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.
T cell epitopes
T cell epitopes are presented on the surface of an antigen-presenting cell, where they are bound to major histocompatibility complex (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.
B cell epitopes
The part of the antigen that immunoglobulin or antibodies bind to is called a B-cell epitope. B cell epitopes can be divided into two groups: conformational or linear. B cell epitopes are mainly conformational. There are additional epitope types when the quaternary structure is considered. Epitopes that are masked when protein subunits aggregate are called cryptotopes. Neotopes are epitopes that are only recognized while in a specific quaternary structure and the residues of the epitope can span multiple protein subunits. Neotopes are not recognized once the subunits dissociate.
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.
T cell epitopes
MHC class I and II epitopes can be reliably predicted by computational means alone, although not all in-silico T cell epitope prediction algorithms are equivalent in their accuracy. There are two main methods of predicting peptide-MHC binding: data-driven and structure-based. Structure based methods model the peptide-MHC structure and require great computational power. Data-driven methods have higher predictive performance than structure-based methods. Data-driven methods predict peptide-MHC binding based on peptide sequences that bind MHC molecules. By identifying T-cell epitopes, scientists can track, phenotype, and stimulate T-cells.
B cell epitopes
There are two main methods of epitope mapping: either structural or functional studies. Methods for structurally mapping epitopes include X-ray crystallography, nuclear magnetic resonance, and electron microscopy. X-ray crystallography of Ag-Ab complexes is considered an accurate way to structurally map epitopes. Nuclear magnetic resonance can be used to map epitopes by using data about the Ag-Ab complex. This method does not require crystal formation but can only work on small peptides and proteins. Electron microscopy is a low-resolution method that can localize epitopes on larger antigens like virus particles.
Methods for functionally mapping epitopes often use binding assays such as western blot, dot blot, and/or ELISA to determine antibody binding. Competition methods look to determine if two monoclonal antibodies (mABs) can bind to an antigen at the same time or compete with each other to bind at the same site. Another technique involves high-throughput mutagenesis, an epitope mapping strategy developed to improve rapid mapping of conformational epitopes on structurally complex proteins. Mutagenesis uses randomly/site-directed mutations at individual residues to map epitopes. B-cell epitope mapping can be used for the development of antibody therapeutics, peptide-based vaccines, and immunodiagnostic tools.
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 characterization. Common epitopes used for this purpose are Myc-tag, HA-tag, FLAG-tag, GST-tag, 6xHis, V5-tag and OLLAS. Peptides can also be bound by proteins that form covalent bonds to the peptide, allowing irreversible immobilisation. These strategies have also been successfully applied to the development of "epitope-focused" vaccine design.
The first epitope-based vaccine was developed in 1985 by Jacob et al. Epitope-based vaccines stimulate humoral and cellular immune responses using isolated B-cell or T-cell epitopes. These vaccines can use multiple epitopes to increase their efficacy. To find epitopes to use for the vaccine, in silico mapping is often used. Once candidate epitopes are found, the constructs are engineered and tested for vaccine efficiency. While epitope-based vaccines are generally safe, one possible side effect is cytokine storms.
A neoantigenic determinant is an epitope on a neoantigen, which is a newly formed antigen that has not been previously recognized by the immune system. Neoantigens are often associated with tumor antigens and are found in oncogenic cells. Neoantigens and, by extension, neoantigenic determinants can be formed when a protein undergoes further modification within a biochemical pathway such as glycosylation, phosphorylation or proteolysis. This, by altering the structure of the protein, can produce new epitopes that are called neoantigenic determinants as they give rise to new antigenic determinants. Recognition requires separate, specific antibodies.
- Epitope binning
- Polyclonal B cell response
- Protein tag
- TimeSTAMP protein labelling
- 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.
- Steers NJ, Currier JR, Jobe O, Tovanabutra S, Ratto-Kim S, Marovich MA, et al. (June 2014). "Designing the epitope flanking regions for optimal generation of CTL epitopes". Vaccine. 32 (28): 3509–3516. doi:10.1016/j.vaccine.2014.04.039. PMID 24795226.
- Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular biology of the cell (4th ed.). New York: Garland Science. p. 1401. ISBN 978-0815332183.
- Sanchez-Trincado, Jose L.; Gomez-Perosanz, Marta; Reche, Pedro A. (2017). "Fundamentals and Methods for T- and B-Cell Epitope Prediction". Journal of Immunology Research. 2017: 1–14. doi:10.1155/2017/2680160. PMC 5763123. PMID 29445754.
- El-Manzalawy Y, Honavar V (November 2010). "Recent advances in B-cell epitope prediction methods". Immunome Research. 6 Suppl 2 (Suppl 2): S2. doi:10.1186/1745-7580-6-S2-S2. PMC 2981878. PMID 21067544.
- Regenmortel, Marc H.V. (2009). "What is a B-Cell Epitope?". Epitope Mapping Protocols. Methods in Molecular Biology. Vol. 524. pp. 3–20. doi:10.1007/978-1-59745-450-6_1. ISBN 978-1934115176. PMID 19377933.
- Koren, E.; Groot, Anne De; Jawa, V.; Beck, K.; Boone, T.; Rivera, D.; Li, L.; Mytych, D.; Koscec, M.; Weeraratne, D.; Swanson, S.; Martin, W. (1 January 2007). "Clinical validation of the 'in silico' prediction of immunogenicity of a human recombinant therapeutic protein". Institute for Immunology and Informatics Faculty Publications. 124 (1): 26–32. doi:10.1016/j.clim.2007.03.544. PMID 17490912. S2CID 12867280.
- De Groot, Anne S.; Martin, William (May 2009). "Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics". Clinical Immunology. 131 (2): 189–201. doi:10.1016/j.clim.2009.01.009. PMID 19269256.
- Peters, Bjoern; Nielsen, Morten; Sette, Alessandro (26 April 2020). "T Cell Epitope Predictions". Annual Review of Immunology. 38 (1): 123–145. doi:10.1146/annurev-immunol-082119-124838. PMID 32045313. S2CID 211085860.
- Ahmad, Tarek A.; Eweida, Amrou E.; El-Sayed, Laila H. (December 2016). "T-cell epitope mapping for the design of powerful vaccines". Vaccine Reports. 6: 13–22. doi:10.1016/j.vacrep.2016.07.002.
- Potocnakova, Lenka; Bhide, Mangesh; Pulzova, Lucia Borszekova (2016). "An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction". Journal of Immunology Research. 2016: 1–11. doi:10.1155/2016/6760830. PMC 5227168. PMID 28127568.
- Davidson, Edgar; Doranz, Benjamin J. (September 2014). "A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes". Immunology. 143 (1): 13–20. doi:10.1111/imm.12323. PMC 4137951. PMID 24854488.
- Ahmad, Tarek A.; Eweida, Amrou E.; Sheweita, Salah A. (2016). "B-cell epitope mapping for the design of vaccines and effective diagnostics". Trials in Vaccinology. 5: 71–83. doi:10.1016/j.trivac.2016.04.003.
- Walker J, Rapley R (2008). Molecular bio-methods handbook. Humana Press. p. 467. ISBN 978-1603273749.
- Novus, Biologicals. "OLLAS Epitope Tag". Novus Biologicals. Retrieved 23 November 2011.
- Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M (March 2012). "Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin". Proceedings of the National Academy of Sciences of the United States of America. 109 (12): E690–697. Bibcode:2012PNAS..109E.690Z. doi:10.1073/pnas.1115485109. PMC 3311370. PMID 22366317.
- Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, et al. (March 2014). "Proof of principle for epitope-focused vaccine design". Nature. 507 (7491): 201–206. Bibcode:2014Natur.507..201C. doi:10.1038/nature12966. PMC 4260937. PMID 24499818.
- McBurney SP, Sunshine JE, Gabriel S, Huynh JP, Sutton WF, Fuller DH, et al. (June 2016). "Evaluation of protection induced by a dengue virus serotype 2 envelope domain III protein scaffold/DNA vaccine in non-human primates". Vaccine. 34 (30): 3500–3507. doi:10.1016/j.vaccine.2016.03.108. PMC 4959041. PMID 27085173.
- Parvizpour, Sepideh; Pourseif, Mohammad M.; Razmara, Jafar; Rafi, Mohammad A.; Omidi, Yadollah (June 2020). "Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches". Drug Discovery Today. 25 (6): 1034–1042. doi:10.1016/j.drudis.2020.03.006. PMID 32205198. S2CID 214629963.
- Hans-Werner V (2005). "Neoantigen-Forming Chemicals". Encyclopedic Reference of Immunotoxicology. p. 475. doi:10.1007/3-540-27806-0_1063. ISBN 978-3540441724.
- Neoantigen. (n.d.) Mosby's Medical Dictionary, 8th edition. (2009). Retrieved February 9, 2015 from Medical Dictionary Online
- 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
- Rubinstein ND, Mayrose I, Martz E, Pupko T (September 2009). "Epitopia: a web-server for predicting B-cell epitopes". BMC Bioinformatics. 10: 287. doi:10.1186/1471-2105-10-287. PMC 2751785. PMID 19751513.
- Rubinstein ND, Mayrose I, Pupko T (February 2009). "A machine-learning approach for predicting B-cell epitopes". Molecular Immunology. 46 (5): 840–847. doi:10.1016/j.molimm.2008.09.009. PMID 18947876.
- Saravanan V, Gautham N (October 2015). "Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor". Omics. 19 (10): 648–658. doi:10.1089/omi.2015.0095. PMID 26406767.
- Singh H, Ansari HR, Raghava GP (2013). "Improved method for linear B-cell epitope prediction using antigen's primary sequence". PLOS ONE. 8 (5): e62216. Bibcode:2013PLoSO...862216S. doi:10.1371/journal.pone.0062216. PMC 3646881. PMID 23667458.
- 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
- Epitopes at the US National Library of Medicine Medical Subject Headings (MeSH)