Characterization of Prion Protein (PrP)-Derived Peptides That Discriminate Full-Length${\rm PrP}^{{\rm Sc}}$from${\rm PrP}^{{\rm C}}

On our initial discovery that prion protein (PrP)-derived peptides were capable of capturing the pathogenic prion protein$({\rm PrP}^{{\rm Sc}})$, we have been interested in how these peptides interact with${\rm PrP}^{{\rm Sc}}$. After screening peptides from the entire human PrP sequence, we found two peptides (PrP₁₉₋₃₀ and PrP₁₀₀₋₁₁₁) capable of binding full-length${\rm PrP}^{{\rm Sc}}$in plasma, a medium containing a complex mixture of other proteins including a vast excess of the normal prion protein$({\rm PrP}^{{\rm C}})$. The limit of detection for captured${\rm PrP}^{{\rm Sc}}$was calculated to be 8 amol from a ≈10⁵-fold dilution of 10% (wt/vol) human variant Creutzfeldt-Jakob disease brain homogenate, with >3,800-fold binding specificity to${\rm PrP}^{{\rm Sc}}$over${\rm PrP}^{{\rm C}}$. Through extensive analyses, we show that positively charged amino acids play an important, but not exclusive, role in the interaction between the peptides and${\rm PrP}^{{\rm Sc}}$. Neither hydrophobic nor polar interactions appear to correlate with binding activity. The$\text{peptide}-{\rm PrP}^{{\rm Sc}}$interaction was not sequence-specific, but amino acid composition affected binding. Binding occurs through a conformational domain that is only present in${\rm PrP}^{{\rm Sc}}$, is species-independent, and is not affected by proteinase K digestion. These and other findings suggest a mechanism by which cationic domains of${\rm PrP}^{{\rm C}}$may play a role in the recruitment of${\rm PrP}^{{\rm C}}$to${\rm PrP}^{{\rm Sc}}$.