Fig. 3: Molecular dynamics simulations of KimA in a lipid bilayer.
From: Structural basis of proton-coupled potassium transport in the KUP family
a Cut-away views of KimA dimer in a membrane, taken from the CG simulation data. The protein backbone is shown as grey surface and the POPE lipids as green, yellow and blue spheres. b Representative plot of the angle between the TM domains over time for the CG simulations; n = 4 independent simulations (see Supplementary Fig. 5 for full data and a schematic of how the angles were computed). c Upright dimer position as determined using ~2 µs of fully atomistic simulation. Protein shown as grey cartoon, lipid phosphates as semi-transparent blue circles. n = 3 repeats, with the upright dimer sampled in 2/3. d Views from atomistic simulation showing the lipid molecules (as coloured spheres) present between the KimA monomer.
