Parallel In-register Intermolecular β-Sheet Architectures for Prion-seeded Prion Protein (PrP) Amyloids

Background: The structures of infectious mammalian prions remain unclear. Results: Based in part on NMR data, we developed models with single PrP molecules spanning the entire cross-section of prion fibrils. Conclusion: These models are consistent with many empirical features of prion amyloids. Significance: We provide a new basis for conceptualizing and experimentally evaluating the structures and propagation of infectious prions. Structures of the infectious form of prion protein (e.g. PrPSc or PrP-Scrapie) remain poorly defined. The prevalent structural models of PrPSc retain most of the native -helices of the normal, noninfectious prion protein, cellular prion protein (PrPC), but evidence is accumulating that these helices are absent in PrPSc amyloid. Moreover, recombinant PrPC can form amyloid fibrils in vitro that have parallel in-register intermolecular -sheet architectures in the domains originally occupied by helices 2 and 3. Here, we provide solid-state NMR evidence that the latter is also true of initially prion-seeded recombinant PrP amyloids formed in the absence of denaturants. These results, in the context of a primarily -sheet structure, led us to build detailed models of PrP amyloid based on parallel in-register architectures, fibrillar shapes and dimensions, and other available experimentally derived conformational constraints. Molecular dynamics simulations of PrP(90-231) octameric segments suggested that such linear fibrils, which are consistent with many features of PrPSc fibrils, can have stable parallel in-register -sheet cores. These simulations revealed that the C-terminal residues approximate to 124-227 more readily adopt stable tightly packed structures than the N-terminal residues approximate to 90-123 in the absence of cofactors. Variations in the placement of turns and loops that link the -sheets could give rise to distinct prion strains capable of faithful template-driven propagation. Moreover, our modeling suggests that single PrP monomers can comprise the entire cross-section of fibrils that have previously been assumed to be pairs of laterally associated protofilaments. Together, these insights provide a new basis for deciphering mammalian prion structures.