Editing Epitope (section)

{{Short description|Chemical entity which can be bound by an antibody}}
An '''epitope''', also known as '''antigenic determinant''', is the part of an [[antigen]] that is recognized by the [[immune system]], specifically by [[antibody|antibodies]], [[B cell]]s, or [[T cell]]s. The part of an antibody that binds to the epitope is called a [[paratope]]. Although epitopes are usually [[exogenous antigen|non-self proteins]], sequences derived from the host that can be recognized (as in the case of autoimmune diseases) are also epitopes.<ref>{{cite journal |last1=Mahmoudi Gomari |first1=Mohammad |last2=Saraygord-Afshari |first2=Neda |last3=Farsimadan |first3=Marziye |last4=Rostami |first4=Neda |last5=Aghamiri |first5=Shahin |last6=Farajollahi |first6=Mohammad M. |title=Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry |journal=Biotechnology Advances |date=1 December 2020 |volume=45 |pages=107653 |doi=10.1016/j.biotechadv.2020.107653 |pmid=33157154 |s2cid=226276355 }}</ref>

The epitopes of [[protein]] antigens are divided into two categories, [[conformational epitope]]s and [[linear epitope]]s, based on their structure and interaction with the paratope.<ref>{{cite journal | vauthors = Huang J, Honda W | title = CED: a conformational epitope database | journal = BMC Immunology | volume = 7 | pages = 7 | date = April 2006 | pmid = 16603068 | pmc = 1513601 | doi = 10.1186/1471-2172-7-7 | doi-access = free }}</ref>   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.<ref>{{cite journal | vauthors = Anfinsen CB | title = Principles that govern the folding of protein chains | journal = Science | volume = 181 | issue = 4096 | pages = 223–230 | date = July 1973 | pmid = 4124164 | doi = 10.1126/science.181.4096.223 | bibcode = 1973Sci...181..223A }}</ref><ref>{{cite journal | vauthors = Bergmann CC, Tong L, Cua R, Sensintaffar J, Stohlman S | title = Differential effects of flanking residues on presentation of epitopes from chimeric peptides | journal = Journal of Virology | volume = 68 | issue = 8 | pages = 5306–10 | date = August 1994 | pmid = 7518534 | pmc = 236480 | doi = 10.1128/JVI.68.8.5306-5310.1994 }}</ref><ref>{{cite journal | vauthors = Bergmann CC, Yao Q, Ho CK, Buckwold SL | title = Flanking residues alter antigenicity and immunogenicity of multi-unit CTL epitopes | journal = Journal of Immunology | volume = 157 | issue = 8 | pages = 3242–9 | date = October 1996 | doi = 10.4049/jimmunol.157.8.3242 | pmid = 8871618 | s2cid = 24717835 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Briggs S, Price MR, Tendler SJ | title = Fine specificity of antibody recognition of carcinoma-associated epithelial mucins: antibody binding to synthetic peptide epitopes | journal = European Journal of Cancer | volume = 29A | issue = 2 | pages = 230–7 | date = 1993 | pmid = 7678496 | doi = 10.1016/0959-8049(93)90181-E }}</ref><ref>{{cite journal | vauthors = Craig L, Sanschagrin PC, Rozek A, Lackie S, Kuhn LA, Scott JK | title = The role of structure in antibody cross-reactivity between peptides and folded proteins | journal = Journal of Molecular Biology | volume = 281 | issue = 1 | pages = 183–201 | date = August 1998 | pmid = 9680484 | doi = 10.1006/jmbi.1998.1907 }}</ref>  90% of epitopes are conformational.<ref>{{cite journal |last1=Ferdous |first1=Saba |last2=Kelm |first2=Sebastian |last3=Baker |first3=Terry S. |last4=Shi |first4=Jiye |last5=Martin |first5=Andrew C. R. |title=B-cell epitopes: Discontinuity and conformational analysis |journal=Molecular Immunology |date=1 October 2019 |volume=114 |pages=643–650 |doi=10.1016/j.molimm.2019.09.014 |pmid=31546099 |s2cid=202747810 |url=https://discovery.ucl.ac.uk/id/eprint/10081794/ }}</ref>