Skip to main content

Structural Characterization of Food Allergens by Nuclear Magnetic Resonance Spectroscopy

  • Protocol
  • First Online:
Food Allergens

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2717))

Abstract

As allergies, especially those triggered by food, are becoming more and more prevalent, it is of increasing importance to fully understand the structures and dynamic behaviors of allergenic proteins along with their interactions with potential natural ligands. Therefore, we have established a solid routine to achieve structural characterization of food allergens, especially for birch pollen-related cross-reactive proteins from the class 10 of pathogenesis-related proteins (PR-10), by nuclear magnetic resonance (NMR) spectroscopy. Following expression of the desired allergen in Escherichia coli in isotope-labeled minimal media, the three-dimensional solution structures of these proteins can be determined, and insight into ligand binding mechanics and structural dynamic properties are accessible through NMR spin relaxation experiments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Sicherer SH, Sampson HA (2014) Food allergy: epidemiology, pathogenesis, diagnosis, and treatment. J Allergy Clin Immunol 133:291–307; quiz 308. https://doi.org/10.1016/j.jaci.2013.11.020

    Article  CAS  PubMed  Google Scholar 

  2. Longo G, Berti I, Burks AW et al (2013) IgE-mediated food allergy in children. Lancet 382:1656–1664. https://doi.org/10.1016/S0140-6736(13)60309-8

    Article  CAS  PubMed  Google Scholar 

  3. de Silva D, Geromi M, Panesar SS et al (2014) Acute and long-term management of food allergy: systematic review. Allergy 69:159–167. https://doi.org/10.1111/all.12314

    Article  PubMed  Google Scholar 

  4. Lack G (2012) Update on risk factors for food allergy. J Allergy Clin Immunol 129:1187–1197. https://doi.org/10.1016/j.jaci.2012.02.036

    Article  PubMed  Google Scholar 

  5. Marrs T, Bruce KD, Logan K et al (2013) Is there an association between microbial exposure and food allergy? A systematic review. Pediatr Allergy Immunol 24(311–320):e318. https://doi.org/10.1111/pai.12064

    Article  Google Scholar 

  6. Han Y, Kim J, Ahn K (2012) Food allergy. Korean J Pediatr 55:153–158. https://doi.org/10.3345/kjp.2012.55.5.153

    Article  PubMed  PubMed Central  Google Scholar 

  7. Ortolani C, Ispano M, Pastorello E et al (1988) The oral allergy syndrome. Ann Allergy 61:47–52

    CAS  PubMed  Google Scholar 

  8. Ebner C, Birkner T, Valenta R et al (1991) Common epitopes of birch pollen and apples--studies by western and northern blot. J Allergy Clin Immunol 88:588–594. https://doi.org/10.1016/0091-6749(91)90152-e

    Article  CAS  PubMed  Google Scholar 

  9. Bohle B, Werfel T (2022) Treatment approaches to food allergy. Handb Exp Pharmacol 268:173–193. https://doi.org/10.1007/164_2021_496

    Article  CAS  PubMed  Google Scholar 

  10. Nothegger B, Reider N, Covaciu CE et al (2020) Allergen-specific immunotherapy with apples: selected cultivars could be a promising tool for birch pollen allergy. J Eur Acad Dermatol Venereol 34:1286–1292. https://doi.org/10.1111/jdv.16201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Valenta R, Ferreira F, Focke-Tejkl M et al (2010) From allergen genes to allergy vaccines. Annu Rev Immunol 28:211–241. https://doi.org/10.1146/annurev-immunol-030409-101218

    Article  CAS  PubMed  Google Scholar 

  12. Linhart B, Valenta R (2012) Vaccines for allergy. Curr Opin Immunol 24:354–360. https://doi.org/10.1016/j.coi.2012.03.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zuidmeer-Jongejan L, Fernandez-Rivas M, Poulsen LK et al (2012) FAST: towards safe and effective subcutaneous immunotherapy of persistent life-threatening food allergies. Clin Transl Allergy 2:5. https://doi.org/10.1186/2045-7022-2-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Eidelpes R, Hofer F, Rock M et al (2021) Structure and zeatin binding of the peach allergen Pru p 1. J Agric Food Chem 69:8120–8129. https://doi.org/10.1021/acs.jafc.1c01876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Führer S, Kamenik AS, Zeindl R et al (2021) Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens. Sci Rep 11:4173. https://doi.org/10.1038/s41598-021-83705-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ahammer L, Grutsch S, Kamenik AS et al (2017) Structure of the major apple allergen Mal d 1. J Agric Food Chem 65:1606–1612. https://doi.org/10.1021/acs.jafc.6b05752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Matricardi PM, Kleine-Tebbe J, Hoffmann HJ et al (2016) EAACI molecular allergology user’s guide. Pediatr Allergy Immunol 27 Suppl 23:1–250. https://doi.org/10.1111/pai.12563

    Article  CAS  PubMed  Google Scholar 

  18. Tollinger M, Skrynnikov NR, Mulder FA et al (2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123:11341–11352. https://doi.org/10.1021/ja011300z

    Article  CAS  PubMed  Google Scholar 

  19. Grutsch S, Fuchs JE, Freier R et al (2014) Ligand binding modulates the structural dynamics and compactness of the major birch pollen allergen. Biophys J 107:2972–2981. https://doi.org/10.1016/j.bpj.2014.10.062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Moschen T, Wunderlich CH, Spitzer R et al (2015) Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed Engl 54:560–563. https://doi.org/10.1002/anie.201409779

    Article  CAS  PubMed  Google Scholar 

  21. Delaglio F, Grzesiek S, Vuister GW et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293. https://doi.org/10.1007/BF00197809

    Article  CAS  PubMed  Google Scholar 

  22. Vranken WF, Boucher W, Stevens TJ et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696. https://doi.org/10.1002/prot.20449

    Article  CAS  PubMed  Google Scholar 

  23. Shen Y, Bryan PN, He Y et al (2010) De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds. Protein Sci 19:349–356. https://doi.org/10.1002/pro.303

    Article  CAS  PubMed  Google Scholar 

  24. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223. https://doi.org/10.1007/s10858-009-9333-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Schwieters CD, Bermejo GA, Clore GM (2018) Xplor-NIH for molecular structure determination from NMR and other data sources. Protein Sci 27:26–40. https://doi.org/10.1002/pro.3248

    Article  CAS  PubMed  Google Scholar 

  26. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73. https://doi.org/10.1016/s1090-7807(02)00014-9

    Article  CAS  PubMed  Google Scholar 

  27. Case DA, Ben-Shalom IY, Brozell SR et al (2018) AMBER 2018 University of California, San Francisco

    Google Scholar 

  28. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795. https://doi.org/10.1002/prot.21165

    Article  CAS  PubMed  Google Scholar 

  29. Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926

    Article  CAS  Google Scholar 

  30. Adelman SA, Doll JD (1976) Generalized Langevin equation approach for atom/solid-surface scattering: general formulation for classical scattering off harmonic solids. J Chem Phys 64:2375–2388

    Article  CAS  Google Scholar 

  31. Berendsen HJC, Postma JPM, van Gunsteren WF et al (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  32. Ciccotti G, Ryckaert JP (1986) Molecular dynamics simulation of rigid molecules. Comput Phys Rep 4:345–392

    Article  CAS  Google Scholar 

  33. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N-log(N) method for Ewald sums large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  34. Baldwin AJ (2014) An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange. J Magn Reson 244:114–124. https://doi.org/10.1016/j.jmr.2014.02.023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Morin S, Linnet TE, Lescanne M et al (2014) Relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics 30:2219–2220. https://doi.org/10.1093/bioinformatics/btu166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Grutsch S, Fuchs JE, Ahammer L et al (2017) Conformational flexibility differentiates naturally occurring bet v 1 isoforms. Int J Mol Sci 18:1192. https://doi.org/10.3390/ijms18061192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Führer S, Unterhauser J, Zeindl R et al (2022) The structural flexibility of PR-10 food allergens. Int J Mol Sci 23:8252. https://doi.org/10.3390/ijms23158252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Tollinger M, Kloiber K, Agoston B et al (2006) An isolated helix persists in a sparsely populated form of KIX under native conditions. Biochemistry 45:8885–8893. https://doi.org/10.1021/bi0607305

    Article  CAS  PubMed  Google Scholar 

  39. Fielding L (2003) NMR methods for the determination of protein-ligand dissociation constants. Curr Top Med Chem 3:39–53. https://doi.org/10.2174/1568026033392705

    Article  CAS  PubMed  Google Scholar 

  40. Fielding L, Rutherford S, Fletcher D (2005) Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems. Magn Reson Chem 43:463–470. https://doi.org/10.1002/mrc.1574

    Article  CAS  PubMed  Google Scholar 

  41. Religa TL, Ruschak AM, Rosenzweig R, Kay LE (2011) Site-directed methyl group labeling as an NMR probe of structure and dynamics in supramolecular protein systems: applications to the proteasome and to the ClpP protease. J Am Chem Soc 133:9063–9068. https://doi.org/10.1021/ja202259a

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Martin Tollinger .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Zeindl, R., Unterhauser, J., Röck, M., Eidelpes, R., Führer, S., Tollinger, M. (2024). Structural Characterization of Food Allergens by Nuclear Magnetic Resonance Spectroscopy. 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_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3453-0_10

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3452-3

  • Online ISBN: 978-1-0716-3453-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics