4.1 : Ligand Binding Sites

Activities of most proteins depend on their interactions with other molecules or ions,  known as ligands. Although ligands are able to bind to proteins, not every ligand binds to every protein. 

Instead, a ligand binds only to a specific region on a protein’s surface called the binding site. But how do ligand binding sites ensure selectivity when proteins sit in a mixed ligand soup?

The particular arrangement of amino acids in a protein forms a complementary binding site on its surface for a specific ligand.  However, complementary shapes are not enough for ligand binding. 

Chemical interactions hold the ligand and the protein together. Generally, these interactions are non-covalent, reversible, and weak. Therefore, many of these interactions need to occur simultaneously during ligand binding.

For example, the larger the surface area of interaction, the more Van der Waals interactions can happen. These forces work best for large ligands. For others, the specific conformation of the binding site enables hydrogen bonding or electrostatic interactions. 

But if the ligand binding site can form hydrogen bonds, why doesn’t it form hydrogen bonds with the water in its surroundings? The answer lies in the shape of the ligand binding site.

As an example, in this protein, the orientation of the amino acids forms a cavity, which restricts the access of water molecules. For individual water molecules, entering the cavity is energetically unfavorable as they have to break their hydrogen bonds with other water molecules. 

Yet, the ligand will readily form hydrogen bonds with the polar amino acids in the binding site because the specific protein-ligand interactions are energetically more favorable than their interactions with water molecules.

Polar amino acids also form electrostatic interactions with a ligand. For instance, the negatively-charged glutamate in this binding site attracts the positively-charged ligand. A mutation in this sequence that turns this negatively charged glutamate into a positively charged lysine eliminates ligand binding.

Taken together, the exact sequence and orientation of the amino acids relative to each other determine the chemical reactivity and selectivity of the ligand binding site.