Accessibility of the S6 residues to the intracellular solution in the TRPV1 open and closed states. The open and closed states data are shown in orange and blue, respectively. The three top panels show the computational results, while the bottom panel shows the experimental data extracted and digitalized from (Salazar et al., 2009). In the simulations, water accessibility is calculated as the overlap between the atomic density of a given S6 residue and that of the intracellular water (the values shown correspond to a sum over all four channel subunits). The open state data correspond to the results obtained for the capsaicin-bound (CAP-bound) open state (Kasimova et al., 2018); the closed state data correspond to the results obtained for the capsaicin-bound closed state and the apo closed state (Liao et al., 2013; Kasimova et al., 2018). The box plots report median and interquartile range with the whiskers representing the SD. The threshold for water accessibility was chosen to be zero. In the experiments, accessibility to the intracellular solution is measured as an effect on current after application of a thiol-modifying reagent. The dashed lines highlight the hypothetical upper gate according to Salazar et al. (2009) and I679 (the gate at the level of the S6 bundle crossing).