Prion protein amyloid formation under native-like conditions involves refolding of the C-terminal alpha-helical domain.

Transmissible spongiform encephalopathies are associated with conformational conversion of the cellular prion protein, PrP(C), into a proteinase K-resistant, amyloid-like aggregate, PrP(Sc). Although the structure of PrP(Sc) remains enigmatic, recent studies have afforded increasingly detailed characterization of recombinant PrP amyloid. However, all previous studies were performed using amyloid fibrils formed in the presence of denaturing agents that significantly alter the folding state(s) of the precursor monomer. Here we report that PrP amyloid can also be generated under physiologically relevant conditions, where the monomeric protein is natively folded. Remarkably, site-directed spin labeling studies reveal that these fibrils possess a beta-core structure nearly indistinguishable from that of amyloid grown under denaturing conditions, where the C-terminal alpha-helical domain of the PrP monomer undergoes major refolding to a parallel and in-register beta-structure upon conversion. The structural similarity of fibrils formed under drastically different conditions strongly suggests that the common beta-sheet architecture within the approximately 160-220 core region represents a distinct global minimum in the PrP conversion free energy landscape. We also show that the N-terminal region of fibrillar PrP displays conformational plasticity, undergoing a reversible structural transition with an apparent pK(a) of approximately 5.3. The C-terminal region, on the other hand, retains its beta-structure over the pH range 1-11, whereas more alkaline buffer conditions denature the fibrils into constituent PrP monomers. This profile of pH-dependent stability is reminiscent of the behavior of brain-derived PrP(Sc), suggesting a substantial degree of structural similarity within the beta-core region of these PrP aggregates.