Fig. 4: Molecular dynamics reveals PC1-PC2 domain transformations are similar between AcrB and MdtF^V610F, but different in MdtF^WT.

A Cumulative average of the pseudo contacts at the PC1-PC2 cleft, calculated using a cut-off of 10 Å between C_a atoms and averaged from the simulation replicas of AcrB, MdtF^WT and MdtF^V610F (left to right). This plot represents the distribution of residue-residue pseudo contacts throughout the simulation trajectory. Contacts in the experimental reference structure are highlighted. Lesser contacts correspond to the cleft opening whereas higher number of contacts correspond to closing. B Extreme conformations of the PC1-PC2 cleft observed in the MD simulations. PC2 is represented as yellow spheres, PC1 is shown in light blue, and the beta sheets of PC1 and PC2 are depicted in blue and red, respectively. Note that MdtF^WT and MdtF^V610F has distinct orientation of A675 and S676 in the PC2 domain for ‘access’ protomer, as shown by the brown surface and highlighted by the black rectangle.