Rhodopsins excited state

Because the high quantum yield originates from the high-rate isomerization, which competes with other relaxation processes in the excited state of rhodopsin, ultrafast laser spectroscopies were applied to investigate the isomerization process of the retinal chromophore. Picosecond time-resolved spectroscopy was appHed to the photochemistry of rhodopsin, and the formation of the primary intermediates was reported, such as photorhodopsin and bathorhodopsin at room temperature. - - However, the time resolution needed to be improved in order to detect the cis-tram isomerization process in the excited state of rhodopsin. The direct observation of the rhodopsin excited state was reported in 1991, in which the primary intermediate photorhodopsin formed from the excited state of rhodopsin within 200 fs. Later, the effects of oscillatory features with a period of 550 fs (60 cm ) on the formation kinetics of photorhodopsin, were observed, suggesting that the primary step in vision is a vibrationally coherent process. 

As shown by the calculations of bacteriorhodopsin (Section 2.3.2.1), ONIOM is an excellent tool for excited-state reactions in biology. The important rhodopsin system has been studied both by TD-B3LYP Amber [80] and CASSCF Amber [81]. Another example of the combination of CASSCF with Amber for the surrounding protein can be found for the yellow protein [82],... 

The Photoactive Yellow Protein (PYP) is the blue-light photoreceptor that presumably mediates negative phototaxis of the purple bacterium Halorhodospira halophila [1]. Its chromophore is the deprotonated trans-p-coumaric acid covalently linked, via a thioester bond, to the unique cystein residue of the protein. Like for rhodopsins, the trans to cis isomerization of the chromophore was shown to be the first overall step of the PYP photocycle, but the reaction path that leads to the formation of the cis isomer is not clear yet (for review see [2]). From time-resolved spectroscopy measurements on native PYP in solution, it came out that the excited-state deactivation involves a series of fast events on the subpicosecond and picosecond timescales correlated to the chromophore reconfiguration [3-7]. On the other hand, chromophore H-bonding to the nearest amino acids was shown to play a key role in the trans excited state decay kinetics [3,8]. In an attempt to evaluate further the role of the mesoscopic environment in the photophysics of PYP, we made a comparative study of the native and denatured PYP. The excited-state relaxation path and kinetics were monitored by subpicosecond time-resolved absorption and gain spectroscopy. 

To summarize, Jean shows that coherence can be created in a product as a result of nonadiabatic curve crossing even when none exists in the reactant [24, 25]. In addition, vibrational coherence can be preserved in the product state to a significant extent during energy relaxation within that state. In barrierless processes (e.g., an isomerization reaction) irreversible population transfer from one well to another occurs, and coherent motion can be observed in the product regardless of whether the initially excited state was prepared vibrationally coherent or not [24]. It seems likely that these ideas are crucial in interpreting the ultrafast spectroscopy of rhodopsins [17], where coherent motion in the product is directly observed. Of course there may be many systems in which relaxation and dephasing are much faster in the product than the reactant. In these cases lack of observation of product coherence does not rule out formation of the product in an essentially ballistic manner. 

C. The steps following the formation of bathorhodopsin have progressively higher thermal activation energies. They can be blocked by lowering the temperature below the temperatures indicated on the left. Asterisk indicates the excited state of rhodopsin. 

Isomerization of the retinal Schiff s base can occur when the molecule is excited with light, because the C-l 1-C-12 bond loses much of its double-bond character in the excited state. The valence bond diagrams of figure S2.7 illustrate this point. In the ground state of rhodopsin, the potential energy barrier to rotation about the C-l 1-C-l2 bond is on the order of 30 kcal/mol. This barrier essentially vanishes in the excited state. In fact, the energy of the excited molecule probably is minimal when the C-11 -C-l2 bond is twisted by about 90° (fig. S2.8). The excited molecule oscillates briefly about this intermediate conformation, and when it decays back to a ground state it usually settles into the ail-trans isomer, bathorhodopsin. 

Andruniow T, Ferre N, Olivucci M (2004) Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level. Proc. Natl. 

Low temperature experiments have shown the formation of hypso intermediates from several species [99,103,105-107]. The study of early photoconversion processes in squid [108], which also involved the evaluation of the relative quantum yields among the four pigments (squid rhodopsin, squid batho-, hypso- and isorhodopsin) showed that hypsorhodopsin is a common intermediate of rhodopsin and isorhodopsin there is no direct conversion between rhodopsin and isorhodopsin bathorhodopsin is not converted directly to hypsorhodopsin and both rhodopsin and isorhodopsin convert more efficiently to bathorhodopsin than to hypsorhodopsin. While a temperature dependence of the relaxation processes from the excited state of rhodopsin, and an assumption that batho could be formed from one of the high vibrational levels of the ground state hypso have been invoked to explain these findings [108], the final clarification of this matter awaits results from subpicosecond laser photolysis experiments at liquid helium temperature. 

In a model proposed by Lewis [228] the effect of the excited state of retinal on the conformational state of the protein is considered to be the first step of the excitation mechanism. Charge redistribution in the retinal by excitation with light would have the consequence of vibrationally exciting and perturbing the ground state conformation of the protein, i.e., excited retinal would induce transient charge density assisted bond rearrangements (e.g., proton translocation). Subsequently, retinal would assume such an isomeric and conformational state so as to stabilize maximally the new protein structure established. In this model, 11-m to trans isomerization would not be involved in the primary process, but would serve to provide irreversibility for efficient quantum detection. It was also proposed that either the 9-m-retinal (in isorhodopsin) or the 11-m-retinal (in rhodopsin) could yield the same, common... 

Fig. 17. Adiabatic potential of rhodopsin as a function of torsional angle around the 11,12 bond. Curves a and b represent adiabatic potentials of Schiff base in the ground state and in the excited state. Curves c and d represent adiabatic potentials of rhodopsin in the ground and excited states respectively. Rhodopsin (A) by absorption of photon goes to excited state (B), isomerization occurs (C), it then goes nonradiatively to D and to E and finally it dissociates totally into retinal and opsin. Adapted from Kakitani and Kakitani [203],...

Fig. 19. Potential energy curves and energy relationships in rhodopsin. Curve I Excited state of rhodopsin and bathorhodopsin. Curve II Ground state of rhodopsin and bathorhodopsin. Curve 111 Ground stale of isolated chromophore. Symbols , and 2 are quantum yields for reaching the single potential minimum along the 11,12 torsional coordinate. From Rosenfeld et al. [201].

Table 4-3. The first excited states of rhodopsin (Rh), bacteriorhodopsin (bR), sensoryrhodopsin II (sRII), and human blue cone pigment (HB) calculated by the SAC-CI and other methods...

RetinalS. The structure and photophysics of rhodopsins are intimately related to the spectroscopic properties of their retiny1-polyene chromophore in its protein-free forms, such as the aldehyde (retinal), the alcohol (retinol or vitamin A), and the corresponding Schiff bases. Since most of the available spectroscopic information refers to retinal isomers (48-55), we shall first center the discussion on the aldehyde derivatives. Three bands, a main one (I) around 380 nm and two weaker transitions at 280 nm and 250 nm (II and III), dominate the spectrum of retinals in the visible and near ultraviolet (Fig. 2). Assignments of these transitions are commonly made in terms of the lowest tt, tt excited states of linear polyenes, the spectroscopic theories of which have been extensively discussed in the past decade (56-60). In terms of the idealized C2h point group of, for example, all-trans butadiene, transitions are expected from the Ta ground state to B , A, and A" excited states... 

The process entails shifting of double bonds along the polyene chain, with the formation of a "retro-retinal" structure. Peters et al. (301) interpreted their observations by identifying PBAT with an excited state of rhodopsin, where single proton transfer toward the Schiff base nitrogen leads to the formation of bathorhodopsin. This approach has been supported by the theoretical interpretation of the spectrum of rhodopsin in terms of a nonprotonated Schiff base (214-216). A mechanism involving deprotonation of the Schiff base has also been suggested (310). All these models do not require cis-trans isomerization as a primary event in the chromo-phore. 

Figure 10. Schematic potential energy curves accounting for the primary event in vision. I. Excited state of rhodopsin and bathorhodopsin. II. Ground state of rhodopsin and bathorhodop-sin. III. Ground state of the isolated PRSB chromophore. E] and E2 are estimated from the equilibrium constants IC = [rhodopsin]/ [11-cis retinal][opsin] < 10 and K2 + [bathorhodopsin]/[all-trans retinal][opsin] < 10"2, respectively. With E3 = 1 kcal, this leads to E4 = E2 + Ei - E3 > 13 kcal. The value estimated from thermal noise data in photoreceptors is E4 = 30 kcal. Note that according to the isomerization model (Section III-B-l-c),...

AIMD simulations have also been carried out on the chromophore present in the rhodopsin photoreceptor (retinal). In the primary event of vision, retinal passes from the ground state (GS) to an excited state (ES) and isomerizes from 11-cis to all-trans within 200 fs. A series of papers [46-50] have analyzed the GS isomerization process. More recently, calculations were extended to the first singlet ES [51] within a recently developed scheme for singlet state dynamics [52]. This work characterizes structural and energetic changes during the photoisomerization process and points to the crucial role of environment effects. 

Retinal as Visual Pigment Model Spectroscopy and Physical Chemistry. As in previous years, several theoretical, spectroscopic, and photochemical studies of retinal (136) and related compounds, especially Schiffs bases, have been reported,and in many cases the main aim was to obtain information relevant to the functioning of rhodopsin and related visual pigments. Particularly valuable are surveys of the year s literature on the photochemistry of polyenes, excited states of biomolecules,and recent developments in the molecular biology of vision. 

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. 

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