Evaluation of available IgE-binding epitope data and its utility in bioinformatics (1)
Proteins that share a high degree of similarity throughout their entire length are often homologous. Homologous proteins share secondary structure and common 3-D folds. Homologous proteins are more likely to share allergenic crossreactive conformational and linear epitopes than unrelated proteins; however, the degree of similarity (amino acid/structural) between homologs varies widely. A window size of eight amino acids was recommended. Since this original recommendation, many IgE- binding epitopes have been identified for a number of foods and aeroallergens.
The requirement that IgE be crosslinked on effector cells in order to release the mediators of allergic symptoms dictates that there should be at least two high affinity IgE-binding epitopes on a single allergen. While conformational IgE-binding epitopes are prevalent and important to the aetiology of aeroallergen-mediated allergic reactions, in some cases linear epitopes are important to food allergens, mainly because the immune system will encounter them only after they have been partially denatured and digested by the human GI tract. The tertiary structure of Bet v 1 contains three surface patches that have conserved-amino acid sequences and structures with proteins from a variety of foods including cherry, apple, hazelnut, peach, carrot, celery, and soya.
Advances in peptide chemistry allowed for the cost-effective synthesis of overlapping peptides that represent the entire allergen amino acid sequence. Most peptide synthesis technologies utilizing Fmoc chemistry recommend production of peptides no longer than 15 amino acids. This is a direct consequence of the fact that each coupling reaction that adds an additional amino acid is not 100% efficient. Even coupling reactions that occur at 97% efficiency will result in some nonsense peptides as the length of the chain is increased. The number of nonsense peptides begins to become significant after 15 coupling reactions. Conformational IgE-binding epitopes on the house dust mite-allergen Der p 2 were first demonstrated by disrupting disulfide bonds known to stabilize the tertiary structure of the allergen. By pooling patient sera, IgEs in low concentrations or that are specific to a single patient may be diluted to such an extent that they will not be detected. This could lead to an under representation of the IgE-binding peptides of a specific allergen. Conversely, using pooled patient sera may lead to incorrect identification of certain epitopes as being overrepresented in the population. whatever approach is developed, it should be remembered that bioinformatics is but one tool in the array of analytical methods for determining potential allergenicity, by itself it does not imply a novel protein to be an allergen.
