Cryo-EM of prion strains from the same genotype of host identifies conformational determinants

Abstract

Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors [anchorless (a) 22L]. Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.

Copper drives prion protein phase separation and modulates aggregation

“…Eleven of 13 tyrosine residues are in the C-terminal half of PrP that forms the protease and denaturation-resistant core of pathological PrP aggregates ( 1 ), likely explaining why oxidation-induced dityrosine cross-linking favors PrP aggregation. Cryo–electron microscopy (cryo-EM)–derived structures of 263 K, aRML, wtRML, and a22L prion fibrils [Protein Data Bank (PDB) IDs: 5o3l, 7qig, 7lna, and 8efu] ( 60 ) suggest the potential for establishing cross-links between closely positioned pairs of tyrosine residues. Although dityrosines were not observed in these cryo-EM models, tyrosine rings might adopt ortho-ortho conformation to form cross-links.…”

The smallest infectious substructure encoding the prion strain structural determinant revealed by spontaneous dissociation of misfolded prion protein assemblies

“…The hypothesis of the existence of two independent folding domains finds a solid structural basis in the comparison of the cryo-EM structures of 263K, aRML, a22L and ME7 (Fig. 8A and B) [9]. Based on these structures, the PrP 95-168 residues adopt a quasicommune fold for the four strains, while the fold of the segment corresponding to 176-231 varies from one strain to another (Fig.…”

“…This dynamic balance between a highly aggregated state and the dimeric state fundamentally contrasts with the canonical amyloid fold of prion infectious particles. The cryo-EM structures reveal a mono-brin amyloid organization with protomers in a parallel-in-register intermolecular β-sheet (PIRIBS)-based fold [9–12]. Small oligomeric species associated with or in the vicinity of 263K fibrils were also observed on cryo-EM images [11], highlighting the coexistence of at least two species.…”

“…At the molecular level, these biological differences are the consequence of differences in the structure of PrP Sc . How the strain structural determinant (SSD) is encoded in the fold of PrP Sc assemblies remains unclear, despite the structure of protease-resistant PrP Sc assemblies from four strains being currently known [9–12]. Nonetheless, the SSD governs the biochemical properties of PrP Sc assemblies, such as the type of PrP Sc fragments generated after proteolysis [2, 13], apparent resistance to unfolding [14, 15], and size distribution of PrP Sc assemblies at the terminal stage of the disease [16–18].…”

Strain‐dependent role of copper in prion disease through binding to histidine residues in the N‐terminal domain of prion protein

“…Strain‐dependent prion susceptibility has been explained by the strain‐dependent conversion of PrP C into PrP Sc . PrP Sc molecules from different strains have been demonstrated to adopt different conformations (Artikis et al, 2022; Hoyt, Alam, et al, 2022; Hoyt, Standke, et al, 2022; Kraus et al, 2021; Manka, Wenborn, Betts, et al, 2023; Manka, Wenborn, Collinge, & Wadsworth, 2023). RML‐PrP Sc has a major PK cleavage site around residue 90, whereas BSE‐PrP Sc is cleaved between His95 and the asparagine at codon 96 (Hayashi et al, 2005; Mange et al, 2004), suggesting different conformations between RML‐ and BSE‐PrP Sc s. The conformational compatibility between PrP C and PrP Sc is an important factor in determining the conversion efficiency of PrP C into PrP Sc .…”