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. 2022 Oct;29(10):962-965.
doi: 10.1038/s41594-022-00833-4. Epub 2022 Sep 12.

Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers

Qiuye Li  1 , Christopher P Jaroniec  2 , Witold K Surewicz  3
Affiliations

Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers

Qiuye Li et al. Nat Struct Mol Biol. 2022 Oct.

Abstract

One of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with the Y145Stop mutation that is associated with a familial prion disease. This structural insight allows us not only to explain previous biochemical findings, but also provides direct support for the conformational adaptability model of prion transmissibility barriers.

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Conflict of interest statement

Competing Interests

The authors declare no competing interests.

Figures

Extended Data Fig. 1
Extended Data Fig. 1. Morphology of huPrP23–144 amyloid fibrils.
a, Cryo-EM image showing the sole morphology with an apparent twist observed for these fibrils, the same fibril morphology was observed in at least 600 images. b, Manually assembled full pitch of huPrP23–144 fibrils from multiple 2D class averages. The entire fibril has a thickness of ~20 nm and the highly ordered amyloid core has a thickness of ~10 nm. c, AFM image of huPrP23–144 fibrils. A representative fibril in the green box is enlarged to show the left-handed twist, the same fibril morphology was observed in at least 20 images.
Extended Data Fig. 2
Extended Data Fig. 2. Fourier shell correlation curves for huPrP23–144 amyloid fibrils.
Fourier shell correlation between two independently refined half-maps is shown in red and Fourier shell correlation between the map and the atomic model is shown in blue.
Extended Data Fig. 3
Extended Data Fig. 3. Non-planar architecture of two representative huPrP23–144 protofilaments assembled through large hydrophobic interfaces.
Subunit n in protofilament A interacts with two subunits in protofilament B (subunits m and m+1); subunit m+1 in protofilament B interacts with two subunits in protofilament A (subunits n and n+1). Such a non-planar conformation results in rugged surfaces at fibril ends, with N-terminal residues at the top end and C-terminal residues at the bottom end exposed to water. A similar non-planar assembly is observed for subunits in protofilaments C and D.
Extended Data Fig. 4
Extended Data Fig. 4. Comparison of the structural model for huPrP23–144 fibrils determined herein by cryo-EM (a) with the low-resolution model previously suggested based on ssNMR data, (b).
Selected residues involved in close interactions between side-chains in these two models are labeled in red (Ala117-Ile139), yellow (Ala115-Leu125), and green (Gly119-Ser135).
Extended Data Fig. 5
Extended Data Fig. 5. Cryo-EM structure of amyloid fibrils generated from moPrP23–144.
a-b, Two types of polymorphs can be found in AFM images (a) and cryo-EM micrographs (b). Polymorph 1 (red arrows) showed a larger left-handed twist like huPrP23–144 fibrils, and polymorph 2 (green arrows) showed a much smaller right-handed twist. The same fibril morphologies were observed in at least 1,000 cryo-EM images or 20 AFM images for each type of sample. c, Manually assembled half-pitch of both polymorphs from multiple 2D class averages. d, 3D maps of moPrP23–144 and huPrP23–144 fibrils represented by a central slice perpendicular to the fibril axis. Polymorph 1 of moPrP23–144 fibrils (red) showed the same fold as that in huPrP23–144 fibrils (purple). Polymorph 2 of moPrP23–144 fibrils (green) showed a distinctly different fold. e-f, An atomic model built based on the map for polymorph 1 of moPrP23–144 fibrils, with a map resolution of 3.92 Å and model resolution of 4.49 Å. The backbone fold in this model is identical to that in huPrP23–144 fibrils. The structure of polymorph 2 of moPrP23–144 fibrils could not be determined due to poor quality of cryo-EM data for this polymorphic form.
Extended Data Fig. 6
Extended Data Fig. 6. The structural model illustrating seeding reaction at the top end of huPrP23–144 fibrils in the presence of huPrP23–144 and ShaPrP23–144 substrates.
Two representative protofilaments (A and B) are shown only. a, Top and side views of a preformed huPrP23–144 fibril (seed) with solvent-exposed hydrophobic side chains shown in blue. b, Top view of a preformed huPrP23–144 fibril (grey) with a newly recruited and converted subunit of huPrP23–144 (orange). c, Top view of a preformed huPrP23–144 fibril (grey) with a newly recruited subunit of ShaPrP23–144 (red). Adaptation of ShaPrP23–144 to the structure of huPrP23–144 seed would lead to significant intermolecular steric clashes between bulky, elongated side chains of M112 and M139 (as indicated by the yellow star), explaining a cross-seeding barrier.
Extended Data Fig. 7
Extended Data Fig. 7. The structural model illustrating seeding reaction at the bottom end of huPrP23–144 fibrils in the presence of huPrP23–144 and ShaPrP23–144 substrates.
Two representative protofilaments (A and B) are shown for illustrative purposes. a, Bottom and side views of a preformed huPrP23–144 fibril (seed) with solvent-exposed hydrophobic side chains shown in blue. b, Bottom view of a preformed huPrP23–144 fibril (grey) with a newly recruited (to protofilament A) and converted subunit of huPrP23–144 (orange). c, Bottom view of a preformed huPrP23–144 fibril (grey) with a newly recruited (to protofilament A) and converted first subunit of ShaPrP23–144 (red). Due to non-planar structure, C-terminal hydrophobic residues at this end of protofilament B are protruding to water. Thus, recruitment of the first ShaPrP subunit would not result in any steric clashes. d, Bottom view of a preformed huPrP23–144 fibril (grey) with a second newly recruited (to protofilament B) and converted subunit of huPrP23–144 (orange). e, Bottom view of a preformed huPrP23–144 fibril (grey) with a second recruited (to protofilament B) subunit of ShaPrP23–144 (red). Adaptation of this subunit to the structure of the huPrP23–144 seed would lead to intermolecular steric clashes between side chains of M139 and M112 (as indicated by the yellow star), explaining a cross-seeding barrier.
Extended Data Fig. 8
Extended Data Fig. 8. The backbone cryo-EM structures of PrP amyloid fibrils including recombinant huPrP23–144 fibrils determined herein (a, PDB 7RL4), recombinant huPrP94–178 fibrils (b, PDB 6UUR), brain-derived 263K prions (c, PDB 7LNA), recombinant huPrP23–231 fibrils (d, PDB 6LNI), and recombinant E196K huPrP23–231 fibrils (e, PDB 7DWV).
The core of huPrP23–144 fibrils is marked as red.
Fig. 1
Fig. 1. Cryo-EM structure of huPrP23–144 amyloid fibrils.
a Cryo-EM density map showing a left-handed twisted helix with a half-pitch of 351 Å and a classical parallel, in-register β-sheet architecture. b The top view of the atomic model superimposed on the cryo-EM density map. The amyloid core contains four identical protofilaments. Two outer protofilaments with greater accessibility to water are depicted in purple; two inner protofilaments are depicted in white. c One representative subunit of the fibril core with β-strands shown in orange. d Amino acid sequence for the highly ordered core of huPrP23–144 fibrils. N- and C-terminal solvent-inaccessible hydrophobic residues are shown in red and blue, respectively. e Schematic representation of one cross-sectional layer of the amyloid core, with β-strands shown as thicker lines. f Hydrophobicity of the cross-section of protofilaments A and B, with hydrophobicity levels colored according to Kyte-Doolittle (top view). g One cross-sectional layer of protofilaments B and C shown as atomic model superimposed on the cryo-EM map (top view). Extra unassigned densities (likely representing side chains of residues outside the core region) are indicated by green arrows; residues within the amyloid core involved in the inter-protofilament interactions are indicated by red circles.
Fig. 2
Fig. 2. Solvent-exposed amino acid residues at the top and bottom ends of huPrP23–144 fibrils.
At the top end of the fibril, two clusters of hydrophobic residues (M112/A116/A117 and A120/V122) in protofilaments B and C (yellow and orange, a) or protofilaments A and D (pink and blue, b) are exposed to the solvent. At the bottom end of the fibril, two clusters of hydrophobic residues (M129/A133 and I139/F141) in protofilaments A and D (pink and blue, c) or protofilaments B and C (yellow and orange, d) are exposed to the solvent.
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References

    1. Prusiner SB Prions. Proceedings of the National Academy of Sciences 95, 13363–13383 (1998). - PMC - PubMed
    1. Cobb NJ & Surewicz WK Prion diseases and their biochemical mechanisms. Biochemistry 48, 2574–2585 (2009). - PMC - PubMed
    1. Caughey B & Kraus A Transmissibility versus pathogenicity of self-propagating protein aggregates. Viruses 11, 1044 (2019). - PMC - PubMed
    1. Kitamoto T, Iizuka R & Tateishi J An amber mutation of prion protein in gerstmann-sträussler syndrome with mutant PrP plaques. Biochemical and Biophysical Research Communications 192, 525–531 (1993). - PubMed
    1. Ghetti B et al. Vascular variant of prion protein cerebral amyloidosis with τ-positive neurofibrillary tangles: The phenotype of the stop codon 145 mutation in PRNP. Proc Natl Acad Sci U S A 93, 744–748 (1996). - PMC - PubMed

References (to Methods)

    1. Morillas M, Swietnicki W, Gambetti P & Surewicz WK Membrane environment alters the conformational structure of the recombinant human prion protein. Journal of Biological Chemistry 274, 36859–36865 (1999). - PubMed
    1. Yu G, Li K & Jiang W Antibody-based affinity cryo-EM grid. Methods 100, 16–24 (2016). - PMC - PubMed
    1. Bokori-Brown M et al. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein. Nature Communications 7, 1–7 (2016). - PMC - PubMed
    1. Mastronarde DN Automated electron microscope tomography using robust prediction of specimen movements. Journal of Structural Biology 152, 36–51 (2005). - PubMed
    1. Zheng SQ et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods 14, 331–332 (2017). - PMC - PubMed

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