References:
1. Gupta, R.S., et al., Prevalence and Severity of Food Allergies Among US Adults. JAMA Netw Open, 2019. 2 (1): p. e185630.
2. Chong, K.W., et al., Reaction phenotypes in IgE-mediated food allergy and anaphylaxis. Annals of Allergy, Asthma & Immunology, 2020.124 (5): p. 473-478.
3. Fischer, D., et al., Anaphylaxis. Allergy, Asthma & Clinical Immunology, 2018. 14 (2): p. 54.
4. Weinberger, T. and S. Sicherer, Current perspectives on tree nut allergy: a review. Journal of asthma and allergy, 2018.11 : p. 41-51.
5. Maloney, J.M., et al., The use of serum-specific IgE measurements for the diagnosis of peanut, tree nut, and seed allergy. J Allergy Clin Immunol, 2008. 122 (1): p. 145-51.
6. García, B.E. and M.T. Lizaso, Cross-reactivity syndromes in food allergy. J Investig Allergol Clin Immunol, 2011. 21 (3): p. 162-70; quiz 2 p following 170.
7. Dreskin, S.C., et al., The importance of the 2S albumins for allergenicity and cross-reactivity of peanuts, tree nuts, and sesame seeds. Journal of Allergy and Clinical Immunology.
8. Maleki, S.J., et al., Computationally predicted IgE epitopes of walnut allergens contribute to cross-reactivity with peanuts. Allergy, 2011. 66 (12): p. 1522-1529.
9. Nesbit, J.B., et al., Epitopes with similar physicochemical properties contribute to cross reactivity between peanut and tree nuts.Mol Immunol, 2020. 122 : p. 223-231.
10. Shewry, P.R., J.A. Napier, and A.S. Tatham, Seed storage proteins: structures and biosynthesis. Plant Cell, 1995. 7 (7): p. 945-56.
11. Shewry, P.R., et al., Plant protein families and their relationships to food allergy. Biochem Soc Trans, 2002. 30 (Pt 6): p. 906-10.
12. Müntz, K., Proteases and proteolytic cleavage of storage proteins in developing and germinating dicotyledonous seeds. Journal of Experimental Botany, 1996. 47 (5): p. 605-622.
13. Lawrence, M.C., et al., Structure of phaseolin at 2.2 A resolution. Implications for a common vicilin/legumin structure and the genetic engineering of seed storage proteins. J Mol Biol, 1994.238 (5): p. 748-76.
14. Zhang, J., et al., An Ancient Peptide Family Buried within Vicilin Precursors. ACS Chemical Biology, 2019. 14 (5): p. 979-993.
15. Yamada, K., et al., Multiple functional proteins are produced by cleaving Asn-Gln bonds of a single precursor by vacuolar processing enzyme. J Biol Chem, 1999. 274 (4): p. 2563-70.
16. Downs, M.L., et al., Characterization of Low Molecular Weight Allergens from English Walnut (Juglans regia). Journal of Agricultural and Food Chemistry, 2014. 62 (48): p. 11767-11775.
17. Aalberse, R.C., et al., Identification of the amino-terminal fragment of Ara h 1 as a major target of the IgE-binding activity in the basic peanut protein fraction. Clin Exp Allergy, 2020. 50 (3): p. 401-405.
18. Ivanciuc, O., et al., The property distance index PD predicts peptides that cross-react with IgE antibodies. Mol Immunol, 2009.46 (5): p. 873-83.
19. Ivanciuc, O., et al., Structural analysis of linear and conformational epitopes of allergens. Regul Toxicol Pharmacol, 2009.54 (3 Suppl): p. S11-9.
20. Midoro-Horiuti, T., et al., Structural basis for epitope sharing between group 1 allergens of cedar pollen. Mol Immunol, 2006.43 (6): p. 509-18.
21. Lu, W., et al., Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs. Mol Immunol, 2018. 99 : p. 1-8.
22. Fushman, D., et al., Backbone dynamics of ribonuclease T1 and its complex with 2’GMP studied by two-dimensional heteronuclear NMR spectroscopy. J Biomol NMR, 1994. 4 (1): p. 61-78.
23. Mueller, G.A., et al., Backbone dynamics of the RNase H domain of HIV-1 reverse transcriptase. Biochemistry, 2004. 43 (29): p. 9332-42.
24. Favier, A. and B. Brutscher, Recovering lost magnetization: polarization enhancement in biomolecular NMR. J Biomol NMR, 2011.49 (1): p. 9-15.
25. Ghosh, D., et al., Primary identification, biochemical characterization, and immunologic properties of the allergenic pollen cyclophilin cat R 1. J Biol Chem, 2014. 289 (31): p. 21374-85.
26. Braun, B.A., C.H. Schein, and W. Braun, D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors. bioRxiv : the preprint server for biology, 2020: p. 2020.08.13.249649.
27. Oparin, P.B., et al., Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.Biochem J, 2012. 446 (1): p. 69-77.
28. Payne, C.D., et al., Defining the Familial Fold of the Vicilin-Buried Peptide Family. J Nat Prod, 2020. 83 (10): p. 3030-3040.
29. Dall’Antonia, F. and W. Keller, SPADE web service for prediction of allergen IgE epitopes. Nucleic Acids Res, 2019.47 (W1): p. W496-w501.
30. Burks, A.W., et al., Mapping and mutational analysis of the IgE-binding epitopes on Ara h 1, a legume vicilin protein and a major allergen in peanut hypersensitivity. Eur J Biochem, 1997.245 (2): p. 334-9.
31. Cong, Y.J., et al., Characterisation of the IgE-binding immunodominant epitopes on Ara h1. Food and Agricultural Immunology, 2008. 19 (3): p. 175-185.
32. Beyer, K., et al., Measurement of peptide-specific IgE as an additional tool in identifying patients with clinical reactivity to peanuts. J Allergy Clin Immunol, 2003. 112 (1): p. 202-7.
33. Ng, Y.-M., et al., Structural characterization and anti-HIV-1 activities of arginine/glutamate-rich polypeptide Luffin P1 from the seeds of sponge gourd (Luffa cylindrica). Journal of Structural Biology, 2011. 174 (1): p. 164-172.
34. Nesbit, J.B., et al., Identification and assessment of the IgE epitopes of Ara h 1 and Jug r 2 leader sequences. Journal of Allergy and Clinical Immunology, 2018. 141 (2): p. AB179.
35. Willison, L.N., et al., Pistachio vicilin, Pis v 3, is immunoglobulin E-reactive and cross-reacts with the homologous cashew allergen, Ana o 1. Clin Exp Allergy, 2008. 38 (7): p. 1229-38.
36. Wang, F., et al., Ana o 1, a cashew (Anacardium occidental) allergen of the vicilin seed storage protein family. J Allergy Clin Immunol, 2002. 110 (1): p. 160-6.
37. Ivanciuc, O., et al., Characteristic motifs for families of allergenic proteins. Molecular Immunology, 2009. 46 (4): p. 559-568.
38. Ling, C., et al., Expression and refolding of mite allergen pro-Der f1 from inclusion bodies in Escherichia coli. Protein Expr Purif, 2015. 109 : p. 93-8.
39. Park, S.S., et al., Primary structure and allergenic activity of trypsin inhibitors from the seeds of buckwheat (Fagopyrum esculentum Moench). FEBS Lett, 1997. 400 (1): p. 103-7.
40. Micsonai, A., et al., Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy. Proc Natl Acad Sci U S A, 2015. 112 (24): p. E3095-103.
41. Micsonai, A., et al., BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res, 2018. 46 (W1): p. W315-w322.
42. Hura, G.L., et al., Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods, 2009. 6 (8): p. 606-12.
43. Dyer, K.N., et al., High-throughput SAXS for the characterization of biomolecules in solution: a practical approach.Methods Mol Biol, 2014. 1091 : p. 245-58.
44. Classen, S., et al., Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr, 2013. 46 (Pt 1): p. 1-13.
45. Putnam, C.D., et al., X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys, 2007. 40 (3): p. 191-285.
46. Farrow, N.A., et al., Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry, 1994. 33 (19): p. 5984-6003.
47. Dall’Antonia, F., et al., Prediction of IgE-binding epitopes by means of allergen surface comparison and correlation to cross-reactivity. J Allergy Clin Immunol, 2011. 128 (4): p. 872-879.e8.
48. Shen, Y., et al., TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR, 2009. 44 (4): p. 213-23.
49. Lee, W., et al., PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.Bioinformatics, 2011. 27 (12): p. 1727-8.
50. Rosato, A., et al., CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods, 2009. 6 (9): p. 625-6.
51. Güntert, P. and L. Buchner, Combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR, 2015.62 (4): p. 453-71.
52. Bhattacharya, A., R. Tejero, and G.T. Montelione, Evaluating protein structures determined by structural genomics consortia.Proteins, 2007. 66 (4): p. 778-95.
53. Sánchez-Ruano, L., B. de la Hoz, and J. Martínez-Botas,Clinical utility of microarray B-cell epitope mapping in food allergies: A systematic review. Pediatr Allergy Immunol, 2020.31 (2): p. 175-185.