The three dimensional structure of an insect olfactory receptor, MhOR5, from the jumping bristletail Machilis hrabei, provides insight into the ligand gating mechanism of OR ion channels. The binding site for eugenol in MhOR5 is occluded, both in the liganded and unliganded structures. Using molecular dynamics simulation, we found tunnels to the ligand site that open on a nanosecond time scale. Tunnels open into the lipid bilayer and also to the protein's exterior surface. We examined AlphaFold models of 21 Drosophila melanogaster ORs, using AutoDock software to predict binding sites for ligands known to activate the ion channel. We found all bound to sites analogous to the eugenol site in MhOR5, with 19 having tunnels to the lipid bilayer and 16 with tunnels to the exterior surface. We examined a subset of 11 D. melanogaster ORs for AutoDock predictions of binding to DEET. In 9 of 11, the predicted DEET binding site overlapped with the predicted ligand binding site, including 3 ligands known to stimulate repellent behavior and 6 ligands known to be attractants. It is possible that, for some of the ORs with attractant ligands, the access tunnels act as filters to prevent DEET's access to the ligand binding site, even though it would bind there if it could get in. However, neurons containing three of the attractant ORs were previously reported to be activated by DEET, indicating that DEET can simultaneously stimulate both attraction and repellency. This is consistent with the idea of DEET as a "confusant".
