Figure 2
From: Differences in the mechanical unfolding pathways of apo- and copper-bound azurins
Steered molecular dynamics (SMD) simulation of apo-azurin. (A) 2D topology of apo-azurin. See Table S5 for β-strand assignment. (B) Three SMD force-versus-extension (FX) traces showing two force peaks of apo-azurin in C-terminal pulling simulations. (C) (Top) Overlay of 10 FX traces showing two TSs obtained by using different initial structures from NVT equilibrium of 100 ns. An average FX trace is also shown (solid black line). (Bottom) Geometric centres (GCs) of β-strands are calculated using the Cα atoms of the constituting residues. GC-GC distance change of adjacent β-strands as a function of unfolding extension during C-terminal pulling of apo-azurin from 10 trajectories. Data for N-terminal pulling simulations is shown in Fig. S9.
