File:Atomic-level-characterization-of-transport-cycle-thermodynamics-in-the-glycerol-3-ncomms9393-s2.ogv

English: Supplementary Movie 1 IF-to-OF conformational transition of apo and Pi-bound GlpT, along with phosphate binding/unbinding in the IF and OF states, representing a full thermodynamic cycle. This trajectory is reconstructed using the post-hoc string method (PHSM) based on our final bias-exchange umbrella sampling (BEUS) simulation set (Set 13). The free energies estimated along the 150 images (representing this cyclic transition pathway) reveal that substrate binding lowers the free energy barrier of the IF-to-OF transition. The ensemble-averaged pore radius for each image was calculated with HOLE (Smart et al., J. Mol. Graphics, 14, 354-360 (1996)) using all protein and phosphate atoms.