Bioinformatic Screening and Detection of relevant Cross-Reactive IgE-binding Epitopes

Allergen cross-reactivity is based on shared IgE-binding which is due to shared sequence and higher level structure (charge and shape). Protein allergens can be uniquely related by cross-reactivity and specific IgE binding epitopes can be important in predicting cross-reactivity potential. Refining the measures of sequence similarity may be used to establish criteria that identify potential epitope homology among groups of allergens. Selected allergens were examined using IgE binding epitope sequences and these were used to determine how the FASTA algorithm could be used to identify a threshold of similarity. The allergens peanut Ara h 1 and Ara h 2, shrimp tropomyosin Pen a 1, and Birch tree pollen allergen, Bet v 1 were sources of known epitopes. Each epitope or set of epitopes was inserted into random amino acid sequence to create hypothetical proteins used as queries to an allergen database. A statistical measure of sequence similarity (E-value) was used to identify a threshold. Hypothetical proteins were examined for alignments with allergens and each was noted for the ability to match the epitope’s source allergen as well as match any cross-reactive or other homologous allergens. A minimum FASTA E-value range was identified that could identify the presence of homologous allergens and which could be used to screen novel proteins for cross-reactivity potential.