Academic Journal
Προβολή σε EDS

An Overview of Epitopes and Methods for Antibody Epitope Mapping.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: An Overview of Epitopes and Methods for Antibody Epitope Mapping.
Συγγραφείς: Nilvebrant J; School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden., Berndt Thalén N; School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden., Rockberg J; School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden. johanr@biotech.kth.se., Malm M; School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden. magdalena.malm@biotech.kth.se.
Πηγή: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2937, pp. 1-11.
Τύπος έκδοσης: Journal Article; Review
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
Imprint Name(s): Publication: Totowa, NJ : Humana Press
Original Publication: Clifton, N.J. : Humana Press
Ιατρικοί όροι (MeSH): Epitope Mapping*/methods , Epitopes*/immunology , Epitopes*/chemistry , Epitopes*/genetics , Antibodies*/immunology , Antibodies*/chemistry, Computational Biology/methods ; Antigens/immunology ; Antigens/chemistry ; Humans ; Animals
Περίληψη: Antibodies are protein molecules indispensable for many therapeutic, diagnostic, and research purposes due to their exquisite ability to selectively recognize and bind a given antigen. The particular area of the antigen recognized by the antibody is called the epitope, and mapping of such epitopes can provide important mechanistic insights and indicate for what applications an antibody might be useful. Even though the nature of epitopes can be complex, epitopes in protein antigens are broadly grouped into linear or discontinuous epitopes depending on the positioning of the epitope residues in the antigen sequence and the requirement of structure. Specialized methods for mapping the two different classes of epitopes have been developed. While different in their detail, all of the experimental methods rely on assessing the binding of the antibody to the antigen or a set of antigen mimics. Classical epitope mapping methods, utilizing truncated proteins, small numbers of synthesized peptides, and structural analyses of antibody-antigen complexes, have been significantly refined. Current state-of-the-art methods involve combinations of mutational scanning, protein display, and high throughput screening in conjunction with bioinformatic analyses of large datasets. In line with the significant development of in silico protein structure prediction in recent years, computerized approaches for epitope prediction have also matured considerably.
(© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
References: Barlow DJ, Edwards MS, Thornton JM (1986) Continuous and discontinuous protein antigenic determinants. Nature 322:747–748. https://doi.org/10.1038/322747a0. (PMID: 10.1038/322747a02427953)
Getzoff ED, Tainer JA, Lerner RA et al (1988) The chemistry and mechanism of antibody binding to protein antigens. In: Dixon FJ (ed) Advances in immunology. Academic, pp 1–98.
Laver WG, Air GM, Webster RG et al (1990) Epitopes on protein antigens: misconceptions and realities. Cell 61:553–556. https://doi.org/10.1016/0092-8674(90)90464-p. (PMID: 10.1016/0092-8674(90)90464-p1693095)
Morris GE (1996) Overview. Choosing a method for epitope mapping. Methods Mol Biol 66:1–9. https://doi.org/10.1385/0-89603-375-9:1. (PMID: 10.1385/0-89603-375-9:18959699)
Van Regenmortel MHV (1996) Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods 9:465–472. https://doi.org/10.1006/meth.1996.0054. (PMID: 10.1006/meth.1996.0054)
Jemmerson R (1987) Antigenicity and native structure of globular proteins: low frequency of peptide reactive antibodies. Proc Natl Acad Sci USA 84:9180–9184. https://doi.org/10.1073/pnas.84.24.9180. (PMID: 10.1073/pnas.84.24.91802447585299716)
Van Regenmortel MHV (2009) What is a B-cell epitope? Methods Mol Biol 524:3–20. https://doi.org/10.1007/978-1-59745-450-6_1. (PMID: 10.1007/978-1-59745-450-6_119377933)
Uhlen M, Bandrowski A, Carr S et al (2016) A proposal for validation of antibodies. Nat Methods 13:823–827. https://doi.org/10.1038/nmeth.3995. (PMID: 10.1038/nmeth.39952759540410335836)
Volk A-L, Hu FJ, Berglund MM et al (2016) Stratification of responders towards eculizumab using a structural epitope mapping strategy. Sci Rep 6:31365. https://doi.org/10.1038/srep31365. (PMID: 10.1038/srep31365275098434980765)
Zhang B, Hu Y, Chen L et al (2020) Mining of epitopes on spike protein of SARS-CoV-2 from COVID-19 patients. Cell Res 30:702–704. https://doi.org/10.1038/s41422-020-0366-x. (PMID: 10.1038/s41422-020-0366-x326121997327194)
Ghotloo S, Maghsood F, Golsaz-Shirazi F et al (2022) Epitope mapping of neutralising anti-SARS-CoV-2 monoclonal antibodies: implications for immunotherapy and vaccine design. Rev Med Virol 32:e2347. https://doi.org/10.1002/rmv.2347. (PMID: 10.1002/rmv.2347353940939111153)
Chavda VP, Yao Q, Vora LK et al (2022) Fast-track development of vaccines for SARS-CoV-2: the shots that saved the world. Front Immunol 13:961198. https://doi.org/10.3389/fimmu.2022.961198. (PMID: 10.3389/fimmu.2022.961198362630309574046)
Lyu X, Zhao Q, Hui J et al (2022) The global landscape of approved antibody therapies. Antib Ther 5:233–257. https://doi.org/10.1093/abt/tbac021. (PMID: 10.1093/abt/tbac021362132579535261)
Brooks BD, Miles AR, Abdiche YN (2014) High-throughput epitope binning of therapeutic monoclonal antibodies: why you need to bin the fridge. Drug Discov Today 19:1040–1044. https://doi.org/10.1016/j.drudis.2014.05.011. (PMID: 10.1016/j.drudis.2014.05.01124880105)
Ladner RC (2007) Mapping the epitopes of antibodies. Biotechnol Genet Eng Rev 24:1–30. https://doi.org/10.1080/02648725.2007.10648092. (PMID: 10.1080/02648725.2007.1064809218059626)
Atassi MZ (1984) Antigenic structures of proteins. Their determination has revealed important aspects of immune recognition and generated strategies for synthetic mimicking of protein binding sites. Eur J Biochem 145:1–20. https://doi.org/10.1111/j.1432-1033.1984.tb08516.x. (PMID: 10.1111/j.1432-1033.1984.tb08516.x6208027)
Gershoni JM, Roitburd-Berman A, Siman-Tov DD et al (2007) Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs 21:145–156. https://doi.org/10.2165/00063030-200721030-00002. (PMID: 10.2165/00063030-200721030-00002175167107100438)
Abbott WM, Damschroder MM, Lowe DC (2014) Current approaches to fine mapping of antigen-antibody interactions. Immunology 142:526–535. https://doi.org/10.1111/imm.12284. (PMID: 10.1111/imm.12284246355664107663)
Johansson LC, Stauch B, Ishchenko A et al (2017) A bright future for serial femtosecond crystallography with XFELs. Trends Biochem Sci 42:749–762. https://doi.org/10.1016/j.tibs.2017.06.007. (PMID: 10.1016/j.tibs.2017.06.007287331165600683)
Koide S (2009) Engineering of recombinant crystallization chaperones. Curr Opin Struct Biol 19:449–457. https://doi.org/10.1016/j.sbi.2009.04.008. (PMID: 10.1016/j.sbi.2009.04.008194776322736338)
Kühlbrandt W (2014) The resolution revolution. Science 343:1443–1444. https://doi.org/10.1126/science.1251652. (PMID: 10.1126/science.125165224675944)
Merino F, Raunser S (2017) Electron cryo-microscopy as a tool for structure-based drug development. Angew Chem Int Ed Eng 56:2846–2860. https://doi.org/10.1002/anie.201608432. (PMID: 10.1002/anie.201608432)
Wu S, Avila-Sakar A, Kim J et al (2012) Fabs enable single particle cryoEM studies of small proteins. Structure 20:582–592. https://doi.org/10.1016/j.str.2012.02.017. (PMID: 10.1016/j.str.2012.02.017224831063322386)
Geysen HM, Meloen RH, Barteling SJ (1984) Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc Natl Acad Sci USA 81:3998–4002. https://doi.org/10.1073/pnas.81.13.3998. (PMID: 10.1073/pnas.81.13.39986204335345355)
Forsström B, Axnäs BB, Stengele K-P et al (2014) Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays. Mol Cell Proteomics 13:1585–1597. https://doi.org/10.1074/mcp.M113.033308. (PMID: 10.1074/mcp.M113.033308247051234047477)
Timmerman P, Puijk WC, Meloen RH (2007) Functional reconstruction and synthetic mimicry of a conformational epitope using CLIPS technology. J Mol Recognit 20:283–299. https://doi.org/10.1002/jmr.846. (PMID: 10.1002/jmr.84618074397)
Meloen RH, Puijk WC, Slootstra JW (2000) Mimotopes: realization of an unlikely concept. J Mol Recognit 13:352–359. https://doi.org/10.1002/1099-1352(200011/12)13:6<352::AID-JMR509>3.0.CO;2-C. (PMID: 10.1002/1099-1352(200011/12)13:6<352::AID-JMR509>3.0.CO;2-C11114068)
Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383–386. https://doi.org/10.1126/science.7529940. (PMID: 10.1126/science.75299407529940)
Chakraborti S, Prabakaran P, Xiao X et al (2005) The SARS coronavirus S glycoprotein receptor binding domain: fine mapping and functional characterization. Virol J 2:73. https://doi.org/10.1186/1743-422X-2-73. (PMID: 10.1186/1743-422X-2-73161223881236967)
Dall’Acqua W, Goldman ER, Lin W et al (1998) A mutational analysis of binding interactions in an antigen−antibody protein−protein complex. Biochemistry 37:7981–7991. https://doi.org/10.1021/bi980148j. (PMID: 10.1021/bi980148j9609690)
Van Regenmortel MH (1989) Structural and functional approaches to the study of protein antigenicity. Immunol Today 10:266–272. https://doi.org/10.1016/0167-5699(89)90140-0. (PMID: 10.1016/0167-5699(89)90140-02478146)
Chao G, Cochran JR, Wittrup KD (2004) Fine epitope mapping of anti-epidermal growth factor receptor antibodies through random mutagenesis and yeast surface display. J Mol Biol 342:539–550. https://doi.org/10.1016/j.jmb.2004.07.053. (PMID: 10.1016/j.jmb.2004.07.05315327953)
Thalén NB, Karlander M, Lundqvist M et al (2024) Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping. Commun Biol 7:1–11. https://doi.org/10.1038/s42003-024-06508-8. (PMID: 10.1038/s42003-024-06508-8)
Rockberg J, Löfblom J, Hjelm B et al (2008) Epitope mapping of antibodies using bacterial surface display. Nat Methods 5:1039–1045. https://doi.org/10.1038/nmeth.1272. (PMID: 10.1038/nmeth.127219029907)
Kowalsky CA, Faber MS, Nath A et al (2015) Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem 290:26457–26470. https://doi.org/10.1074/jbc.M115.676635. (PMID: 10.1074/jbc.M115.676635262968914646304)
Najar TA, Khare S, Pandey R et al (2017) Mapping protein binding sites and conformational epitopes using cysteine labeling and yeast surface display. Structure 25:395–406. https://doi.org/10.1016/j.str.2016.12.016. (PMID: 10.1016/j.str.2016.12.01628132782)
Van Blarcom T, Rossi A, Foletti D et al (2015) Precise and efficient antibody epitope determination through library design, yeast display and next-generation sequencing. J Mol Biol 427:1513–1534. https://doi.org/10.1016/j.jmb.2014.09.020. (PMID: 10.1016/j.jmb.2014.09.02025284753)
Garrett ME, Itell HL, Crawford KH et al (2020) Phage-DMS: a comprehensive method for fine mapping of antibody epitopes. iScience 23:101622. https://doi.org/10.1016/j.isci.2020.101622. (PMID: 10.1016/j.isci.2020.101622330891107566095)
Kumar N, Bajiya N, Patiyal S et al (2023) Multi-perspectives and challenges in identifying B-cell epitopes. Protein Sci 32:e4785. https://doi.org/10.1002/pro.4785. (PMID: 10.1002/pro.47853773348110578127)
Petersen RL (2017) Strategies using bio-layer interferometry biosensor technology for vaccine research and development. Biosensors 7:49. https://doi.org/10.3390/bios7040049. (PMID: 10.3390/bios7040049290880965746772)
Paus E, Haugen MH, Olsen KH et al (2011) TD-11 workshop report: characterization of monoclonal antibodies to S100 proteins. Tumour Biol 32:1–12. https://doi.org/10.1007/s13277-010-0073-1. (PMID: 10.1007/s13277-010-0073-120652782)
Opuni KFM, Al-Majdoub M, Yefremova Y et al (2018) Mass spectrometric epitope mapping. Mass Spectrom Rev 37:229–241. https://doi.org/10.1002/mas.21516. (PMID: 10.1002/mas.2151627403762)
Coales SJ, Tuske SJ, Tomasso JC et al (2009) Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry. Rapid Commun Mass Spectrom 23:639–647. https://doi.org/10.1002/rcm.3921. (PMID: 10.1002/rcm.392119170039)
Pandit D, Tuske SJ, Coales SJ et al (2012) Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking. J Mol Recognit 25:114–124. https://doi.org/10.1002/jmr.1169. (PMID: 10.1002/jmr.116922407975)
Ray-Saha S, Huber T, Sakmar TP (2014) Antibody epitopes on G protein-coupled receptors mapped with genetically encoded photoactivatable cross-linkers. Biochemistry 53:1302. https://doi.org/10.1021/bi401289p. (PMID: 10.1021/bi401289p24490954)
Dahl L, Kotliar IB, Bendes A et al (2023) Multiplexed selectivity screening of anti-GPCR antibodies. Sci Adv 9:eadf9297. https://doi.org/10.1126/sciadv.adf9297. (PMID: 10.1126/sciadv.adf92973713417310156119)
The Nobel Prize in Physics 2024. In: NobelPrize.org. https://www.nobelprize.org/prizes/physics/2024/press-release/ . Accessed 28 Oct 2024.
The Nobel Prize in Chemistry 2024. In: NobelPrize.org. https://www.nobelprize.org/prizes/chemistry/2024/press-release/ . Accessed 28 Oct 2024.
Greenbaum JA, Andersen PH, Blythe M et al (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 20:75–82. https://doi.org/10.1002/jmr.815. (PMID: 10.1002/jmr.81517205610)
Sela-Culang I, Ofran Y, Peters B (2015) Antibody specific epitope prediction-emergence of a new paradigm. Curr Opin Virol 11:98–102. https://doi.org/10.1016/j.coviro.2015.03.012. (PMID: 10.1016/j.coviro.2015.03.012258374664456244)
Van Regenmortel MHV (2014) Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition. J Mol Recognit 27:627–639. https://doi.org/10.1002/jmr.2394. (PMID: 10.1002/jmr.239425277087)
De Groot AS (2006) Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov Today 11:203–209. https://doi.org/10.1016/S1359-6446(05)03720-7. (PMID: 10.1016/S1359-6446(05)03720-716580597)
Nielsen M, Andreatta M (2016) NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med 8:33. https://doi.org/10.1186/s13073-016-0288-x. (PMID: 10.1186/s13073-016-0288-x270291924812631)
Blythe MJ, Flower DR (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14:246. https://doi.org/10.1110/ps.041059505. (PMID: 10.1110/ps.041059505155765532253337)
Huang P-S, Boyken SE, Baker D (2016) The coming of age of de novo protein design. Nature 537:320–327. https://doi.org/10.1038/nature19946. (PMID: 10.1038/nature1994627629638)
Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2. (PMID: 10.1038/s41586-021-03819-2342658448371605)
Abramson J, Adler J, Dunger J et al (2024) Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630:493–500. https://doi.org/10.1038/s41586-024-07487-w. (PMID: 10.1038/s41586-024-07487-w3871883511168924)
Cho H-S, Mason K, Ramyar KX et al (2003) Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab. Nature 421:756–760. https://doi.org/10.1038/nature01392. (PMID: 10.1038/nature0139212610629)
Contributed Indexing: Keywords: Antibody; Antigen; Epitope; Epitope mapping; Peptide; Prediction; Structural biology
Substance Nomenclature: 0 (Epitopes)
0 (Antibodies)
0 (Antigens)
Entry Date(s): Date Created: 20250702 Date Completed: 20250702 Latest Revision: 20250702
Update Code: 20260130
DOI: 10.1007/978-1-0716-4591-8_1
PMID: 40593411
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:1940-6029
DOI:10.1007/978-1-0716-4591-8_1