Chemical specificity

Chemical specificity is the ability of binding site of a macromolecule (such as a protein) to bind specific ligands. The fewer ligands a protein can bind, the greater its specificity.

Specificity describes the strength of binding between a given protein and ligand. This relationship can be described by a dissociation constant, which characterizes the balance between bound and unbound states for the protein-ligand system. In the context of a single enzyme and a pair of binding molecules, the two ligands can be compared as stronger or weaker ligands (for the enzyme) on the basis of their dissociation constants. (A lower value corresponds to a stronger binding.)

Specificity for a set of ligands is unrelated to the ability of an enzyme to catalyze a given reaction, with the ligand as a substrate.

If a given enzyme has a high chemical specificity, this means that the set of ligands to which it binds is limited, such that neither binding events nor catalysis can occur at an appreciable rate with additional molecules.

An example of a protein-ligand pair whose binding activity can be highly specific is the antibody-antigen system. Affinity maturation typically leads to highly specific interactions, whereas naive antibodies are promiscuous and bind a larger number of ligands. Conversely, an example of a protein-ligand system that can bind substrates and catalyze multiple reactions effectively is the Cytochrome P450 system, which can be considered a promiscuous enzyme due to its broad specificity for multiple ligands. Proteases are a group of enzymes that show a broad range of cleavage specificities. Promiscuous proteases as digestive enzymes unspecifically degrade peptides, whereas highly specific proteases are involved in signaling cascades.

The interactions between the protein and ligand substantially affect the specificity between the two entities. Electrostatic interactions and Hydrophobic interactions are known to be the most influential in regards to where specificity between two molecules is derived from. The strength of these interactions between the protein and ligand often positively correlate with their specificity for one another.

The specificity of a binding process is strongly dependent of the flexibility of the binding partners. A rigid protein is very restricted in its binding possibilities. A flexible protein can adapt its conformation to a larger number of ligands and thus is more promiscuous. As the binding process usually leads to a rigidification of both binding partners in the complex, binding of a flexible protein usually comes with an entropic penalty. This is the main reason for the frequently found positive correlation of binding affinity and binding specificity. Antibodies show a strong correlation between rigidity and specificity. This correlation extends far beyond the paratope of the antibodies

Enzyme specificity refers to the interactions between any particular enzyme and its corresponding substrate. In addition to the specificity in binding its substrates, correct proximity and orientation as well as binding the transition state provide an additional layer of enzyme specificity.