ON THE STATE OF CHROMOPHORE PROTONATION IN RHODOPSIN: IMPLICATION FOR PRIMARY PHOTOCHEMISTRY IN VISUAL PIGMENTS

Resonance Raman multicomponent spectra of bovine rhodopsin, isorhodopsin, and bathorhodopsin are obtained at low temperature. Application of the double beam, 'pump-probe' technique allows an extraction of the rhodopsin and bathorhodopsin spectra in both protonated and deuterated media. Our results show that the Schiff bases of both rhodopsin and bathorhodopsin are fully protonated and the degree of protonation is unaffected by the rhodopsin-bathorhodopsin transformation. Further, the data support the concept or cis-trans isomerization as occurring in this transition. The effect of these results on various models for the primary photochemical event in vision is discussed.     

PROTON TRANSFER IN THE PRIMARY PROCESS OF VISION

Abstract— Proton transfer was theoretically examined as a possible primary process of vision. The motion of protons in the adiabatic potential of the Schiff base hydrogen bond was investigated in terms of quantum mechanics. The probability of proton transfer from the Schiff base nitrogen (i.e. the unprotonation of Schiff base) was found to increase as the retinal rotated around 11–12. double bond by 90°. The results also suggested that the proton transfer can take place before or during the transition from the excited to ground state (excited state proton transfer). We proposed that such excited state proton transfer is one of the elementary processes in primary visual photochemistry, and this process leads to the unprotonated visual pigment, hyposorhodopsin, which has been experimentally verified as one of the primary photoproducts of rhodopsin. The probability of this process could be comparable to the conventional process leading to the protonated intermediate, bathorhodopsin. The relation of these results with the recent experimental data is discussed.     

Retinal counterion switch mechanism in vision evaluated by molecular simulations

Photoisomerization of the retinylidene chromophore of rhodopsin is the starting point in the vision cascade. A counterion switch mechanism that stabilizes the retinal protonated Schiff base (PSB) has been proposed to be an essential step in rhodopsin activation. On the basis of vibrational and UV-visible spectroscopy, two counterion switch models have emerged. In the first model, the PSB is stabilized by Glu181 in the meta I state, while in the most recent proposal, it is stabilized by Glu113 as well as Glu181. We assess these models by conducting a pair of microsecond scale, all-atom molecular dynamics simulations of rhodopsin embedded in a 99-lipid bilayer of SDPC, SDPE, and cholesterol (2:2:1 ratio) varying the starting protonation state of Glu181. Theoretical simulations gave different orientations of retinal for the two counterion switch mechanisms, which were used to simulate experimental 2H NMR spectra for the C5, C9, and C13 methyl groups. Comparison of the simulated 2H NMR spectra with experimental data supports the complex-counterion mechanism. Hence, our results indicate that Glu113 and Glu181 stabilize the retinal PSB in the meta I state prior to activation of rhodopsin.     

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.     

Interaction of chromophore, 11-<Emphasis Type="Italic">cis</Emphasis>-retinal,with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study

A molecular dynamics study of the dark adapted visual pigment rhodopsin molecule was carried out. The interaction of the chromophore group, 11-cis-retinal, with the nearest amino acid residues in the chromophore center of the molecule, namely, in the region of the protonated Schiff base linkage, was analyzed. Most likely, the interaction of the CH=NH bond with the negatively charged amino acid residue Glu113 cannot be described as a simple electrostatic interaction of two oppositely charged groups. One can propose that not only Glu113 but also Glu181 and Ser186 are involved in stabilization of the protonated Schiff base linkage. Accord-ing to calculations, Glu181 interacts, as the counter-ion, with the Schiff base indirectly via Ser186. The intramolecular mechanisms of protonated Schiff base stabilization in rhodopsin are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 19–27, January, 2007.     

Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants

We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.     

POWER- AND TIME-RESOLVED RESONANCE RAMAN STUDIES AND CONFORMATIONAL CHANGES IN BACTERIORHODOPSIN

Abstract— By comparing the resonance Raman spectra of the retinal of the intermediates of bacteriorho-dopsin (obtained by using fixed flow with residence of time of 10 ps. variable laser power and frequency as well as computer subtraction techniques) with those of model compounds and with each other, the following possible conclusions can be obtained: (1) There exists stronger interaction between the retinal and the opsin in bacteriorhodopsin than that present in rhodopsin. (2) Conformational changes seem to take place during the dark light adaptation process as well as during the photosynthetic cycle. (3) The appearance of the spectrum of the retinal in the fingerprint region for the bL₅₅₀ and bM₄₁₂ intermediates is similar despite large shifts in their optical absorption maxima. This might argue against the theory that proposes ground state retinal conformational changes to explain the observed red shift in the optical spectra of retinal upon combining with the opsin. (4) Contrary to bM ₄₁₂ , the bL₅₅₀ species seems to be protonated. The fact that loss of proton does not seem to change the retinal conformation greatly might suggest that the protein and its ionic environment might carry the larger share of the load in the deprotonation process.     

THE FORMATION OF TWO FORMS OF BATHORHODOPSIN AND THEIR OPTICAL PROPERTIES

Abstract— Using two kinds of rhodopsin preparations (digitonin extract and rod outer segments suspension), we measured changes in absorption spectra during the conversion of rhodopsin or isorhodopsin to a photosteady state mixture composed of rhodopsin, isorhodopsin and bathorhodopsin by irradiation with blue light (437 nm) at 77 K and during the reversion of bathorhodopsin to a mixture of rhodopsin and isorhodopsin by irradiation with red light (> 650 nm) at 77 K. The reaction kinetics could be expressed with only one exponential in the former case and with two exponentials in the latter case. These data suggest that both rhodopsin and isorhodopsin are composed of a single molecular species, while bathorhodopsin is composed of two molecular species, designated as bathorhodopsin₁ and bathorhodopsin₂. The absorption spectra of these bathorhodopsin were calculated by two different methods (kinetic method and warming-cooling method). The former was based on the kinetics of the conversion of two forms of bathorhodopsin by irradiation with the red light. The spectra obtained by this method were consistent with those obtained by the warming-cooling method. Bathorhodopsin₁ and bathorhodopsin₂ have Λ_max at 555 and 538 nm, respectively. The two forms of bathorhodopsin are interconvertible in the light, but not in the dark. Thus, we suggest that a rhodopsin molecule in the excited state relaxes to either bathorhodopsin₁ or bathorhodopsin₂ through one of the two parallel pathways.     

Ground states of σ-bonded molecules—VIII MINDO Calculations for species involved in nitration by acetyl nitrate

It is shown that the MINDO semiempirical SCF MO method gives good values for heats of formation of inorganic species and ions as well as neutral molecules. Calculations are reported for the various species that could be involved in nitrations by nitric acid in acetic anhydride; it is concluded that the active agent is protonatedacetyl nitr acetyl nitrate protonated at the ether-type oxygen.     

Absorption studies of neutral retinal Schiff base chromophores

The neutral retinal Schiff base is connected to opsin in UV sensing pigments and in the blue-shifted meta-II signaling state of the rhodopsin photocycle. We have designed and synthesized two model systems for this neutral chromophore and have measured their gas-phase absorption spectra in the electrostatic storage ring ELISA with a photofragmentation technique. By comparison to the absorption spectrum of the protonated retinal Schiff base in vacuo, we found that the blue shift caused by deprotonation of the Schiff base is more than 200 nm. The absorption properties of the UV absorbing proteins are thus largely determined by the intrinsic properties of the chromophore. The effect of approaching a positive charge to the Schiff base was also studied, as well as the susceptibility of the protonated and unprotonated chromophores to experience spectral shifts in different solvents.     

INVESTIGATION INTO THE SPECTROSCOPY AND PHOTOISOMERIZATION OF A SERIES OF POLY (ETHYLENE GLYCOL) PEPTIDE SCHIFF BASES OF 11-cis RETINAL

Abstract— The 11-cis and all-trans isomers of a series of poly(ethylene glycol)-oligopeptide - Schiff bases as models for rhodopsin were synthesized and studied. Absorption data for certain of the PEG-peptide Schiff bases demonstrated that no intramolecular hydrogen-bonding (or protonation) occurs between the Schiff base and an acidic amino acid residue, as was previously thought. Photoisomerization of the 11-cis protonated and unprotonated Schiff bases were examined using both steady state and laser flash techniques. Also with 355 nm excitation (and additionally 532 nm in one case), an approximate 40% increase in quantum yield of isomerization (φ) occurred for all protonated PEG-peptide Schiff bases compared to the H⁺-n-butylamine counterparts (in methanol). In one case, a > 100% increase in φ was found in dichloromethane. These data show that PEG-oligopeptide Schiff bases are still further improved models for rhodopsin compared to their n-butylamine analogs.     

INTERACTION OF RHODOPSIN, G-PROTEIN AND KINASE IN OCTOPUS PHOTORECEPTORS

Light induced phosphorylation of octopus rhodopsin was greatly enhanced by guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S), suggesting that the kinases are involved in regulating interaction between rhodopsin and G-protein. We determined phosphorylated peptides of octopus rhodopsin in the presence or absence of GTP gamma S. Possible phosphorylation sites for octopus rhodopsin enhanced by GTP gamma S were Thr329, Thr330 and/or Thr336, which suggest that the G-protein associates with cytoplasmic loops including C-terminal peptide in the seventh helix of octopus rhodopsin.     

Modulating rhodopsin receptor activation by altering the pKa of the retinal Schiff base

The visual pigment rhodopsin is a seven-transmembrane (7-TM) G protein-coupled receptor (GPCR). Activation of rhodopsin involves two pH-dependent steps: proton uptake at a conserved cytoplasmic motif between TM helices 3 and 6, and disruption of a salt bridge between a protonated Schiff base (PSB) and its carboxylate counterion in the transmembrane core of the receptor. Formation of an artificial pigment with a retinal chromophore fluorinated at C14 decreases the intrinsic pKa of the PSB and thereby destabilizes this salt bridge. Using Fourier transform infrared difference and UV-visible spectroscopy, we characterized the pH-dependent equilibrium between the active photoproduct Meta II and its inactive precursor, Meta I, in the 14-fluoro (14-F) analogue pigment. The 14-F chromophore decreases the enthalpy change of the Meta I-to-Meta II transition and shifts the Meta I/Meta II equilibrium toward Meta II. Combining C14 fluorination with deletion of the retinal beta-ionone ring to form a 14-F acyclic artificial pigment uncouples disruption of the Schiff base salt bridge from transition to Meta II and in particular from the cytoplasmic proton uptake reaction, as confirmed by combining the 14-F acyclic chromophore with the E134Q mutant. The 14-F acyclic analogue formed a stable Meta I state with a deprotonated Schiff base and an at least partially protonated protein counterion. The combination of retinal modification and site-directed mutagenesis reveals that disruption of the protonated Schiff base salt bridge is the most important step thermodynamically in the transition from Meta I to Meta II. This finding is particularly important since deprotonation of the retinal PSB is known to precede the transition to the active state in rhodopsin activation and is consistent with models of agonist-dependent activation of other GPCRs.     

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.     

STRUCTURE OF HYPSORHODOPSIN: ANALYSIS BY FOURIER TRANSFORM INFRARED SPECTROSCOPY AT 10 K

Abstract— Vibrational bands of hypsorhodopsin in the difference Fourier transform infrared spectra were identified as the bands which arose after formation of isorhodopsin by successive irradiations of bovine rhodopsin at 10 K with >500 nm light, and also as the bands disappeared upon conversion to bathorhodopsin by warming. The chromophore bands were assigned by the bands which shifted upon deuterium substitution of the polyene chain of the retinylidene chromophore. The presence of chromophore bands which shift by D₂O exchange clearly shows that the Schiff base chromophore of hypsorhodopsin is protonated. The amide I bands and several other protein bands of hypsorhodopsin appeared at the same frequencies as those of bathorhodopsin, but they are different from those of rhodopsin and isorhodopsin. Furthermore, like bathorhodopsin, hypsorhodopsin displays the C_l—H out-of-plane bending mode which is weakly coupled with C₁₂-_-–H out-of-plane mode. These facts show that hypsorhodopsin has a chromophore conformation and chromophore-opsin interaction more similar to bathorhodopsin than to rhodopsin and isorhodopsin.     

Coupling of protonation switches during rhodopsin activation

Recent studies of the activation mechanism of rhodopsin involving Fourier-transform infrared spectroscopy and a combination of chromophore modifications and site-directed mutagenesis reveal an allosteric coupling between two protonation switches. In particular, the ring and the 9-methyl group of the all-trans retinal chromophore serve to couple two proton-dependent activation steps: proton uptake by a cytoplasmic network between transmembrane (TM) helices 3 and 6 around the conserved ERY (Glu-Arg-Tyr) motif and disruption of a salt bridge between the retinal protonated Schiff base (PSB) and a protein counterion in the TM core of the receptor. Retinal analogs lacking the ring or 9-methyl group are only partial agonists--the conformational equilibrium between inactive Meta I and active Meta II photoproduct states is shifted to Meta I. An artificial pigment was engineered, in which the ring of retinal was removed and the PSB salt bridge was weakened by fluorination of C14 of the retinal polyene. These modifications abolished allosteric coupling of the proton switches and resulted in a stabilized Meta I state with a deprotonated Schiff base (Meta I(SB)). This state had a partial Meta II-like conformation due to disruption of the PSB salt bridge, but still lacked the cytoplasmic proton uptake reaction characteristic of the final transition to Meta II. As activation of native rhodopsin is known to involve deprotonation of the retinal Schiff base prior to formation of Meta II, this Meta I(SB) state may serve as a model for the structural characterization of a key transient species in the activation pathway of a prototypical G protein-coupled receptor.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

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.     

EVIDENCE FOR A MAGNESIUM DEPENDENT ATPase IN BOVINE ROD OUTER SEGMENT DISK MEMBRANES*†

Abstract—In the presence of Mg²⁺ and adenosine triphosphate (ATP), a rapid. light-induced, light-scattering transient is observed from bovine rod outer segments (ROS). This light-scattering transient we have labelled 'A'. Ca²⁺ cannot replace Mg²⁺. nor can guanosine triphosphate (GTP) replace ATP. 'A' is observed at ATP concentrations as low as a few μM.
The half-time of 'A', 60 ms at 20° and 20 ms at 37°, is consistent with a process possibly involved in visual transduction.
'A' has the action spectrum of rhodopsin bleaching and its amplitude is strictly proportional to the fraction of rhodopsin bleached per flash. 'A' can be regenerated by 11- cis retinal.
Inhibition studics with ATP analogues, which cannot be hydrolysed and fail to evoke an 'A' response, reveal that an ATP hydrolysis process has to precede illumination in order for 'A' to occur.
On the basis of the above findings. it is proposed that there is a Mg²⁺ dependent ATPase in ROS that allows the disk membrane to assume a new membrane state which, upon illumination, is altered. giving rise to the structural phenomenon monitored as light-scattering transient 'A'.     

RECONSTITUTION OF SQUID RHODOPSIN IN RHABDOMAL MEMBRANES

Abstract— Squid opsin which is capable of combining with 11- cis or 9- cis retinal to reconstitute photo-pigment has been prepared by irradiation of rhabdomal membranes with orange light (> 530 nm) in the presence of 0.2 M hydroxylamine. When the irradiation is carried out either at concentrations of hydroxylamine higher than 0.2 M or with light of wavelength shorter than 530 nm, rhodopsin in the membranes is bleached quickly, but the ability of the resultant opsin to form rhodopsin is greatly reduced.
The optimum pH for rhodopsin regeneration in rhabdomal membranes was found to be between 6.5 and 8.5. The rate of regeneration of rhodopsin increases with raising temperature, and at about 20°C it is almost the same as that of isorhodopsin. Even after solubilization in digitonin solution, opsin still preserves the ability to reform rhodopsin.
All- trans retinal can be incorporated into retinochrome-bearing membranes, in which it is isomerized into 11- cis isomer by the photoisomerase activity of retinochrome. Rhabdomal membranes retaining active opsin can take up 11- cis retinal from retinochrome membranes so as to synthesize rhodopsin.