Epitope Mapping: B‐Cell Epitopes

Abstract

Antigen–antibody interaction is a key event in humoral immune response to invading pathogen. All of the macromolecular components of living organism (proteins, carbohydrates, lipids and nucleic acids) are potential antigens. A specific antibody recognises antigen at discrete regions known as antigenic determinants or B‐cell epitopes. Most of the antigen surface may become part of epitopes after recognition with specific antibodies; however, the exact selection mechanism of why certain regions become B‐cell epitopes is not fully understood. The epitope mapping is the process of identification and characterisation of the antibody‐binding site on the antigen, although the term is also applied more broadly to receptor–ligand interactions unrelated to the immune system. With an ever‐increasing number of available pathogen genomes, mapping of epitopes becomes the central issue of vaccine development. Precise identification of epitope is crucial for understanding the molecular basis of immunity and autoimmunity and allows to replace an antigen in the immunisation, antibody production and serodiagnosis.

Key Concepts

  • Virtually any surface‐exposed residue of antigen may become part of epitope after interactions with the antibody. The exact selection mechanism governing the antibody recognition of the corresponding epitope is not known.
  • The experimental methods developed to identify the epitopes depend on the unique features of the reaction between an antigen and its complementary antibody.
  • Structural methods interpret the protein structure comprising residues in direct contact with an antibody.
  • Functional methods identify and characterise residues important for binding within structurally defined epitope and are based on detection of binding of antibody to antigen fragments.
  • Identification of B‐cell epitopes is extensively employed in the development of diagnostic tests, therapeutics and vaccines.
  • The epitope‐based subunit vaccines became a promising alternative to traditional vaccines; however, low immunogenicity and low affinity of raised antibodies present major drawbacks of these types of vaccines.

Keywords: epitope; antigen; antibody; immunoassay; site‐directed mutagenesis; phage display; mass spectrometry

Figure 1. Alanine scanning library.
Figure 2. Synthetic overlapping fragments.
Figure 3. Biopanning procedure involves the following: 1. The immobilised antibodies are presented to the phage‐displayed library allowing the binding; this step is referred as panning. 2. After incubation, unbound and nonspecific phages are washed away. 3. The specific phages containing epitopes can be released by elution. 4. The eluted phages are used for E. coli infection in order to amplify phage clones or to isolate the individual clone. 5. The sequence of DNA insert is identified, and the peptide sequence of epitope is deduced.
close

References

Abbott WM, Damschroder MM and Lowe DC (2014) Current approaches to fine mapping of antigen‐antibody interactions. Immunology 142 (4): 526–535.

Atassi MZ and Smith JA (1978) A proposal for the nomenclature of antigenic sites in peptides and proteins. Immunochemistry 15 (8): 609–610.

Barlow DJ, Edwards MS and Thornton JM (1986) Continuous and discontinuous protein antigenic determinants. Nature 322 (6081): 747–748.

Brown MC, Joaquim TR, Chambers R, et al. (2011) Impact of immunization technology and assay application on antibody performance – a systematic comparative evaluation. PLoS One 6 (12): e28718.

Coales SJ, Tuske SJ, Tomasso JC and Hamuro Y (2009) Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on‐line proteolysis, liquid chromatography and mass spectrometry. Rapid Communications in Mass Spectrometry 23 (5): 639–647.

Davidson E and Doranz BJ (2014) A high‐throughput shotgun mutagenesis approach to mapping B‐cell antibody epitopes. Immunology 143 (1): 13–20.

Dreier B and Pluckthun A (2011) Ribosome display: a technology for selecting and evolving proteins from large libraries. Methods in Molecular Biology 687: 283–306.

El‐Kased RF, Koy C, Lorenz P, et al. (2011) A novel mass spectrometric epitope mapping approach without immobilization of the antibody. Journal of Proteomics & Bioinformatics 4: 001–009.

Fiorucci S and Zacharias M (2014) Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces. Methods in Molecular Biology 1184: 365–374.

Gershoni JM, Roitburd‐Berman A, Siman‐Tov DD, et al. (2007) Epitope mapping: the first step in developing epitope‐based vaccines. BioDrugs 21 (3): 145–156.

Hager‐Braun C and Tomer KB (2005) Determination of protein‐derived epitopes by mass spectrometry. Expert Review of Proteomics 2 (5): 745–756.

Huang J, Gutteridge A, Honda W and Kanehisa M (2006) MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 7: 451.

Infante YC, Pupo A and Rojas G (2014) A combinatorial mutagenesis approach for functional epitope mapping on phage‐displayed target antigen: application to antibodies against epidermal growth factor. MAbs 6 (3): 637–648.

Krawczyk K, Liu X, Baker T, et al. (2014) Improving B‐cell epitope prediction and its application to global antibody‐antigen docking. Bioinformatics 30 (16): 2288–2294.

Lo Conte L, Chothia C and Janin J (1999) The atomic structure of protein‐protein recognition sites. Journal of Molecular Biology 285 (5): 2177–2198.

Lucic V, Rigort A and Baumeister W (2013) Cryo‐electron tomography: The challenge of doing structural biology in situ. Journal of Cell Biology 202 (3): 407–419.

Mayrose I, Penn O, Erez E, et al. (2007) Pepitope: epitope mapping from affinity‐selected peptides. Bioinformatics 23 (23): 3244–3246.

Mazzoni MR, Porchia F and Hamm HE (2009) Proteolytic fragmentation for epitope mapping. Methods in Molecular Biology 524: 77–86.

Morris GE (2005) Epitope mapping. Methods in Molecular Biology 295: 255–268.

Peng HP, Lee KH, Jian JW and Yang AS (2014) Origins of specificity and affinity in antibody‐protein interactions. Proceedings of the National Academy of Sciences of the United States of America 111 (26): E2656–E2665.

Pereboeva LA, Pereboev AV, Wang LF and Morris GE (2000) Hepatitis C epitopes from phage‐displayed cDNA libraries and improved diagnosis with a chimeric antigen. Journal of Medical Virology 60 (2): 144–151.

Rubinstein ND, Mayrose I, Halperin D, et al. (2008) Computational characterization of B‐cell epitopes. Molecular Immunology 45 (12): 3477–3489.

Safsten P (2009) Epitope mapping by surface plasmon resonance. Methods in Molecular Biology 524: 67–76.

Santona A, Carta F, Fraghi P and Turrini F (2002) Mapping antigenic sites of an immunodominant surface lipoprotein of Mycoplasma agalactiae, AvgC, with the use of synthetic peptides. Infection and Immunity 70 (1): 171–176.

Wagstaff JL, Taylor SL and Howard MJ (2013) Recent developments and applications of saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy. Molecular bioSystems 9 (4): 571–577.

Wilson DS, Keefe AD and Szostak JW (2001) The use of mRNA display to select high‐affinity protein‐binding peptides. Proceedings of the National Academy of Sciences of the United States of America 98 (7): 3750–3755.

Zander H, Reineke U, Schneider‐Mergener J and Skerra A (2007) Epitope mapping of the neuronal growth inhibitor Nogo‐A for the Nogo receptor and the cognate monoclonal antibody IN‐1 by means of the SPOT technique. Journal of Molecular Recognition 20 (3): 185–196.

Further Reading

Ahmad TA, Eweida AE and Sheweita SA (2016) B‐cell epitope mapping for the design of vaccines and effective diagnostics. Trials in Vaccinology 5: 71–83.

Carter JM and Loomis‐Price L (2004) B cell epitope mapping using synthetic peptides. Current Protocols in Immunology 60: 9.4.1–9.4.23.

Galan A, Comor L, Horvatic A, et al. (2016) Library‐based display technologies: where do we stand? Molecular Biosystems 12 (8): 2342–2358.

Obungu VH, Gelfanova V and Huang L (2013) Epitope mapping of antibodies by mass spectroscopy: a case study. Methods in Molecular Biology 988: 291–302.

Van Regenmortel MH (2009) What is a B‐cell epitope? In: Schutkowski M and Reineke U (eds) Epitope Mapping Protocols. Methods in Molecular Biology (Methods and Protocols), vol. 524. New York, USA: Humana Press.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Borszekova Pulzova, Lucia(May 2018) Epitope Mapping: B‐Cell Epitopes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002624.pub3]