Complexity: How Unique is the Epitope?

Exhibit 1. An immunological complexity profile as defined by EpiQuest-C. Shown is a simple case of reviewing the complexity of different areas of the protein in order to exclude from future areas for choosing the antigen (this may be an area of the molecule, expressed as a fusion protein, or a peptide selected as an epitope). The areas of low complexity may elicit an antibody, but this antibody will be cross-reactive with many other proteins.The area that definitely should be excluded is framed on the graph.

Immunogenicity (B-epitopes) and Complexity (below) profiles for NS1 protein of Dengue virus 2. Note the difference in complexity of the epitopes, and see Exhibit 2 for more detail/

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When one selects an epitope, whether B or T, or plans using some area of protein to induce an immune response (i.e. as antigen for immunization, or part of a recombinant vaccine), it is usually highly desirable, that the response is specific, that is, directed against the chosen molecule (of the family of the molecules), but not against other proteins. One of the protein domain characteristics that allows to evaluate this is a domain complexity: the higher it is, the more likely this region will be unique for a particular molecule (domain of the molecule). Our algorithm is designed to address primarily the immunological complexity, that is likely that immune response to a particular peptide will not recognize other proteins.

Exhibit 2. Complexity and uniqueness of an epitope. There are 3 immunodominant epitopes in the sequence of NS1 protein of Dengue virus; the analysis is performed for a particular isolate from South America. Imagine that one would like to select epitopes for diagnostic assay that analyses the presence of antibodies to immunodomiant epitopes of the virus. All 3 epitopes, in case of infection, elicit the response, but we would like to know how specific would be an assay, based on a particular epitope.

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