Paper Citing NAMD - Abstract
Chapron, Yves; Charlet, Laurent; Sahai, Nita
Fate of pathological prion (PrP(sc)92-138) in soil and water: prion-clay nanoparticle molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1802-1816, 2014
Pathogenic prion protein scrapie (PrPsc) may contaminate soils for decades and remain in water in colloidal suspension, providing infection pathways for animals through the inhalation of ingested dust and soil particles, and drinking water. We used molecular dynamics simulations to understand the strong binding mechanism of this pathogenic peptide with clay mineral surfaces and compared our results to experimental works. We restricted our model to the moiety PrP(92-138), which is a portion of the whole PrPsc molecule responsible for infectivity and modeled it using explicit solvating water molecules in contact with a pyrophyllite cleavage plane. Pyrophyllite is taken as a model for common soil clay, but it has no permanent structural charge. However, partial residual negative charges occur on the cleavage plane slab surface due to a slab charge unbalance. The charge is isotropic in 2D and it was balanced with K+ ions. After partially removing potassium ions, the peptide anchors to the clay surface via up to 10 hydrogen bonds, between protonated lysine or histidine residues and the oxygen atoms of the siloxane cavities. Our results provide insight to the mechanism responsible for the strong association between the PrPsc peptide and clay nanoparticles and the associations present in contaminated soil and water which may lead to the infection of animals.
