All-atom simulation of the HET-s prion replication
Fig 5
Order of β-strand formation along the HET-s propagation pathway.
The median value of the reaction progress variable Q at which each residue of the rungs assumes the β-strand conformation is reported. Blue dots correspond to residues in the N-terminal rung while red dots correspond to residues in the C-terminal rung. Dots shown in transparency indicate residues not achieving a stable β-strand conformation. Horizontal bars span between the first and the third quartile of the distribution. The vertical dashed line delineates the average reaction progress at which half of the rungs-residues are incorporated into β-strand conformation. In the propagation starting from the fibril N-terminus (A) the residues of the C-terminal rung of the converting monomer are incorporated first (mean Q = 0.44), followed by the residues in the N-terminal rung (mean Q = 0.69). The opposite sequence of events is observed when propagation starts from the fibril C-terminus (B): the residues of the N-terminal rung of the converting monomer are incorporated first (mean Q = 0.42), followed by the residues in the C-terminal rung (mean Q = 0.81).