MD simulation analysis

VMD⁴⁶ with in-house scripts, GROMACS, and MOE software were used for visualization and analyses. The calculations of residue distance were performed by using GROMACS code g_bond. For tyrosine toggle switch, we measured the distance between the oxygen atoms of the side chains of Y219^5.58 and Y302^7.53 throughout MD simulation. For interdomain distance, the distance between C_α atoms of residues A238 and E276 of G_αi-protein were measured. The hydrogen bonding network was calculated by using “Hydrogen Bonds” implemented in VMD for the MD trajectories of various systems. The water density maps were created by using GROMACS code g_densmap which analyzed the MD trajectories of various systems. The kink angle of TM6 with time for various simulation systems was calculated by using GROMACS code g_angle which three C_α atoms of residues (I245^6.41, P254^6.50, and G258^6.54) were selected to measure the angle of TM6. The rotational angle of α5-helix of G_αi-protein was calculated by using GROMACS code g_helixorient which calculated the coordinates and direction of the average axis inside the helix.