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

Nature volume 480, pages 268–272 (2011)Cite this article

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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.

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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.

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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)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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)

    Article  CAS  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)

    Article  CAS  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)

    Article  ADS  CAS  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)

    Article  ADS  CAS  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)

    Article  ADS  CAS  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)

    Article  CAS  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)

    Article  CAS  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)

    Article  ADS  CAS  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)

    Article  CAS  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)

    Article  CAS  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)

    Article  CAS  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)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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)

    Article  CAS  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)

    Article  CAS  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)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  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)

    Article  CAS  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)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  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)

    Article  CAS  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)

    Article  CAS  Google Scholar 

  28. Ishima, R. & Torchia, D. A. Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R20a ≠ R20b. J. Biomol. NMR 34, 209–219 (2006)

    Article  CAS  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)

    Article  ADS  CAS  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)

    Article  ADS  CAS  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)

    Article  CAS  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.).

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Nicolas L. Fawzi, Jinfa Ying & G. Marius Clore

  2. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Rodolfo Ghirlando

  3. National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Dennis A. Torchia

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  1. Nicolas L. Fawzi
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All authors contributed extensively to the work described in this paper.

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Correspondence to G. Marius Clore.

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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

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