8] Predicting location of continuous epitopes in proteins from their primary structures

Abstract

This chapter describes epitopes that are considered as “functional epitopes”—that is, portions or fragments of a protein that are able to bind to antibody in an immunoassay—and not as “contact epitopes” or “energetic epitopes” identifiable only in structural studies. The most common way of classifying epitopes is into continuous and discontinuous epitopes. The label “continuous epitope” is given to any short linear peptide fragment of an antigen that is able to bind to antibodies raised against the intact protein. In most cases, these antibodies cross-react only weakly with linear peptide fragment of the antigen. A more extreme viewpoint has been advocated, according to which all continuous epitopes represent “unfoldons”—that is, unfolded regions of the antigen that cross-react only with antibodies specific for the denatured protein. Such antibodies may be present in antisera raised against the protein, because some of the antigen molecules used for immunization is denatured or they could be obtained by immunization with peptide fragments.