds preferentially to the R state, thereby shifting the equilibrium to that state. Since the mechanism is concerted, binding of one F6P to the first subunit provides an additional three subunits in the R state, hence the cooperativity of F6P binding and catalysis. ATP binds to both states, so there is no shift in the equilibrium and hence there is no cooperativity of ATP binding. The inhibitor PEP preferentially binds to the effector binding site of molecules in the T state and as a result the equilibrium is shifted to the inactive state. By contrast the activator ADP preferentially binds to the effector site of molecules in the R state and as a result shifts the equilibrium to the R state with its four available, catalytically competent, active sites per molecule. 

Schirmer, T., Evans, P.R. Structural basis of the allosteric behaviour of phosphofructokinase. Nature 343 140-145, 1990. 

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. 

Inhibition of a regulatory enzyme by a feedback inhibitor does not conform to any normal inhibition pattern, and the feedback inhibitor F bears little structural similarity to A, the substrate for the regulatory enzyme. F apparently acts at a binding site distinct from the substrate-binding site. The term allosteric is apt, because F is sterically dissimilar and, moreover, acts at a site other than the site for S. Its effect is called allosteric Inhibition. 

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. 

Freire, E. (2000). Can allosteric regulation be predicted from structure Proc. Natl. Acad. Sci. U.S.A. 97 11680-11682. 

The influence of pH on the affinity of Hb for oxygen known as the Bohr-effect indicates that protons retain the allosteric regulation of oxygen transport. It is also an indirect confirmation of the ability of Hb and Im Hb for transporting carbon dioxide. The values of the Bohr-effect d log P50/d pH for Hb and Im Hb are close to each other in the pH range 7.1-7.4. It is possible that the effect of the micro-environment of carboxylic CP on immobilized Hb and its polyfunctional interaction represents the interaction between Hb and the structural elements inside the red cell [99]. 

Die cytosolic loop between TMs 13 and 14 (KCO I) and TMs 16-17 (KCO II) were identified as critical for KatpCO binding to SURs (Fig. 4d). T1286 and Ml 290 appeared to be particularly important. Close local association of sulfonylurea and KCO binding regions might represent the structural basis for negative allosteric coupling of the sites. 

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