Fig. 7. Equilibrium between retinal isomers and dynamics at the retinal binding pocket.

a Proposed scheme of retinal isomer equilibrium formed after illumination. The isomerization pathways taking place after red (625 nm) illumination of protonated species are indicated with red arrows. The isomerization pathways taking place after blue (400 nm) illumination of the deprotonated species are indicated with violet arrows. The thickness of the arrows represents the likelihood of the isomerization to take place, as predicted from HPLC analysis of the extracted chromophore (Fig. 2). Nevertheless, the efficiency of all isomerization pathways is very low. The red illumination may induce double and single isomerization. The more likely double isomerization would result in an equilibrium shift between the 13-trans/15-anti and 13-cis/15-syn (upper row of the panel). The single isomerization would drive a photocycle and result in deprotonation (a shift between the upper row indicated isomers and the lower row indicated isomers). The blue illumination of deprotonated species would result in a backreaction with a strong preference towards the population of 13-cis/15-syn isomer. b According to our models, the voltage-dependent dynamics of the intracellular part of helix D modulate the side-chain orientation of D125 in helix D. The reorientations of D125 in Archon1 result in the reorganization of the hydrogen bonding network involving the RSBH⁺. The key residues are indicated. c The key residues and their interactions are indicated in the homology model of Archon1.