Crystal structure of a human prion protein fragment reveals a motif for oligomer formation

Abstract

The structural transition of the prion protein from α-helical- to β-sheet-rich underlies its conversion into infectious and disease-associated isoforms. Here we describe the crystal structure of a fragment from human prion protein consisting of the disulfide-bond-linked portions of helices 2 and 3. Instead of forming a pair-of-sheets steric zipper structure characteristic of amyloid fibers, this fragment crystallized into a β-sheet-rich assembly of hexameric oligomers. This study reveals a never before observed structural motif for ordered protein aggregates and suggests a possible mechanism for self-propagation of misfolded conformations by such nonamyloid oligomers.

Figure 1

Structure of hexameric oligomer formed by DBPrP fragments reveals a symmetric, tightly packed, prismatic assembly of β-sheets. (a) The hexamer is shown in two orientations, looking along the side of the prismatic assembly on the left, and down its quasisymmetric threefold axis represented as a triangle on the right. Dashed grey lines are intended to draw attention to the three four-stranded β-sheets that define the hexamer. The main chain is represented as cartoon β-strands and side-chains as sticks. Each subunit is a different color, starting with chain A in orange with chains B through F arranged clockwise. This color scheme is consistent with panels c, d and e. (b) A side view of the oligomer with one segment removed reveals the tight complementary packing of hydrophobic sidechains as pink spheres at the interior and exclusion of hydrophilic sidechains as green spheres at its exterior. (c) A schematic representation of one dimeric β-sheets illustrates the arrangement of hydrogen bonds (dashed lines) between strands. Hydrogen bonds drawn in light blue are not observed in all six subunits within the hexamer due to conformational flexibility of the strand termini. Side chains which protrude towards the exterior of the hexamer are depicted as larger circles. Smaller pink circles highlight hydrophobic residues that form a hydrophobic cluster along one of its interior faces. A black oval represents a twofold symmetry within the association of two subunits. (d) A molecular stick representation with a transparent overlay of cartoon β-strands shows the same dimeric β-sheet diagramed in panel c. (e) A similar molecular representation of the interaction between edge strands of two adjacent β-sheets shows the Asp178 sidechain twisting away from the hydrophobic interior of the hexamer. In doing so it hydrogen bonds to the peptide backbone, and prevents the association of edge strands around the circumference of the hexamer.

Figure 2

An interaction between hexamers is mediated through backbone hydrogen bonding. (a) A cartoon representation of symmetry related hexamers in different colors illustrates their head-to-tail association along the c-axis of the unit cell (grey box). (b) A detailed molecular view of one of these interactions shows that they are mediated through hydrogen bonding of the peptide backbone between two edge strands of adjacent hexamers, forming a short anti-parallel β-sheet. (c) A schematic of this interaction shows the pattern of backbone hydrogen bonds between His177 and Cys179 from the two involved edge strands. The diagram is cut-off where interactions are the same as that described for individual hexamers (Fig. 1).