Value of eight-amino-acid matches in predicting the allergenicity status of proteins: An empirical bioinformatic investigation

Clinical and Molecular Allergy

Volumn 7, Issue , 2009, Pages

  Herman, Rod A ^a   Song, Ping ^a   ThirumalaiswamySekhar, Arvind ^a  

^a DOW AGROSCIENCES LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ALLERGENICITY; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; BIOINFORMATICS; CONTROLLED STUDY; CROSS REACTION; DATA BASE; FOOD ALLERGY; NONHUMAN; PREDICTION; SENSITIZATION; SEQUENCE ALIGNMENT;

EID: 71149115883     PISSN: None     EISSN: 14767961     Source Type: Journal    
DOI: 10.1186/1476-7961-7-9     Document Type: Article

References (32)

1. Codex Alimentarius Commission Alinorm 03/34: Joint FAO/WHO Food Standard Programme. Codex Alimentarius Commission, Twenty-Fifth Session, 30 July 2003, Rome, Italy. Appendix III: Guideline for Conduct of Food Safety Assessment of Foods Derived from Recombinant-DNA Plants; Appendix IV: Annex on Assessment of Possible Allergenicity. 2003, 47-60. Geneva: Codex Alimentarius Commission.
2. Ladics GS. Current Codex guidelines for assessment of potential protein allergenicity. Food Chem Toxicol 2008, 46:S20-S23. 10.1016/j.fct.2008.07.021, 18708115.
3. FAO/WHO (World Health Organization) Evaluation of Allergenicity of Genetically Modified Foods. Report of Joint FAO/WHO Expert Consultation. 2001, Rome: Food and Agriculture Organization of the United Nations.
4. Schnell S, Herman RA. Should digestion assays be used to estimate persistence of potential allergens in safety tests for novel proteins?. Clin Mol Allergy 2009, 7:1. 2632610, 19146693, 10.1186/1476-7961-7-1.
5. Maleki SJ, Chung S-Y, Champagne ET, Raufman J-P. The effects of roasting on the allergenic properties of peanut proteins. Allergy Clin Immunol 2000, 106:763-768.
6. Sathe SK, Teuber SS, Roux KH. Effects of food processing on the stability of allergens. Biotechnol Adv 2005, 23:413-429.
7. Herman RA, Storer NP, Gao Y. Digestion assays in allergenicity assessment of transgenic proteins. Environ Health Perspect 2006, 114:1154-1157. 1552003, 16882518.
8. Herman RA, Woolhiser MM, Ladics GS, Korjagin VA, Schafer BW, Storer NP, Green SB, Kan L. Stability of a set of allergens and non-allergens in simulated gastric fluid. Int J Food Sci Nutr 2007, 58:125-141. 10.1080/09637480601149640, 17469768.
9. Fu T-J, Abbott UR, Hatzos C. Digestibility of food allergens and nonallergenic proteins in simulated gastric fluid and simulated intestinal fluid - a comparative study. J Agric Food Chem 2002, 50:7154-7160. 10.1021/jf020599h, 12428975.
10. Silvanovich A, Nemeth MA, Song P, Herman R, Tagliani L, Bannon GA. The value of short amino acid sequence matches for prediction of protein allergenicity. Tox Sci 2006, 90:252-258.
11. Stadler MB, Stadler BM. Allergenicity prediction by protein sequence. FASEB J 2003, 17:1141-1143.
12. Goodman RE, Vieths S, Sampson HA, Hill D, Ebisawa M, Taylor SL, van Ree R. Allergenicity assessment of genetically modified crops - what makes sense?. Nat Biotech 2008, 26:73-81.
13. Thomas K, Herouet-Guicheney C, Ladics G, McClain S, MacIntosh S, Privalle L, Woolhiser M. Current and future methods for evaluating the allergenic potential of proteins: International workshop report 23-25 October 2007. Food Chem Tox 2008, 46:3219-3225.
14. Cressman RF, Ladics G. Further evaluation of the utility of "sliding window" FASTA in predicting cross-reactivity with allergenic proteins. Regul Toxicol Pharmacol 2009, 54:S20-S25. 10.1016/j.yrtph.2008.11.006, 19114081.
15. Goodman RE. Performing IgE serum testing due to informatic matches in the allergenicity assessment of GM crops. Food Chem Toxicol 2008, 46:S24-S34. 10.1016/j.fct.2008.07.023, 18715545.
16. Kennedy MW, Brass A, McCruden AB, Price NC, Kelly SM, Cooper A. The ABA-1 allergen of the parasitic nematode Ascaris suum: fatty acid and retinoid binding function and structural characterization. Biochem 1995, 34:6700-6710.
17. Ishikawa M, Ishida M, Shimakura K, Nagashima Y, Shiomi K. Purification and IgE-binding epitopes of a major allergen in gastropod Turbo cornutus. Biosci Biotechnol Biochem 1998, 62:1337-1343. 10.1271/bbb.62.1337, 9720216.
18. Swoboda I, Jilek A, Ferreira F, Engel E, Hoffmann-Sommergruber K, Scheiner O, Kraft D, Breiteneder H, Pittenauer E, Schmid E, Vicente O, Heberle-Bors E, Ahorn H, Breitenbach M. Isoforms of Bet v 1, the major birch pollen allergen, analyzed by liquid chromatography, mass spectrometry, and cDNA cloning. J Bio Chem 1995, 270:2607-2613.
19. Spuergin P, Mueller H, Walter M, Sciltz E, Forster J. Allergenic epitopes of bovine αS1-casein recognized by human IgE and IgG. Allergy 1996, 51:306-312.
20. Wallner M, Erler A, Hauser M, Klinglmayr E, Gadermaier G, Vogel L, Mari A, Bohle B, Briza P, Ferreira F. Immunologic characterization of isoforms of Car b 1 and Que a 1, the major hornbeam and oak pollen allergens. Allergy 2009, 64:452-460. 10.1111/j.1398-9995.2008.01788.x, 19170672.
21. Sone T, Morikubo K, Miyahara M, Komiyama N, Shimizu K, Tsunoo H, Kino K. T cell epitopes in Japanese cedar (Cryptomeria japonica) pollens: choice of major T cell epitopes in Cry j 1 and Cry j 2 toward design of the peptide-based immunotherapeutics for management of Japanese cedar pollinosis. J Immunol 1998, 161:448-457.
22. Joseph LM, Hymowitz T, Schmidt MA, Herman EM. Evaluation of Glycine germplasm for nulls of the immunodominant allergen P34/Gly m Bd 30k. Crop Sci 2006, 46:1755-1763.
23. Hoffman DR, Sakell RH, Schmidt M. Sol i 1, the phospholipase allergen of imported fire and venom. J Allergy Clin Immunol 2005, 115:611-616. 10.1016/j.jaci.2004.11.020, 15753912.
24. Matsuo H, Kohno K, Niihara H, Morita E. Specific IgE determinant to epitope peptides of ω-5 gliadin and high molecular weight glutenin subunit is a useful tool for diagnosis of wheat-dependent exercise-induced anaphylaxis. J Immunol 2005, 175:8116-8122.
25. Klinglmayr E, Hauser M, Zimmermann F, Dissertori O, Lackner P, Wopfner N, Ferreira F, Wallner M. Identification of B-cell epitopes of Bet v 1 involved in cross-reactivity with food allergens. Allergy 2009, 64:647-651. 10.1111/j.1398-9995.2008.01844.x, 19154550.
26. Pearson WR. Flexible sequence similarity searching with FASTA3 program package. Methods in Molecular Biology 1999, 185-219. Totowa NJ: Humana Press Inc, Misener S, Krawetz SA.
27. Breiteneder H, Radauer C. A classification of plant food allergens. J Allergy Clin Immunol 2004, 113:821-830. 10.1016/j.jaci.2004.01.779, 15131562.
28. Shen H-D, Chou H, Tam MF, Chang C-Y, Lai H-Y, Wang S-R. Molecular and immunological characterization of Pen ch 18, the vacuolar serine protease major allergen of Penicillium chrysogenum. Allergy 2003, 58:993-1002. 10.1034/j.1398-9995.2003.00107.x, 14510716.
29. Ferreir F, Hawranek T, Gruber P, Wopfner N, Mari A. Allergenic cross-reactivity: from gene to clinic. Allergy 2004, 59:243-267. 10.1046/j.1398-9995.2003.00407.x, 14982506.
30. Clouier S, Rampitsch C, Penner GA, Lukow OM. Cloning and expression of a LMW-I glutenin gene. J Cereal Sci 2001, 33:143-154.
31. Sordet C, Culerrier R, Granier C, Rancé F, Didier A, Barre A, Rougé P. Expression of jug r 1, the 2S albumin allergen from walnut (Juglans regia), as correctly folded and functional recombinant protein. Peptides 2009, 30:1213-1221. 10.1016/j.peptides.2009.03.007, 19540419.
32. Hileman RE, Silvanovich A, Goodman RE, Rice EA, Holleschak G, Astwood JD, Hefle SL. Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int Arch Allergy Immunol 2002, 128:280-291. 10.1159/000063861, 12218366.