Epitope Mapping: B‐Cell Epitopes


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.


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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.

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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.

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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]