The region of a protein that associates with a ligand, known as the ligand’s binding site, usually consists of a cavity in the protein surface formed by a particular arrangement of amino acids. These amino acids can belong to different portions of the polypeptide chain that are brought together when the protein folds (Figure 3–38). Separate regions of the protein surface generally provide binding sites for different ligands, allowing the protein’s activity to be regulated, as we shall see later. And other parts of the protein act as a handle to position the protein in the cell—an example is the SH2 domain discussed previously, which often moves a protein containing it to particular intracellular sites in response to signals.
Although the atoms buried in the interior of the protein have no direct contact with the ligand, they form the framework that gives the surface its contours and its chemical and mechanical properties. Even small changes to the amino acids in the interior of a protein molecule can change its three-dimensional shape enough to destroy a binding site on the surface.
The Surface Conformation of a Protein Determines Its Chemistry
The impressive chemical capabilities of proteins often require that the chemical groups on their surface interact in ways that enhance the chemical reactivity of one or more amino acid side chains. These interactions fall into two main categories.
First, the interaction of neighboring parts of the polypeptide chain may restrict the access of water molecules to that protein’s ligand-binding sites. Because water molecules readily form hydrogen bonds that can compete with ligands for sites
Figure 3–37 The selective binding of a protein to another molecule. Many weak bonds are needed to enable a protein to bind tightly to a second molecule, or ligand. A ligand must therefore fit precisely into a protein’s binding site, like a hand into a glove, so that a large number of noncovalent bonds form between the protein and the ligand. (A) Schematic; (B) space-filling model. (PDB code: 1G6N.)
Figure 3–38 The binding site of a protein. (A) The folding of the polypeptide chain typically creates a crevice or cavity on the protein surface. This crevice contains a set of amino acid side chains disposed in such a way that they can form noncovalent bonds only with certain ligands. (B) A close-up of an actual binding site, showing the hydrogen bonds and electrostatic interactions formed between a protein and its ligand. In this example, a molecule of cyclic AMP is the bound ligand.
on the protein surface, a ligand will form tighter hydrogen bonds (and electrostatic interactions) with a protein if water molecules are kept away. It might be hard to imagine a mechanism that would exclude a molecule as small as water from a protein surface without affecting the access of the ligand itself. However, because of the strong tendency of water molecules to form water–water hydrogen bonds, water molecules exist in a large hydrogen-bonded network (see Panel 2–2, pp. 92–93). In effect, a protein can keep a ligand-binding site dry, increasing that site's reactivity, because it is energetically unfavorable for individual water molecules to break away from this network—as they must do to reach into a crevice on a protein’s surface.
Second, the clustering of neighboring polar amino acid side chains can alter their reactivity. If protein folding forces together a number of negatively charged side chains against their mutual repulsion, for example, the affinity of the site for a positively charged ion is greatly increased. In addition, when amino acid side chains interact with one another through hydrogen bonds, normally unreactive groups (such as the –CH2OH on the serine shown in Figure 3–39) can become reactive, enabling them to be used to make or break selected covalent bonds.
The surface of each protein molecule therefore has a unique chemical reactivity that depends not only on which amino acid side chains are exposed, but also on their exact orientation relative to one another. For this reason, two slightly different conformations of the same protein molecule can differ greatly in their chemistry.