PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure
Figure 7
PoreWalker results for the 3D-structures of the KcsA K+ channel at low (1k4c) and high (1bl8) concentration of K+.
(A),(C)-PoreWalker visual representation (xz-plane section, z-coordinate>0 only, x-axis corresponding to the pore axis of KcsA K+ channel at low (1k4c, A) and high (1bl8, C) concentration of K+. Pore-lining atoms and residues are coloured in orange and blue, respectively, and the rest of the protein is shown in green. Red spheres represent pore centres at 3Å steps and their size is proportional to the pore diameter at that point. IN and OUT indicate the cytoplasmic and periplasmic side of the pore, respectively. (B)-Diameter profiles calculated by PoreWalker standard protocol (3Å steps, solid line), HOLE (1Å steps, dotted line) and PoreWalker-1Å steps (dashed line). The internal pore, the internal cavity and the selectivity filter are highlighted in orange, blue and red, respectively. (D)-Diameter profiles calculated by PoreWalker standard protocol for the low-K+ (solid line) and high-K+ (dotted line) KcsaA channel structures. The entrance of the selectivity filter is shown in green and is found at the pore height highlighted by a green box in the channel structures (A for the low-K+ channel and C for the high-K+ channel). (E)–(F) Different conformation of the Thr75s lining the entrance of the selectivity filter in the low-K+ (E) and high-K+ (F) channels. Backbone and sidechain oxygens are coloured in dark pink and red, respectively, and their atomic volume is shown by dots. Red spheres represent the pore centres at the entrance of the selectivity filter and their size is proportional to the pore diameter predicted for that point (0.92Å and 3.63Å for the low-K+ (E) and high-K+ (F) channels, respectively).