The interaction between separated sites on a protein molecule is now known to depend on a conformational change in the protein: binding at one of the sites causes a shift from one folded shape to a slightly different folded shape. During feedback inhibition, for example, the binding of an inhibitor at one site on the protein causes the protein to shift to a conformation that incapacitates its active site located elsewhere in the protein.
It is thought that most protein molecules are allosteric. They can adopt two or more slightly different conformations, and a shift from one to another caused by the binding of a ligand can alter their activity. This is true not only for enzymes but also for many other proteins, including receptors, structural proteins, and motor proteins. In all instances of allosteric regulation, each conformation of the protein has somewhat different surface contours, and the protein’s binding sites for ligands are altered when the protein changes shape. Moreover, as we discuss next, each ligand will stabilize the conformation that it binds to most strongly, and thus—at high enough concentrations—will tend to “switch” the protein toward the conformation that the ligand prefers.
The effects of ligand binding on a protein follow from a fundamental chemical principle known as linkage. Suppose, for example, that a protein that binds glucose also binds another molecule, X, at a distant site on the protein’s surface. If the binding site for X changes shape as part of the conformational change in the protein induced by glucose binding, the binding sites for X and for glucose are said to be coupled. Whenever two ligands prefer to bind to the same conformation of an allosteric protein, it follows from basic thermodynamic principles that each ligand must increase the affinity of the protein for the other. For example, if the shift of a protein to a conformation that binds glucose best also causes the binding site for X to fit X better, then the protein will bind glucose more tightly when X is present than when X is absent. In other words, X will positively regulate the protein’s binding of glucose (Figure 3–57).
Conversely, linkage operates in a negative way if two ligands prefer to bind to different conformations of the same protein. In this case, the binding of the first ligand discourages the binding of the second ligand. Thus, if a shape change caused by glucose binding decreases the affinity of a protein for molecule X, the binding of X must also decrease the protein’s affinity for glucose (Figure 3–58). The linkage relationship is quantitatively reciprocal, so that, for example, if glucose has a very large effect on the binding of X, X has a very large effect on the binding of glucose.
The relationships shown in Figures 3–57 and 3–58 apply to all proteins, and they underlie all of cell biology. The principle seems so obvious in retrospect that we now take it for granted. But the discovery of linkage in studies of a few enzymes in the 1950s, followed by an extensive analysis of allosteric mechanisms in proteins in the early 1960s, had a revolutionary effect on our understanding of biology. Since molecule X in these examples binds at a site on the enzyme that is distinct from the site where catalysis occurs, it need not have any chemical relationship to the substrate that binds at the active site. Moreover, as we have just seen, for enzymes that are regulated in this way, molecule X can either turn the enzyme on (positive regulation) or turn it off (negative regulation). By such a mechanism, allosteric proteins serve as general switches that, in principle, can allow one molecule in a cell to affect the fate of any other.