The Structure of the Infectious Prion Protein Constrains Potential Prion Replication Mechanisms

Abstract

X-ray fiber diffraction and cryo electron microscopy revealed that the infectious prion protein, PrPSc, contains a four-rung beta-solenoid structure as a key element of its self-propagating conformation. In particular, amyloid fibrils with their regular and repetitive nature allowed important insights into the structure of PrPSc. X-ray fiber diffraction revealed a height of 19.2 Å per molecule of PrPSc along the fibril axis. Meridional diffraction signals at 4.8, 6.4, and 9.6 Å indicated four rungs of beta structure (4 x 4.8 Å = 19.2 Å), while the lack of a ∼10 Å equatorial reflection implied a beta-solenoid configuration. Unprocessed cryo EM micrographs of PrPSc fibrils displayed 4.8 Å spacings, confirming the cross-beta structure. 3D reconstructions of individual PrPSc fibrils indicated a molecular height of ∼17.7 Å, in good agreement with the X-ray fiber diffraction results. Moreover, single particle averaging of short fibril segments revealed periodicities of ∼2 and ∼4 nm. The first measurement is consistent with the molecular height of PrPSc, while the latter suggests a higher order such as a head-to-head dimerization. The four-rung beta-solenoid structure provides insights into the PrPC to PrPSc conversion mechanism. The folding properties of regular beta-solenoid proteins revealed a nearly universal occurrence of “capping structures” that prevent the propagation of the beta-solenoid conformation. These caps consist of short alpha-helices, loops, or other structures and their removal resulted in aggregation and amyloid formation. The absence of capping structures in PrPSc allows the propagation of its beta-solenoid conformation to neighboring PrPC molecules. The putative head-to-head arrangement of the PrPSc dimers implies a role for matching sequences in the conversion mechanism. The fidelity of the templating process, which is a hallmark of the PrPSc propagation, can thus be attributed to molecular properties of the PrPSc structure.