BPS2026 – Computational mapping of prion protein misfolding hotspots: Insights from entropy and simulation

Prion diseases are fatal neurodegenerative disorders caused by misfolding of the prion protein (PrP). The molecular factors that make PrP prone to misfolding remain unclear. We hypothesize that regions with greater sequence and structural variability are less stable and more likely to misfold. We combined sequence entropy analysis across species with φ/ψ dihedral mapping from available PrP structures. Both analyses pointed to the β2-α2 loop and the α3-helix as variable regions. Molecular dynamics simulations tested whether mutations modeled after resistant species alter the behavior of these regions. In particular, the Y225A variant found in rabbit PrP stabilized the β2-α2 loop by favoring a short 3 10 -helix, reducing loop flexibility and hydrophobic exposure. These results suggest that sequence variability contributes to misfolding risk in specific regions of PrP and that even a single change such as Y225A can shift local structure and reduce this risk. Entropy analysis combined with simulation can identify stabilizing mutations and may explain species-specific resistance to prion disease.