Polypeptide Chain Folding in the Hydrophobic Core of Hamster Scrapie Prion: Analysis by X-Ray Diffraction

Abstract

Conversion of the noninfectious, cellular form of the scrapie prion (PrPC) to the infectious form (PrPSc) is thought to be driven by an α-helical to β-sheet conformational transition. The N-truncated polypeptide PrP27–30, which encompasses residues 90–231 of PrPScand from which the truncated peptide is derived by limited proteolysis, assembles into amyloid rods that are rich in the β-sheet conformation. The N-terminal half of PrP27–30, which includes residues 90–145 of PrP (SHa90–145) and contains the two putative α-helical domains H1 (PrP109–122) and H2 (PrP129–141), appears to be particularly crucial in the α → β conversion. To assess their role in this conformational transition, we have analyzed in detail X-ray diffraction patterns from the prion-related peptides A8A (PrP113–120), H1, and SHa90–145. We used iterative Fourier synthesis with β-silk as an initial model for assigning phases. For H1, the lyophilized and acetonitrile-solubilized/dehydrated specimens gave two different electron density maps. The former showed that the β-sheets were composed of small side chains as in A8A. The latter showed two types of β-sheets having smaller and larger side chains, suggesting a turn. Such a turn was not observed in the lyophilized H1, indicating that the internal turn in H1 depends on the physical–chemical environment. In SHa90–145, the β-chains are assembled in ≈40 Å-wide crystal domains (termed β-crystallites), and the electron density maps of these crystallites showed evidence for turns within both the H1 and H2 domains. The molecular folding of H1–H2 is compared here with the recent NMR solution structure of recombinant hamster prion, and the effect of pH on the conformational change is discussed. The most compact structure based on the X-ray diffraction analysis showed that the N-terminal, smaller residues of H2 fold back and are hydrogen-bonded with the C-terminal, smaller residues of H1. Similar folding is observed in the NMR solution structure. Comparison of the NMR structures at different pH with the X-ray diffraction results suggests that histidine and lysine residues in the N-terminal sequence of PrP may figure in the α → β structure transition of PrP.