Differences in dynamics of dimeric and monomeric human prion protein revealed by molecular dynamics simulations

Chie Motono1, Masakazu Sekijima2, Satoshi Yamasaki,Kiyotoshi Kaneko,and Yutaka Akiyama
1c-motono@aist.go.jp, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology; 2sekijima@cbrc.jp, Computational Biology Research Center , National Institute of Advanced Industrial Science and Technology

Conversion of normal cellular prion protein (PrPC) to its pathogenic isoform, PrPSc is a central event in prion pathogenesis. Although the three-dimensional structures of monomeric and dimeric human prion protein (HuPrP) have been revealed by NMR spectroscopy and X-ray crystallography, the molecular details of conversion from PrPC to PrPSc, the dynamics, and functions of PrPC remain unclear. In this study, we performed molecular dynamics (MD) simulations on monomeric and dimeric HuPrP at 300K and 500K for 10 ns to investigate the differences in the dynamics of the monomer and the dimer HuPrP. Simulations were also carried out with Asp178Asn and acidic pH known as a disease-associated factor. Our results indicate that the dynamics of the dimer and monomer were largely similar (e.g. unfolding process of helices and elongation of β-sheet). However, additional secondary structure elements formed in the dimer might result in showing the differences dynamics between the monomer and dimer (e.g. the greater retention of dimeric than monomeric tertiary structure).