The Crystal Structure of the Globular Domain of Sheep Prion Protein

Abstract

The prion protein PrP is a naturally occurring polypeptide that becomes transformed from a normal conformation to that of an aggregated form, characteristic of pathological states in fatal transmissible spongiform conditions such as Creutzfeld-Jacob Disease and Bovine Spongiform Encephalopathy. We report the crystal structure, at 2 A resolution, of residues 123-230 of the C-terminal globular domain of the ARQ allele of sheep prion protein (PrP). The asymmetric unit contains a single molecule whose secondary structure and overall organisation correspond to those structures of PrPs from various mammalian species determined by NMR. The globular domain shows a close association of helix-1, the C-terminal portion of helix-2 and the N-terminal portion of helix-3, bounded by the intramolecular disulphide bond, 179-214. The loop 164-177, between beta2 and helix-2 is relatively well structured compared to the human PrP NMR structure. Analysis of the sheep PrP structure identifies two possible loci for the initiation of beta-sheet mediated polymerisation. One of these comprises the beta-strand, residues 129-131 that forms an intra-molecular beta-sheet with residues 161-163. This strand is involved in lattice contacts about a crystal dyad to generate a four-stranded intermolecular beta-sheet between neighbouring molecules. The second locus involves the region 188-204, which modelling suggests is able to undergo a partial alpha-->beta switch within the monomer. These loci provide sites within the PrPc monomer that could readily give rise to early intermediate species on the pathway to the formation of aggregated PrPSc containing additional intermolecular beta-structure.

Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations

“…For PrP, the first [8] and most abundant structural information has been obtained by nuclear magnetic resonance techniques (NMR), which has resulted in experimentally derived models of PrP of a wide variety of species [64][65][66][67][68][69][70]. For human and sheep PrP, structures determined by X-ray crystallography have also been reported, both with and without antibodies bound [71][72][73][74][75]. The overall structure of PrP that has emerged from these studies is largely identical for the different species and conditions.…”

“…To increase conformational sampling, replica-exchange MD simulations were performed by De Simone et al [63], based on the crystal structure of sheep PrP [73] (res. 125-230).…”

Misfolding of the prion protein: linking biophysical and biological approaches

“…More recently, high resolution crystallographic structures were established for sheep PrP variants [32,43]. They showed the same global fold as other mammalian species determined by NMR.…”

Caprine PrP variants harboring Asp-146, His-154 and Gln-211 alleles display reduced convertibility upon interaction with pathogenic murine prion protein in scrapie infected cells

“…In particular, substitution of the wild type and positively charged Arg-154 by Histidine, would be expected to reduce the strength of the ionic interaction between residue at position 154 and the negatively charged Asp-150. 67 Since codon 154 resides within helix1, 30 introduction of the His-154 polymorphism is expected to reduce its regional stability. Moreover, this polymorphism results in altered charge distribution at the C-terminal part of helix1, which has been shown to affect conversion efficiency.…”

“…30 A structural model of the molecule's globular domain depicting tested alleles' localization, generated using the pdb.viewer software, is shown in Figure 5A. Predictions of amino acid alteration effects on hydrogen bond formation relative to wild type, identified 2 groups of variants: a) variants with no impact on hydrogen bond formation relative to wild type (Asp-146, His-154) and b) variants diminishing hydrogen bonds present in the wild type allele (Gln-211 and Lys-222).…”