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. 2010 Aug 5;107(34):15075–15080. doi: 10.1073/pnas.1007071107

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Fig. 3. — Spatial distribution of pore waters and structural stability of the bundle. (A) Average number of water molecules localized within the pocket between the His and the Trp tetrads. (B) The water oxygen density from the simulation of the state (light blue shading) is plotted together with the experimental one (red surfaces). The overall structure of the bundle is also presented (gray shading) and the sidechains of some of functionally relevant residues are highlighted as sticks: Val27 (blue), His37 (orange), and Trp41 (green). (C) The rmsd of the heavy atoms from the initial (X-ray) structure is plotted as a function of MD simulation time for the protonation states (red), (gold), (purple), and 4⁺ (blue), respectively.

Inline graphic — Spatial distribution of pore waters and structural stability of the bundle. (A) Average number of water molecules localized within the pocket between the His and the Trp tetrads. (B) The water oxygen density from the simulation of the state (light blue shading) is plotted together with the experimental one (red surfaces). The overall structure of the bundle is also presented (gray shading) and the sidechains of some of functionally relevant residues are highlighted as sticks: Val27 (blue), His37 (orange), and Trp41 (green). (C) The rmsd of the heavy atoms from the initial (X-ray) structure is plotted as a function of MD simulation time for the protonation states (red), (gold), (purple), and 4⁺ (blue), respectively.