Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR

Abstract

Exchange dynamics between molecules free in solution and bound to the surface of a large supramolecular structure, a polymer, a membrane or solid support are important in many phenomena in biology and materials science. Here we present a novel and generally applicable solution NMR technique, known as dark-state exchange saturation transfer (DEST), to probe such exchange phenomena with atomic resolution. This is illustrated by the exchange reaction between amyloid-β (Aβ) monomers and polydisperse, NMR-invisible (‘dark’) protofibrils, a process of significant interest because the accumulation of toxic, aggregated forms of Aβ, from small oligomers to very large assemblies, has been implicated in the aetiology of Alzheimer’s disease1,2,3,4,5,6. The 15N-DEST experiment imprints with single-residue-resolution dynamic information on the protofibril-bound species in the form of 15N transverse relaxation rates (15N-R2) and exchange kinetics between monomers and protofibrils onto the easily observed two-dimensional 1H–15N correlation spectrum of the monomer. The exchanging species on the protofibril surface comprise an ensemble of sparsely populated states where each residue is either tethered to (through other residues) or in direct contact with the surface. The first eight residues exist predominantly in a mobile tethered state, whereas the largely hydrophobic central region and part of the carboxy (C)-terminal hydrophobic region are in direct contact with the protofibril surface for a significant proportion of the time. The C-terminal residues of both Aβ40 and Aβ42 display lower affinity for the protofibril surface, indicating that they are likely to be surface exposed rather than buried as in structures of Aβ fibrils7,8,9,10, and might therefore comprise the critical nucleus for fibril formation11,12. The values, however, are significantly larger for the C-terminal residues of Aβ42 than Aβ40, which might explain the former’s higher propensity for rapid aggregation and fibril formation13,14.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: 15 N DEST and Δ R 2 for Aβ40.
Figure 2: Kinetic schemes for monomer exchange on the surface of Aβ protofibrils.
Figure 3: Comparison of residue-specific fitted parameters describing the ensemble of protofibril-bound states.

References

  1. Lashuel, H. A. & Lansbury, P. T. Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins? Q. Rev. Biophys. 39, 167–201 (2006)

    CAS  Article  Google Scholar 

  2. Walsh, D. M. & Selkoe, D. J. Aβ oligomers – a decade of discovery. J. Neurochem. 101, 1172–1184 (2007)

    CAS  Article  Google Scholar 

  3. Glabe, C. G. Structural classification of toxic amyloid oligomers. J. Biol. Chem. 283, 29639–29643 (2008)

    CAS  Article  Google Scholar 

  4. Querfurth, H. W. & LaFerla, F. M. Mechanisms of disease: Alzheimer’s disease. N. Engl. J. Med. 362, 329–344 (2010)

    CAS  Article  Google Scholar 

  5. Ahmed, M. et al. Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils. Nature Struct. Mol. Biol. 17, 561–567 (2010)

    CAS  Article  Google Scholar 

  6. Fukumoto, H. et al. High-molecular-weight beta-amyloid oligomers are elevated in cerebrospinal fluid of Alzheimer patients. FASEB J. 24, 2716–2726 (2010)

    CAS  Article  Google Scholar 

  7. Petkova, A. T. et al. A structural model for Alzheimer’s β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99, 16742–16747 (2002)

    ADS  CAS  Article  Google Scholar 

  8. Luhrs, T. et al. 3D structure of Alzheimer’s amyloid-β(1–42) fibrils. Proc. Natl Acad. Sci. USA 102, 17342–17347 (2005)

    ADS  CAS  Article  Google Scholar 

  9. Paravastu, A. K., Leapman, R. D., Yau, W. M. & Tycko, R. Molecular structural basis for polymorphism in Alzheimer’s β-amyloid fibrils. Proc. Natl Acad. Sci. USA 105, 18349–18354 (2008)

    ADS  CAS  Article  Google Scholar 

  10. Petkova, A. T., Yau, W. M. & Tycko, R. Experimental constraints on quaternary structure in Alzheimer’s β-amyloid fibrils. Biochemistry 45, 498–512 (2006)

    CAS  Article  Google Scholar 

  11. Fawzi, N. L., Okabe, Y., Yap, E. H. & Head-Gordon, T. Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer’s Aβ1–40 peptide. J. Mol. Biol. 365, 535–550 (2007)

    CAS  Article  Google Scholar 

  12. Powers, E. T. & Powers, D. L. Mechanisms of protein fibril formation: nucleated polymerization with competing off-pathway aggregation. Biophys. J. 94, 379–391 (2008)

    ADS  CAS  Article  Google Scholar 

  13. Jarrett, J. T., Berger, E. P. & Lansbury, P. T., Jr The carboxy terminus of the beta amyloid protein is critical for the seeding of amyloid formation: implications for the pathogenesis of Alzheimer’s disease. Biochemistry 32, 4693–4697 (1993)

    CAS  Article  Google Scholar 

  14. Riek, R., Guntert, P., Dobeli, H., Wipf, B. & Wuthrich, K. NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two Alzheimer peptides with widely different plaque-competence, Aβ(1–40)(ox) and Aβ(1–42)(ox). Eur. J. Biochem. 268, 5930–5936 (2001)

    CAS  Article  Google Scholar 

  15. Fawzi, N. L., Ying, J., Torchia, D. A. & Clore, G. M. Kinetics of amyloid β monomer-to-oligomer exchange by NMR relaxation. J. Am. Chem. Soc. 132, 9948–9951 (2010)

    CAS  Article  Google Scholar 

  16. Teplow, D. B. et al. Elucidating amyloid β-protein folding and assembly: a multidisciplinary approach. Acc. Chem. Res. 39, 635–645 (2006)

    CAS  Article  Google Scholar 

  17. Mastrangelo, I. A. et al. High-resolution atomic force microscopy of soluble Aβ42 oligomers. J. Mol. Biol. 358, 106–119 (2006)

    CAS  Article  Google Scholar 

  18. Pimplikar, S. W. Reassessing the amyloid cascade hypothesis of Alzheimer’s disease. Int. J. Biochem. Cell Biol. 41, 1261–1268 (2009)

    CAS  Article  Google Scholar 

  19. Scheidt, H. A., Morgado, I., Rothemund, S., Huster, D. & Fandrich, M. Solid-state NMR spectroscopic investigation of Aβ protofibrils: implication of a β-sheet remodeling upon maturation into terminal amyloid fibrils. Angew. Chem. 50, 2837–2840 (2011)

    CAS  Article  Google Scholar 

  20. Hou, L. M. et al. Solution NMR studies of the Aβ(1–40) and Aβ(1–42) peptides establish that the met35 oxidation state affects the mechanism of amyloid formation. J. Am. Chem. Soc. 126, 1992–2005 (2004)

    CAS  Article  Google Scholar 

  21. Yan, Y. & Wang, C. Aβ42 is more rigid than Aβ40 at the C terminus: implications for Aβ aggregation and toxicity. J. Mol. Biol. 364, 853–862 (2006)

    CAS  Article  Google Scholar 

  22. McConnell, H. M. Reaction rates by nuclear magnetic resonance. J. Chem. Phys. 28, 430–431 (1958)

    ADS  CAS  Article  Google Scholar 

  23. Helgstrand, M., Hard, T. & Allard, P. Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange. J. Biomol. NMR 18, 49–63 (2000)

    CAS  Article  Google Scholar 

  24. Lee, J., Culyba, E. K., Powers, E. T. & Kelly, J. W. Amyloid-β forms fibrils by nucleated conformational conversion of oligomers. Nature Chem. Biol. 7, 602–609 (2011)

    CAS  Article  Google Scholar 

  25. Carulla, N. et al. Molecular recycling within amyloid fibrils. Nature 436, 554–558 (2005)

    ADS  CAS  Article  Google Scholar 

  26. Carulla, N., Zhou, M., Giralt, E., Robinson, C. V. & Dobson, C. M. Structure and intermolecular dynamics of aggregates populated during amyloid fibril formation studied by hydrogen/deuterium exchange. Acc. Chem. Res. 43, 1072–1079 (2010)

    CAS  Article  Google Scholar 

  27. Hansen, D. F., Vallurupalli, P. & Kay, L. E. Measurement of methyl group motional parameters of invisible, excited protein states by NMR spectroscopy. J. Am. Chem. Soc. 131, 12745–12754 (2009)

    CAS  Article  Google Scholar 

  28. Ishima, R. & Torchia, D. A. Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R20aR20b. J. Biomol. NMR 34, 209–219 (2006)

    CAS  Article  Google Scholar 

  29. Ruschak, A. M., Religa, T. L., Breuer, S., Witt, S. & Kay, L. E. The proteasome antechamber maintains substrates in an unfolded state. Nature 467, 868–871 (2010)

    ADS  CAS  Article  Google Scholar 

  30. Sugase, K., Dyson, H. J. & Wright, P. E. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447, 1021–1025 (2007)

    ADS  CAS  Article  Google Scholar 

  31. Sklenar, V., Torchia, D. & Bax, A. Measurement of 13C longitudinal relaxation using 1H detection. J. Magn. Reson. 73, 375–379 (1987)

    ADS  CAS  Google Scholar 

  32. Delaglio, F. et al. NmrPipe – a multidimensional spectral processing system based on Unix pipes. J. Biomol. NMR 6, 277–293 (1995)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank R. Tycko for discussions, D. Baber, D. Garrett and M. Cai for NMR technical assistance, F. Shewmaker for performing dot blots, and W. Qiang, B. Chen and K. Thurber for assistance with atomic force microscopy and electron microscopy imaging. This work was supported by the intramural program of the National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health and the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (to G.M.C.).

Author information

Authors and Affiliations

Authors

Contributions

All authors contributed extensively to the work described in this paper.

Corresponding author

Correspondence to G. Marius Clore.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Text and Data, Supplementary Figures 1-12 with legends, Supplementary Table 1 and additional references. (PDF 4851 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fawzi, N., Ying, J., Ghirlando, R. et al. Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR. Nature 480, 268–272 (2011). https://doi.org/10.1038/nature10577

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10577

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing