Photochemistry of the Retinal Chromophore in Microbial Rhodopsins

Abstract

Microbial rhodopsins are photoreceptive membrane proteins of microorganisms that express diverse photobiological functions. All-trans-retinylidene Schiff base, the so-called all-trans-retinal, is a chromophore of microbial rhodopsins, which captures photons. It isomerizes into the 13-cis form upon photoexcitation. Isomerization of retinal leads to sequential conformational changes in the protein, giving rise to active states that exhibit biological functions. Despite the rapidly expanding diversity of microbial rhodopsin functions, the photochemical behaviors of retinal were considered to be common among them. However, the retinal of many recently discovered rhodopsins was found to exhibit new photochemical characteristics, such as highly red-shifted absorption, isomerization to 7-cis and 11-cis forms, and energy transfer from a secondary carotenoid chromophore to the retinal, which is markedly different from that established in canonical microbial rhodopsins. Here, I review new aspects of retinal found in novel microbial rhodopsins and highlight the emerging problems that need to be addressed to understand noncanonical retinal photochemistry.

Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins

“…Fluorescence and photoisomerization of the chromophore in opsin-based photosensitive proteins have been investigated for decades [7,8,98,99]. Recently, the research in this area has been facilitated by application of rhodopsins as tools for optogenetics [100][101][102], which is, along with photopharmacology [103][104][105][106], a widely used approach to control and monitor biological cell activity using light.…”

“…The first path converts the chromophore back to the initial form, and the second path leads to the successful photoisomerization reaction that initiates a series of processes required for a rhodopsin to perform its biological function. In rhodopsins, the protein environment facilitates the photoisomerization of a chromophore, since it is the process that is directly related to rhodopsin functioning, and, as a rule, photoisomerization in rhodopsins occurs very efficiently (e.g., photoisomerization quantum yields in bovine visual rhodopsin and bacteriorhodopsin are 0.65 and 0.64, respectively) [7][8][9]. On the contrary, fluorescence is a side process for rhodopsin functions, and the radiative pathway is suppressed in these proteins.…”

Chromophore–Protein Interactions Affecting the Polyene Twist and π–π* Energy Gap of the Retinal Chromophore in Schizorhodopsins

“…The polyene chain of the retinal chromophore is situated between two specific aromatic residues, while an additional aromatic residue lies on the side of the polyene plane. These interactions play key roles in regulating the retinal chromophore in rhodopsins . It is widely accepted that the selectivity of the photoisomerization site is determined by the steric effect due to residues surrounding the retinal chromophore in proteins because the photoproducts of all- trans -retinal derivatives in organic solvents are in the 7- cis , 9- cis , 11- cis , and 13- cis forms (numbering of the positions of the skeletal carbon atoms in the retinal chromophore is shown in Figure ).…”

Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin

“…The resulting rPSB isomer triggers the formation of opsin conformers that, ultimately, drive biological functions such as vision in contribute to the solar energy capture. 18 Despite these facts, only a limited number of studies have targeted the rPSB isomerization diversity in both animal [19][20][21] and microbial [22][23][24][25][26][27] rhodopsins. For this reason, we present a computational study of the photoisomerization mechanism and dynamics of a member of a recently discovered rhodopsin family and compare the results to those obtained for the evolutionarily distant dim-light visual pigment of vertebrates.…”