Tunnel connects lipid bilayer to occluded odorant-binding site of insect olfactory receptor.

Mh OR5, an insect olfactory receptor (OR), has an occluded binding site for the odorant eugenol in both the open and closed states of the ion channel. We used atomistic molecular dynamics simulation (MD) and steered molecular dynamics to examine possible tunnels to the odorant binding site from the protein surface. Four high probability tunnels were identified in the MD results. Surprisingly, three of the tunnels connect the ligand binding site to the lipid bilayer. We found sharp 30%–50% increases or decreases in tunnel bottleneck areas over 70 nsec MD trajectories, both in the ligand-bound and unliganded OR structures. Steered MD showed that eugenol follows the tunnels to the protein surface, and the potential of mean force is quantitatively consistent with the known affinity of eugenol for Mh OR5. We examined AlphaFold-generated models of 21 other insect ORs, and we found that 19 had odorant binding sites and tunnels in similar positions to Mh OR5. The possibility of a tunnel between the odorant binding site and the lipid bilayer in insect ORs suggests new experiments to test molecular mechanisms for insect odorant reception. [Display omitted] • The insect olfactory receptor Mh OR5 was analyzed by molecular dynamics simulation. • Tunnels connect occluded ligand-binding sites to the exterior and to the lipid bilayer. • Tunnel bottlenecks undergo large area fluctuations over 5–10 ns. • Steered molecular dynamics shows ligand can enter or exit Mh OR5 via the tunnels. [ABSTRACT FROM AUTHOR]