Figure 6

Binding mode of βK in the secondary channel (MD simulations E2a and E2b). A) Superimposed snapshots of βK binding to PqsD at 0 and 30 ns. βK at 0 and 30 ns is shown as purple sticks and as green ball and sticks respectively. Important residues are shown as cyan lines at 30 ns and as orange lines at 0 ns. The red arrows indicate the conformational shift from the initial (yellow) to the final (blue) conformation of PqsD in the MD simulation E2b; Phe218 flips out in presence of βK. B) Schematic representation of βK in the secondary channel. Polar amino acids are illustrated in purple and hydrophobic amino acids in green circles. Hydrogen bonds and CH-pi interactions are shown as green arrows and dotted lines. C) Decomposed energy contributions per residue (at least for one MD >0.5 kcal/mol) determined by MM-GBSA methods for the MD simulations E2a (cyan) and E2b (chain A – red; chain B – black).