Full atomistic model of prion structure and conversion

• DOI: 10.1371/journal.ppat.1007864
• Publication Date: 2019-07-11T17:40:52Z
• Authors: Giovanni Spagnolli; Marta Rigoli; Simone Orioli; Alejandro M. Sevi...; Pietro Faccioli; Holger Wille; Emiliano Biasini; Jesús R. Requena
• Keywords: Models, Molecular; 0301 basic medicine; Animals; Cryoelectron Microscopy; Mice; Models; Molecular; Molecular Dynamics Simulation; PrPC Proteins; PrPSc Proteins; Prions; Protein Conformation; Protein Structure; Quaternary; PrPSc Proteins; QH301-705.5; Prions; Protein Conformation; Animals; Cryoelectron Microscopy; Mice; Models, Molecular; Molecular Dynamics Simulation; PrPC Proteins; PrPSc Proteins; Prions; Protein Conformation; Protein Structure, Quaternary; Cryoelectron Microscopy; RC581-607; Molecular Dynamics Simulation; Mice; 03 medical and health sciences; Animals; PrPC Proteins; Immunologic diseases. Allergy; Biology (General); Protein Structure, Quaternary; Research Article

AbstractPrions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular prion protein (PrPC), is the only one known to cause epidemic and epizootic episodes(1). Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-β-Sheet (PIRIBS)(2) or β-solenoid conformations(3). Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung β-solenoid (4RβS)(4, 5). Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4RβS architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring β-solenoid. Importantly, the 4RβS arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. Our results provide the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.SignificanceSince the original hypothesis by Stanley Prusiner, prions have represented enigmatic agents diverging from the classical concept of genetic inheritance. However, the structure of PrPSc, the infectious isoform of the cellular prion protein (PrPC), has so far remained elusive, mostly due to technical challenges posed by its aggregation propensity. Here, we present a new high resolution model of PrPSc derived from the integration of a wide array of recent experimental constraints. By coupling the information of such model with a newly developed computational method, we reconstructed for the first time the conformational transition of PrPC to PrPSc. This study offers a unique workbench for designing therapeutics against prion diseases, and a physically-plausible mechanism explaining how protein conformation could self-propagate.