Figure 7: MD simulations.

(a) The top view and (b) the side view of the two Ca²⁺ bound membrane-channel system before simulations using the Drude polarizable force field. After 30 ns simulation, the pore closes in the system (c) without any Ca²⁺ at the S_Ca site, whereas the selectivity filter pore remains open and permeable to water in the system (d) with two Ca²⁺ bound at the S_Ca site. The NaKTs channel is shown in yellow cartoon presentation with the front and back subunits hidden in (b–d) for the sake of clarity. POPC lipids are shown as grey lines with their phosphates in orange spheres. Ca²⁺ ions are indicated by purple spheres. The other ions including K⁺ (light pink), Na⁺ (yellow) and Cl⁻ (green) are shown as well. Surface rendering (marine) is used to show the water accessible regions in the system. The molecular presentation is created using PyMOL. (e,f) show the time series of D_inner in the zero and two S_Ca Ca²⁺ systems with −500 mV TM potential, respectively. The lighter-coloured points are instantaneous values of D_inner and the lines show the running averages. The two D_inner in one tetramer channel are distinguished by different colours.