The molecular structure of a curl-shaped retinal isomer

Structural Impact of Selected Retinoids on Model Photoreceptor Membranes

Photoreceptor membranes have a unique lipid composition. They contain a high level of polyunsaturated fatty acids including the most unsaturated fatty acid in nature, docosahexaenoic acid (22:6), and are enriched in phosphatidylethanolamines. The phospholipid composition and cholesterol content of the subcellular components of photoreceptor outer segments enables to divide photoreceptor membranes into three types: plasma membranes, young disc membranes, and old disc membranes. A high degree of lipid unsaturation, extended exposure to intensive irradiation, and high respiratory demands make these membranes sensitive to oxidative stress and lipid peroxidation. Moreover, all-trans retinal (AtRAL), which is a photoreactive product of visual pigment bleaching, accumulates transiently inside these membranes, where its concentration may reach a phototoxic level. An elevated concentration of AtRAL leads to accelerated formation and accumulation of bisretinoid condensation products such as A2E or AtRAL dimers. However, a possible structural impact of these retinoids on the photoreceptor-membrane properties has not yet been studied. In this work we focused just on this aspect. The changes induced by retinoids, although noticeable, seem not to be significant enough to be physiologically relevant. This is, however, an positive conclusion because it can be assumed that accumulation of AtRAL in photoreceptor membranes will not affect the transduction of visual signals and will not disturb the interaction of proteins engaged in this process.

Trajectory surface hopping molecular dynamics simulations for retinal protonated Schiff-base photoisomerization

Global switching trajectory surface hopping molecular dynamics simulations are performed using accurate on-the-fly (TD)CAM-B3LYP/6-31G potential energy surfaces to study retinal protonated Schiff-base photoisomerization up to S₁ excitation. The simulations detected two-layer conical intersection networks: one is at an energy as high as 8 eV and the other is in the energy range around 3-4 eV. Six conical intersections within the low-layer energy region that correspond to active conical intersections under experimental conditions are found via the use of pairwise isomers, within which nonadiabatic molecular dynamics simulations are performed. Eight isomer products are populated with simulated sampling trajectories from which the simulated quantum yield in the gas phase is estimated to be 0.11 (0.08) moving from the all-trans isomer to the 11-cis (11-cis to all-trans) isomer in comparison with an experimental value of 0.09 (0.2) in the solution phase. Each conical intersection is related to one specific twist angle accompanying a related CC double bond motion during photoisomerization. Nonplanar distortion of the entire dynamic process has a significant role in the formation of the relevant photoisomerization products. The present simulation indicates that all hopping points show well-behaved potential energy surface topology, as calculated via the conventional TDDFT method, at conical intersections between S₁ and S₀ states. Therefore, the present nonadiabatic dynamics simulations with the TDDFT method are very encouraging for simulating various large systems related to retinal Schiff-base photoisomerization in the real world.

The effect of protein environment on photoexcitation properties of retinal

Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.

Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP

The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.

Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies

We have investigated the protonation state and photoabsorption spectrum of Schiff-base (SB) nitrogen bound 11-cis-retinal in human blue and mouse UV cone visual pigments as well as in bovine rhodopsin by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. We have employed both multireference (MRCISD+Q, MR-SORCI+Q, and MR-DDCI2+Q) and single reference (TD-B3LYP and RI-CC2) QM methods. The calculated ground-state and vertical excitation energies show that UV-sensitive pigments have deprotonated SB nitrogen, while violet-sensitive pigments have protonated SB nitrogen, in agreement with some indirect experimental evidence. A significant blue shift of the absorption maxima of violet-sensitive pigments relative to rhodopsins arises from the increase in bond length alternation of the polyene chain of 11-cis-retinal induced by polarizing fields of these pigments. The main counterion is Glu113 in both violet-sensitive vertebrate pigments and bovine rhodopsin. Neither Glu113 nor the remaining pigment has a significant influence on the first excitation energy of 11-cis-retinal in the UV-sensitive pigments that have deprotonated SB nitrogen. There is no charge transfer between the SB and beta-ionone terminals of 11-cis-retinal in the ground and first excited states.

Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin

Engineering squid rhodopsin with modified retinal analogues is essential for understanding the conserved steric and electrostatic interaction networks that govern the architecture of the Schiff base binding site. Depriving the retinal of its steric and electrostatic contacts affects the positioning of the Schiff-base relative to the key residues Asn87, Tyr111, and Glu180. Displacement of the W1 and W2 positions and the impact on the structural rearrangements near the Schiff base binding region reiterates the need for the presence of internal water molecules and the accessibility of binding sites to them. Also, the dominant role of the Glu180 counterion in inducing the S(1)/S(2) state reversal for SBR is shown for the first time in squid rhodopsin.