Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the active site of the protein.

Binding site linkages can cause either positive or negative regulation of ligand binding to other sites. In cases where both ligands prefer to bind to the same conformation of a protein, binding at one site increases the affinity of the other site for its respective ligand. This is known as a positive linkage. On the other hand, if the ligands prefer binding to different conformations, binding of one ligand will make it difficult for the second ligand to bind to the protein. This is known as a negative linkage.

Binding sites linkages can regulate a protein’s function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process can serve as an inhibitor. UTP and CTP, the end products of the pyrimidine synthesis pathway, inhibit the activity of ATCase, the enzyme that catalyzes the first essential step of this pathway. Binding of UTP and CTP to the enzyme negatively regulates the linked catalytic site when the concentration of pyrimidines is high, relative to the concentration of purines in the cell. This phenomenon is known as feedback inhibition and is essential in maintaining the right amounts of metabolites in an organism.