What is an Epitope?

Antibodies target discrete sites on molecules know as epitopes or antigenic determinants. Protein epitopes are groupings of amino acid residues at the surface of a target protein specifically recognised by antibodies. Epitopes are either linear or conformational based on the topographical arrangement of epitope residues at the protein surface. Linear epitopes are a continuous sequence of amino acids typically ranging from six to twenty residues in length. Conformational epitopes are formed by spatially discontinuous amino acid groupings that are brought together at the protein surface as a consequence of protein chain folding or dynamic movement.

In our lengthy experience, linear epitopes may come together at the surface of a protein to form conformational epitopes. The extent to which this occurs across a proteome is currently unknown, but it is a subject of investigation at Epitope Informatics.

Quaternary epitopes are found in association with quaternary protein structures. Protomers are the structural units of oligomeric proteins. A quaternary epitope may be located in a single protein of a multimeric complex, or it may span multiple protomers, being formed de novo by their interaction. Quaternary epitopes formed across multiple protomers are no longer recognised by antibodies when oligomeric subunits dissociate.

Cryptic epitopes are epitopes that are hidden as a result of protein conformational change or when protein subunits aggregate.