The biological function of antibodies is to bind to pathogens and their products, and to facilitate their removal from the body. An antibody generally recognizes only a small region on the surface of a large molecule such as a polysaccharide or protein. The structure recognized by an antibody is called an antigenic determinant or epitope. Some of the most important pathogens have polysaccharide coats, and antibodies that recognize epitopes formed by the sugar subunits of these molecules are essential in providing immune protection against such pathogens. In many cases, however, the antigens that provoke an immune response are proteins. For example, many protective antibodies against viruses recognize viral coat proteins. In all such cases, the structures recognized by the antibody are located on the surface of the protein. Such sites are likely to be composed of amino acids from different parts of the polypeptide chain that have been brought together by protein folding. Antigenic determinants of this kind are known as conformational or discontinuous epitopes because the structure recognized is composed of segments of the protein that are discontinuous in the amino acid sequence of the antigen but are brought together in the three-dimensional structure. In contrast, an epitope composed of a single segment of polypeptide chain is termed a continuous or linear epitope. Although most antibodies raised against intact, fully folded proteins recognize discontinuous epitopes, some will bind to peptide fragments of the protein. Conversely, antibodies raised against peptides of a protein or against synthetic peptides corresponding to part of its sequence are occasionally found to bind to the natural folded protein. This makes it possible, in some cases, to use synthetic peptides in vaccines that aim to raise antibodies against a pathogen’s protein.
The interaction between an antibody and its antigen can be disrupted by high salt concentrations, by extremes of pH, by detergents, and sometimes by competition with high concentrations of the pure epitope itself. The binding is therefore a reversible noncovalent interaction. The forces, or bonds, involved in these noncovalent interactions are outlined in Fig. 4.9. Electrostatic interactions occur between charged amino acid side chains, as in salt bridges. Most antibody–antigen interactions involve at least one electrostatic interaction. Interactions also occur between electric dipoles, as in hydrogen bonds, or can involve short-range van der Waals forces. High salt concentrations and extremes of pH disrupt antigen–antibody binding by weakening electrostatic interactions and/or hydrogen bonds. This principle is employed in the purification of antigens by using affinity columns of immobilized antibodies (or in the purification of antibody by using antigens in a like manner) (see Appendix I, Section A-3). Hydrophobic interactions occur when two hydrophobic surfaces come together to exclude water. The strength of a hydrophobic interaction is proportional to the surface area that is hidden from water, and for some antigens, hydrophobic interactions probably account for most of the binding energy. In some cases, water molecules are trapped in pockets in the interface between antigen and antibody. These trapped water molecules, especially those between polar amino acid residues, may also contribute to binding and hence to the specificity of the antibody.
The contribution of each of these forces to the overall interaction depends on the particular antibody and antigen involved. A striking difference between antibody interactions with protein antigens and most other natural protein– protein interactions is that antibodies often have many aromatic amino acids