Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes

Abstract

Similarities in sequences and 3D structures of allergenic proteins provide vital clues to identify clinically relevant immunoglobulin E (IgE) cross-reactivities. However, experimental 3D structures are available in the Protein Data Bank for only 5% (45/829) of all allergens catalogued in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP). Here, an automated procedure was used to prepare 3D-models of all allergens where there was no experimentally determined 3D structure or high identity (95%) to another protein of known 3D structure. After a final selection by quality criteria, 433 reliable 3D models were retained and are available from our SDAP Website. The new 3D models extensively enhance our knowledge of allergen structures. As an example of their use, experimentally derived "continuous IgE epitopes" were mapped on 3 experimentally determined structures and 13 of our 3D-models of allergenic proteins. Large portions of these continuous sequences are not entirely on the surface and therefore cannot interact with IgE or other proteins. Only the surface exposed residues are constituents of "conformational IgE epitopes" which are not in all cases continuous in sequence. The surface exposed parts of the experimental determined continuous IgE epitopes showed a distinct statistical distribution as compared to their presence in typical protein-protein interfaces. The amino acids Ala, Ser, Asn, Gly and particularly Lys have a high propensity to occur in IgE binding sites. The 3D-models will facilitate further analysis of the common properties of IgE binding sites of allergenic proteins.

Figure 1

Correlation plot of sequence identity and RMSD values between the 3D-models and their templates in the aligned regions.

Figure 2

Most of the 3D-models have >98% of their residues in allowed areas of the Ramachandran Plots.

Figure 3

Distribution of the PROCHECK overall g-factor of the 3D-models and their corresponding templates.

Figure 4

Linear epitopes map to a hydrophilic, lysine rich face of the 3D-model of the weed pollen allergen Par j 1. Charged residues on the surface of linear epitopes are labeled. a) surface electrostatic potential, b) ribbon plot showing the surface exposed side chains of the linear epitopes, colored to indicate the different epitopes; c–f: rotations around the y-axis, starting from the orientation of panel a, showing the epitopes colored coded as in b). This face is positively charged while the back side is predominantly negative.

Figure 5

Linear epitopes of the allergens a) Ara h 1 from peanut and b) Asp f 13 from a fungus are only partially surface exposed. The surface is transparent and the different epitopes are demarcated by different colors.

Figure 6

The propensities of the amino acids, relative to their overall occurrence in the protein sequence, to occur on the surfaces of proteins (a) or in the epitope or interface residues (b), The propensities for occurrence in IgE binding sites are based on the surface exposed residues of linear IgE epitopes determined for 16 allergens (3 experimental structures, 13 3D-models). The propensities for occurrence in the interface are based on a previous study of 72 protein complexes (Negi and Braun, 2007).