All-atom simulation of the HET-s prion replication
Fig 6
Principal component analysis of the HET-s propagation trajectories.
Graphs (A) and (D) represent the free energy landscape in the principal component plane of the trajectories propagating from the fibril N- and C-terminus respectively. The letters “U”, “I” and “T” indicate the unstructured, intermediate the final (target) state, respectively. The residue contacts were classified in three categories: contacts between Cα in the same rung (intra-rung), contacts between Cα belonging to different rungs (inter-rung) and contacts between Cα of the converting monomer and Cα of the structured fibril (monomer-fibril). The contribution of these sets of the two principal components is shown in bar plots (B) for the N-terminal propagation and (E) for the C-terminal propagation. Images (C) and (F) show representative protein conformations sampled from the intermediate state, for the N-terminal and C-terminal propagations, respectively.