Reaction pathways bacteriorhodopsin

Figure 4.3 shows photochemical reactions in visual (Fig. 4.3A) and archaeal (Fig. 4.3B) rhodopsins. In visual rhodopsins, the 11-as-retinal is isomerized into the a -trans form. The selectivity is 100%, and the quantum yield is 0.67 for bovine rhodopsin [20]. In archaeal rhodopsins, the all-trans-retinal is isomerized into the 13-cis form. The selectivity is 100%, and the quantum yield is 0.64 for bacteriorhodopsin [21]. Squid and octopus possess a photoisomerase called retino-chrome, which supplies the 11-ris-retinal for their rhodopsins through the specific photoreaction. Retinochrome possesses all-trans-retinal as the chromophore, and the all-trans-retinal is isomerized into the 11-cis form with a selectivity of 100% [22]. Thus, the photoproduct is different between archaeal rhodopsins and retinochrome, the aU-trans form being converted into the 13-cis and 11-cis forms, respectively. This fact implies that protein environment determines the reaction pathways of photoisomerization in their excited states. 

HPLC analysis also revealed that the protonated Schiff base of all-traws-retinal in solution is isomerized predominantly into the 11-cis form (82% 11-cis, 12% 9-cis, and 6% 13-ds in methanol) [23]. The 11-cis form as a photoproduct is the nature of retinochrome, not those of archaeal rhodopsins. This suggests that the protein environment of retinochrome serves as the intrinsic property of the photoisomerization of the retinal chromophore. In contrast, it seems that the protein environment of archaeal rhodopsins forces the reaction pathway of the isomerization to change into the 13-cis form. In this regard, it is interesting that the quantum yield of bacteriorhodopsin (0.64) is 4—5 times higher than that in solution (-0.15) [21,23], The altered excited state reaction pathways in archaeal rhodopsins never reduce the efficiency. Rather, archaeal rhodopsins discover the reaction pathway from the all-trans to 13-cis form efficiently. Consequently, the system of efficient isomerization reaction is achieved as well as in visual rhodopsins. Structural and spectroscopic studies on archaeal rhodopsins are also reviewed in Section 4.3. 

The great dielectric asymmetry of the two half-membrane charge transfer pathways in bacteriorhodopsin is in contrast with the situation in the photosynthetic reaction centre complex. In the latter case, both halves of the membraneous protein are very hydrophobic and equally contribute to Ar/j formation [7,24]. 

Fig. 5. Suggested scheme for the photocycle of bacteriorhodopsin [114-116], The photoreaction produces state J, the other reactions represent the pathway of thermal relaxation back to the initial state. Where release and uptake are shown, they refer to exchange of the proton with the aqueous...

Proton transfer is closely linked to the structure of the reaction-center protein. Since protons are present in the external aqueous medium, the (reduced) quinone molecules are buried inside the interior ofthe reaction-center protein, therefore protonation would seem to require some kind of channel for the passage of water molecules. However, at least until recently (see below), there was no evidence for the presence of channels large enough to accommodate water molecules. An alternative mechanism might involve a chain of ionizable amino acids which extends from the surface of the protein to the interior where the reduced quinone is located, forming a pathway along which protons may be transported. Such a mechanism has been likened to a bucket brigade or relay station and shown to exist in such proteins as bacteriorhodopsin, ATP synthase and cytochrome oxidase. 

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