A molecular dynamics study on the conformational stability of PrP 180-193 helix II prion fragment

Molecular dynamics of PrP 180-193 has allowed us to investigate the stability of the alpha-helical conformation of the zwitterionic peptide (L-1) and the neutralized (L-2). In water, the helical structure of L-1 is unstable; in L-2, the alpha-helix breaks up in the middle at Gln186, and the two resulting connected helices are stable. The hydrophobic enviroment decreases the stability of the helical structure of L-1, this effect is more evident for L-2 for which the unfolding of the C-terminus is followed by the formation of an intramolecular hydrogen bond connecting His(187) with Thr(191).