Atomistic Simulations of Ion Channels - Computational Neuroscience: A Comprehensive Approach - page 58

Figure 2.10
Overview of the simulation system (A), including a definition of the four sites (S1 to
S4) in the selectivity filter (B). (A) The KcsA channel (shown using two polypeptide
chains out of the four) is embedded in a lipid bilayer. The structure of KcsA can
be thought of as made up of a selectivity filter formed by the TVGYG-motifs of the
P-loop, a central cavity, and an intracellular gate where the cavity-lining M2 helices
pack closely together so as to occlude the central pore. (B) The water molecules and
K + ions in the filter are in the configuration: W(S0)-K1(S1)-W(S2)-K2(S3)-e(S4)-
W(C), where S0 is the extracellular mouth, C is the cavity, and e indicates that a
site is empty. This corresponds to the initial configuration of simulation KA13C.
Reproduced with permission from [104].