Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein

[Display omitted] ► We applied the recently proposed MC(CRA)/MD scheme to the prion protein. ► The MC/MD simulations revealed structural changes that were not observed in MD simulations. ► This work further demonstrates the potential advantages of MC/MD simulations. In this paper we present the results of mixed Monte Carlo/Molecular Dynamics (MC/MD) simulations of the D178N mutant of the human prion protein. We have used the MC moves for polypeptide sampling known as Concerted Rotations with Angles (CRA) to selectively sample the region of the prion protein comprising the β-sheet and one of the α-helices. The results indicate that the MC/MD simulations sample the phase space substantially faster than regular Molecular Dynamics simulations starting with the same initial conditions. This work further indicates the MC/MD technique as a potentially powerful simulation tool, allowing the selective sampling of a region of a physical system that is deemed important.