5.2 All proteins bind other molecules
All proteins bind to other molecules (generically termed ligands). Ligands that can bind to proteins include:
ions, e.g. Ca2+;
small molecules, e.g. H2O, O2 and CO2, glucose, ATP, GTP, NAD;
macromolecules, i.e. proteins, lipids, polysaccharides, nucleic acids.
These interactions are specific and key to the protein's function and, of course, are critically dependent on the conformation of the protein. As we have seen with Src, protein conformation can be plastic; that is, proteins shift and adapt in response to interactions with specific ligands, thereby changing their activity and their capacity for further interactions.
Regardless of the nature of the ligand, the following general principles apply to the binding activity of proteins.
The interaction between a protein and a ligand is always specific; in other words, the protein discriminates between many different molecules and binds only one particular molecule or one of a number of very closely related (i.e. chemically and structurally similar) molecules.
Interactions are driven by the formation of non-covalent bonds, i.e. hydrogen bonds, ionic bonds, van der Waals forces and/or hydrophobic interactions.
Protein–ligand interactions range from weak and transient to strong and persistent, depending on the summative strength of the non-covalent bonds. Ligands that bind strongly tend to ‘fit’ the protein particularly well, like the correct piece of a jigsaw, thereby maximising the number of non-covalent bonds that can form between the ligand and the amino acid residues of the protein.
The part of the protein that binds the ligand is called the ligand binding site. A protein may have binding sites for more than one ligand, though they usually are located in different parts of the protein.
Ligand binding sites are often clefts or ‘pockets’ at the protein surface and can be formed by amino acids from different parts of the polypeptide when it folds (Figure 31).
A measure of the strength of binding of a ligand to a protein is given by the equilibrium dissociation constant, (KD).