An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. For example, the epitope is the specific piece of the antigen that an antibody binds to. The part of an antibody that binds to the epitope is called a paratope. Although epitopes are usually non-self proteins, sequences derived from the host that can be recognized (as in the case of autoimmune diseases) are also epitopes.
The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their structure and interaction with the paratope. A conformational epitope is composed of discontinuous sections of the antigen's amino acid sequence. These epitopes interact with the paratope based on the 3-D surface features and shape or tertiary structure of the antigen. The proportion of epitopes that are conformational is unknown.
By contrast, linear epitopes interact with the paratope based on their primary structure. A linear epitope is formed by a continuous sequence of amino acids from the antigen.
T cell epitopes
T cell epitopes are presented on the surface of an antigen-presenting cell, where they are bound to MHC molecules. In humans, professional antigen-presenting cells are specialized to present MHC class II peptides, whereas most nucleated somatic cells present MHC class I peptides. T cell epitopes presented by MHC class I molecules are typically peptides between 8 and 11 amino acids in length, whereas MHC class II molecules present longer peptides, 13-17 amino acids in length, and non-classical MHC molecules also present non-peptidic epitopes such as glycolipids.
Epitopes are sometimes cross-reactive. This property is exploited by the immune system in regulation by anti-idiotypic antibodies (originally proposed by Nobel laureate Niels Kaj Jerne). If an antibody binds to an antigen's epitope, the paratope could become the epitope for another antibody that will then bind to it. If this second antibody is of IgM class, its binding can upregulate the immune response; if the second antibody is of IgG class, its binding can downregulate the immune response.
Epitopes are often used in proteomics and the study of other gene products. Using recombinant DNA techniques genetic sequences coding for epitopes that are recognized by common antibodies can be fused to the gene. Following synthesis, the resulting epitope tag allows the antibody to find the protein or other gene product enabling lab techniques for localisation, purification, and further molecular characterisation. Common epitopes used for this purpose are Myc-tag, HA-tag, FLAG-tag, GST-tag, 6xHis and OLLAS. Peptides can also be bound by proteins that form covalent bonds to the peptide, allowing irreversible immobilisation.
- Epitope binning
- Epitope mapping
- Conformational epitope
- Polyclonal B cell response
- Protein tag
- Huang, J.; Honda, W. (2006). "CED: a conformational epitope database". BMC Immunology 7: 7. doi:10.1186/1471-2172-7-7. PMC 1513601. PMID 16603068. Retrieved April 8, 2010.
- Alberts (2002). Molecular Biology of the Cell. New York: Garland Science. p. 1401.
- Koren, E.; AS De Groot (July 7, 2007). "Clinical validation of the "in silico" prediction of immunogenicity of a human recombinant therapeutic protein". Clinical Immunology 124 (1). doi:10.1016/j.clim.2007.03.544.
- De Groot, Anne; W. Martin (May 2009). "Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics". Clinical Immunology 131 (2). doi:10.1016/j.clim.2009.01.009.
- Walker, John; Ralph Rapley (2008). Molecular biomethods handbook. Humana Press. p. 467. ISBN 1-60327-374-3.
- Novus, Biologicals. "OLLAS Epitope Tag". Novus Biologicals. Retrieved 23 November 2011.
- Zakeri, B. (2012). "Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin". Proceedings of the National Academy of Sciences 109 (12): E690–7. doi:10.1073/pnas.1115485109. PMC 3311370. PMID 22366317.
- Antibodies bind to conformational shapes on the surfaces of antigens (Janeway Immunobiology Section 3.8)
- Antigens can bind in pockets or grooves, or on extended surfaces in the binding sites of antibodies (Janeway Immunobiology Figure 3.8)
Epitope prediction methods
- LBEEP : Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor. 
- Lbtope: Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence. PLoS ONE 8(5): e62216
- BCEP: Prediction of B-cell epitopes using protein 3D structures.
- MHCBN: A database of MHC/TAP binder and T-cell epitopes
- Bcipep: A database of B-cell epitopes
- SYFPEITHI - First online database of T cell epitopes
- IEDB - Database of T and B cell epitopes with annotation of recognition context - NIH funded
- ANTIJEN - T and B cell epitope database at the Jenner institute, UK
- IMGT/3Dstructure-DB - Three-dimensional structures of B and T cell epitopes with annotation of IG and TR - IMGT, Montpellier, France
- SEDB: A Structural Epitope Database- Pondicheery University, DIT funded