The primary photoisomerization reactions of the all-trans to 13-cis and 11-cis to all-trans retinal protonated Schiff base (RPSB) in microbial and animal rhodopsins, respectively, occur on a subpicosecond time scale with high quantum yields. At the same time, the isolated RPSB exhibits slower excited-state decay, in particular, in its all-trans form, and hence the interaction with the protein environment is capable of changing the time scale as well as the specificity of the reaction. Here, by using the high-level QM/MM calculations, we provide a comparative study of the primary photoresponse of cis and trans RPSB isomers in both the initial forms and first photoproducts of microbial Krokinobacter eikastus rhodopsin 2 (KR2) and Halobacterium salinarum bacteriorhodopsin (BR), and animal Bos taurus visual rhodopsin (Rho). By simulating photoabsorption band shapes of RPSB inside the proteins, we show that its photoresponse is highly mode-specific for the forward reactions, resulting in excitation of those vibrational modes that facilitate particular double-bond isomerization. The reverse reaction shows specificity only for 13-cis isomers in microbial rhodopsins, whereas the specificity is lost for all-trans RPSB in visual rhodopsin. This indicates evolutionary highly tuned 11-cis chromophore-protein interactions in visual rhodopsin. We also highlight the differences in the photoresponse of RPSB in two microbial rhodopsins and discuss the implications to their excited-state dynamics.
