Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine
Figure 7
Free energy profiles of parallel β-sheets (GNNQQNY and NNQQ).
(A) Open/solid circle: calculation based on MD with/without PBC in the filament axis. The exposed edge in the case without PBC elevates the overall energy level. (B) In the case when the inter-peptide distance d was adjusted, we used the CPT dynamics to maintain a constant pressure while the axial length of the simulation box fluctuated. Error bars in all graphs denote standard deviations. Values of individual energy terms are in Tables 2 and S2.