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Review
. 2022 Aug;298(8):102181.
doi: 10.1016/j.jbc.2022.102181. Epub 2022 Jun 23.

Structural biology of ex vivo mammalian prions

Efrosini Artikis  1 , Allison Kraus  2 , Byron Caughey  3
Affiliations
Review

Structural biology of ex vivo mammalian prions

Efrosini Artikis et al. J Biol Chem. 2022 Aug.

Abstract

The structures of prion protein (PrP)-based mammalian prions have long been elusive. However, cryo-EM has begun to reveal the near-atomic resolution structures of fully infectious ex vivo mammalian prion fibrils as well as relatively innocuous synthetic PrP amyloids. Comparisons of these various types of PrP fibrils are now providing initial clues to structural features that correlate with pathogenicity. As first indicated by electron paramagnetic resonance and solid-state NMR studies of synthetic amyloids, all sufficiently resolved PrP fibrils of any sort (n > 10) have parallel in-register intermolecular β-stack architectures. Cryo-EM has shown that infectious brain-derived prion fibrils of the rodent-adapted 263K and RML scrapie strains have much larger ordered cores than the synthetic fibrils. These bona fide prion strains share major structural motifs, but the conformational details and the overall shape of the fibril cross sections differ markedly. Such motif variations, as well as differences in sequence within the ordered polypeptide cores, likely contribute to strain-dependent templating. When present, N-linked glycans and glycophosphatidylinositol (GPI) anchors project outward from the fibril surface. For the mouse RML strain, these posttranslational modifications have little effect on the core structure. In the GPI-anchored prion structures, a linear array of GPI anchors along the twisting fibril axis appears likely to bind membranes in vivo, and as such, may account for pathognomonic membrane distortions seen in prion diseases. In this review, we focus on these infectious prion structures and their implications regarding prion replication mechanisms, strains, transmission barriers, and molecular pathogenesis.

Keywords: N-linked glycosylation; amyloid; cryo-EM; glycosylphosphatidylinositol anchor; infectious disease; neurodegenerative disease; prion; prion disease; protein aggregation; protein structure.

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Conflict of interest statement

Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article.

Figures

Figure 1
Figure 1
Recent models for prion fibrils.A, monomeric subunit of the 263K prion within its parallel in-register intermolecular β-sheet or stack (PIRIBS) architecture (38, 39). B, monomeric subunit within a 4-rung β-solenoid (4RβS) architecture hypothesized initially for the anchorless RML (aRML) prion (50), but see contrary data demonstrating PIRIBS architecture for this strain (41). Spacing of cross-β strands in both models is ∼4.9 Å (C). This is also the spacing of each monomer in the PIRIBS structure, whereas in the 4RβS model the monomers span 19.2 Å along the fibril axis (C). Glycosylation sites (D) at positions N181 and N197 (hamster numbering, PIRIBS) and N180 and N196 (mouse numbering, 4RβS) are labeled in green and a disulfide bond between C179 and C214 (PIRIBS) and C178 and C213 (4RβS) is colored in yellow. Note: an extra glycine residue at position 53 in the hamster PrP sequence shifts the hamster-mouse sequence alignment for subsequent residues. The lower panels show the distribution of hydrophobic residues in orange (E) and the electrostatic surface (F) (red and blue indicate negative and positive charges, respectively).
Figure 2
Figure 2
Ordered core structures of synthetic prion fibrils derived from cryo-EM.A, the two protofilaments of the rhu PrP94–178 (M129 variant) (61) are traced in blue. Hydrophobic residues at the interface of the two protofilaments are shown in orange. B, the two protofilaments of the rhu PrP23–231 fibril (62) with highlighted glycosylated sidechains (green) and disulfide bond (yellow). Salt-bridges formed between K194 and E196 at the interface of opposing protofibrils are colored by heteroatom (carbon, cyan; oxygen, red; nitrogen, blue). C, protofilaments of the E196K mutant (63) with highlighted as in glycosylated sidechains (green; N181 and N197), the disulfide bond (yellow; C179 and C214), and the E196K mutation (purple).
Figure 3
Figure 3
Comparison of 263K and aRML prion structures. Cross-sections of the (A) 263K and (B) aRML fibril (4-monomer segments) highlighting analogous β-arch motifs (N β-arch, cyan; middle β-arch, green; disulfide β-arch, pink). C, tips of N β-arches of 263K (left) and aRML (right) with hydrophobic residues in orange. D, disulfide β-arches (pink) with respective disulfide bonds (yellow), glycosylation sites (green), and hydrophobic residues (orange). E, steric zippers (blue) formed between tips middle β-arches and respective N-terminal residues. The 263 K structure illustrated in this figure includes residues 194 to 196 which were not specified in PDB ID 7LNA. aRML, anchorless RML; PDB, Protein Data Bank.
Figure 4
Figure 4
Conversion of PrPCto PrPSc. Schematic of membrane bound PrPC (only the ordered C-terminal domain determined by solution NMR (81) is shown) with GPI-anchor (green) and N-linked glycan moieties (blue) in POPC lipid bilayer. Insets depict representative GPI anchors and glycans. Membrane-bound 263K pentamer is shown with N-linked glycans (blue) and GPI anchor (green) determined by cryo-EM (39). A cluster of positively charged residues near the N terminus is marked with red asterisks. The inset on the right shows top view of a single polypeptide chain with arrows at positions G119 and V179 (left) and a side view of three stacked monomers (silver, blue, and purple) exhibiting fibril staggering and the diagonal orientation of G119 and V179 of the silver monomer. Also shown is a speculative conversion intermediate with PrPC’s β1–helix 1-β2 loop peeled away from helices 2 & 3 (113) as well as an inset listing types of cofactors that can affect prion propagation in vitro (88, 89, 91, 92, 93) and might therefore be peripherally associated with prion fibrils. GPI, glycophosphatidylinositol.
Figure 5
Figure 5
Potential transmission barrier mechanisms. Sidechain representations (purple, red) of the eight residue variations between mouse and hamster sequences are displayed on the monomer chains (aRML and 263K, respectively). Two residues (mouse: I138, Y154; hamster: M139, N155) implicated in cross species barrier mechanisms are displayed in red. Insets show mouse residues I138 (A) and Y154 (B) and corresponding hamster resides M139 (C) and N155 (D) and their sidechain orientations relative to those of neighboring residues (cyan) and give insight into the surrounding chemical environment. aRML, anchorless RML.
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