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Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils

Nature Structural & Molecular Biology volume 27, pages 660–667 (2020)Cite this article

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Abstract

Amyloid deposits consisting of fibrillar islet amyloid polypeptide (IAPP) in pancreatic islets are associated with beta-cell loss and have been implicated in type 2 diabetes (T2D). Here, we applied cryo-EM to reconstruct densities of three dominant IAPP fibril polymorphs, formed in vitro from synthetic human IAPP. An atomic model of the main polymorph, built from a density map of 4.2-Å resolution, reveals two S-shaped, intertwined protofilaments. The segment 21-NNFGAIL-27, essential for IAPP amyloidogenicity, forms the protofilament interface together with Tyr37 and the amidated C terminus. The S-fold resembles polymorphs of Alzheimer’s disease (AD)-associated amyloid-β (Aβ) fibrils, which might account for the epidemiological link between T2D and AD and reports on IAPP–Aβ cross-seeding in vivo. The results structurally link the early-onset T2D IAPP genetic polymorphism (encoding Ser20Gly) with the AD Arctic mutation (Glu22Gly) of Aβ and support the design of inhibitors and imaging probes for IAPP fibrils.

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Fig. 1: Comparison of reconstructed IAPP polymorphs.
Fig. 2: Architecture of the main polymorph, PM1.
Fig. 3: Secondary structure and hydrogen bonding in PM1.
Fig. 4: Structural comparison of PM1 with fibrillar IAPP peptide and Aβ fibril models.

Data availability

The structure of IAPP PM1 has been deposited in the Protein Data Bank under accession code PDB 6Y1A. The cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under accession codes EMD-10669 (PM1), EMD-10670 (PM2) and EMD-10671 (PM3).

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Acknowledgements

We thank P.J. Peters and C. López-Iglesias for advice and helpful discussions, H. Duimel for help with sample preparation and the M4I Division of Nanoscopy of Maastricht University for microscope access and support. The authors gratefully acknowledge the computing time granted by the Jülich Aachen Research Alliance High-Performance Computing (JARA-HPC) Vergabegremium and VSR commission on the supercomputer JURECA at Forschungszentrum Jülich. We acknowledge support from a European Research Council (ERC) Consolidator grant (no. 726368; W.H.), the Alzheimer Forschung Initiative e.V. and Alzheimer Nederland (project no. 19082CB; R.B.G.R. and G.F.S.), the Russian Science Foundation (RSF; project no. 20-64-46027; L.G. and D.W.) and the Helmholtz Association Initiative and Networking Fund (project no. ZT-I-0003; K.R.P. and G.F.S.).

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  1. These authors contributed equally: Christine Röder, Tatsiana Kupreichyk.

Authors and Affiliations

  1. Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany

    Christine Röder, Tatsiana Kupreichyk, Lothar Gremer, Luisa U. Schäfer, Karunakar R. Pothula, Dieter Willbold, Wolfgang Hoyer & Gunnar F. Schröder

  2. Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany

    Christine Röder, Tatsiana Kupreichyk, Lothar Gremer, Luisa U. Schäfer, Karunakar R. Pothula, Dieter Willbold, Wolfgang Hoyer & Gunnar F. Schröder

  3. Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Christine Röder, Tatsiana Kupreichyk, Lothar Gremer, Dieter Willbold & Wolfgang Hoyer

  4. The Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands

    Raimond B. G. Ravelli

  5. Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Gunnar F. Schröder

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Contributions

L.G., W.H., T.K. and G.F.S. conceived the study. T.K. and L.G. performed and analyzed fibril preparation and AFM experiments. R.G.B.R. performed cryo-EM experiments and the initial data analysis. C.R., T.K. and G.F.S. performed image processing and initial reconstruction. C.R. and G.F.S. performed reconstruction, model building and refinement. L.U.S., K.R.P. and G.F.S. performed molecular dynamics simulations and structure fitting. C.R., T.K., G.F.S., W.H., L.G., K.R.P. and L.U.S. wrote the manuscript. D.W. and all other authors discussed the results and commented on the manuscript.

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Correspondence to Wolfgang Hoyer or Gunnar F. Schröder.

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Extended data

Extended Data Fig. 1 Comparison of described IAPP polymorphs.

a, Single fibril cut-outs of polymorphs PM1, PM2 and PM3 from AFM images (top row) and cryo-EM micrographs (bottom row); single box size is 100 × 250 nm. b, Height profiles of individual fibrils extracted from AFM images. c, Height distribution histogram, showing the highest number of counts for the plane background surface around 0 nm and a distinct peak around 2.2 nm. The peak around 2.2 nm includes both PM1 and PM2 which are non-distinguishable in sense of height distribution. Moreover, a pronounced shoulder on the right corresponds to the presence of lower amounts of PM3 as well as the overlaps of single PM1/PM2 fibrils. For the height distribution analysis, histograms from six height images of 5 × 5 µm size and a resolution of 1024 × 1024 pixels were obtained, binned and presented in one graph. An example of the image used can be seen in Supplementary Figure 2.

Extended Data Fig. 2 Overview of IAPP polymorphs.

a, Typical height profile AFM image used for polymorph distribution analysis. b, Cryo-EM micrographs showing 370 × 370 nm areas. c, AFM overview images showing 1 × 1 µm areas. Arrows indicate the presence of PM1 (red), PM2 (green) and PM3 (blue).

Extended Data Fig. 3 DireX analysis of polymorph 2 (PM2).

The table contains the Cwork and Cfree values from DireX fitting of 21-residue-long sequence snippets (black box) of IAPP in both possible Cα-chain directions into a density layer of PM2 together with the respective amino acid sequence. The results are ranked according to their Cfree values. Highlighted (green box) is the most favorable sequence fit. Atomic models of the four most favorable sequence snippets are shown at the bottom. Note that some models, for example model 2, can be excluded since they are incompatible with the disulfide bond between residues Cys2 and Cys7.

Extended Data Fig. 4 Hydrophobicity plot of the fibril displayed as top view.

Hydrophobicity levels of the IAPP polymorph 1 (PM1) fibril are colored according to Kyte-Doolittle in the hydrophobicity score range −4.5 (white) to 4.5 (gold). One hydrophobic cluster spans the entire diagonal of the fibril cross-section. This hydrophobic streak is surrounded by highly ordered polar clusters.

Extended Data Fig. 5 Results of molecular dynamics simulations of IAPP polymorph 1 (PM1).

Superimposed snapshots from a 250 ns simulation displaying only the backbone (a) or all atoms (except for solvent and hydrogen) (b). c, Showing the RMSD from the deposited structure of PM1 (PDB ID 6Y1A) for two 250 ns simulations (black and grey lines, respectively). d, Showing the RMSD of a single chain from the deposited structure during the two 250 ns simulations. e, Showing the atomic root mean square fluctuations (RMSF) for each residue calculated over each 250 ns simulation.

Extended Data Fig. 6 FSC Analysis of polymorph 1 (PM1).

FSC curves from the even/odd test (solid black) from the gold-standard refinement yields a resolution of 4.2 Å (using the 0.143 criterion). The even/odd FSC curve is fitted (red) with the model function 1/(1+exp((x-A)/B)) (with A = 0.1947 and B = 0.026) to obtain a more robust resolution estimate.

Extended Data Fig. 7 FSC analysis of polymorph 2 (PM2).

FSC curves from the even/odd test (solid black) from the gold-standard refinement yields a resolution of 4.2 Å (using the 0.143 criterion). The even/odd FSC curve is fitted (green) with the model function 1/(1+exp((x-A)/B))) (with A = 0.194789 and B = 0.02427) to obtain a more robust resolution estimate.

Extended Data Fig. 8 FSC analysis of Polymorph 3 (PM3).

FSC curves from the even/odd test (solid black) from the gold-standard refinement yields a resolution of 8.1 Å (using the 0.143 criterion). The even/odd FSC curve is fitted (light blue) with the model function 1/(1+exp((x-A)/B)) (with A = 0.0772 and B = 0.0256) to obtain a more robust resolution estimate.

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Röder, C., Kupreichyk, T., Gremer, L. et al. Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils. Nat Struct Mol Biol 27, 660–667 (2020). https://doi.org/10.1038/s41594-020-0442-4

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  • DOI: https://doi.org/10.1038/s41594-020-0442-4

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