pH-dependent transitions in xanthorhodopsin

Xanthorhodopsin (XR), the light-driven proton pump of the halophilic eubacterium Salinibacter ruber, exhibits substantial homology to bacteriorhodopsin (BR) of archaea and proteorhodopsin (PR) of marine bacteria, but unlike them contains a light-harvesting carotenoid antenna, salinixanthin, as well as retinal. We report here the pH-dependent properties of XR. The pKa of the retinal Schiff base is as high as in BR, i.e. > or =12.4. Deprotonation of the Schiff base and the ensuing alkaline denaturation cause large changes in the absorption bands of the carotenoid antenna, which lose intensity and become broader, making the spectrum similar to that of salinixanthin not bound to XR. A small redshift of the retinal chromophore band and increase of its extinction, as well as the pH-dependent amplitude of the M intermediate indicate that in detergent-solubilized XR the pKa of the Schiff base counterion and proton acceptor is about 6 (compared to 2.6 in BR, and 7.5 in PR). The protonation of the counterion is accompanied by a small blueshift of the carotenoid absorption bands. The pigment is stable in the dark upon acidification to pH 2. At pH < 2 a transition to a blueshifted species absorbing around 440 nm occurs, accompanied by loss of resolution of the carotenoid absorption bands. At pH < 3 illumination of XR with continuous light causes accumulation of long-lived photoproduct(s) with an absorption maximum around 400 nm. The photocycle of XR was examined between pH 4 and 10 in solubilized samples. The pH dependence of recovery of the initial state slows at both acid and alkaline pH, with pKas of 6.0 and 9.3. The decrease in the rates with pKa 6.0 is apparently caused by protonation of the counterion and proton acceptor, and that at high pH reflects the pKa of the internal proton donor, Glu94, at the times in the photocycle when this group equilibrates with the bulk.     

PHOTOCHEMISTRY OF METHYLATED RHODOPSINS

Abstract— Rhodopsin, in which the active-site Schiff-base lysine has been chemically modified by monomethylation, is unable to form the deprotonated Schiff base bleaching intermediate, rnetarhodop-sin II. The photochemistry of the methylated Schiff base rhodopsin stops at the metarhodopsin I stage, which then slowly decays to all-trans retinal and opsin. Methylation of the non active-site lysines does not block the photochemical transformation but does speed up the formation and decay of the metarhodopsins.     

Micellar effects on photoprocesses in retinyl polyenes

The effects of micellar solubilization on excited-state properties of several retinyl polyenes have been examined primarily by nanosecond laser flash photolysis. The relative intensity of band system III (254–256 nm) in the ground state absorption spectrum of 11-cis retinal decreases significantly on going from methanol to micellar solutions, suggesting that the 12-s-trans form of 11-cis retinal is relatively favored in the organized media. In addition to microsecond transient phenomena due to triplets, the laser flash photolysis of all-trans and 11-cis retinal and all-trans retinyl Schiff base incorporated into micelles leads to ‘permanent’ absorption changes attributable to photoisomerization (in the case of retinals) and protonation and/or complexation with water (in the case of Schiff base). All-trans retinol and retinyl acetate in micellar solutions undergo ionic photodissociation leading to long-lived retinyl carbocation (λ_max = 585–600 nm), the process being monophotonic in the case of retinyl acetate and predominantly bipho-tonic in the case of retinol. The trends in the location of ground-state absorption maxima (^IB_u^+*←^IA_g) and triplet yield of retinals, and photodissociation yield of retinyl acetate suggest that the polarity of the environment probed by the polyene systems increases in the order: Triton X-100 < CTAB < NaLS.     

MOLECULAR MECHANISMS IN VISUAL PIGMENT REGENERATION

The photochemical bleaching of vertebrate rhodopsin results in the cis to trans isomerization of the 11-cis-retinal protonated Schiff base. Hydrolysis of the Schiff base leads to the formation of opsin and all-trans-retinal. In order for vision to proceed, the enzymatic trans to cis isomerization of a retinoid must occur. Since retinoids exist as alcohols, aldehydes, or esters in the eye, there are potentially nine different routes for isomerization. Moreover, 11-cis-retinoids are approximately 4 kcal/mol higher in energy than their all-trans isomers. Thus, not only must the isomerization route be defined, but an energy source must be identified to power this process. It was discovered that the energy is provided for in a minimally two-step process involving membrane phospholipids as the energy source. First, all-trans-retinol (vitamin A) is esterified in the retinal pigment epithelium by lecithin retinol acyl transferase to produce an all-trans-retinyl ester. Second, this ester is directly transformed into 11-cis-retinol by an isomerohydrolase enzyme, in a process that couples the negative free energy of hydrolysis of the acyl ester to the formation of the strained 11-cis-retinoid.     

LIGHT-INDUCED PERTURBATION OF AROMATIC RESIDUES IN BOVINE RHODOPSIN AND BACTERIORHODOPSIN*

Light-induced changes in the UV absorption spectrum of bovine rod outer segment membranes were measured by conventional difference spectroscopy and by flash photolysis methods. Different thermal intermediates of rhodopsin (lumirhodopsin, metarhodopsin I, metarhodopsin II, and meta-rhodopsin III) have absorption spectra in the ultraviolet which differ from the rhodopsin spectrum and from each other. The spectra associated with metarhodopsin I, metarhodopsin II, and metarhodopsin III are characteristic of perturbation of a small number of tyr. and/or trp residues, most likely one trp residue. These aromatic residues are in the neighborhood of the retinal Schiff base and undergo coordinated changes of interaction with retinal during the bleaching sequence. At the metarhodopsin II stage, the magnitude of the UV spectral changes is consistent with the exposure of a previously shielded trp residue to an aqueous environment. The present results are consistent with previous spectral studies which limit the extent of light-induced conformational changes to regions of the protein in the neighborhood of the retinal Schiff base. An analogous study was made on light-adapted purple membranes of Halobacterium halobium. The UV absorption spectrum associated with the deprotonated Schiff base intermediate of the trans-bacteriorhodopsin cycle is indicative, in part, of aromatic residue perturbation. However, significant changes in the secondary and tertiary structures of the bacterio-rhodopsin protein characteristic of a delocalized conformational change are unlikely at this intermediate stage.     

Carotenoid response to retinal excitation and photoisomerization dynamics in xanthorhodopsin

We present a comparative study of xanthorhodopsin, a proton pump with the carotenoid salinixanthin serving as an antenna, and the closely related bacteriorhodopsin. Upon excitation of retinal, xanthorhodopsin exhibits a wavy transient absorption pattern in the region between 470 and 540 nm. We interpret this signal as due to electrochromic effect of the transient electric field of excited retinal on salinixanthin. The spectral shift decreases during the retinal dynamics through the ultrafast part of the photocycle. Differences in dynamics of bacteriorhodopsin and xanthorhodopsin are discussed.     

Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.     

Activity switches of rhodopsin

Rhodopsin, the visual pigment of the rod photoreceptor cell contains as its light-sensitive cofactor 11-cis retinal, which is bound by a protonated Schiff base between its aldehyde group and the Lys296 side chain of the apoprotein. Light activation is achieved by 11-cis to all-trans isomerization and subsequent thermal relaxation into the active, G protein-binding metarhodopsin II state. Metarhodopsin II decays via two parallel pathways, which both involve hydrolysis of the Schiff base eventually to opsin and released all-trans retinal. Subsequently, rhodopsin's dark state is regenerated by a complicated retinal metabolism, termed the retinoid cycle. Unlike other retinal proteins, such as bacteriorhodopsin, this regeneration cycle cannot be short cut by light, because blue illumination of active metarhodopsin II does not lead back to the ground state but to the formation of largely inactive metarhodopsin III. In this review, mechanistic details of activating and deactivating pathways of rhodopsin, particularly concerning the roles of the retinal, are compared. Based on static and time-resolved UV/Vis and FTIR spectroscopic data, we discuss a model of the light-induced deactivation. We describe properties and photoreactions of metarhodopsin III and suggest potential roles of this intermediate for vision.     

Novel retinylidene iminium salts for defining opsin shifts: synthesis and intrinsic chromophoric properties

Retinal Schiff bases serve as chromophores in many photoactive proteins that carry out functions such as signalling and light-induced ion translocation. The retinal Schiff base can be found as neutral or protonated, as all-trans, 11-cis or 13-cis isomers and can adopt different conformations in the protein binding pocket. Here we present the synthesis and characterisation of isomeric retinylidene iminium salts as mimics blocked towards isomerisation at the C11 position and conformationally restrained. The intrinsic chromophoric properties are elucidated by gas phase absorption studies. These studies reveal a small blue-shift in the S0-->S1 absorption for the 11-locked derivative as compared to the unlocked one. The gas phase absorption spectra of all the cationic mimics so far investigated show almost no absorption in the blue region. This observation stresses the importance of protein interactions for colour tuning, which allows the human eye to perceive blue light.     

A resonance Raman study of octopus bathorhodopsin with deuterium labeled retinal chromophores.

The resonance Raman spectrum of octopus bathorhodopsin in the fingerprint region and in the ethylenic-Schiff base region have been obtained at 80 K using the "pump-probe" technique as have its deuterated chromophore analogues at the C7D; C8D; C8,C7D2; C10D; C11D; C11, C12D2; C14D; C15D; C14, C15D2; and N16D positions. While these data are not sufficient to make definitive band assignments, many tentative assignments can be made. Because of the close spectral similarity between the octopus bathorhodopsin spectrum and that of bovine bathorhodopsin, we conclude that the essential configuration of octopus bathorhodopsin's chromophore is all-trans like. The data suggest that the Schiff base, C = N, configuration is trans (anti). The observed conformationally sensitive fingerprint bands show pronounced isotope shifts upon chromophore deuteration. The size of the shifts differ, in certain cases, from those found for bovine bathorhodopsin. Thus, the internal mode composition of the fingerprint bands differs somewhat from bovine bathorhodopsin, suggesting a somewhat different in situ chromophore conformation. An analysis of the NH bend frequency, the Schiff base C = N stretch frequency, and its shift upon Schiff base deuteration suggests that the hydrogen bonding between the protonated Schiff base with its protein binding pocket is weaker in octopus bathorhodopsin than in bovine bathorhodopsin but stronger than that found in bacteriorhodopsin's bR568 pigment.     

Pressure-induced isomerization of retinal on bacteriorhodopsin as disclosed by fast magic angle spinning NMR

Bacteriorhodopsin (bR) is a retinal protein in purple membrane of Halobacterium salinarum, which functions as a light-driven proton pump. We have detected pressure-induced isomerization of retinal in bR by analyzing 15N cross polarization-magic angle spinning (CP-MAS) NMR spectra of [zeta-15N]Lys-labeled bR. In the 15N-NMR spectra, both all-trans and 13-cis retinal configurations have been observed in the Lys N(zeta) in protonated Schiff base at 148.0 and 155.0 ppm, respectively, at the MAS frequency of 4 kHz in the dark. When the MAS frequency was increased up to 12 kHz corresponding to the sample pressure of 63 bar, the 15N-NMR signals of [zeta-15N]Lys in Schiff base of retinal were broadened. On the other hand, other [zeta-15N]Lys did not show broadening. Subsequently, the increased signal intensity of [zeta-15N]Lys in Schiff base of 13-cis retinal at 155.0 ppm was observed when the MAS frequency was decreased from 12 to 4 kHz. These results showed that the equilibrium constant of [all-trans-bR]/[13-cis-bR] in retinal decreased by the pressure of 63 bar. It was also revealed that the structural changes induced by the pressure occurred in the vicinity of retinal. Therefore, microscopically, hydrogen-bond network around retinal would be disrupted or distorted by a constantly applied pressure. It is, therefore, clearly demonstrated that increased pressure induced by fast MAS frequencies generated isomerization of retinal from all-trans to 13-cis state in the membrane protein bR.     

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

Here we improved our hybrid QM/MM methodology (Houjou et al. J Phys Chem B 2001, 105, 867) for evaluating the absorption maxima of photoreceptor proteins. The renewed method was applied to evaluation of the absorption maxima of several retinal proteins and photoactive yellow protein. The calculated absorption maxima were in good agreement with the corresponding experimental data with a computational error of <10 nm. In addition, our calculations reproduced the experimental gas-phase absorption maxima of model chromophores (protonated all-trans retinal Schiff base and deprotonated thiophenyl-p-coumarate) with the same accuracy. It is expected that our methodology allows for definitive interpretation of the spectral tuning mechanism of retinal proteins.     

A POSSIBLE MECHANISM FOR THE ROLE OF N-RETINYLIDENE PHOSPHATIDYL ETHANOLAMINE IN THE REGENERATION OF RHODOPSIN

Abstract— A series of molecular orbital calculations on a model Schiff base comparable to protonated N -retinylidene phosphatidyl ethanolamine isomers has been made. The effect of the charged oxygen atoms of the phosphate moiety on the distribution of positive charge along the polyene chain of these isomers has been calculated. The stabilizing coulombic energy of interaction of these opposite charges and the possibility of free rotation around carbonxarbon double bonds in the electronically excited state has led to the conclusion that an 11- cis Schiff base isomer is the most probable product of the photoisomerization of an all-trans Schiff base.
The formation of a stable unprotonated all-trans Schiff base in aqueous detergent dispersion and its subsequent conversion to the protonated form, both with absorption spectra in conformity with the literature, is demonstrated.     

Mechanism of G-protein activation by rhodopsin

Rhodopsin is a member of the family of G-protein-coupled receptors (GPCRs), and is an excellent molecular switch for converting light signals into electrical response of the rod photoreceptor cells. Light initiates cis-trans isomerization of the retinal chromophore of rhodopsin and leads to the formation of several thermolabile intermediates during the bleaching process. Recent investigations have identified spectrally distinguishable two intermediate states that can interact with the retinal G-protein, transducin, and have elucidated the functional sharing of these intermediates. The initial contact with GDP-bound G-protein occurs in the meta-Ib intermediate state, which has a protonated Schiff base as its chromophore. The meta-Ib intermediate in the complex with the G-protein converts to the meta-II intermediate with releasing GDP from the alpha-subunit of the G protein. Meta-II has a de-protonated Schiff base chromophore and induces binding of GTP to the alpha-subunit of the G-protein. Thus, the GDP-GTP exchange reaction, namely G-protein activation, by rhodopsin proceeds through at least two steps, with conformational changes in both rhodopsin and the G-protein.     

A molecular spring for vision

Light absorption by the visual pigment rhodopsin leads to vision via a complex signal transduction pathway that is initiated by the ultrafast and highly efficient photoreaction of its chromophore, the retinal protonated Schiff base (RPSB). Here, we investigate this reaction in real time by means of unrestrained molecular dynamics simulations of the protein in a membrane mimetic environment, treating the chromophore at the density functional theory level. We demonstrate that a highly strained all-trans RPSB is formed starting from the 11-cis configuration (dark state) within approximately 100 fs by a minor rearrangement of the nuclei under preservation of the saltbridge with Glu113 and virtually no deformation of the binding pocket. Hence, the initial step of vision can be understood as the compression of a molecular spring by a minor change of the nuclear coordinates. This spring can then release its strain by altering the protein environment.     

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base.

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.     

Rhodopsin regeneration is accelerated via noncovalent 11-cis retinal-opsin complex--a role of retinal binding pocket of opsin

The regeneration of bovine rhodopsin from its apoprotein opsin and the prosthetic group 11-cis retinal involves the formation of a retinylidene Schiff base with the epsilon-amino group of the active lysine residue of opsin. The pH dependence of a Schiff base formation in solution follows a typical bell-shaped profile because of the pH dependence of the formation and the following dehydration of a 1-aminoethanol intermediate. Unexpectedly, however, we find that the formation of rhodopsin from 11-cis retinal and opsin does not depend on pH over a wide pH range. These results are interpreted by the Matsumoto and Yoshizawa (Nature 258 [1975] 523) model of rhodopsin regeneration in which the 11-cis retinal chromophore binds first to opsin through the beta-ionone ring, followed by the slow formation of the retinylidene Schiff base in a restricted space. We find the second-order rate constant of the rhodopsin formation is 6100+/-300 mol(-1) s(-1) at 25 degrees C over the pH range 5-10. The second-order rate constant is much greater than that of a model Schiff base in solution by a factor of more than 10(7). A previous report by Pajares and Rando (J Biol Chem 264 [1989] 6804) suggests that the lysyl epsilon-NH(2) group of opsin is protonated when the beta-ionone ring binding site is unoccupied. The acceleration of the Schiff base formation in rhodopsin is explained by stabilization of the deprotonated form of the lysyl epsilon-NH(2) group which might be induced when the beta-ionone ring binding site is occupied through the noncovalent binding of 11-cis retinal to opsin at the initial stage of rhodopsin regeneration, followed by the proximity and orientation effect rendered by the formation of noncovalent 11-cis retinal-opsin complex.     

Absorption of schiff-base retinal chromophores in vacuo

The absorption spectrum of the all-trans retinal chromophore in the protonated Schiff-base form, that is, the biologically relevant form, has been measured in vacuo, and a maximum is found at 610 nm. The absorption of retinal proteins has hitherto been compared to that of protonated retinal in methanol, where the absorption maximum is at 440 nm. In contrast, the new gas-phase absorption data constitute a well-defined reference for spectral tuning in rhodopsins in an environment devoid of charges and dipoles. They replace the misleading comparison with absorption properties in solvents and lay the basis for reconsidering the molecular mechanisms of color tuning in the large family of retinal proteins. Indeed, our measurement directly shows that protein environments in rhodopsins are blue- rather than red shifting the absorption. The absorption of a retinal model chromophore with a neutral Schiff base is also studied. The data explain the significant blue shift that occurs when metharhodopsin I becomes deprotonated as well as the purple-to-blue transition of bacteriorhodopsin upon acidification.     

The photoreaction of vacuum-dried rhodopsin at low temperature: evidence for charge stabilization by water

The photoreaction of vacuum-dried rhodopsin was monitored by UV-visible absorption spectroscopy. The results indicate that in dry rhodopsin, isorhodopsin and lumirhodopsin a protonation equilibrium exists between the protonated and the non-protonated Schiff base. On hydration the water stabilizes the protonated forms. In metarhodopsin-I the protein itself is able to stabilize the protonated Schiff base. The direct involvement of water in the retinal binding site was demonstrated by measuring the rhodopsin-bathorhodopsin FTIR difference spectra of rhodopsin hydrated with H2O and H2(18)O. The results are discussed with respect to the problem of charge stabilization and energy storage.     

PURPLE MEMBRANE ANALOGS SYNTHESIZED FROM C17 ALDEHYDE

Abstract— All- trans , 11- cis and 9- cis isomers of the C₁₇ aldehyde analogs of retinal bound with purple membrane apoprotein, probably through a Schiff base linkage at the normal retinal binding site. The complex formed from C₁₇ aldehyde and purple membrane apoprotein was slowly decomposed by 10m M hydroxylamine. The C₁₇ aldehyde competitively inhibited the regeneration of purple membrane from all- trans -retinal and purple membrane apoprotein. The differential ability of the different isomers to inhibit the regeneration suggests that purple membrane has a binding site for the side chain of retinal in addition to the Schiff base binding site.