Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals

We investigate the conformations of the full chicken prion protein (ChPrP1-267) in solution at neutral pH with molecular dynamics simulations. We focus on the persistence of its secondary structure motifs using a recently proposed protein chirality indicator [A. Pietropaolo et al. , Proteins 2008, 70, 667–677]. From this, we find a high rigidity of helix 2 (ChPrP178-195) and of the hexarepeat domain, which is turn rich, and a plasticity of the short b-sheet, consistent with the available NMR structural details. We also determine the extent of solvation for each residue, revealing local minima for such structured regions. These features hint at a possible origin of the high resistance to proteolysis of the avian prion proteins and of its capability in preventing the aggregation in comparison to mammals.