Insights of Amino Acid Usage Patterns Among Allergenic and Non-allergenic Proteins

Abstract

Food allergies are a major public health problem that, at times, are seen to cause immunological cross-reactivity involving IgE and different families of allergens. This study investigates the amino acid usage patterns within four primary allergen families: Cupin, Bet v 1, Cap, and Tropomyosin. The aims of this work were to compare the structural and compositional features of allergenic and non-allergenic proteins based on several computational analysis, which included correspondence analysis using RAAU data, solubility analysis of the proteins, and well as Multiple Sequence Alignment. Sequences of amino acids for allergens and non-allergens were obtained from public databases, and the sequences were compared. For the purpose of clustering the RAAU data, correspondence analysis (CoAn) was performed to find out the cluster pattern. When allergens were biplot against non-allergens within the allergen families from the CoAn biplots, it was evident that the two groups had significant qualitative variations in their amino acid signatures. Notably, Cupin allergens had differences in the distribution of the few amino acids viz., methionine, proline, and histidine, unlike the other groups, which were mostly characterized by the distribution of glutamine, glutamic acid, and tryptophan. Bet v 1 homolog allergens had a higher glycine content, affecting protein folding and possible allergenicity. However, tropomyosin allergens did not have a specific amino acid relationship that one could deduce, which needed more study. The study also determined conserved motifs in each of the allergen families by multiple sequence alignments and comparisons that were at least 70% identical. It is assumed that these conserved motifs play a role in protein stability, allergenicity, and patterns of interactions with the immune system. This knowledge about conserved sequences can be valuable for the development of allergen-specific treatments and tests. Solubility was determined by the principles of physicochemical properties using the SoluProt 1.0 tool. According to the assessment of the structural characteristics, the Cupin, CAP, and tropomyosin families of allergens displayed relatively low insolubility compared to non-allergenic proteins, while Bet v 1 allergens were relatively soluble. Similar differences may be postulated to affect the stability and interaction of these proteins with the immune system and thus their allergenic effects.