Figure 2: Equilibrium MD simulations of LLO and Y406A.

From: Engineering a pH responsive pore forming protein

Figure 2: Equilibrium MD simulations of LLO and Y406A.
Figure 2

(a) Y406A mutant is more flexible than LLO, which is evident from radius of gyration (Rg) of domains D1-D3. Domain D4 is excluded from calculations of Rg to prevent the interference of highly mobile D4 in both variants30. (b) The distance between Cα atoms of residues A/Y406 and Y212 (entire residues shown as red and magenta spheres, respectively, in panel (d)). Two major peaks (black arrows) at ~100 ns and ~630 ns correspond to partial opening of D2-D3 interface. (c) The distance between K316 and D320 centers of mass for LLO and Y406A is 0.66 ± 0.1 nm and 0.59 ± 0.04 nm, respectively. (d) Residues A/Y406 as red spheres and Y212 as magenta spheres in the structure of LLO. (e) Residues K316 as magenta spheres and D320 as green spheres in the structure of LLO (f) Aligned backbone traces of LLO and Y406A mutant (grey). D1 was used to align the snapshots from the MD simulation. Residues 406 and 212 are visible as magenta spheres. (g) Dynamics of K316 and D320 side chains. Backbone trace of one α-helix from HB2 is shown as black lines. Side chain atoms of K316 and D320 are shown as grey dots.