Grantee Research Project Results

2012 Progress Report: Prediction of Allergenicity by Linear and Conformational Epitopes

EPA Grant Number: R834823
Title: Prediction of Allergenicity by Linear and Conformational Epitopes
Investigators: Braun, Werner , Schein, Catherine H. , Ivanciuc, Ovidiu I
Institution: The University of Texas Medical Branch - Galveston
EPA Project Officer: Aja, Hayley
Project Period: September 15, 2010 through September 30, 2014
Project Period Covered by this Report: September 15, 2011 through September 14,2012
Project Amount: $425,000
RFA: Approaches to Assessing Potential Food Allergy from Genetically Engineered Plants (2009) RFA Text | Recipients Lists
Research Category: Human Health

Objective:

Recombinant genetic tools are increasingly used by the biotechnology industry to introduce novel proteins into crops for protection against pesticides, as plant-incorporated protectants (PIP) or to increase the nutritional value. Appropriate safeguards must be in place to insure that this will not introduce new proteins that are potentially allergenic in the plants. The goal of this project is to provide quantitative bioinformatics criteria to determine the potential allergenicity of transgenic proteins in food products and PIPs from allergen specific motifs.

Progress Summary:

We maintained and expanded our Structural Data Base of Allergenic Proteins (SDAP) as a user friendly web server to the allergenic community, regularly updated the data base for new detected allergens, and introduced new bioinformatics tools on the web site. SDAP is used heavily by the allergenic community with approximately 1500 unique users who submit more than 100,000 requests each month. The usefulness of 3D models in SDAP was assessed by an objective comparison of 3D models in SDAP to experimental structures recently released in the Protein Data Bank. The comparison of the 3D models in SDAP to their experimental structures, determined after our modeling efforts, showed the high quality for backbone fold and IgE mapping if the identity between the allergen sequence and the sequence of the template structure is higher than 25%. We also extended the generation of allergen specific motifs to 17 protein families, designed peptides that correspond to the allergen specific motifs of peanut allergens, and tested the IgE binding affinity of those peptides with serum from patients allergic to peanuts.

Our studies are important to provide a solid scientific foundation in the general discussion on the potential risk of genetically modified (GM) foods. The statistical results and the novel bioinformatics tools can help EPA formulate more specific bioinformatics guidelines for companies that would like to bring new recombinant crops to the market place. Because food allergies can result in fatal reactions, the allergenic potential of genetically engineered food products needs to be carefully assessed prior to their entry into the market. There is a vital need for faster and reliable methods to evaluate the potential allergenicity of proteins that have not previously been part of the food supply. Our novel approaches can reduce some uncertainty for those crops that may be potentially allergenic for some sensitive subpopulation.

Future Activities:

(1) We will continue updating the SDAP data base with novel allergens and 3D models.

(2) We will continue testing the validity of our motif search method with experimental data, and publish the results.

(3) We will apply our 3D search methods for new allergens with known conformational epitopes, and publish the results.

Journal Articles on this Report : 4 Displayed | Download in RIS Format

Publications Views
Other project views:	All 19 publications	6 publications in selected types	All 6 journal articles

Publications
Type	Citation	Project	Document Sources
Journal Article	Nesbit JB, Hurlburt BK, Schein CH, Cheng H, Wei H, Maleki SJ. Ara h 1 structure is retained after roasting and is important for enhanced binding to IgE. Molecular Nutrition and Food Research 2012;56(11):1739-1747.	R834823 (2012) R834823 (2013) R834823 (Final) R834066 (Final)	Abstract from PubMed Abstract: Wiley-Abstract Exit
Journal Article	Power TD, Ivanciuc O, Schein CH, Braun W. Assessment of 3D models for allergen research. Proteins 2013;81(4):545-554.	R834823 (2012) R834823 (2013) R834823 (Final)	Full-text from PubMed Abstract from PubMed Associated PubMed link Abstract: Wiley Online-Abstract Exit
Journal Article	Schein CH, Bowen DM, Lewis JA, Choi K, Paul A, van der Heden van Noort GJ, Lu W, Filippov DV. Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. BMC Bioinformatics 2012;13(Suppl 13):S9.	R834823 (2012) R834823 (2013) R834823 (Final) R834066 (Final)	Full-text from PubMed Abstract from PubMed Associated PubMed link Full-text: BioMed Central-Full Text HTML Exit Other: BioMed Central-Full Text PDF Exit
Journal Article	Tiwari R, Negi SS, Braun B, Braun W, Pomes A, Chapman MD, Goldblum RM, Midoro-Horiuti T. Validation of a phage display and computational algorithm by mapping a conformational epitope of Bla g 2. International Archives of Allergy and Immunology 2012;157(4):323-330.	R834823 (2012) R834823 (2013) R834823 (Final) R833137 (Final)	Full-text from PubMed Abstract from PubMed Associated PubMed link Full-text: Karger-Full Text HTML Exit Other: Karger-Full Text PDF Exit

Supplemental Keywords:

relational database, large scale 3D modeling of proteins, WHO/EFSA recommendations for risk assessment of proteins

Relevant Websites:

http://fermi.utmb.edu/SDAP/ Exit (Home page of the Structural Database of Allergenic Proteins [SDAP])

Progress and Final Reports:

Original Abstract

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.