The analysis of ligand-protein complex structures deposited in the Protein Data Bank (PDB) shows that the majority of small organic molecules interact with specific surface regions on their macromolecular targets forming pocket-like indentations, called binding sites or binding pockets.
Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges. The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process.
The majority of these pockets are within a 6 Å distance from protein interfaces. Accordingly, in about half of ligand-bound protein-protein complexes, amino acids from both sides of a protein interface are involved in direct contacts with at least one ligand. Statistically, ligands are closer to a protein-protein interface than a random surface patch of the same solvent accessible surface area. Similar results are obtained in an analysis of the ligand distribution around domain-domain interfaces of 1,416 non-redundant, two-domain protein structures.
A cavity on the surface or in the interior of a protein that contains suitable properties for binding a ligand is usually known as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are present on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket.
Different classes of protein pocket dynamics
(1) appearance/disappearance of a subpocket in an existing pocket
(2) appearance/disappearance of an adjacent pocket on the protein surface in the direct vicinity of an already existing pocket
(3) pocket breathing, which may be caused by side-chain fluctuations or backbone or interdomain vibrational motion
(4) opening/closing of a channel or tunnel, connecting a pocket inside the protein with solvent, including lid motion
(5) the appearance/disappearance of an allosteric pocket at a site on a protein distinct from an already existing pocket with binding of a ligand to the allosteric binding site affecting the original pocket.