Modeling PrPSc Generation Through Deformed Templating

Deformed templating is the process by which self-replicating protein conformations with a given cross-beta folding pattern can seed formation of an alternative self-replicating state with different cross-beta folding pattern. In particular, uninfectious but propagative PrP amyloid can transform into abona fideinfectious conformer, PrP(Sc)through deformed templating. The process can take many rounds of replication (if taking placein vitro) or even several passages of the evolving PrP conformers through successive brains ifin vivo, through experimental transmission. In all cases, deformed templating involves a forced conversion in which there is a mismatch between the template and the substrate and/or the templating environment, typically a recombinant PrP amyloid, adept at converting recombinant PrP under denaturing conditions (e.g., presence of chaotropic agents), encountering a glycosylated, GPI-anchored PrP (c) substrate under physiological conversion conditions. Deformed templating is characterized by emergence of intermediate conformers that exhibit biochemical characteristics that are intermediate between those of the initial PrP amyloid and the final PrP(Sc)conformers. Here, we took advantage of the recent elucidation of the structure of a PrP amyloid by cryo-EM and the availability of a physically plausible atomistic model of PrP(Sc)that we have recently proposed. Using modeling and Molecular Dynamics (MD) approaches, we built a complete molecular modelization of deformed templating, including an atomistic model of a glycosylated intermediate conformer and a modified model of PrPSc. Among other unanticipated outcomes, our results show that fully glycosylated PrP can be stacked in-register, and how 4-rung beta-solenoid (4R beta S) PrP architectures can share key structural motifs with parallel-in register intermolecular sheet (PIRIBS) PrP amyloids. Our results shed light on the mechanisms of prion replication.