Figure 5: Alterations in interdomain hydrophobic interactions between LF and DF domains after ATP-binding.
From: Relative motions between left flipper and dorsal fin domains favour P2X4 receptor activation
(a) A superposition of the resting (grey, PDB ID code 3H9V) and open (pink, PDB ID code 4DW1) structures of zfP2X4 (upper panel) to show the alterations of hydrophobic interactions among I208, L217, V291 and K193 (displayed in sticks and surrounded with mesh for emphasis in lower panel). Green arrows denote the movement of key residues from the closed state to the ATP-bound open state. (b–e) Three-dimensional projection of the free-energy (kcal mol−1) surface showing the lowest free-energy paths passing from resting to open states of zfP2X4 receptors. CVr and CVo indicate the CVs at the resting and open states, respectively. The red arrows depict the lowest free-energy paths passing from resting to open states; the blue arrows denote the ‘transition’ state corresponding to higher potential energy along transition process. Similar results were obtained in two other independent metadynamics runs for each interaction pair.
