Fig. 3: MD simulations of peptide-BamA interactions.

RMSD of lumen binders over the course of the simulation demonstrate the conformational stability of A CP1 and B CP2 in the closed state. Snapshots of CP1 and CP2 in three replicates are displayed on the right. The initial position of the peptides and their position after 50 ns are shown in cyan and pink, respectively. C The hole radius profile for the Apo BamA closed (PDB 9CS0) and open (PDB 5LJO²²) structures are represented by the black and blue lines, respectively. The computation of the average hole radius from the 50 ns of the MD simulations for Apo BamA starting in the open state are shown in green, and the three replicates of BamA + CP2 are shown in brown, red, and yellow. Crosshairs indicate the hole radius of each simulation at a Z-coordinate of 14 Å. D The computation of the average hole radius from the first 25 ns of the MD simulations for Apo BamA (green) and replicate 1 of BamA + CP2 (brown) are shown. E RMSD values of the CP2 peptide bound to BamA in an open state over the course of the three 50 ns simulations are shown. The data in C and D are presented as mean values and error bars represent the standard deviation.