Abstract
The identification of T-cell epitopes is a critical step in the understanding of the immunologic mechanisms such as food allergy. Epitope screening in silico by bioinformatic tools can be used to identify T-cell epitopes, which can save time and resources. In this chapter, a multiparametric approach to predict and assess major histocompatibility complex (MHC) class II binding T-cell epitopes using bioinformatics was introduced for food allergens. Furthermore, the ability of predicted T-cell epitopes to induce interleukin (IL)-4, as well as the allergenicity potential based on the sequence analysis and population coverage of epitopes were also determined. The molecular docking approach was further used to explore the binding ability between epitopes and human leukocyte antigen (HLA) class II molecules. The amino acids that might be responsible for binding to HLA class II molecules and their binding interactions were analyzed.
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References
Bohle B (2006) T-cell epitopes of food allergens. Clin Rev Allergy Immunol 30(2):97–108
Bøgh KL, Madsen CB (2016) Food allergens: is there a correlation between stability to digestion and allergenicity? Crit Rev Food Sci Nutr 56(9):1545–1567
Ahmad TA, Eweida AE, El-Sayed LH (2016) T-cell epitope map** for the design of powerful vaccines. Vaccine Rep 6:13–22
Chapoval S, Dasgupta P, Dorsey NJ et al (2010) Regulation of the T helper cell type 2 (Th2)/T regulatory cell (Treg) balance by IL-4 and STAT6. J Leukoc Biol 87(6):1011–1018
Zhu J, Paul WE (2008) CD4 T cells: fates functions and faults. Blood 112(5):1557–1569
Olatunde AC, Hale JS, Lamb TJ (2021) Cytokine-skewed Tfh cells: functional consequences for B cell help. Trends Immunol 42(6):536–550
Wang C, Wang Y, Liu G et al (2020) Food allergomics based on high-throughput and bioinformatics technologies. Food Res Int 130:108942
UniProt Consortium (2020) UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 49(D1):D480–D489
Pundir S, Martin MJ, O’Donovan C et al (2016) UniProt tools. Curr Protoc Bioinformatics 53(1):1–29
Vita R, Mahajan S, Overton JA et al (2019) The immune epitope database (IEDB): 2018 update. Nucleic Acids Res 47(D1):D339–D343
Bui HH, Sidney J, Dinh K et al (2006) Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 7(1):1–5
Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28(1):235–242
Dhanda SK, Gupta S, Vir P et al (2013) Prediction of IL4 inducing peptides. Clin Dev Immunol 2013:1–9
Dimitrov I, Bangov I, Flower DR et al (2014) AllerTOP v. 2 – a server for in silico prediction of allergens. J Mol Model 20(6):1–6
Kalyanaraman N (2018) In silico prediction of potential vaccine candidates on capsid protein of human bocavirus 1. Mol Immunol 93:193–205
Vanga SK, Wang J, Singh A et al (2019) Simulations of temperature and pressure unfolding in soy allergen Gly m 4 using molecular modeling. J Agric Food Chem 67(45):12547–12557
Geng T, Liu K, Frazier R et al (2015) Development of a sandwich ELISA for quantification of Gly m 4, a soybean allergen. J Agric Food Chem 63(20):4947–4953
Vita R, Overton JA, Greenbaum JA et al (2015) The immune epitope database (IEDB) 3.0. Nucleic Acids Res 43(D1):D405–D412
Wang P, Sidney J, Kim Y et al (2010) Peptide binding predictions for HLA DR DP and DQ molecules. BMC Bioinformatics 11(1):1–12
Sidney J, Assarsson E, Moore C et al (2008) Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res 4(1):1–14
Jensen KK, Andreatta M, Marcatili P et al (2018) Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154(3):394–406
Nielsen M, Lundegaard C, Lund O (2007) Prediction of MHC class II binding affinity using SMM-align a novel stabilization matrix alignment method. BMC Bioinformatics 8(1):1–12
Sturniolo T, Bono E, Ding J et al (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 17(6):555–561
Reynisson B, Alvarez B, Paul S et al (2020) NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res 48(W1):W449–W454
Wang P, Sidney J, Dow C et al (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 4(4):e1000048
Greenbaum J, Sidney J, Chung J et al (2011) Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenetics 63(6):325–335
Paul S, Arlehamn CSL, Scriba TJ et al (2015) Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. J Immunol Methods 422:28–34
Kaur H, Garg A, Raghava GPS (2007) PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept Lett 14(7):626–631
Arumugam AC, Agharbaoui FE, Khazali AS et al (2022) Computational-aided design: minimal peptide sequence to block dengue virus transmission into cells. J Biomol Struct Dyn 40(11):5026–5035
Zhou F, He S, Zhang Y et al (2022) Prediction and characterization of the T cell epitopes for the major soybean protein allergens using bioinformatics approaches. Proteins 90(2):418–434
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The authors pay high tribute to the experts and scholars who have devoted themselves to the study of food allergy and immunology.
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He, S., Zhou, F. (2024). Characterization of T-Cell Epitopes in Food Allergens by Bioinformatic Tools. In: Cabanillas, B. (eds) Food Allergens. Methods in Molecular Biology, vol 2717. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3453-0_6
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DOI: https://doi.org/10.1007/978-1-0716-3453-0_6
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