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.
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.
Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants. Nature. 1986;322:747–8.
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.
Berzofsky JA. Intrinsic and extrinsic factors in protein antigenic structure. Science. 1985;229:932–40.
Berzofsky JA, Schechter AN. The concepts of crossreactivity and specificity in immunology. Mol Immunol. 1981;18:751–63.
Blalok J. Complementarity of peptides specified by “sense” and “antisense” strands of DNA. Trends Biotechnol. 1990;8:140–4.
Blythe MJ, Flower DR. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci. 2005;14:246–8.
Boeyé A, Rombaut B. The proteins of poliovirus. Prog Med Virol. 1992;62:139–66.
Boquet D, Déry O, Forbert Y, Grassi J, Couraud JY. Is hydropathic complementarity involved in antigen-antibody binding? Mol Immunol. 1995;32:303–8.
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.
Braden BC, Poljak RJ. Structural features of the reactions between antibodies and protein antigens. FASEB J. 1995;9:9–16.
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.
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.
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.
DeLano WL. Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol. 2002;12:14–20.
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.
Dougherty W, Willis L, Johnston RE. Topographic analysis of tobacco etch virus capsid protein epitopes. Virology. 1985;144:66–72.
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.
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.
Frison EA, Stace-Smith R. Cross-reacting and heterospecific monoclonal antibodies produced against arabis mosaic nepovirus. J Gen Virol. 1992;73:2525–30.
Getzoff ED, Tainer JA, Lerner RA, Geysen HM. The chemistry and mechanism of antibody binding to protein antigens. Adv Immunol. 1988;43:1–98.
Geysen HM, Rodda SJ, Mason TJ. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol Immunol. 1986;23:709–15.
Ghosh G, Cambell AM. Multispecific monoclonal antibodies. Immunol Today. 1986;7:217–22.
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.
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.
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.
Hans D, Young PR, Fairlie DP. Current status of short synthetic peptides as vaccines. Med Chem. 2006;2:627–46.
Harper M, Lema F, Boulot G, Poljak RJ. Antigen specificity and cross-reactivity of monoclonal anti-lysozyme antibodies. Mol Immunol. 1987;24:97–108.
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.
Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981;78:3824–8.
James LC, Roversi P, Tawfik DS. Antibody multi-specificity mediated by conformational diversity. Science. 2003;299:1362–7.
Landsteiner K. The specificity of serological reactions. New York: Dover Publications; 1962. p. 330.
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.
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.
Laver WG, Air GM, Webster RG, Smith-Gill SJ. Epitopes on protein antigens: misconceptions and realities. Cell. 1990;61:553–6.
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.
Lerner RA. Antibodies of predetermined specificity in biology and medicine. Adv Immunol. 1984;36:1–44.
Loor F. On the existence of heterospecific antibodies in sera from rabbits immunized against tobacco mosaic virus determinants. Immunology. 1971;21:557–64.
Mäkelä O. Single lymph node cells producing heteroclitic bacteriophage antibody. J Immunol. 1965;95:378–86.
Mazumdar PH. Species and specificity. Cambridge: Cambridge University Press; 1995.
Medawar PB, Medawar JS. The life science. London: Granada Publishing; 1978.
Meloen RH, Puyk WC, Sloostra JW. Mimotopes: realization of an unlikely concept. J Mol Recognit. 2000;13:352–9.
Moodie SL, Mitchell JBO, Thornton JM. Protein recognition of adenylate: an example of a fuzzy recognition template. J Mol Biol. 1996;263:486–500.
Mullen LM, Nair SP, Ward JM, Rycroft AN, Henderson B. Phage display in the study of infectious diseases. Trends Microbiol. 2006;14:141–7.
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.
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.
Novotny J, Bruccoleri RE, Carlson WD, Handschumacher M, Haber E. Antigenicity of myohemerythrin. Science. 1987;238:1584–6.
Odorico M, Pellequer JL. BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit. 2003;16:20–2.
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.
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.
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.
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.
Roberts VA, Getzoff ED, Tainer JA. In: Van Regenmortel MHV, editor. Structure of antigens, vol. 3. Boca Raton, FL: CRC; 1993. p. 31–53.
Rosen R. Life itself. New York: Columbia University Press; 1991.
Schroer JA, Bender T, Feldmann T, Kim KJ. Mapping epitopes on the insulin molecule using monoclonal antibodies. Eur J Immunol. 1983;13:693–700.
Shepard JF, Secor GA, Purcifull DE. Immunochemical cross-reactivity between the dissociated capsid proteins of PVY group plant viruses. Virology. 1974;58:464–75.
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.
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.
Thornton JM, Sibanda BL. Amino and carboxy-terminal regions in globular proteins. J Mol Biol. 1983;167:443–60.
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.
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.
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.
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.
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.
Van Oss CJ. Hydrophobic, hydrophilic and other interactions in epitope-paratope binding. Mol Immunol. 1995;32:199–211.
Van Regenmortel, Plant virus serology MHV. Adv Virus Res. 1966;12:207–71.
Van Regenmortel MHV. Serology and immunochemistry of plant viruses. New-York: Academic; 1982. p. 268.
Van Regenmortel MHV. The conformational specificity of viral epitopes. FEMS Microbiol Lett. 1992a;100:483–7.
Van Regenmortel MHV. Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods. 1996;9:465–72.
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.
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.
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.
Van Regenmortel MHV. Antigenicity and immunogenicity of synthetic peptides. Biologicals. 2001a;29:209–13.
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.
Van Regenmortel MHV. The rational design of biological complexity: a deceptive metaphor. Proteomics. 2007;7:965–75.
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.
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.
Walter G. Production and use of antibodies against synthetic peptides. J Immunol Methods. 1986;88:149–61.
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.
Wilson IA, Stanfield RL. Antibody-antigen interactions: new structures and new conformational changes. Curr Opin Struct Biol. 1994;4:857–67.
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.
Zolla-Pazner S. Identifying epitopes of HIV-1 that induce protective antibodies. Nat Rev Immunol. 2004;4:199–210.
Zwick MB. The membrane-proximal external region of HIV-1 gp41: a vaccine target worth exploring. AIDS. 2005;19:1725–37.
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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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