Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106–126

The present paper aims at exploring the elongation of the PrP106–126 fibril under acid environments through molecular dynamics simulation. It shows that influenced by the edge strands of the fibril, single PrP106–126 peptide forms ββ-sheet and becomes a new element of the fibril. Under acidic condition, single PrP106–126 fragment presents a much larger variety of conformations than it does under neural condition. However, acidic condition does not largely affect the stability of the PrP106–126 fibril. Consequently, the speed of the fibril elongation can be dramatically increased by lowering the pH value of the solution. The pH values are adjusted by either altering the protonation state of the residues or adding hydronium ions or hydroxyl ions.