Modeling of the resting and inactivated states of MscS based on the crystal structure predicts simultaneous changes at the TM2–TM3 and TM3b–β domain interfaces. (A and B) Displayed are MD-equilibrated models of the inactivated (A) and resting (B) states in the explicit lipid bilayer. (C and D) The details of TM cage domain interactions with critical side chains shown for the inactivated (C) and resting (D) state where the gate (L105 and L109) is coupled to the peripheral helices through the hydrophobic TM2–TM3 (F68, L72–L111, and L115) contact. The model of the inactivated state resembles the crystal conformation (PDB ID 2OAU); however, the splay of the peripheral TM1 and TM2 helices (ocher and green) is less. In both conformations, D62 residing on the TM1–TM2 loop forms a salt bridge with either R128 in the inactivated or R131 in the resting state. The resting state model predicts straightening of the crystallographic G113 kink, a substantial separation of TM3b (dark blue) from the β cytoplasmic domain (purple), and a translation of the gate region upward.