Figure 5. In blue, the average loop positions from the EOT ensemble of EmrE is presented in terms of the fraction of configurations for which each loop occupies the cytoplasm.
In red, the corresponding average loop position from the EOT ensemble of EmrE mutants; for each loop, the presented result is for the charge mutation associated with that loop.
Figure 5—figure supplement 1. The average loop positions from the EOT ensemble of six EmrE mutants is presented in terms of the fraction of configurations for which each loop occupies the cytoplasm.
The first column (dark gray) shows loop positions from the control simulation protocol. To test the effect of the hydrophobicity of TMD1, the second column (blue) presents results in which all four beads in TMD1 are modeled with the very hydrophobic L CG bead-type. This modification is seen to have a very minor effect on the EOT ensemble. To test the effect of negatively charged EmrE residues in the simulation, the third column (red) presents results in which a charge of −2 is assigned to bead 4 in loop L2 and bead 3 in loop L4, thus matching the profile of negative charges in the EmrE sequence (Figure 1—figure supplement 1). The figure shows that including negative charges consistently shifts the positions of loop L4 toward the periplasm and L5 toward the cytoplasm. The small magnitude of these shifts and their uniformity across all mutants suggests that the negative charges in EmrE play a small role in understanding the shifts in topology of the mutants studied here.