Figure 2.

PIP₂ mediates intra- and inter-subunit contacts. (A) Identified PIP₂ binding pocket in the structure of TRPV1. (B) Residues proposed as mediators of PIP₂ interaction to the channel. (C) K710 is located at the distal end of the TD helix and interacts with Q498 located at the bottom of TM2. (D) Predicted/potential cation-π interactions connecting the TRP box of the TD helix with the TM4-TM5 helix and N-terminal region. In order to get a better placement of the lateral chains of the available structure, the TRPV1 channel (PDB ID 3J5P) was embedded in lipids (POPC), and placed in a periodic box containing water and ions (140 mM KCl). After 5 ns of all-atom MD simulations using the NAMD/CHARMM32 force-field, the channel was visualized using VMD.