Helix-coil transition of PrP106-126: Molecular dynamic study

A set of 34 molecular dynamic (MD) simulations totaling 305 ns of simulation time of the prion protein‐derived peptide PrP106–126 was performed with both explicit and implicit solvent models. The objective of these simulations is to investigate the relative stability of the α‐helical conformation of the peptide and the mechanism for conversion from the helix to a random‐coil structure. At neutral pH, the wild‐type peptide was found to lose its initial helical structure very fast, within a few nanoseconds (ns) from the beginning of the simulations. The helix breaks up in the middle and then unwinds to the termini. The spontaneous transition into the random coil structure is governed by the hydrophobic interaction between His111 and Val122. The A117V mutation, which is linked to GSS disease, was found to destabilize the helix conformation of the peptide significantly, leading to a complete loss of helicity approximately 1 ns faster than in the wild‐type. Furthermore, the A117V mutant exhibits a different mechanism for helix‐coil conversion, wherein the helix begins to break up at the C‐terminus and then gradually to unwind towards the N‐terminus. In most simulations, the mutation was found to speed up the conversion through an additional hydrophobic interaction between Met112 and the mutated residue Val117, an interaction that did not exist in the wild‐type peptide. Finally, the β‐sheet conformation of the wild‐type peptide was found to be less stable at acidic pH due to a destabilization of the His111–Val122, since at acidic pH this histidine is protonated and is unlikely to participate in hydrophobic interaction. Proteins 2001;45:382–396. © 2001 Wiley‐Liss, Inc.