Heterologous Stacking of Prion Protein Peptides Reveals Structural Details of Fibrils and Facilitates Complete Inhibition of Fibril Growth

Fibrils play an important role in the pathogenesis of amyloidosis; however, the underlying mechanisms of the growth process and the structural details of fibrils are poorly understood. Crucial in the fibril formation of prion proteins is the stacking of PrP monomers. We previously proposed that the structure of the prion protein fibril may be similar as a parallel left-handed β-helix. The β-helix is composed of spiraling rungs of parallel β-strands, and in the PrP model residues 105–143 of each PrP monomer can contribute two β-helical rungs to the growing fibril. Here we report data to support this model. We show that two cyclized human PrP peptides corresponding to residues 105–124 and 125–143, based on two single rungs of the left-handed β-helical core of the human PrP^Sc fibril, show spontaneous cooperative fibril growth in vitro by heterologous stacking. Because the structural model must have predictive value, peptides were designed based on the structure rules of the left-handed β-helical fold that could stack with prion protein peptides to stimulate or to block fibril growth. The stimulator peptide was designed as an optimal left-handed β-helical fold that can serve as a template for fibril growth initiation. The inhibiting peptide was designed to bind to the exposed rung but frustrate the propagation of the fibril growth. The single inhibitory peptide hardly shows inhibition, but the combination of the inhibitory with the stimulatory peptide showed complete inhibition of the fibril growth of peptide huPrP-(106–126). Moreover, the unique strategy based on stimulatory and inhibitory peptides seems a powerful new approach to study amyloidogenic fibril structures in general and could prove useful for the development of therapeutics.Transmissible spongiform encephalopathies are neurodegenerative disorders in a wide range of mammalian species, including Creutzfeldt-Jacob disease in man, scrapie in sheep, and bovine spongiform encephalopathy in cattle. The deposition of aggregated prion protein fibrils on and in neurons is regarded to be the source of these neurodegenerative diseases and is frequently associated with occurrence of Congo red positivity (1–3). The fibrils are formed by the conformational change of the prion protein (PrP^c)² into the scrapie form (PrP^Sc). The misfolded conformer of the prion protein (PrP^Sc) is considered as the causative agent in these diseases according to the protein-only hypothesis (4). Studies have shown the toxicity of fibrils of the full-length recombinant mammalian prion protein as well as soluble β-rich oligomers to cultured cells and primary neurons (5).It is still unknown how much of the whole PrP^Sc molecule is involved in the fibril growth. It is shown that the N-terminal part of PrP, specifically residues 112–141, can go through conformational changes involving β-strand formation, which subsequently triggers fibril growth (6–8), and solid state NMR studies showed that residues 112–141 are part of the highly ordered core of huPrP-(23–144) (9). It was previously shown that peptides based on the 89–143 region of the human PrP protein can form fibrils rich in β-sheet structure which are biologically active in transgenic mice (10). Within this region it is the huPrP-(106–126) peptide that is the smallest known region of PrP that forms fibrils that are toxic and resemble the physiological properties of PrP^Sc (11–16). The formation of PrP^Sc is considered to be a two-step event; first, there is the binding between PrP^c and PrP^Sc and subsequently the conformational conversion from PrP^c into PrP^Sc occurs. Mutation studies in a prion-infected neuroblastoma cell line showed that in mouse PrP the regions 101–110 and 136–158 are crucial for the binding and conversion events, respectively (17). Because prevention of fibril growth is the prime therapeutic target, detailed structural knowledge of the fibril is essential for understanding the mechanism of fibril growth. However, structural analysis of amyloid fibrils is hampered by insolubility, isomorphism, and aggregation. X-ray diffraction of several amyloid fibrils revealed a so-called cross-β diffraction pattern which indicates that the fibrils contain β-strands perpendicular to the fibril axis and hydrogen bonds in parallel (18, 19). Thus, for fibril growth the β-strands have to stack on top of each other. Several structures have been suggested to explain the structure of the stacked β-strands; e.g. a parallel in register organization of stacked β hairpins (24) or the comparable dry steric zipper structure (25). Previously, we and other groups suggested that the β-sheet structures in the PrP^Sc fibril may be similar to the topologically most simple class of β-sheets; that is, the parallel left-handed β-helix (Fig. 1A) (6, 20, 21). The left-handed β helix is formed by triangular progressive coils (rungs) of 18–20 residues. Each rung is formed by three hexapeptide motifs, which results in an approximate 3-fold symmetry. Backbone-backbone hydrogen bonding and stacking of the side chains in adjacent rungs contribute to the folding of β-helical rungs. We suggested that each PrP^Sc monomer contributes two left-handed β-helical rungs to the fibril, comprising residues 105–124 and 125–143 (Fig. 1A). This two-rung structural model was recently confirmed for amyloid fibrils of the HET-s prion by NMR analysis (22). In contrast to fibrils which are composed of homologous stacks of identical peptides, e.g. the Aβ peptide (23), the PrP^Sc fibril is more complex because it is composed of heterologous stacks of at least two peptides. For homologous stacking of two identical peptides, the complementarity issue is relatively simple because the identical side chains are in register (e.g. Ile-Ile, Val-Val stacking, and Asn ladders). However, in the case of heterologous stacking, the side chains of the additional heterologous peptide needs to be complementary with the other peptide to allow fibril growth.Open in a separate windowFIGURE 1.A, theoretical model of the fibrillogenic core of PrP^Sc. In the PrP^Sc model based on the left-handed β-helix structure, each PrP^Sc monomer contributes two stacked rungs to the fibril (different color for each monomer). The protofibril is formed by consecutive stacking of the two windings. The stack of two rungs provides enough elevation to accommodate the remaining part (residues ∼ 146–253) of the PrP^Sc molecule (20). B, the left-handed β-helix structure of LpxA-based on x-ray crystallography. In the left-handed β-helix structure of LpxA (PDB code 1LXA) rungs 6 and 7 are indicated (red) that were used for the heterologous stacking studies. Linear and cyclized peptides based on rung 6 and rung 7 were modified to satisfy the ideal left-handed β-helix motif (see “LpxA Peptides” under “Results”) and tested for their intrinsic and cooperative fibrillogenicity. C, left-handed β-helical rung based on rung 6 of LpxA. The rung is formed by three hexapeptide motifs, which results in an approximate 3-fold symmetry. A left-handed β-helical rung can be cyclized by a disulfide bridge after the introduction of a cysteine at position 2 of the first hexapeptide and position 1 of the fourth hexapeptide (according to the numbering used for the hexapeptide repeats in the left-handed β-helix).To investigate whether the suggested rungs 105–123 and 125–143 from human PrP could be complementary (20), we studied the homologous stacking and the heterologous stacking of linear and cyclized prion protein peptides comprising the huPrP-(105–143) region (KTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGS). Qualitative and semiquantitative analysis were done by electron microscopy and Congo red staining. The quantification of the fibril formation was assessed by thioflavin S staining, in which the addition of polyanions (e.g. heparin) enhance the β-sheet formation of peptides comprising the 82–143 region of PrP and improve the reproducibility of the fibril growth (24). This study provides first evidence of heterologous stacking by two isolated putative β-strand layers (or rungs) of the human prion protein with fibril formation as a result. The left-handed β-helix structure provided insight for the “stack-and-stop” approach. With this approach a mix of a stimulatory peptide and an inhibitory peptide could completely block fibril formation. The stimulatory peptide was based on the 125–143 region that was optimized to serve as a folding template for the consecutive stacking of the 106–126 peptide. This cooperative fibril growth was completely inhibited by the inhibitory peptide based on peptides 106–126 with strategic d-amino acid and/or proline substitutions. The findings in this study support models in which the sequential strands in a fibril must somehow spiral up- or downward along the fibril axis, e.g. like the hypothetical left-handed β-helical structure of PrP^Sc fibrils (20). Furthermore, it allows the development of well defined small protein modules which can be used for structure studies of the 82–143 domain of PrP^Sc and the development of therapeutics.