Structural analysis of linear and conformational epitopes of allergens

Abstract

In many countries regulatory agencies have adopted safety guidelines, based on bioinformatics rules from the WHO/FAO and EFSA recommendations, to prevent potentially allergenic novel foods or agricultural products from reaching consumers. We created the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to combine data that had previously been available only as flat files on Web pages or in the literature. SDAP was designed to be user friendly, to be of maximum use to regulatory agencies, clinicians, as well as to scientists interested in assessing the potential allergenic risk of a protein. We developed methods, unique to SDAP, to compare the physicochemical properties of discrete areas of allergenic proteins to known IgE epitopes. We developed a new similarity measure, the property distance (PD) value that can be used to detect related segments in allergens with clinical observed cross-reactivity. We have now expanded this work to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to known IgE epitopes. In complementary work we show how sequence motifs characteristic of allergenic proteins in protein families can be used as fingerprints for allergenicity.

Fig. 1

Example of the information content for allergens in SDAP, illustrated here for the allergen Ole e 8. Links to software tools, other websites and information in other databases for this protein, can be direct accessed from this page.

Fig. 2

Implementation of the FAO/WHO allergenicity guidelines in the SDAP Website. A user supplied sequence can be pasted into the window, and the FASTA search run according to the user selected criteria.

Fig. 3

Evaluation of criterion 1 of the WHO/FAO rules: A protein is classified as an allergen if the sequence identity to an allergen is higher than a given threshold in a window of 80 aa residues. The fraction of positive controls (SDAP allergens) in blue and the fraction of negative controls (set of non-allergenic proteins) in red satisfying criterion 1 are given as a function of the threshold value. A cutoff value of 35–40% identities most allergens, but classifies about 6% of the control group as allergenic.

Fig. 4

PDB structures of allergens from three Pfam families: PF00112, Papain family cysteine protease: (a) Act c 1, 2ACT; (b) Car p 1, 1KHQ. PF01620, Ribonuclease (pollen allergen): (c) Phl p 5, 1L3P; (d) Phl p 6, 1NLX. PF02221, ML domain: (e) Der f 2, 1XWV; (f) Der p 2, 1KTJ.

Fig. 5

(A) Section of an alignment of the English walnut protein Jug r 1 with related allergens (from black walnut, castor bean, sesame, Brazil nut, and buckwheat) in the same Pfam (PF00190, Cupin). (B) PCPMer analysis of this section of the alignment. Single positions are colored to indicate a continuum between variability (red) and conservation (blue). PCP motifs are listed at increasing relative entropy values from 1.0 to 1.8.

Fig. 6

IgE epitopes mapped on the MPACK model of Par j 1: (a) ribbon plot and (b) solvent accessible surface.