Fig 4. Temperature dependent states.

Top: free energy landscapes, and bottom: representative snapshots are shown for simulations at three different temperatures modelled with a strong hydrophobic temperature dependence, α = 60. The snapshots of the peptides are representative for the low free energy conformations; the circle represents the exact order parameters for the snapshot in the corresponding free energy landscape. Within the snapshots the seed fibril is indicated in a lighter shade (see caption Fig 1 for colour coding). At high temperatures only transient (external) contacts are formed and the protein molecules that are not part of the seed remain in their monomeric form. At intermediate temperatures the free peptides adopt a regular, fibrillar structure at the end of the seed. At low temperatures the heatmap shows that there is not a single distinct conformation with a low free energy: the simulated free peptides are attached to the seed fibril, but no hydrophobic core is formed between the peptides.