Investigation of the chromophore binding cavity in the 11-cis acceptable microbial rhodopsin MR

Rhodopsins are photoactive molecules functioning as photo-energy or photo-signal converters with the chromophore retinal. Recently we characterized a unique microbial rhodopsin (middle rhodopsin, MR) which can also bind 11-cis retinal besides all-trans and 13-cis retinal at a particular ratio. In this study, we investigated the structural characteristics around the retinal binding cavity in MR. The results suggest that the space of the retinal binding site of MR is less restricted to the retinal chromophore and the presence of the 11-cis conformer is regulated by the residues located around the retinal. Furthermore, although the triple mutant of MR has identical residues with the well-studied microbial rhodopsin bacteriorhodopsin (BR) within 5 Å from the retinal, the absorption maximum and retinal composition of MR did not reach those of BR, indicating that some long-range effect(s) (>5 Å) is also important for the maintenance of the chemical properties of MR.