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Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

Abstract

Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies1 as well as with normal cellular functions2,3, and frequently form during protein denaturation4,5. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-d-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer’s disease, and a non-natural l-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-β-sheet ‘steric zippers’, the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.

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Figure 1: Design and characterization of peptide inhibitors of amyloid fibril formation.
Figure 2: Designed d -peptide delays tau K12 fibril formation in a sequence-specific manner.
Figure 3: Mechanism of interaction.
Figure 4: Designed non-natural peptide inhibits 248 PAP 286 fibril formation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported GGVLVN structure have been deposited in the Protein Data Bank with accession code 3PPD.

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Acknowledgements

We thank M. I. Ivanova, J. Corn, T. Kortemme, D. Anderson, M. R. Sawaya, M. Phillips, S. Sambashivan, J. Park, M. Landau, A. Laganowsky, Q. Zhang, R. Clubb, F. Guo, T. Yeates, J. Nowick, J. Zheng and M. J. Thompson for discussions; the HHMI, NIH, NSF, Gates Foundation and Joint Center for Translational Medicine for support; R. Peterson for help with NMR experiments; E. Mandelkow for providing tau constructs; R. Riek for providing amyloid-β; and J. Stroud for amyloid-β preparation. Support came from the Damon Runyon Cancer Research Foundation (J.K.), the Ruth L. Kirschstein National Research Service Award (H.W.C.), the programme for junior professors by the Ministry of Science, Baden-Württemberg (J.M.), and a UCLA-IGERT bioinformatics traineeship (S.A.S.).

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Authors

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S.A.S., J.K., D.B., J.M. and D.E. designed the project. J.K. and S.A.S. created the design protocol. J.K. designed the d-peptides. L.J. expanded the design methodology and designed the non-natural amino-acid peptides. S.A.S., H.W.C. and A.Z. performed the fluorescence experiments and electron microscopy, and analysed kinetic data. A.Z. determined the structure of GGVLVN. O.Z. performed the HIV infectivity experiments. J.T.S. determined the tau fibril elongation rates. S.A.S. performed the NMR experiments. S.A.S., J.K. and D.E. wrote the manuscript and coordinated contributions by other authors.

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Correspondence to David Eisenberg.

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The authors declare no competing financial interests.

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Sievers, S., Karanicolas, J., Chang, H. et al. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature 475, 96–100 (2011). https://doi.org/10.1038/nature10154

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