Structure of allergens and structure based epitope predictions

Abstract

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

What makes an allergen?

“…Therefore, allergens have been clustered according to their common structural, biochemical and functional features to less than 2% of all known protein families [7][8][9][10]. It has been proposed that the sensitization capacity of allergens is dedicated to specific molecular features.…”

“…There is a general consensus that the molecular basis of allergenicity probably is not defined on the epitope level. Common rules for the main allergen-IgE binding sites cannot be deduced because of the diverse physicochemical properties of the proteins [8]. In line with this, the IgE-epitope repertoire is too large to make specific IgE epitopes, a realistic target for allergenicity prediction [11].…”

Recombinant Allergens in Structural Biology, Diagnosis, and Immunotherapy

“…SDAP also provides 458 models for allergen and isoallergen structures. In their 2014 paper, Dall'Antonia et al [19 ]presented 103 structures of allergens from the PDB. Structural information on allergens is helpful in reconstructing the evolutionary history of protein architectures where amino acid sequence comparisons fail to reveal sequence similarities.…”

The Occurrence of Sequences Identical with Epitopes from the Allergen Pen a 1.0102 Among Food and Non-Food Proteins

“…Increasing the length of common fragments suggests increasing the likelihood of cross-reactivity between proteins. Additional restriction is recommended [Dall'Antonia et al, 2014]. The secondary structure of peptide should mimic the structure of the corresponding fragment of entire protein.…”