Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: insight into dynamics and properties.
A central theme in prion protein research is the detection of the process that underlies the conformational transition from the normal cellular prion form (PrP(C)) to its pathogenic isoform (PrP(Sc)). Although the three-dimensional structures of monomeric and dimeric human prion protein (HuPrP) have been revealed by NMR spectroscopy and x-ray crystallography, the process underlying the conformational change from PrP(C) to PrP(Sc) and the dynamics and functions of PrP(C) remain unknown. The dimeric form is thought to play an important role in the conformational transition. In this study, we performed molecular dynamics (MD) simulations on monomeric and dimeric HuPrP at 300 K and 500 K for 10 ns to investigate the differences in the properties of the monomer and the dimer from the perspective of dynamic and structural behaviors. Simulations were also undertaken with Asp178Asn and acidic pH, which is known as a disease-associated factor. Our results indicate that the dynamics of the dimer and monomer were similar (e.g., denaturation of helices and elongation of the beta-sheet). However, additional secondary structure elements formed in the dimer might result in showing the differences in dynamics and properties between the monomer and dimer (e.g., the greater retention of dimeric than monomeric tertiary structure).
Sekijima
Masakazu
M
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan. sekijima@cbrc.jp
Motono
Chie
C
Yamasaki
Satoshi
S
Kaneko
Kiyotoshi
K
Akiyama
Yutaka
Y
D001665:Binding Sites; D001704:Biopolymers / Q000737:chemistry; D003198:Computer Simulation; D019281:Dimerization; D006801:Humans; D046911:Macromolecular Substances; D008958:Models, Molecular; D009038:Motion; D018621:PrPC Proteins / Q000737:chemistry; D018620:PrPSc Proteins / Q000737:chemistry; D011328:Prions / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D001704:Biopolymers; D046911:Macromolecular Substances; D018621:PrPC Proteins; D018620:PrPSc Proteins; D011328:Prions