Allergy is immune-related hypersensitivity of the organism to otherwise harmless substances. The World Allergy Organization emphasizes that allergic diseases should be recognized as a significant public health problem. Allergic reactions are triggered by allergens, mostly proteins, which cause an immediate hypersensitivity reaction mediated by IgE antibodies. A common phenomenon is cross-reactivity, in which an antibody formed against one antigen recognizes and reacts with another, structurally similar antigen. Proteins that share a relatively high similarity in primary amino acid sequence are identified as potentially cross-reactive. However, there are examples of proteins that, despite having little similarity in the primary sequence with the allergen, cross-react due to similarity in the three-dimensional structure. In this master's thesis, we want to demonstrate that the similarity between the three-dimensional structures of known allergens and cross-reactive food proteins is generally higher than the similarity of their primary structures. As a typical example of a known allergen, we used the Bet v 1 allergen from birch pollen. We first searched the literature for food proteins that had been experimentally proven to be cross-reactive with Bet v 1. Then, using the COMPASS bioinformatics tool, we compared the primary structures of three Bet v 1 isoforms with the entire database of allergenic proteins COMPARE and included only cross-reactive food proteins in further analysis. In the second step, we performed a comparison of three-dimensional structures of proteins from food with three Bet v 1 isoforms, for which we found experimentally determined structures. The comparison was carried out with the PDBeFold bioinformatics tool, which uses the method of secondary structural matching. We compared the similarity of proteins at the primary and tertiary levels and found that the investigated cross-reactive proteins share very different degrees of similarity in the amino acid sequence, while in all cases they exhibit high similarity in three-dimensional structures. Thus, the structural similarity of cross-reactive proteins from food with Bet v 1 is in most cases higher at the tertiary level than at the primary level.
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