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Abstract

The antigenicity of proteins resides in different types of antigenic determinants known as continuous and discontinuous epitopes, cryptotopes, neotopes, and mimotopes. All epitopes have fuzzy boundaries and can be identified only by their ability to bind to certain antibodies. Antigenic cross-reactivity is a common phenomenon because antibodies are always able to recognize a considerable number of related epitopes. This places severe limits to the specificity of antibodies. Antigenicity, which is the ability of an epitope to react with an antibody, must be distinguished from its immunogenicity or ability to induce antibodies in a competent vertebrate host. Failure to make this distinction partly explains why no successful peptide-based vaccines have yet been developed. Methods for predicting the epitopes of proteins are discussed and the reasons for the low success rate of epitope prediction are analyzed.

In: Schutkowski M., Reineke U. (eds) Epitope Mapping Protocols. Methods in Molecular Biology (Methods and Protocols), vol 524. Humana Press, 2009,

Marc H V Van Regenmortel

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References

  • Al Moudallal Z, Briand JP, Van Regenmortel MHV. Monoclonal antibodies as probes of the antigenic structure of tobacco mosaic virus. EMBO J. 1982;1:1005–10.

    Article  PubMed  PubMed Central  Google Scholar 

  • Alexander H, Alexander S, Getzoff ED, Tainer JA, Geysen HM, Lerner RA. Altering the antigenicity of proteins. Proc Natl Acad Sci U S A. 1992;89:3352–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants. Nature. 1986;322:747–8.

    Article  CAS  PubMed  Google Scholar 

  • Benjamin DC, Berzofsky JA, East IJ, Gurd FRN, Hannum C, Leach SJ, Margoliash E, Michael JG, Miller A, Prager EM, Reichlin M, Sercaz EE, Smith-Gill SJ, Todd PE, Wilson AC. The antigenic structure of proteins: a reappraisal. Annu Rev Immunol. 1984;2:67–101.

    Article  CAS  PubMed  Google Scholar 

  • Berzofsky JA. Intrinsic and extrinsic factors in protein antigenic structure. Science. 1985;229:932–40.

    Article  CAS  PubMed  Google Scholar 

  • Berzofsky JA, Schechter AN. The concepts of crossreactivity and specificity in immunology. Mol Immunol. 1981;18:751–63.

    Article  CAS  PubMed  Google Scholar 

  • Blalok J. Complementarity of peptides specified by “sense” and “antisense” strands of DNA. Trends Biotechnol. 1990;8:140–4.

    Article  Google Scholar 

  • Blythe MJ, Flower DR. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci. 2005;14:246–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boeyé A, Rombaut B. The proteins of poliovirus. Prog Med Virol. 1992;62:139–66.

    Google Scholar 

  • Boquet D, Déry O, Forbert Y, Grassi J, Couraud JY. Is hydropathic complementarity involved in antigen-antibody binding? Mol Immunol. 1995;32:303–8.

    Article  CAS  PubMed  Google Scholar 

  • Bothner B, Dong XF, Bibbs L, Johnson JE, Siuzdak G. Evidence of viral capsid dynamics using limited proteolysis and mass spectrometry. J Biol Chem. 1998;9:673–6.

    Article  Google Scholar 

  • Braden BC, Poljak RJ. Structural features of the reactions between antibodies and protein antigens. FASEB J. 1995;9:9–16.

    Article  CAS  PubMed  Google Scholar 

  • Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 2007;68:294–304.

    Article  CAS  PubMed  Google Scholar 

  • Cunningham BC, Wells JA. Comparison of a structural and a functional epitope. J Mol Biol. 1993;234:554–63. https://doi.org/10.1006/jmbi.1993.1611.

    Article  CAS  PubMed  Google Scholar 

  • Darst SA, Robertson CR, Berzofsky JA. Adsorption of the protein antigen myoglobin affects the binding of conformation-specific monoclonal antibodies. Biophys J. 1988;53:533–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DeLano WL. Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol. 2002;12:14–20.

    Article  CAS  PubMed  Google Scholar 

  • Delmastro P, Meola A, Monaci P, Cortese R, Galfre G. Immunogenicity of filamentous phage displaying peptide mimotopes after oral administration. Vaccine. 1997;15:1276–85.

    Article  CAS  PubMed  Google Scholar 

  • Dougherty W, Willis L, Johnston RE. Topographic analysis of tobacco etch virus capsid protein epitopes. Virology. 1985;144:66–72.

    Article  CAS  PubMed  Google Scholar 

  • Folgori A, Tafi R, Meola A, Felici F, Galfré G, Cortese R, Monaci P, Nicosia A. A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera. EMBO J. 1994;13:2236–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Foote J, Eisen HN. Kinetic and affinity limits on antibodies produced during immune responses. Proc Natl Acad Sci U S A. 1995;92:1254–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frison EA, Stace-Smith R. Cross-reacting and heterospecific monoclonal antibodies produced against arabis mosaic nepovirus. J Gen Virol. 1992;73:2525–30.

    Article  CAS  PubMed  Google Scholar 

  • Getzoff ED, Tainer JA, Lerner RA, Geysen HM. The chemistry and mechanism of antibody binding to protein antigens. Adv Immunol. 1988;43:1–98.

    Article  CAS  PubMed  Google Scholar 

  • Geysen HM, Rodda SJ, Mason TJ. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol Immunol. 1986;23:709–15.

    Article  CAS  PubMed  Google Scholar 

  • Ghosh G, Cambell AM. Multispecific monoclonal antibodies. Immunol Today. 1986;7:217–22.

    Article  CAS  PubMed  Google Scholar 

  • Greenbaum JA, Andersen PH, Blythe M, Bui H-H, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit. 2007;20:75–82.

    Article  CAS  PubMed  Google Scholar 

  • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins. 2002;47:409–43.

    Article  CAS  PubMed  Google Scholar 

  • Hanin V, Déry O, Boquet D, Sagot MA, Créminon C, Couraud JY, Grassi J. Importance of hydropathic complementarity for the binding of the neuropeptide substance P to a monoclonal antibody: equilibrium and kinetic studies. Mol Immunol. 1997;34:829–38.

    Article  CAS  PubMed  Google Scholar 

  • Hans D, Young PR, Fairlie DP. Current status of short synthetic peptides as vaccines. Med Chem. 2006;2:627–46.

    Article  CAS  PubMed  Google Scholar 

  • Harper M, Lema F, Boulot G, Poljak RJ. Antigen specificity and cross-reactivity of monoclonal anti-lysozyme antibodies. Mol Immunol. 1987;24:97–108.

    Article  CAS  PubMed  Google Scholar 

  • Haste-Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci. 2006;15:2558–67.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981;78:3824–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • James LC, Roversi P, Tawfik DS. Antibody multi-specificity mediated by conformational diversity. Science. 2003;299:1362–7.

    Article  CAS  PubMed  Google Scholar 

  • Landsteiner K. The specificity of serological reactions. New York: Dover Publications; 1962. p. 330.

    Google Scholar 

  • Larralde OG, Martinez R, Camacho F, Amin N, Aguilar A, Talavera A, Stott DL, Perez EM. Identification of hepatitis A virus mimotopes by phage display, antigenicity and immunogenicity. J Virol Methods. 2007;140:49–58.

    Article  CAS  PubMed  Google Scholar 

  • Laune D, Molina F, Ferrieres G, Mani JC, Cohen P, Simon D, Bernardi T, Piechaczyk M, Pau B, Granier C. Systematic exploration of the antigen binding activity of synthetic peptides isolated from the variable regions of immunoglobulins. J Biol Chem. 1997;272:30937–44.

    Article  CAS  PubMed  Google Scholar 

  • Laver WG, Air GM, Webster RG, Smith-Gill SJ. Epitopes on protein antigens: misconceptions and realities. Cell. 1990;61:553–6.

    Article  CAS  PubMed  Google Scholar 

  • Leinikki P, Lehtinen M, Hyöty H, Parkkonen P, Kantanen ML, Hakulinen J. Synthetic peptides as diagnostic tools in virology. Adv Virus Res. 1993;42:149–86.

    Article  CAS  PubMed  Google Scholar 

  • Lerner RA. Antibodies of predetermined specificity in biology and medicine. Adv Immunol. 1984;36:1–44.

    Article  CAS  PubMed  Google Scholar 

  • Loor F. On the existence of heterospecific antibodies in sera from rabbits immunized against tobacco mosaic virus determinants. Immunology. 1971;21:557–64.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mäkelä O. Single lymph node cells producing heteroclitic bacteriophage antibody. J Immunol. 1965;95:378–86.

    PubMed  Google Scholar 

  • Mazumdar PH. Species and specificity. Cambridge: Cambridge University Press; 1995.

    Google Scholar 

  • Medawar PB, Medawar JS. The life science. London: Granada Publishing; 1978.

    Google Scholar 

  • Meloen RH, Puyk WC, Sloostra JW. Mimotopes: realization of an unlikely concept. J Mol Recognit. 2000;13:352–9.

    Article  CAS  PubMed  Google Scholar 

  • Moodie SL, Mitchell JBO, Thornton JM. Protein recognition of adenylate: an example of a fuzzy recognition template. J Mol Biol. 1996;263:486–500.

    Article  CAS  PubMed  Google Scholar 

  • Mullen LM, Nair SP, Ward JM, Rycroft AN, Henderson B. Phage display in the study of infectious diseases. Trends Microbiol. 2006;14:141–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muller S. Use of antipeptide antibodies in molecular and cellular biology. In: Van Regenmortel MHV, Muller S, editors. Synthetic peptides as antigens. Amsterdam: Elsevier; 1999b. p. 215–35.

    Chapter  Google Scholar 

  • Muller S, Plaue S, Couppez M, Van Regenmortel MHV. Comparison of different methods for localizing antigenic regions in histone H2A. Mol Immunol. 1986;23:593–601.

    Article  CAS  PubMed  Google Scholar 

  • Novotny J, Bruccoleri RE, Carlson WD, Handschumacher M, Haber E. Antigenicity of myohemerythrin. Science. 1987;238:1584–6.

    Article  CAS  PubMed  Google Scholar 

  • Odorico M, Pellequer JL. BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit. 2003;16:20–2.

    Article  CAS  PubMed  Google Scholar 

  • Pellequer JL, Westhof E, Van Regenmortel MHV. Predicting the location of continuous epitopes in proteins from their primary structures. Methods Enzymol. 1991;203:176–201.

    Article  CAS  PubMed  Google Scholar 

  • Pellequer JL, Westhof E, Van Regenmortel MHV. Epitope predictions from the primary structure of proteins. In: Wisdom GB, editor. Peptide antigens: a practical approach. Oxford: JRL; 1994. p. 7–25.

    Google Scholar 

  • Ponomarenko JV, Van Regenmortel MHV. B cell epitope prediction. In: Gu J, Bourne PE, editors. Structural bioinformatics. 2nd ed. Hoboken, NJ: John Wiley; 2009. p. 849–79.

    Google Scholar 

  • Quesniaux VFJ, Schmitter D, Schreier M, Van Regenmortel MHV. Monoclonal antibodies to Cyclosporine are representative of the major antibody populations present in antisera of immunized mice. Mol Immunol. 1990;27:227–36.

    Article  CAS  PubMed  Google Scholar 

  • Roberts VA, Getzoff ED, Tainer JA. In: Van Regenmortel MHV, editor. Structure of antigens, vol. 3. Boca Raton, FL: CRC; 1993. p. 31–53.

    Google Scholar 

  • Rosen R. Life itself. New York: Columbia University Press; 1991.

    Google Scholar 

  • Schroer JA, Bender T, Feldmann T, Kim KJ. Mapping epitopes on the insulin molecule using monoclonal antibodies. Eur J Immunol. 1983;13:693–700.

    Article  CAS  PubMed  Google Scholar 

  • Shepard JF, Secor GA, Purcifull DE. Immunochemical cross-reactivity between the dissociated capsid proteins of PVY group plant viruses. Virology. 1974;58:464–75.

    Article  CAS  PubMed  Google Scholar 

  • Shepherd NE, Hoang HN, Abbenante G, Fairlie DP. Single turn peptide alpha helices with exceptional stability in water. J Am Chem Soc. 2004;127:2974–83.

    Article  CAS  Google Scholar 

  • Sundaram R, Lynch MP, Rawale SV, Sun Y, Kazanji M, Kaumaya PT. De novo design of peptide immunogens that mimic the coiled coil region of human T-cell leukemia virus type-1 glycoprotein 21 transmembrane subunit for induction of native protein reactive neutralizing antibodies. J Biol Chem. 2004;279:24141–51.

    Article  CAS  PubMed  Google Scholar 

  • Thornton JM, Sibanda BL. Amino and carboxy-terminal regions in globular proteins. J Mol Biol. 1983;167:443–60.

    Article  CAS  PubMed  Google Scholar 

  • Thornton JM, Edwards MS, Taylor WR, Barlow DJ. Location of “continuous” antigenic determinants in the protruding regions of proteins. EMBO J. 1986;5:409–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Timmerman P, Beld J, Puijk WC, Meloen RH. Rapid and quantitative cyclization of multiple peptide loops onto synthetic scaffolds for structural mimicry of protein surfaces. Chembiochem. 2005;6:821–4.

    Article  CAS  PubMed  Google Scholar 

  • Tropsha A, Kizer JS, Chaiken IM. Making sense from antisense: a review of experimental data and developing ideas on sense-antisense peptide recognition. J Mol Recognit. 1992;5:43–54.

    Article  CAS  PubMed  Google Scholar 

  • Underwood PA. Theoretical considerations of the ability of monoclonal antibodies to detect antigenic differences between closely related variants, with particular reference to heterospecific reactions. J Immunol Methods. 1985;85:295–307.

    Article  CAS  PubMed  Google Scholar 

  • Uversky VN, Oldfield CJ, Dunker AK. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit. 2005;18:343–84.

    Article  CAS  PubMed  Google Scholar 

  • Van Oss CJ. Hydrophobic, hydrophilic and other interactions in epitope-paratope binding. Mol Immunol. 1995;32:199–211.

    Article  PubMed  Google Scholar 

  • Van Regenmortel, Plant virus serology MHV. Adv Virus Res. 1966;12:207–71.

    Article  PubMed  Google Scholar 

  • Van Regenmortel MHV. Serology and immunochemistry of plant viruses. New-York: Academic; 1982. p. 268.

    Google Scholar 

  • Van Regenmortel MHV. The conformational specificity of viral epitopes. FEMS Microbiol Lett. 1992a;100:483–7.

    Article  PubMed  Google Scholar 

  • Van Regenmortel MHV. Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods. 1996;9:465–72.

    Article  PubMed  Google Scholar 

  • Van Regenmortel MHV. From absolute to exquisite specificity. Reflections on the fuzzy nature of species, specificity and antigenic sites. J Immunol Methods. 1998;216:37–48.

    Article  PubMed  Google Scholar 

  • Van Regenmortel MHV. Molecular design versus empirical discovery in peptide-based vaccines. Coming to terms with fuzzy recognition sites and ill-defined structure-function relationships in immunology. Vaccine. 1999b;18:216–21. https://doi.org/10.1016/S0264-410X(99)00192-9.

    Article  PubMed  Google Scholar 

  • Van Regenmortel MHV. Molecular dissection of protein antigens and the prediction of epitopes. In: Van Regenmortel MHV, Muller S, editors. Synthetic peptides as antigens. Amsterdam: Elsevier; 1999c. p. 281–317.

    Chapter  Google Scholar 

  • Van Regenmortel MHV. Antigenicity and immunogenicity of synthetic peptides. Biologicals. 2001a;29:209–13.

    Article  PubMed  CAS  Google Scholar 

  • Van Regenmortel MHV. Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines. J Mol Recognit. 2006;19:183–7.

    Article  PubMed  CAS  Google Scholar 

  • Van Regenmortel MHV. The rational design of biological complexity: a deceptive metaphor. Proteomics. 2007;7:965–75.

    Article  PubMed  CAS  Google Scholar 

  • Van Regenmortel MHV, Pellequer J-L. Predicting antigenic determinants in proteins: looking for unidimensional solutions to a three-dimensional problem? Pept Res. 1994;7:224–8.

    PubMed  Google Scholar 

  • Von Sengbusch P, Wittman HG. Serological and physicochemical properties of the wild strain and two mutants of tobacco mosaic virus with the same amino acid exchange in different positions of the protein chain. Biochem Biophys Res Commun. 1965;18:780–7.

    Article  Google Scholar 

  • Walter G. Production and use of antibodies against synthetic peptides. J Immunol Methods. 1986;88:149–61.

    Article  CAS  PubMed  Google Scholar 

  • Westhof E, Altschuh D, Moras D, Bloomer AC, Mondragon A, Klug A, Van Regenmortel MHV. Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature. 1984;311:123–6.

    Article  CAS  PubMed  Google Scholar 

  • Wilson IA, Stanfield RL. Antibody-antigen interactions: new structures and new conformational changes. Curr Opin Struct Biol. 1994;4:857–67.

    Article  CAS  PubMed  Google Scholar 

  • Zimmermann D, Van Regenmortel MHV. Spurious cross-reactions between plant viruses and monoclonal antibodies can be overcome by saturating ELISA plates with milk proteins. Arch Virol. 1989;106:15–22.

    Article  CAS  PubMed  Google Scholar 

  • Zolla-Pazner S. Identifying epitopes of HIV-1 that induce protective antibodies. Nat Rev Immunol. 2004;4:199–210.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zwick MB. The membrane-proximal external region of HIV-1 gp41: a vaccine target worth exploring. AIDS. 2005;19:1725–37.

    Article  PubMed  Google Scholar 

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Van Regenmortel, M.H.V. (2019). What Is a B Cell Epitope. In: HIV/AIDS: Immunochemistry, Reductionism and Vaccine Design. Springer, Cham. https://doi.org/10.1007/978-3-030-32459-9_1

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