Proteins are the fundamental components of living cells involved with complex biological processes, such as nutrition transport, immune responding, tissue contraction, and gene expression. Most proteins function through interacting with other biomolecules, such as peptides, nucleic acid, lipoprotein, proteins, etc. (Table 1). The nature of these interactions or bindings is typically reversible so that a cell can rapidly respond to changes in its metabolic and external environment. Although reversible, these interactions are specific such that a protein can recognize and bind their specific ligands from thousands of different molecules surrounded it.
Table 1.Biological Functions of Protein-ligand Interactions.A variety of protein and ligand types presented with a diverse sets of functions.
A molecule that binds reversibly to the protein, or receptor, is known as a ligand, which may be any type of molecule including another protein, a peptide, DNA, RNA, a small organic molecule, or a metal ion. Proteins and ligands are usually complementary in size, shape, charge, hydrophobicity, and hydrophilicity. These ligands bind to proteins through non-covalent interactions, which are critical in biology. The site on the protein where the ligand binds is called the binding site. However, one particular protein may have several binding sites each corresponding to a different ligand.
To fully describe a biologically relevant protein-ligand interaction, there are many pieces of information that must be known, including:
Each of the above parameters contributes to completely describing the distinct protein-ligand pair and its function in biology. These parameters can be obtained by several techniques.
Table 2. Biophysical Experimental Techniques. There are wide ranges of methods to study the binding of ligands to macromolecular receptors like proteins based on a number of different physical properties.
In order to determine the association constant, the value of the free peptide concentration can be measured or a change in the biological or chemical properties of the bound ligand, the bound receptor, or the complex must be detected. Dialysis or chromatographic techniques are often used to detect the concentration of the ligand, whereas spectroscopic techniques can measure a change in some property of the components of the system (such as bound ligand, bound receptor, or complex). In addition, it is also possible to perform competitive assays in which the equilibrium constant is deduced for one ligand binding to the protein when it competes with a ligand of known binding affinity.
Using these experimental results, the protein-ligand binding can be described quantitatively by the equilibrium constant. K. Data can also be analyzed to determine the number of ligand binding sites. By measuring the dependence of K on ionic strength, pH, and other variables, more can be learned about the specific intermolecular forces involved in the binding interface.