An epitope is a localized molecular region or portion on the surface of an antigen that can elicit or provoke an immune response. When an antibody binds to a protein or peptides it recognizes a relatively small area on the surface of the protein or peptide. These recognition sites are known as "epitopes." Sugars, lipids or amino acids as well as other molecules can be part of an epitope.
Epitopes are recognized by antibodies, B cells, or T cells, molecules and cells of the immune system. The recognition sites of an antibody that interact and recognizes the epitope is called a paratope. Usually epitopes are derived from non-self proteins but peptide sequences derived from host protein that are recognized as well are also epitopes.
Epitopes of antigens originating from proteins can be divided into two categories.
A, "conformational epitopes," and, B, "linear epitopes."
The nature of these epitopes is based on their structure and interaction with the paratope. A conformational epitope contains a structured section of amino acids which can contain partial sections of the antigen's amino acid sequence. This type of epitopes can interact with the paratope via 3-D surface features and shape which is determined by the tertiary structure of the antigen. Linear epitopes on the other hand interact with the paratope throw their primary amino acid sequence structure forming a linear epitope through a continuous sequence of amino acids present in the antigen.
Peptide binding by target molecules such as by MHC proteins can be monitored using fluorogenic peptide base biosensors.