Steric hindrance between chromophore substituents as the driving force of rhodopsin photoisomerization: 10-methyl-13-demethyl retinal containing rhodopsin

Tuning Two-Photon Absorption in Rhodopsin Chromophore via Backbone Modification: The Story Told by CC2 and TD-DFT

We investigate here a systematic way to tune two-photon transition strengths (δ2PA) and two-photon absorption (2PA) cross sections (σ2PA) of the rhodopsin's chromophore 11-cis-retinal protonated Schiff base (RPSB) via the modulation of the methyl groups pattern along its polyene chain. Our team employed the resolution of identity, coupled cluster approximate second order (RI-CC2) method with Dunning's aug-cc-pVDZ basis set, to determine the structural impact on δ2PA, as well as its correlation to both transition dipole moments and permanent electric dipole moments. Seven structures were probed in vacuo, including five-double-bond-conjugated model of the native chromophore, shortened by the β-ionone ring (RPSB5), and its de/methylated analogues: 9-methyl, 13-methyl, planar and twisted models of 9,10-dimethyl and 9,10,13-trimethyl. Our results demonstrate that the magnitude of δ2PA is dictated by both the position and number of methylated groups attached to its polyene chain as well as the degree of dihedral twist that is introduced due to the de/methylation. In fact, a strong correlation between δ2PA enhancement and the presence of a C13-methyl group in the planar RPSB5 species is found. Trends in δ2PA values follow the trends observed in their corresponding changes in the permanent dipole moment upon the S0-S1 excitation nearly exactly. The assessment of four DFT functionals, i.e., M11, MN15, CAM-B3LYP, and BHandHLYP, previously found most successful in predicting 2PA properties in biological chromophores, points to a long-range-corrected hybrid meta-GGA M11 as the top-performing functional, albeit still delivering underestimated δ2PA and σ2PA values by a factor of 3.3-5.3 with respect to the CC2 results. In the case of global-hybrid meta-NGA (MN15), as well as CAM-B3LYP and BHandHLYP functionals, this factor deteriorates significantly to 6.7-20.9 and is mostly related to significantly lower quality of the ground- and excited-state dipole moments.

Potential therapeutic roles of retinoids for prevention of neuroinflammation and neurodegeneration in Alzheimer's disease

All retinoids, which can be natural and synthetic, are chemically related to vitamin A. Both natural and synthetic retinoids use specific nuclear receptors such as retinoic acid receptors and retinoid X receptors to activate specific signaling pathways in the cells. Retinoic acid signaling is extremely important in the central nervous system. Impairment of retinoic acid signaling pathways causes severe pathological processes in the central nervous system, especially in the adult brain. Retinoids have major roles in neural patterning, differentiation, axon outgrowth in normal development, and function of the brain. Impaired retinoic acid signaling results in neuroinflammation, oxidative stress, mitochondrial malfunction, and neurodegeneration leading to progressive Alzheimer's disease, which is pathologically characterized by extra-neuronal accumulation of amyloid plaques (aggregated amyloid-beta) and intra-neurofibrillary tangles (hyperphosphorylated tau protein) in the temporal lobe of the brain. Alzheimer's disease is the most common cause of dementia and loss of memory in old adults. Inactive cholinergic neurotransmission is responsible for cognitive deficits in Alzheimer's disease patients. Deficiency or deprivation of retinoic acid in mice is associated with loss of spatial learning and memory. Retinoids inhibit expression of chemokines and neuroinflammatory cytokines in microglia and astrocytes, which are activated in Alzheimer's disease. Stimulation of retinoic acid receptors and retinoid X receptors slows down accumulation of amyloids, reduces neurodegeneration, and thereby prevents pathogenesis of Alzheimer's disease in mice. In this review, we described chemistry and biochemistry of some natural and synthetic retinoids and potentials of retinoids for prevention of neuroinflammation and neurodegeneration in Alzheimer's disease.

Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2

This study provides gas-phase S₁ excited-state geometries along with emission and adiabatic energies for methylated/demethylated and ring-locked analogues of protonated Schiff base retinal models comprising system of five conjugated double bonds (PSB5), using second order multiconfiguration perturbation theory (CASPT2). CASPT2 results serve as reference data to assess the performance of CC2 (second-order approximate coupled cluster singles and doubles) and a commonly used CASSCF/CASPT2 protocol, that is, complete active space self-consistent field (CASSCF) geometry optimization followed by CASPT2 energy calculation. We find that the CASSCF methodology fails to locate planar S₁ minimum energy structures for four out of five investigated planar models in contrast to CC2 and CASPT2 methods. However, for those which were found: one planar and two twisted minima, there is an excellent agreement between CASSCF and CASPT2 results in terms of geometrical parameters, one-electron properties, as well as emission and adiabatic energies. CC2 performs well for in-plane S₁ minima and their spectroscopic and electronic properties. However, this picture deteriorates for twisted minima. As expected, the CC2 description of the S₂ electronic state, with strong multireference and significant double excitation character, is very poor, exhibiting errors in transition energies exceeding 1 eV. They may be substantially diminished by recalculating transition energies with CASPT2 method. Our work shows that CASSCF/CASPT2 and CC2 shortcomings may influence gas-phase retinal analogues' excited state description in a dramatic way. © 2017 Wiley Periodicals, Inc.

Molecular Signaling Mechanisms of Natural and Synthetic Retinoids for Inhibition of Pathogenesis in Alzheimer's Disease

Retinoids, which are vitamin A derivatives, interact through retinoic acid receptors (RARs) and retinoid X receptors (RXRs) and have profound effects on several physiological and pathological processes in the brain. The presence of retinoic acid signaling is extensively detected in the adult central nervous system, including the amygdala, cortex, hypothalamus, hippocampus, and other brain areas. Retinoids are primarily involved in neural patterning, differentiation, and axon outgrowth. Retinoids also play a key role in the preservation of the differentiated state of adult neurons. Impairment in retinoic acid signaling can result in neurodegeneration and progression of Alzheimer's disease (AD). Recent studies demonstrated severe deficiencies in spatial learning and memory in mice during retinoic acid (vitamin A) deprivation indicating its significance in preserving memory function. Defective cholinergic neurotransmission plays an important role in cognitive deficits in AD. All-trans retinoic acid is known to enhance the expression and activity of choline acetyltransferase in neuronal cell lines. Activation of RAR and RXR is also known to impede the pathogenesis of AD in mice by inhibiting accumulation of amyloids. In addition, retinoids have been shown to inhibit the expression of chemokines and pro-inflammatory cytokines in microglia and astrocytes, which are activated in AD. In this review article, we have described the chemistry and molecular signaling mechanisms of natural and synthetic retinoids and current understandings of their therapeutic potentials in prevention of AD pathology.

Rhodopsins carrying modified chromophores--the 'making of', structural modelling and their light-induced reactivity

A series of vitamin-A aldehydes (retinals) with modified alkyl group substituents (9-demethyl-, 9-ethyl-, 9-isopropyl-, 10-methyl, 10-methyl-13-demethyl-, and 13-demethyl retinal) was synthesized and their 11-cis isomers were used as chromophores to reconstitute the visual pigment rhodopsin. Structural changes were selectively introduced around the photoisomerizing C11=C12 bond. The effect of these structural changes on rhodopsin formation and bleaching was determined. Global fit of assembly kinetics yielded lifetimes and spectral features of the assembly intermediates. Rhodopsin formation proceeds stepwise with prolonged lifetimes especially for 9-demethyl retinal (longest lifetime τ3 = 7500 s, cf., 3500 s for retinal), and for 10-methyl retinal (τ3 = 7850 s). These slowed-down processes are interpreted as either a loss of fixation (9dm) or an increased steric hindrance (10me) during the conformational adjustment within the protein. Combined quantum mechanics and molecular mechanics (QM/MM) simulations provided structural insight into the retinal analogues-assembled, full-length rhodopsins. Extinction coefficients, quantum yields and kinetics of the bleaching process (μs-to-ms time range) were determined. Global fit analysis yielded lifetimes and spectral features of bleaching intermediates, revealing remarkably altered kinetics: whereas the slowest process of wild-type rhodopsin and of bleached and 11-cis retinal assembled rhodopsin takes place with lifetimes of 7 and 3.8 s, respectively, this process for 10-methyl-13-demethyl retinal was nearly 10 h (34670 s), coming to completion only after ca. 50 h. The structural changes in retinal derivatives clearly identify the precise interactions between chromophore and protein during the light-induced changes that yield the outstanding efficiency of rhodopsin.

Carotenoids and Retinoids: Nomenclature, Chemistry, and Analysis

Carotenoids are polyenes synthesized in plants and certain microorganisms and are pigments used by plants and animals in various physiological processes. Some of the over 600 known carotenoids are capable of metabolic conversion to the essential nutrient vitamin A (retinol) in higher animals. Vitamin A also gives rise to a number of other metabolites which, along with their analogs, are known as retinoids. To facilitate discussion about these important molecules, a nomenclature is required to identify specific substances. The generally accepted rules for naming these important molecules have been agreed to by various Commissions of the International Union of Pure and Applied Chemistry and International Union of Biochemistry. These naming conventions are explained along with comparisons to more systematic naming rules that apply for these organic chemicals. Identification of the carotenoids and retinoids has been advanced by their chemical syntheses, and here, both classical and modern methods for synthesis of these molecules, as well as their analogs, are described. Because of their importance in biological systems, sensitive methods for the detection and quantification of these compounds from various sources have been essential. Early analyses that relied on liquid adsorption and partition chromatography have given way to high-performance liquid chromatography (HPLC) coupled with various detection methods. The development of HPLC coupled to mass spectrometry, particularly LC/MS-MS with Multiple Reaction Monitoring, has resulted in the greatest sensitivity and specificity in these analyses.

Impacts of retinal polyene (de)methylation on the photoisomerization mechanism and photon energy storage of rhodopsin

Similar to native rhodopsin, a two-mode space-saving isomerization mechanism drives the photoreaction in (de)methylated rhodopsin analogues.

Backbone modification of retinal induces protein-like excited state dynamics in solution

The drastically different reactivity of the retinal chromophore in solution compared to the protein environment is poorly understood. Here, we show that the addition of a methyl group to the C═C backbone of all-trans retinal protonated Schiff base accelerates the electronic decay in solution making it comparable to the proton pump bacteriorhodopsin. Contrary to the notion that reaction speed and efficiency are linked, we observe a concomitant 50% reduction in the isomerization yield. Our results demonstrate that minimal synthetic engineering of potential energy surfaces based on theoretical predictions can induce drastic changes in electronic dynamics toward those observed in an evolution-optimized protein pocket.

Retinoid chemistry: synthesis and application for metabolic disease

In this review a discussion of the usual procedures used to synthesize retinoids is followed by an overview of the structure-activity relationships of these molecules. The discussion is then focused on the role and impact of retinoids on metabolic disorders with a particular emphasis on obesity, diabetes, and the metabolic syndrome. In these areas, both natural and synthetic retinoids that are being studied are reviewed and areas where likely future research will occur are suggested. This article is part of a Special Issue entitled Retinoid and Lipid Metabolism.

Photochemistry of Visual Pigment Chromophore Models by Ab Initio Molecular Dynamics

Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.

The chromophore induces a correct folding of the polypeptide chain of bacteriorhodopsin

The pK values of the Schiff bases of several bacteriorhodopsin (BR) preparations have been determined by titration. While for the native protein a high pK of 13 has been reported [Druckmann et al. (1982) Biochemistry 21, 4953], we find that a BR reconstituted from retinal and the apoprotein obtained from the retinal-deficient strain JW5 exhibits a low pK value, 8.5. When the retinal chromophore is added to growing JW5 cells leading to in vivo BR formation, this BR shows a high Schiff base pK, >/=10.2. A value of 9.3 was determined when BR was reconstituted from retinal and BO, obtained from bleaching BR with hydroxylamine. A low pK value of 8.1 was found when 13-trifluoro(CF3)-retinal was used as chromophore for in vitro reconstitution [Sheves et al. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3262], which is confirmed in this study. When we add CF3-retinal to growing JW5 cells, this low pK shifts to 9.1. Besides wild-type protein, the apoprotein from the mutant D96N (from the chromophore-deficient strain L-07) was also used for in vitro reconstitution with either chromophore, retinal or CF3-retinal. Irrespective of the chromophore used, both mutant BRs exhibit low pK values of their Schiff bases of 8.1. Flash photolysis with respect to the rise and decay of the M-photocycle intermediate of wild-type and D96N-mutated BR carrying retinal and CF3-retinal revealed that in both proteins the incorporation of the trifluororetinal leads to a faster rise of the M-intermediate and to a slower decay. Since the apoprotein from the chromophore-deficient JW5 strain of H. salinarium, despite its lower boyant density, is arranged into trimers (according to CD measurements), we propose that the high pK value of the BR Schiff base is induced by long-distance interactions between BR molecules in the purple membrane patches which control the pK of the chromophore.

Vibrational spectrum of the lumi intermediate in the room temperature rhodopsin photo-reaction

The vibrational spectrum (650-1750 cm(-1)) of the lumi-rhodopsin (lumi) intermediate formed in the microsecond time regime of the room-temperature rhodopsin (RhRT) photoreaction is measured for the first time using picosecond time-resolved coherent anti-Stokes Raman spectroscopy (PTR/CARS). The vibrational spectrum of lumi is recorded 2.5 micros after the 3-ps, 500-nm excitation of RhRT. Complementary to Fourier transform infrared spectra recorded at Rh sample temperatures low enough to freeze lumi, these PTR/CARS results provide the first detailed view of the vibrational degrees of freedom of room-temperature lumi (lumiRT) through the identification of 21 bands. The exceptionally low intensity (compared to those observed in bathoRT) of the hydrogen out-of-plane (HOOP) bands, the moderate intensity and absolute positions of C-C stretching bands, and the presence of high-intensity C==C stretching bands suggest that lumiRT contains an almost planar (nontwisting), all-trans retinal geometry. Independently, the 944-cm(-1) position of the most intense HOOP band implies that a resonance coupling exists between the out-of-plane retinal vibrations and at least one group among the amino acids comprising the retinal binding pocket. The formation of lumiRT, monitored via PTR/CARS spectra recorded on the nanosecond time scale, can be associated with the decay of the blue-shifted intermediate (BSI(RT)) formed in equilibrium with the bathoRT intermediate. PTR/CARS spectra measured at a 210-ns delay contain distinct vibrational features attributable to BSI(RT), which suggest that the all-trans retinal in both BSI(RT) and lumiRT is strongly coupled to part of the retinal binding pocket. With regard to the energy storage/transduction mechanism in RhRT, these results support the hypothesis that during the formation of lumiRT, the majority of the photon energy absorbed by RhRT transfers to the apoprotein opsin.