Atomistic Simulations of Ion Channels - Computational Neuroscience: A Comprehensive Approach - page 60

Figure 2.11
Trajectories (along the pore axis) of K + ions (thick black lines) and water molecules
(gray lines) for two simulations with different starting configurations in sites S1-S4:
(A) KA13C; (B) KA02C; Note that, for clarity, not all water molecules within the
filter are shown. The locations on z (pore axis) of the four sites (S1 to S4) defined
by the geometric center of the 8 oxygen atoms are indicated by the thin black lines.
At each point in time, the origin of the coordinate system is defined as the center of
gravity of the 16 oxygen atoms that line the selectivity filter. The black arrow in B
indicates the time at which a K + ion enters the selectivity filter from the extracellular
mouth (S0) of the channel. Reproduced with permission from [104]