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Chapter 11 : Structural Database of Allergenic Proteins (SDAP)
Authors:
Catherine H. Schein1,
Ovidiu Ivanciuc2,
Werner Braun3
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Affiliations:
1: Sealy Center for Structural Biology and Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch 301 University Blvd., Galveston TX 77555–0857;
2: Sealy Center for Structural Biology and Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch 301 University Blvd., Galveston TX 77555–0857;
3: Sealy Center for Structural Biology and Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch 301 University Blvd., Galveston TX 77555–0857
Content Type: Monograph
Publication Year:
2006
Category: Immunology; Applied and Industrial Microbiology
Book DOI:
10.1128/9781555815721
Chapter DOI:
10.1128/9781555815721.ch11
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Abstract:
The Structural Database of Allergenic Proteins (SDAP) brings together data from diverse sources on over 800 allergen sequences and their epitopes in a cross-referenced format. Special methods developed for SDAP, such as the property distance (PD) scale, automatically detect peptides in the ensemble of allergen sequences that have physicochemical properties similar to known immunoglobulin E (IgE) epitopes. Comparing the structure of food allergens with allergenic proteins from exposure to pollens, insect dust, or other aeroallergens can give valuable information about the sensitization process. Any novel protein introduced into a food crop should have a low potential to be an allergen. This chapter deals with database approaches to determine the allergenic potential of a test protein, based on similarity to known allergens. It outlines basic methodology to identify cross-reacting proteins in food sources and predict the potential allergenicity of novel proteins. The chapter concentrates on the SDAP, which has been specifically designed to allow combined analysis of the sequence, structure, and epitopes of allergens. It also shows how SDAP and the methods for sequence and peptide comparison incorporated therein can be used to predict cross-reactive allergens in foods and determine common properties of their IgE epitopes. The second half of the chapter demonstrates how SDAP has allowed one to rapidly collect data pertinent to very basic questions about allergens, such as whether enzymatic activity is related to allergenicity. The chapter provides an overview of the information and methods incorporated into the cross-referenced (MySQL-Linux) lists of data.
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
Figures
Structural Database of Allergenic Proteins (SDAP)
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Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig01
Figure 1.
Basic structure of the SDAP database. The data are contained in cross-referenced lists. The user can send a query by pushing buttons at the site or go to specific search pages and type in a question.
10.1128/9781555815721/f0261-01_thmb.gif
10.1128/9781555815721/f0261-01.gif
Figure 1.
Basic structure of the SDAP database. The data are contained in cross-referenced lists. The user can send a query by pushing buttons at the site or go to specific search pages and type in a question.
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig02
Untitled
10.1128/9781555815721/e0263-01_thmb.gif
10.1128/9781555815721/e0263-01.gif
Untitled
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig03
Untitled
10.1128/9781555815721/e0264-01_thmb.gif
10.1128/9781555815721/e0264-01.gif
Untitled
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig04
Figure 2.
Histogram of PD values obtained for the Ara h 3 IgE epitope VTVRGGLRILSPDRK (
Table 3
) for the lowest-scoring window for each of the SDAP allergens (A) and the scores of all possible sequence windows in the SDAP allergens (B).
10.1128/9781555815721/f0265-01_thmb.gif
10.1128/9781555815721/f0265-01.gif
Figure 2.
Histogram of PD values obtained for the Ara h 3 IgE epitope VTVRGGLRILSPDRK ( Table 3 ) for the lowest-scoring window for each of the SDAP allergens (A) and the scores of all possible sequence windows in the SDAP allergens (B).
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig05
Figure 3.
Model structure of the vicilin allergen Ara h 1 (residues 172 to 586) from peanut, showing the internal dimer axis (i.e., the monomer has two equivalent areas of structure that have different sequences). Two epitopes on opposite sides of the protein (symmetric IgE epitopes) with side chains are shown, and the first and last amino acids are labeled. The template for homology modeling was canavalin from jack bean (PDB file 2CAV_A; resolution, 2 Å), which is 47% identical (162 of 346) with this area of Ara h 1.
10.1128/9781555815721/f0267-01_thmb.gif
10.1128/9781555815721/f0267-01.gif
Figure 3.
Model structure of the vicilin allergen Ara h 1 (residues 172 to 586) from peanut, showing the internal dimer axis (i.e., the monomer has two equivalent areas of structure that have different sequences). Two epitopes on opposite sides of the protein (symmetric IgE epitopes) with side chains are shown, and the first and last amino acids are labeled. The template for homology modeling was canavalin from jack bean (PDB file 2CAV_A; resolution, 2 Å), which is 47% identical (162 of 346) with this area of Ara h 1.
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig06
Figure 4.
Isolated linear epitopes of Ara h 1 (
Burks et al., 1997
), shown as segments of the model shown in
Fig. 3
. The residues with significant (>30%) solvent exposure, according to GETAREA, are labeled; the surface-exposed residues known to play a role in reactivity of the epitope with IgE are underlined.
10.1128/9781555815721/f0268-01_thmb.gif
10.1128/9781555815721/f0268-01.gif
Figure 4.
Isolated linear epitopes of Ara h 1 ( Burks et al., 1997 ), shown as segments of the model shown in Fig. 3 . The residues with significant (>30%) solvent exposure, according to GETAREA, are labeled; the surface-exposed residues known to play a role in reactivity of the epitope with IgE are underlined.
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11fig07
Figure 5.
Use of structure, surface location, and sequence conservation as three ways to indicate potential epitopes of homologs of a protein where the IgE epitopes are known. The location of a known epitope of the cedar pollen allergen Jun a 3 is shown to be in a related position to PR5 allergenic proteins from three foods (Mal d 2 from apples, Pru av 2 from cherry, and Cap a 1 from bell pepper). The epitope (arrow), detected by mapping tryptic fragments of Jun a 3, is shown in black on all structures.
10.1128/9781555815721/f0276-01_thmb.gif
10.1128/9781555815721/f0276-01.gif
Figure 5.
Use of structure, surface location, and sequence conservation as three ways to indicate potential epitopes of homologs of a protein where the IgE epitopes are known. The location of a known epitope of the cedar pollen allergen Jun a 3 is shown to be in a related position to PR5 allergenic proteins from three foods (Mal d 2 from apples, Pru av 2 from cherry, and Cap a 1 from bell pepper). The epitope (arrow), detected by mapping tryptic fragments of Jun a 3, is shown in black on all structures.
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
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Tables
Structural Database of Allergenic Proteins (SDAP)
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Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl01
Table 1.
Web sites with information about allergens
Table 1.
Web sites with information about allergens
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl02
Table 2.
Output of an automatic FASTA search in SDAP starting from the file for allergen Act c 1 of kiwifruit (Actinidia chinensis)
a
Table 2.
Output of an automatic FASTA search in SDAP starting from the file for allergen Act c 1 of kiwifruit (Actinidia chinensis) a
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl03
Table 3.
Sequences most closely related to epitope 3 of Ara h 3 from peanut by PD search
a
Table 3.
Sequences most closely related to epitope 3 of Ara h 3 from peanut by PD search a
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl04
Table 4.
Results of two automatic FASTA searches in SDAP
a
Table 4.
Results of two automatic FASTA searches in SDAP a
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl05
Table 5.
Allergenic molecules from similar enzymatic classes occur in many different sources
Table 5.
Allergenic molecules from similar enzymatic classes occur in many different sources
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11
/content/10.1128/9781555815721.ch11.ch11tbl06
Table 6.
SDAP food allergen classification according to protein type (from the IUIS database)
Table 6.
SDAP food allergen classification according to protein type (from the IUIS database)
Citation:
Schein C, Ivanciuc O, Braun W.
2006.
Structural Database of Allergenic Proteins (SDAP),
p 257-283.
In
Maleki S, Burks A, Helm R (ed),
Food Allergy.
ASM Press, Washington, DC.
doi: 10.1128/9781555815721.ch11