Epitope Mapping

Abstract

Antibodies are an effective line of defense in preventing infectious diseases. Highly potent neutralizing antibodies can intercept a virus before it attaches to its target cell and, thus, inactivate it. This ability is based on the antibodies' specific recognition of epitopes, the sites of the antigen to which antibodies bind. Thus, understanding the antibody/epitope interaction provides a basis for the rational design of preventive vaccines. It is assumed that immunization with the precise epitope, corresponding to an effective neutralizing antibody, would elicit the generation of similarly potent antibodies in the vaccinee. Such a vaccine would be a 'B-cell epitope-based vaccine', the implementation of which requires the ability to backtrack from a desired antibody to its corresponding epitope. In this article we discuss a range of methods that enable epitope discovery based on a specific antibody. Such a reversed immunological approach is the first step in the rational design of an epitope-based vaccine. Undoubtedly, the gold standard for epitope definition is x-ray analyses of crystals of antigen:antibody complexes. This method provides atomic resolution of the epitope; however, it is not readily applicable to many antigens and antibodies, and requires a very high degree of sophistication and expertise. Most other methods rely on the ability to monitor the binding of the antibody to antigen fragments or mutated variations. In mutagenesis of the antigen, loss of binding due to point modification of an amino acid residue is often considered an indication of an epitope component. In addition, computational combinatorial methods for epitope mapping are also useful. These methods rely on the ability of the antibody of interest to affinity isolate specific short peptides from combinatorial phage display peptide libraries. The peptides are then regarded as leads for the definition of the epitope corresponding to the antibody used to screen the peptide library. For epitope mapping, computational algorithms have been developed, such as Mapitope, which has recently been found to be effective in mapping conformational discontinuous epitopes. The pros and cons of various approaches towards epitope mapping are also discussed.

Cloning, Expression and Patient IgE Reactivity of Recombinant Pru du 6, an 11S Globulin from Almond

“…B cell epitopes are typically categorized as being either sequential (linear, continuous) or conformational (discontinuous) [35,58,59,60,61]. Recently, there has been considerable debate over the clinical importance and relevance of the two epitope forms, and several studies have shown conflicting results.…”

Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies

“…Simpler epitopebased vaccines, accentuating neutralizing epitopes, may prove to be an efficient alternative for vaccine design. A better understanding of the dynamics of HIV-1 envelope interactions with its receptors, and in particular those of monomeric gp120, might contribute to the ultimate task of generating such an epitope-based vaccine for AIDS (87). …”

Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing

“…Methods for epitope mapping include X-ray crystallography, NMR spectroscopy, and a variety of antigen manipulation/antibody binding analysis techniques [ Gershoni et al, 2007 ]. The method described here provides a means to use NGS datasets with currently available prediction software to identify candidate epitope sites, reducing the number of target regions for fine mapping via costly and time-consuming mutagenesis methods such as alanine substitution [ Kronqvist et al, 2010 ].…”

“…Use of NGS with prediction methods can help reduce development time for diagnostics, therapeutics and vaccines that require detailed knowledge of antigenic epitopes [Gershoni et al , 2007; Rojas et al , 2014]. For the described protocol, the most time-consuming activity is library generation.…”