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. 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. Conformational and linear epitopes interact with the paratope based on the 3-D conformation adopted by the epitope, which is determined by the surface features of the involved epitope residues and the shape or tertiary structure of other segments of the antigen. A conformational epitope is formed by the 3-D conformation adopted by the interaction of discontiguous amino acid residues. In contrast, a linear epitope is formed by the 3-D conformation adopted by the interaction of contiguous amino acid residues. A linear epitope is not determined solely by the primary structure of the involved amino acids. Residues that flank such amino acid residues, as well as more distant amino acid residues of the antigen affect the ability of the primary structure residues to adopt the epitope's 3-D conformation. 90% of epitopes are conformational.
^Mahmoudi Gomari, Mohammad; Saraygord-Afshari, Neda; Farsimadan, Marziye; Rostami, Neda; Aghamiri, Shahin; Farajollahi, Mohammad M. (1 December 2020). "Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry". Biotechnology Advances. 45: 107653. doi:10.1016/j.biotechadv.2020.107653. PMID 33157154. S2CID 226276355.
^Huang J, Honda W (April 2006). "CED: a conformational epitope database". BMC Immunology. 7: 7. doi:10.1186/1471-2172-7-7. PMC 1513601. PMID 16603068.
^Anfinsen CB (July 1973). "Principles that govern the folding of protein chains". Science. 181 (4096): 223–230. Bibcode:1973Sci...181..223A. doi:10.1126/science.181.4096.223. PMID 4124164.
^Bergmann CC, Tong L, Cua R, Sensintaffar J, Stohlman S (August 1994). "Differential effects of flanking residues on presentation of epitopes from chimeric peptides". Journal of Virology. 68 (8): 5306–5310. doi:10.1128/JVI.68.8.5306-5310.1994. PMC 236480. PMID 7518534.
^Bergmann CC, Yao Q, Ho CK, Buckwold SL (October 1996). "Flanking residues alter antigenicity and immunogenicity of multi-unit CTL epitopes". Journal of Immunology. 157 (8): 3242–3249. PMID 8871618.
^Briggs S, Price MR, Tendler SJ (1993). "Fine specificity of antibody recognition of carcinoma-associated epithelial mucins: antibody binding to synthetic peptide epitopes". European Journal of Cancer. 29A (2): 230–237. doi:10.1016/0959-8049(93)90181-E. PMID 7678496.
^Craig L, Sanschagrin PC, Rozek A, Lackie S, Kuhn LA, Scott JK (August 1998). "The role of structure in antibody cross-reactivity between peptides and folded proteins". Journal of Molecular Biology. 281 (1): 183–201. doi:10.1006/jmbi.1998.1907. PMID 9680484.
^Ferdous, Saba; Kelm, Sebastian; Baker, Terry S.; Shi, Jiye; Martin, Andrew C. R. (1 October 2019). "B-cell epitopes: Discontinuity and conformational analysis". Molecular Immunology. 114: 643–650. doi:10.1016/j.molimm.2019.09.014. PMID 31546099. S2CID 202747810.