Fig. 5. Molecular dynamics simulation of TBP2 gated ion channel.

A Structure of the ion-channel embedded lipid bilayer showing the vertical arrangement of the TBP2 molecules and Na⁺ within the channel. Lipid molecules have been blurred for clarity. B Schematic illustration of ion channel formation. C Number of ions within the ion channel for 500 ns production simulations for the channel-embedded lipid membrane in 0.15 molar NaCl and KCl medium. D Free energy profiles (in kcal/mol) in terms of potential of mean forces (PMF’s) for the passage of Na⁺, K⁺, and Cl^- ions through the ion-channel at 310 K, calculated employing the adaptive biasing force (ABF) module implemented in NAMD 2.12.