Residue mobility as determined by average B-factors.

<p>Values are averaged over all chains in the last 0.5 ns of the MD simulation. High fluctuations are noted for the unstable α helix. Residues in the core have low mobilities with central and C-terminal turn residues exhibiting higher values. The lower packing density of model M4 is reflected in significantly higher motions.</p

Root-mean-square deviation (RMSD) from the initial structure.

<p>Each model displays similar structural variance from the initial configuration. The RMSD for the core atoms rapidly achieves convergence of between 2 and 2.3 Å. The total RMSD shows a consistent increase in change due to the transition of the N-terminal helices to a random coil state. The trajectory of M1 was extended to 2 ns to illustrate that the equilibrium achieved by the core atoms is not impacted by N-terminal motions.</p

Energy contributions for core residues in optimized endpoint structures.

<p>Energy contributions for core residues in optimized endpoint structures.</p

Ensemble averages of structural features in Aβ42 dodecamer models.

<p>Ensemble averages of structural features in Aβ42 dodecamer models.</p

Representative model of a PrP^c complex with Aβ42 dimer.

<p>The N terminus of the PrP^c β-sheet is extended by 2 strands in a model of the double deletion mutant (Δ(51–91,111–125)). A model of Aβ42 dimer (G1) interacts with residues 97–100 of the extended β-sheet in an interfacial manner. The indole sidechain of W99 is shown for orientation. The figure is rendered with MOE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049375#pone.0049375-Molecular1" target="_blank">[31]</a>.</p