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😷 | "Factor X" revealed? The reason why the number of new coronas is less than in Europe and the United States RIKEN


Is "Factor X" found? Why is there less new corona than in Europe and the United States? RIKEN

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Furthermore, it was found that the epitope binds well to HLA-A6 type, which is said to be possessed by nearly 24% of Japanese.

Regarding the factor "Factor X", which is said to have a smaller number of people infected with the new coronavirus in Japan than in Europe and the United States, with HLA ... → Continue reading


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Epitope(British: epitope) IsAntigen determinant(British: antigenic determinant),Immune system,In particularantibody,B cells,T cellsRecognized byantigenIs part of.antibodyIs a pathogenic microorganismHigh molecularSubstance etc.antigenWhen binding to, it does not recognize the whole, but recognizes and binds only to a relatively small specific part of the antigen.This antibody binding site is the antigenEpitopeCalled.EpitopeAntigenicityIs the smallest unit for.Antibodies produced by the invasion of the antigen react only with those having the same or similar epitopes as the antigen.Usually, multiple epitopes are contained in one antigen.The portion of the antibody that binds to the epitopeParatope(British: paratope).Epitopes are usuallyNon-self-proteinHowever, recognizable host-derived genomic sequences (such as autoimmune diseases) are also epitopes.

proteinAntigen epitopes depend on their structure and interaction with paratopes.(English edition(English editionClassified into three[1]..Conformational epitopes and linear epitopes are the three-dimensional conformations that the epitope takes (the surface features of the epitope residues involved and the shape or shape of other segments of the antigen.Tertiary structureInteracts with the paratope based on).Conformational epitopes are formed by a three-dimensional conformation determined by the interaction of discontinuous amino acid residues.In contrast, linear epitopes are formed by a three-dimensional conformation determined by the interaction of successive amino acid residues.Therefore, linear epitopes are the amino acids involved.Primary structureIt's not just determined.Residues adjacent to such amino acid residues, or amino acid residues farther from the antigen, affect the ability of the primary structure residue to take the three-dimensional configuration of the epitope.[2][3][4][5][6]..The proportion of conformational epitopes is unknown[Source required].


T cell epitope

T cell epitopesT cell receptorIt is the antigen part that binds to.T cellsEpitope[7],Antigen presenting cellsPresented on the surface ofMajor histocompatibility complexIt is bound to the (MHC) molecule.For humansProfessional antigen presenting cellsIt is,MHC class IISpecialized to present peptides, but most nucleatedSomatic cells TheMHC class IPeptides are presented. The T cell epitope presented by MHC class I molecules is typically a peptide with a length of 8-11 amino acids, whereas the MHC class II molecule presents a longer peptide with a length of 13-17 amino acids.[8], And non-classical MHC moleculesGlycolipidNon-peptidic epitopes such as are also presented.

B cell epitope

The part of the antigen to which an immunoglobulin or antibody binds is called a B cell epitope.[9].. Like T-cell epitopes, B-cell epitopes can be divided into two groups: conformation and linear.[9].. B cell epitopes are predominantly conformations[10][11]..Considering the quaternary structure, the types of epitopes will increase further.[11]..Epitopes masked by the aggregation of protein subunits(English editionと 呼 ば れ る[11]..Neotopes are epitopes that are recognized only when they are in a particular quaternary structure, and the residue of the epitope can span multiple protein subunits.[11]..Neotope becomes unrecognized when the subunit dissociates[11].

Cross activity

Epitopes sometimesCross reactionWake up.Taking advantage of this property, the immune system is regulated by anti-idiotype antibodies (Nobel laureates).Niels JerneFirst proposed by).When an antibody binds to an epitope of an antigen, the paratope becomes an epitope of another antibody, and another antibody may bind to that epitope.If the secondary antibody is of the IgM class, its binding may upregulate the immune response, and if the secondary antibody is of the IgG class, the binding may downregulate the immune response. There is[Source required].

Epitope mapping

(English editionIs a process of experimentally identifying a site (epitope) at which an antibody binds to a target antigen (usually a protein).Identifying the binding site of an antibody and characterizing it will help discover and develop new therapeutic agents, vaccines, and diagnostics.In addition, by clarifying the characteristics of epitopes, the binding mechanism of antibodies can be elucidated and the protection of intellectual property rights (patents) can be strengthened.

T cell epitope mapping

Although MHC class I and II epitopes can be reliably predicted by computational means alone.[12], Not all in-silico T cell epitope prediction algorithms are comparable in accuracy[13]..There are two main methods for predicting peptide-MHC binding: data-driven and structure-based.[9]..Structure-based methods model peptide-MHC structures and require enormous computational power.[9]..Data-driven methods have higher predictive performance than structure-based methods[9]..Data-driven methods predict peptide-MHC binding based on the peptide sequence that binds to the MHC molecule.[9]..By identifying T cell epitopes, scientists can track, capture, and stimulate T cells.[14].

B cell epitope mapping

Epitope mapping can be broadly divided into two methods: structural research and functional research.[15]..As a method of structurally mapping epitopes,X-ray crystal structure analysis,Nuclear magnetic resonance,electronic microscopeand so on[15].. X-ray crystallography of the Ag-Ab complex is considered to be an accurate method for structurally mapping epitopes.[15]..Nuclear magnetic resonance can be utilized to map epitopes using data on Ag-Ab complexes.[15]..This method does not require crystallization, but can only be used for small peptides and proteins.[15]..Electron microscopy is a low resolution method that can localize epitopes of large antigens such as viral particles.[15].

How to functionally map an epitopeWestern blot,Dot blot, And / orELISABinding assays such as are often used to determine antibody binding.[15]..In the competition method, there are twoMonoclonal antibodyThe purpose is to investigate whether (mAB) can bind to the antigen at the same time or compete with each other to bind to the same site.[15]..Another approach is high-throughput, an epitope mapping strategy developed to rapidly map conformation epitopes on structurally complex proteins.(English editionIs[16]..Mutagenesis involves adding random / site-specific oriented mutations to individual residues to map epitopes.[15].. B-cell epitope mapping can be used to develop antibody therapies, peptide-based vaccines, and immunological diagnostic tools.[15].

Epitope tag

Epitope isProteomicsOften used to study and other gene products.Recombinant DNATechniques can be used to fuse a gene with a gene sequence that encodes an epitope recognized by a common antibody.SynthesisObtained laterEpitope tagAllows antibodies to find proteins and other gene products, enabling experimental techniques for localization, purification, and even investigating molecular properties.Common epitopes used for this purpose are:Myc-tag, HA-tag, FLAG tag, GST tag, 6xHis,[17] V5-tag, OLLAS[18]..In addition, a protein that forms a covalent bond with the peptide binds to the peptide, enabling irreversible immobilization.[19]..These strategies have also been successfully applied to the development of "epitope-focused" vaccine designs.[20][21].

Epitope-based vaccine

The first epitope-based vaccine was developed by Jacob et al. In 1985.[22]..Epitope-based vaccines use isolated B or T cell epitopes.FluidandCellular immunityStimulate the response[22]..These vaccines can be enhanced in efficacy using multiple epitopes.[22]..To find an epitope to use for a vaccinein silicoMapping is often used[22]..Once a candidate epitope is found, its construct is designed and vaccine efficiency verified.[22]..Epitope-based vaccines are generally safe, but one of the possible side effects isCytokine stormIs[22]

Neogenic antigenic determinant

Neogenic antigenic determinant(Neoantigenic determinant) is an epitope on a nascent antigen (a newly formed antigen previously unrecognized by the immune system).[23]..New antigens are oftenTumor antigenRelated to and found in carcinogenic cells[24]..ProteinGlycosylation,Phosphorylation, ま た はProteolysisFurther modifications within such biochemical pathways can lead to the formation of nascent antigens and thus nascent antigenic determinants.It can generate new epitopes by changing the structure of the protein, and this epitope is new.Antigen determinantIt is called a new antigenic determinant because it produces.Individual and specific to recognitionantibodyis necessary.

Reference item


  1. ^ “CED: a conformational epitope database”. BMC Immunology 7: 7. (April 2006). two:10.1186 / 1471-2172-7-7. PMC 1513601. PMID 16603068. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513601/. 
  2. ^ “Principles that govern the folding of protein chains”. Science 181 (4096): 223–30. (July 1973). bibcode1973 Sci ... 181 .. 223A. two:10.1126 / science.181.4096.223. PMID 4124164. 
  3. ^ “Differential effects of flanking residues on presentation of epitopes from chimeric peptides”. Journal of Virology 68 (8): 5306–10. (August 1994). two:10.1128 / JVI.68.8.5306-5310.1994. PMC 236480. PMID 7518534. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC236480/. 
  4. ^ “Flanking residues alter antigenicity and immunogenicity of multi-unit CTL epitopes”. Journal of Immunology 157 (8): 3242–9. (October 1996). PMID 8871618. 
  5. ^ “Fine specificity of antibody recognition of carcinoma-associated epithelial mucins: antibody binding to synthetic peptide epitopes”. European Journal of Cancer 29A (2): 230–7. (1993). two:10.1016 / 0959-8049 (93) 90181-E. PMID 7678496. 
  6. ^ “The role of structure in antibody cross-reactivity between peptides and folded proteins”. Journal of Molecular Biology 281 (1): 183–201. (August 1998). two:10.1006 / jmbi.1998.1907. PMID 9680484. 
  7. ^ “Designing the epitope flanking regions for optimal generation of CTL epitopes”. Vaccine 32 (28): 3509–16. (June 2014). two:10.1016 / j.vaccine.2014.04.039. PMID 24795226. 
  8. ^ Molecular biology of the cell (4th ed.). New York: Garland Science. (2002). P. 1401. ISBN 978-0-8153-3218-3 
  9. ^ a b c d e f “Fundamentals and Methods for T- and B-Cell Epitope Prediction”. Journal of Immunology Research 2017: 2680160. (2017-12-28). two:10.1155/2017/2680160. PMC 5763123. PMID 29445754. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763123/. 
  10. ^ “Recent advances in B-cell epitope prediction methods”. Immunome Research 6 Suppl 2 (Suppl 2): ​​S2. (November 2010). two:10.1186 / 1745-7580-6-S2-S2. PMC 2981878. PMID 21067544. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981878/. 
  11. ^ a b c d e Epitope Mapping Protocols. Methods in Molecular Biology ™. 524. Totowa, NJ: Humana Press. (2009). two:10.1007 / 978-1-59745-450-6. ISBN 978-1-934115-17-6 
  12. ^ “Clinical validation of the“ in silico ”prediction of immunogenicity of a human recombinant therapeutic protein”. Clinical Immunology 124 (1): 26–32. (July 2007). two:10.1016 / j.clim.2007.03.544. PMID 17490912. https://digitalcommons.uri.edu/cgi/viewcontent.cgi?article=1050&context=immunology_facpubs. 
  13. ^ “Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics”. Clinical Immunology 131 (2): 189–201. (May 2009). two:10.1016 / j.clim.2009.01.009. PMID 19269256. 
  14. ^ “T Cell Epitope Predictions”. Annual Review of Immunology 38 (1): 123–145. (April 2020). two:10.1146 / annurev-immunol-082119-124838. PMID 32045313. 
  15. ^ a b c d e f g h i j “An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction”. Journal of Immunology Research 2016: 6760830. (2016). two:10.1155/2016/6760830. PMC 5227168. PMID 28127568. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227168/. 
  16. ^ “A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes”. Immunology 143 (1): 13–20. (September 2014). two:10.1111 / imm.12323. PMC 4137951. PMID 24854488. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137951/. 
  17. ^ Molecular bio-methods handbook. Humana Press. (2008). P. 467. ISBN 978-1-60327-374-9 
  18. ^ Novus, Biologicals. “OLLAS Epitope Tag”. Novus Biologicals. 2011/11/23Browse.
  19. ^ “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): E690-7. (March 2012). bibcode2012PNAS..109E.690Z. two:10.1073 / pnas.1115485109. PMC 3311370. PMID 22366317. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3311370/. 
  20. ^ “Proof of principle for epitope-focused vaccine design”. Nature 507 (7491): 201–6. (March 2014). bibcode2014 Natur.507..201C. two:10.1038 / nature12966. PMC 4260937. PMID 24499818. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260937/. 
  21. ^ “Evaluation of protection induced by a dengue virus serotype 2 envelope domain III protein scaffold / DNA vaccine in non-human primates”. Vaccine 34 (30): 3500–7. (June 2016). two:10.1016 / j.vaccine.2016.03.108. PMC 4959041. PMID 27085173. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959041/. 
  22. ^ a b c d e f “Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches”. Drug Discovery Today 25 (6): 1034–1042. (June 2020). two:10.1016 / j.drudis.2020.03.006. PMID 32205198. 
  23. ^ “Neoantigen-Forming Chemicals”. Encyclopedic Reference of Immunotoxicology(2005). P. 475. two:10.1007 / 3-540-27806-0_1063. ISBN 978-3-540-44172-4 
  24. ^ Neoantigen. (nd) Mosby's Medical Dictionary, 8th edition. (2009). Retrieved February 9, 2015 from Medical Dictionary Online


  • Edited by Masamitsu Kae et al. "Latest Livestock Microbiology" Asakura Shoten 1998 ISBN 4254460198

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Epitope prediction method

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