Solid-State NMR Structure of Amyloid-β Fibrils

  • Protocol
  • First Online:
Protein Aggregation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2551))

Abstract

Amyloid fibrils are involved in a number of diseases and notably play a role in neurodegeneration, where they are present in plaques in the brain. Their structure determination might help in finding ways to interfere with their formation, and ultimately prevent disease, by revealing the structure-function relationship and hel** to design molecules targeting initial assembly steps and further propagation. Here, we describe the different steps in NMR protocols which allowed the 3D structure determination of amyloid-β fibrils.

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

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
EUR 44.95
Price includes VAT (Germany)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 149.79
Price includes VAT (Germany)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
EUR 192.59
Price includes VAT (Germany)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
EUR 267.49
Price includes VAT (Germany)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Tycko R, Bernini A, Venditti V et al (2003) Insights into the amyloid folding problem from solid-state NMR. Biochemistry 42:3151–3159

    Article  CAS  PubMed  Google Scholar 

  2. Wüthrich K (2003) NMR studies of structure and function of biological macromolecules (Nobel Lecture). Angew Chem Int Ed Engl 42:3340–3363

    Article  PubMed  Google Scholar 

  3. Schütz AK, Vagt T, Huber M et al (2015) Atomic-resolution three-dimensional structure of amyloid β fibrils bearing the Osaka mutation. Angew Chem Int Ed Engl 54:331–335

    Article  PubMed  Google Scholar 

  4. Wälti MA, Ravotti F, Arai H et al (2016) Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril. Proc Natl Acad Sci USA 113:E4976–E4984

    Article  PubMed  PubMed Central  Google Scholar 

  5. Colvin MT, Silvers R, Ni QZ et al (2016) Atomic resolution structure of monomorphic Aβ42 Amyloid fibrils. J Am Chem Soc 138(30):9663–9674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Bertini I, Gonnelli L, Luchinat L et al (2011) A new structural model of Aβ 40 Fibrils. J Am Chem Soc 133:16013–16022

    Article  CAS  PubMed  Google Scholar 

  7. Lu J-X, Qiang W, Yau W-M et al (2013) Molecular structure of b-Amyloid Fibrils in Alzheimer’s disease brain tissue. Cell 154:1257–1268

    Article  CAS  PubMed  Google Scholar 

  8. Schledorn M, Meier BH, Böckmann A (2015) Alternative salt bridge formation in Aβ – a hallmark of early-onset Alzheimer’s disease? Front Mol Biosci 2:14

    Article  PubMed  PubMed Central  Google Scholar 

  9. Li D, Liu C (2020) Structural diversity of Amyloid fibrils and advances in their structure determination. Biochemistry 59:639–646

    Article  CAS  PubMed  Google Scholar 

  10. Fujii T, Cheung M, Blanco A et al (2012) Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms. Proc Natl Acad Sci USA 109:4461–4466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Loquet A, Sgourakis NG, Gupta R et al (2012) Atomic model of the type III secretion system needle. Nature 486:276–279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Verasdonck J, Shen DK, Treadgold A et al (2015) Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR. J Struct Biol 192:441–448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Guerrero-Ferreira R, Taylor NM, Arteni A-A et al (2019) Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy. Elife 8:e48907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Stevens TJ, Fogh RH, Boucher W et al (2011) A software framework for analysing solid-state MAS NMR data. J Biomol NMR 51:437–447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Güntert P (2008) Automated structure determination from NMR spectra. Eur Biophys J 38:129–143

    Article  PubMed  Google Scholar 

  16. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38

    Article  CAS  PubMed  Google Scholar 

  17. Goddard TD, Huang CC, Meng EC et al (2018) UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci 27:14–25

    Article  CAS  PubMed  Google Scholar 

  18. Seuring C, Verasdonck J, Ringler P et al (2017) Amyloid fibril polymorphism: almost identical on the atomic level, mesoscopically very different. J Phys Chem B 121(8):1783–1792

    Article  CAS  PubMed  Google Scholar 

  19. Schuetz A, Wasmer C, Habenstein B et al (2010) Protocols for the sequential solid-state NMR spectroscopic assignment of a uniformly labeled 25 kDa protein: HET-s(1-227). ChemBioChem 11:1543–1551

    Article  CAS  PubMed  Google Scholar 

  20. Habenstein B, Bousset L, Sourigues Y et al (2012) A native-like conformation for the C-terminal domain of the prion Ure2p within its fibrillar form. Angew Chem Int Ed Engl 51:7963–7966

    Article  CAS  PubMed  Google Scholar 

  21. De Paëpe G, Lewandowski JR, Loquet A et al (2011) Heteronuclear proton assisted recoupling. J Chem Phys 134:095101

    Article  PubMed  PubMed Central  Google Scholar 

  22. Lange A, Seidel K, Verdier L et al (2003) Analysis of proton−proton transfer dynamics in rotating solids and their use for 3D Structure determination. J Am Chem Soc 125:12640–12648

    Article  CAS  PubMed  Google Scholar 

  23. Wasmer C, Schütz A, Loquet A et al (2009) The molecular organization of the fungal prion HET-s in its amyloid form. J Mol Biol 394:119–127

    Article  CAS  PubMed  Google Scholar 

  24. Van Melckebeke H, Wasmer C, Lange A et al (2010) Atomic-resolution three-dimensional structure of HET-s(218−289) Amyloid fibrils by solid-state NMR spectroscopy. J Am Chem Soc 132:13765–13775

    Article  PubMed  Google Scholar 

  25. Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180

    Article  CAS  PubMed  Google Scholar 

  26. Sborgi L, Ravotti F, Dandey VP et al (2015) Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy. Proc Natl Acad Sci USA 112:13237–13242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Shen Y, Delaglio F, Cornilescu G et al (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wiegand T, Hunkeler A, Däpp A et al (2018) CONFINE-MAS: a magic-angle spinning NMR probe that confines the sample in case of a rotor explosion. J Biomol NMR 72:171–177

    Article  CAS  PubMed  Google Scholar 

  29. Bousset L, Brundin P, Böckmann A et al (2016) An efficient procedure for removal and inactivation of Alpha-synuclein assemblies from laboratory materials. J Parkinsons Dis 6:143–151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Huber M, Ovchinnikova OY, Schütz AK et al (2015) Solid-state NMR sequential assignment of Osaka-mutant amyloid-beta (Aβ1-40 E22Δ) fibrils. Biomol NMR Assign 9:7–14

    Article  CAS  PubMed  Google Scholar 

  31. Ravotti F, Sborgi L, Cadalbert R et al (2015) Sequence-specific solid-state NMR assignments of the mouse ASC PYRIN domain in its filament form. Biomol NMR Assign 10:269–276

    Article  Google Scholar 

  32. Wasmer C, Lange A, Van Melckebeke H et al (2008) Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science 319:1523–1526

    Article  CAS  PubMed  Google Scholar 

  33. Gath J, Bousset L, Habenstein B et al (2014) Yet another polymorph of α-synuclein: solid-state sequential assignments. Biomol NMR Assign 8:395–404

    Article  CAS  PubMed  Google Scholar 

  34. Gath J, Bousset L, Habenstein B et al (2014) Unlike twins: an NMR comparison of two α-synuclein polymorphs featuring different toxicity. PLoS One 9:e90659

    Article  PubMed  PubMed Central  Google Scholar 

  35. Schmidt E, Gath J, Habenstein B et al (2013) Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J Biomol NMR 56:243–254

    Article  CAS  PubMed  Google Scholar 

  36. Gath J, Habenstein B, Bousset L et al (2012) Solid-state NMR sequential assignments of α-synuclein. Biomol NMR Assign 6:51–55

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank all students and post-docs who have developed the protocols in the frame of their project in the two labs. This work was supported by the CNRS and the ETH Zurich.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Anja Böckmann .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Meier, B.H., Böckmann, A. (2023). Solid-State NMR Structure of Amyloid-β Fibrils. In: Cieplak, A.S. (eds) Protein Aggregation. Methods in Molecular Biology, vol 2551. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2597-2_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2597-2_5

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2596-5

  • Online ISBN: 978-1-0716-2597-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Navigation