Protein ligand binding

It is important for cells to be able to react with their surroundings and to do this, cellular molecules need to be able to interact with one another. Most often, cells use proteins to interact and carry out cellular functions. Proteins are able to interact with one another, but it is important that they can interact with non-protein ligands as well. This is achieved through the use of a binding pocket. The binding pocket is a site on the protein that allows the ligand to fit in and non-covalently bond. Non-covalent bonds include ionic and hydrogen bonds as well as van der Waals and hydrophobic interactions. This is not to say that proteins cannot bind to other proteins using a binding pocket, it is just not always used as sometimes the flat surfaces can simply bind two proteins.

               One of the ways that the interactions between proteins and ligands is measured is by their binding affinity. Also known as the dissociation constant, binding affinity is characterized as the concentration of ligand for when half the binding sites in the protein are filled. The smaller the dissociation constant, the tighter the binding interaction will be, meaning there is a strong binding affinity. Conversely, a low dissociation constant means there is a lower affinity for binding.