Fig. 5: Random acceleration molecular dynamics (RAMD) simulations exploring potential exit pathways of non-covalently bound all-trans retinal and decanoate from proteoopsin.
The exit trajectories for the non-covalently bound all-trans retinal (A) or decanoate (B) are shown with spheres representing the centres of mass of the ligands. Similar trajectories were organised into groups labelled 1-6 (coloured individually), where pathway 6 was only observed in decanoate simulations. Top views in (A) and (B) are seen from the extracellular side. Ligands are depicted as ball-and-stick models (black), TMHs are labelled (A–G) and lipid bilayer boundaries (based on the PPM server64) are indicated in the side views.
