Structural and functional approaches to the study of protein antigenicity

Structural and functional approaches to the study of protein antigenicity lead to two different perceptions of the nature of protein epitopes. The structural approach concentrates on the purely spatial arrangements of atoms found in the antigen-antibody complex and shows that at least 15 amino acid residues may be implicated in each epitope. The functional approach, which introduces the additional dimension of time, takes the form of cross-reactive binding measurements and leads to the view that a smaller number of residues are implicated in each epitope. Furthermore, as functional binding assays are irretrievably operational in character, different types of epitopes are identified by the use of different probes. Three current controversies in the field of protein antigenicity are discussed here: the mechanism of antigen-antibody interaction, the suitability of peptides as synthetic vaccines and the value of prediction methods for locating epitopes in proteins.