Waltz, AlphaFold and ESMfold Predictions on a Human Prion Protein Tiled Peptide Library Highlight a C-Terminal Region with Strong Conformational Sensitivity

Abstract

Short, linear sequence motifs within the human prion protein (PrP) may encode local aggregation tendencies that are not apparent from full-length sequence analysis. To map intrinsic amyloidogenic potential across PrP, we generated a complete one-residue-step library of overlapping 15-mer peptides from the 253-residue human PrP sequence and evaluated each peptide using WALTZ in both high-specificity and best-overall-performance modes, with full-length SNPeffect4/WALTZ output used for comparison. Peptide-level WALTZ analysis identified several candidate amyloidogenic regions, including an N-terminal signal-peptide segment spanning approximately residues 8-21/22 that was not detected in the publicly available full-length WALTZ/SNPeffect4 output. Predictions made using AlphaFold 3.0 also identified a short C-terminal area whose representative peptides formed either -helix or pair of {beta}-strands, indicating a region of potential higher susceptibility to conformational dynamics. This computational study supports the use of peptide tiling as a complementary screening strategy for identifying candidate short aggregation-prone motifs in PrP and other misfolding-associated proteins.