Fig. 1

System used for MD simulations and profiles of the TRPV1 channel pore radius. (a) A representative simulation system. hTRPV1 was inserted into a POPC bilayer (yellow wire) and solvated in 150 mM NaCl. Sodium ions and chloride ions are shown as purple spheres and green spheres, respectively. Water molecules are shown as the cyan surface. (b) The pore radius along the z-axis was calculated using the HOLE program. The gray lines indicate the average positions of D625, G644, D647, I680 and E685 calculated by MD run 1. The average pore radius obtained by the three MD runs are shown by the green solid lines, and the shaded areas indicate the standard deviations. The closed-state sqTRPV1 bound to RTX (7LQZ), open-state rTRPV1 (7RQY) bound to RTX and open-state rTRPV1 bound to RTX and double-knot toxin (3J5Q) are shown by the blue, black and red solid lines, respectively. The dashed lines at 1.4 Å and 2.0 Å indicate the minimum pore sizes required for the passage of water molecules and hydrated cations, respectively.