Geometric rules of channel gating inferred from computational models of the P2X receptor transmembrane domain

• The P2X transmembrane domains are assembled by computational modelling.
• The assembly starts from helices relaxed by molecular dynamics simulation.
• The assembled models are relaxed in different lipids by molecular dynamics.
• The packing of L340, A344 and A347 play key roles in channel gating.
• The residue G343 and its packing pocket act as a joint during channel gating.

The P2X receptors are trimeric ATP-gated ion channels and mediate chemical communication between eukaryotic cells. Each P2X subunit contains two transmembrane helices, M1 and M2, and the M2 helix packs around an ion conduction pore. Here, I have reconstructed the three-dimensional models of the zebrafish P2X4 transmembrane domain using spatial restraints on helical packing. The models are stable in lipid bilayers during molecular dynamics simulation and adopt different conformations depending on bilayer hydrophobic thickness. Comparison of these conformations shows that the pore-lining residues L340, A344 and A347 each have multiple packing sites that define the pore configurations. Shift of L340 packing between different sites alters the side-chain orientation that occludes the pore or removes this occlusion. L340, A344 and A347 also gate the pore by expansion–contraction mechanism based on their packing patterns. Finally, pore expansions at the L340 and A344 levels are mutually exclusive, so the P2X gating may involve sequential pore opening at L340 and A344 levels to allow ion conduction. In summary, the current study shows that the computational assembly of the helical membrane protein is not only possible, but also necessary to provide insights into the mechanisms of channel gating.

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