Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment.

The visual pigments of the cones perceive red, green, and blue colors. The monkey green (MG) pigment possesses a unique Cl- binding site; however, its relationship to the spectral tuning in green pigments remains elusive. Recently, FTIR spectroscopy revealed the characteristic structural modifications of the retinal binding site by Cl- binding. Herein, we report the computational structural modeling of MG pigments and quantum-chemical simulation to investigate its spectral redshift and physicochemical relevance when Cl- is present. Our protein structures reflect the previously suggested structural changes. AlphaFold2 failed to predict these structural changes. Excited-state calculations successfully reproduced the experimental red-shifted absorption energies, corroborating our protein structures. Electrostatic energy decomposition revealed that the redshift results from the His197 protonation state and conformations of Glu129, Ser202, and Ala308; however, Cl- itself contributes to the blueshift. Site-directed mutagenesis supported our analysis. These modeled structures may provide a valuable foundation for studying cone pigments.

Early Proton Transfer Reaction in a Primate Blue-Sensitive Visual Pigment.

The proton transfer reaction belongs to one of the key triggers for the functional expression of membrane proteins. Rod and cone opsins are light-sensitive G-protein-coupled receptors (GPCRs) that undergo the cis-trans isomerization of the retinal chromophore in response to light. The isomerization event initiates a conformational change in the opsin protein moiety, which propagates the downstream effector signaling. The final step of receptor activation is the deprotonation of the retinal Schiff base, a proton transfer reaction which has been believed to be identical among the cone opsins. Here, we report an unexpected proton transfer reaction occurring in the early photoreaction process of primate blue-sensitive pigment (MB). By using low-temperature UV-visible spectroscopy, we found that the Lumi intermediate of MB formed in transition from the BL intermediate shows an absorption maximum in the UV region, indicating the deprotonation of the retinal Schiff base. Comparison of the light-induced difference FTIR spectra of Batho, BL, and Lumi showed significant α-helical backbone C=O stretching and protonated carboxylate C=O stretching vibrations only in the Lumi intermediate. The transition from BL to Lumi thus involves dramatic changes in protein environment with a proton transfer reaction between the Schiff base and the counterion resulting in an absorption maximum in the UV region.

Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment.

The visual pigments of humans contain 11-cis retinal as the chromophore of light perception, and its photoisomerization to the all-trans form initiates visual excitation in our eyes. It is well-known that three isomeric states of retinal (11-cis, all-trans, and 9-cis) are in photoequilibrium at very low temperatures such as 77 K. Here we report the lack of formation of the 9-cis form in monkey blue (MB) at 77 K, as revealed by light-induced difference Fourier transform infrared spectroscopy. This indicates that the chromophore binding pocket of MB does not accommodate the 9-cis form, even though it accommodates the all-trans form by twisting the chromophore. Mutation of the blue-specific tyrosine at position 265 to tryptophan, which is highly conserved in other animal rhodopsins, led to formation of the 9-cis form in MB, suggesting that Y265 is one of the determinants of the unique photochemistry in blue pigments. We also found that 9-cis retinal does not bind to MB opsin, implying that the chromophore binding pocket does not accommodate the 9-cis form at physiological temperature. The unique property of MB is discussed on the basis of the results presented here.

A2E Distribution in RPE Granules in Human Eyes.

A2E (N-retinylidene-N-retinylethanolamine) is a major fluorophore in the RPE (retinal pigment epithelium). To identify and characterize A2E-rich RPE lipofuscin, we fractionated RPE granules from human donor eyes into five fractions (F1-F5 in ascending order of density) by discontinuous sucrose density gradient centrifugation. The dry weight of each fraction was measured and A2E was quantified by liquid chromatography/mass spectrometry (LC/MS) using a synthetic A2E homolog as a standard. Autofluorescence emission was characterized by a customer-built spectro-fluorometer system. A significant A2E level was detected in every fraction, and the highest level was found in F1, a low-density fraction that makes up half of the total weight of all RPE granules, contains 67% of all A2E, and emits 75% of projected autofluorescence by all RPE granules. This group of RPE granules, not described previously, is therefore the most abundant RPE lipofuscin granule population. A progressive decrease in autofluorescence was observed from F2 to F4, whereas no autofluorescence emission was detected from the heavily pigmented F5. The identification of a novel and major RPE lipofuscin population could have significant implications in our understanding of A2E and lipofuscin in human RPE.

Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes.

Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force-distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young's modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.

Structural biology of 11-cis-retinaldehyde production in the classical visual cycle.

The vitamin A derivative 11-cis-retinaldehyde plays a pivotal role in vertebrate vision by serving as the chromophore of rod and cone visual pigments. In the initial step of vision, a photon is absorbed by this chromophore resulting in its isomerization to an all-trans state and consequent activation of the visual pigment and phototransduction cascade. Spent chromophore is released from the pigments through hydrolysis. Subsequent photon detection requires the delivery of regenerated 11-cis-retinaldehyde to the visual pigment. This trans-cis conversion is achieved through a process known as the visual cycle. In this review, we will discuss the enzymes, binding proteins and transporters that enable the visual pigment renewal process with a focus on advances made during the past decade in our understanding of their structural biology.

Visual pigment genes and absorbance spectra in the Japanese sardine Sardinops melanostictus (Teleostei: Clupeiformes).

The spectral absorbance of photoreceptor visual pigments and the opsin gene class of the visual pigments was investigated in Sardinops melanostictus. Microspectrophotometric (MSP) measurements showed that the rod photoreceptors had peak absorbance spectra (λmax) at 502 nm. The spectral sensitivity of single cones was centered at 393 nm. Double cones had a λmax of 493/522 nm, but a few displayed a red-shifted absorbance of the long-wave member at 542 nm. The mRNAs of six different opsins were isolated from the retina, retrotranscribed, cloned, and sequenced. Three genes encoded opsins in the green-sensitive class (RH2), and three genes encoded opsins in the red-sensitive class (LWS), the ultraviolet (UV)-sensitive (SWS1) class, and the rod class (RH1). A Southern blot analysis showed that the blue-sensitive (SWS2) opsin gene is absent from this species, hence it was concluded that the λmax of 393 nm was generated from the SWS1 opsin. Phylogenetic analyses of S. melanostictus RH1, LWS, and SWS1 sequences placed them with orthologs from other species (e.g., the cyprinids Danio rerio and Carrasius auratus) in Otomorpha. However, unexpectedly, the RH2 sequences were more similar to orthologs in members of the Euteleosteomorpha (e.g., Oryzias latipes and Takifugu rubripes) than to cyprinid RH2 opsins.

"In situ" observation of the role of chloride ion binding to monkey green sensitive visual pigment by ATR-FTIR spectroscopy.

Long-wavelength-sensitive (LWS) pigment possesses a chloride binding site in its protein moiety. The binding of chloride alters the absorption spectra of LWS; this is known as the chloride effect. Although the two amino acid substitutions of His197 and Lys200 influence the chloride effect, the molecular mechanism of chloride binding, which underlies the spectral tuning, has yet to be clarified. In this study, we applied ATR-FTIR spectroscopy to monkey green (MG) pigment to gain structural information of the chloride binding site. The results suggest that chloride binding stabilizes the ß-sheet structure on the extracellular side loop with perturbation of the retinal polyene chain, promotes a hydrogen bonding exchange with the hydroxyl group of Tyr, and alters the protonation state of carboxylate. Combining with the results of the binding analyses of various anions (Br-, I- and NO3-), our findings suggest that the anion binding pocket is organized for only Cl- (or Br-) to stabilize conformation around the retinal chromophore, which is functionally relevant with absorbing long wavelength light.

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations.

Vision is the dominant sensory modality in many organisms for foraging, predator avoidance, and social behaviors including mate selection. Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye. Sensitivity to individual colors, i.e., peak spectral sensitivities (λmax) of visual pigments, are a function of the type of chromophore and the amino acid sequence of the associated opsin protein in the photoreceptors. Large differences in peak spectral sensitivities can result from minor differences in amino acid sequence of cone opsins. To determine how minor sequence differences could result in large spectral shifts we selected a spectrally-diverse group of 14 teleost Rh2 cone opsins for which sequences and λmax are experimentally known. Classical molecular dynamics simulations were carried out after embedding chromophore-associated homology structures within explicit bilayers and water. These simulations revealed structural features of visual pigments, particularly within the chromophore, that contributed to diverged spectral sensitivities. Statistical tests performed on all the observed structural parameters associated with the chromophore revealed that a two-term, first-order regression model was sufficient to accurately predict λmax over a range of 452-528 nm. The approach was accurate, efficient and simple in that site-by-site molecular modifications or complex quantum mechanics models were not required to predict λmax. These studies identify structural features associated with the chromophore that may explain diverged spectral sensitivities, and provide a platform for future, functionally predictive opsin modeling.

Spectral Tuning Mechanism of Primate Blue-sensitive Visual Pigment Elucidated by FTIR Spectroscopy.

Protein-bound water molecules are essential for the structure and function of many membrane proteins, including G-protein-coupled receptors (GPCRs). Our prior work focused on studying the primate green- (MG) and red- (MR) sensitive visual pigments using low-temperature Fourier transform infrared (FTIR) spectroscopy, which revealed protein-bound waters in both visual pigments. Although the internal waters are located in the vicinity of both the retinal Schiff base and retinal ß-ionone ring, only the latter showed differences between MG and MR, which suggests their role in color tuning. Here, we report FTIR spectra of primate blue-sensitive pigment (MB) in the entire mid-IR region, which reveal the presence of internal waters that possess unique water vibrational signals that are reminiscent of a water cluster. These vibrational signals of the waters are influenced by mutations at position Glu113 and Trp265 in Rh, which suggest that these waters are situated between these two residues. Because Tyr265 is the key residue for achieving the spectral blue-shift in λmax of MB, we propose that these waters are responsible for the increase in polarity toward the retinal Schiff base, which leads to the localization of the positive charge in the Schiff base and consequently causes the blue-shift of λmax.

Spontaneous activation of visual pigments in relation to openness/closedness of chromophore-binding pocket.

Visual pigments can be spontaneously activated by internal thermal energy, generating noise that interferes with real-light detection. Recently, we developed a physicochemical theory that successfully predicts the rate of spontaneous activity of representative rod and cone pigments from their peak-absorption wavelength (λmax), with pigments having longer λmax being noisier. Interestingly, cone pigments may generally be ~25 fold noisier than rod pigments of the same λmax, possibly ascribed to an 'open' chromophore-binding pocket in cone pigments defined by the capability of chromophore-exchange in darkness. Here, we show in mice that the λmax-dependence of pigment noise could be extended even to a mutant pigment, E122Q-rhodopsin. Moreover, although E122Q-rhodopsin shows some cone-pigment-like characteristics, its noise remained quantitatively predictable by the 'non-open' nature of its chromophore-binding pocket as in wild-type rhodopsin. The openness/closedness of the chromophore-binding pocket is potentially a useful indicator of whether a pigment is intended for detecting dim or bright light.

Dimerization of visual pigments in vivo.

It is a deeply engrained notion that the visual pigment rhodopsin signals light as a monomer, even though many G protein-coupled receptors are now known to exist and function as dimers. Nonetheless, recent studies (albeit all in vitro) have suggested that rhodopsin and its chromophore-free apoprotein, R-opsin, may indeed exist as a homodimer in rod disk membranes. Given the overwhelmingly strong historical context, the crucial remaining question, therefore, is whether pigment dimerization truly exists naturally and what function this dimerization may serve. We addressed this question in vivo with a unique mouse line (S-opsin(+)Lrat(-/-)) expressing, transgenically, short-wavelength-sensitive cone opsin (S-opsin) in rods and also lacking chromophore to exploit the fact that cone opsins, but not R-opsin, require chromophore for proper folding and trafficking to the photoreceptor's outer segment. In R-opsin's absence, S-opsin in these transgenic rods without chromophore was mislocalized; in R-opsin's presence, however, S-opsin trafficked normally to the rod outer segment and produced functional S-pigment upon subsequent chromophore restoration. Introducing a competing R-opsin transmembrane helix H1 or helix H8 peptide, but not helix H4 or helix H5 peptide, into these transgenic rods caused mislocalization of R-opsin and S-opsin to the perinuclear endoplasmic reticulum. Importantly, a similar peptide-competition effect was observed even in WT rods. Our work provides convincing evidence for visual pigment dimerization in vivo under physiological conditions and for its role in pigment maturation and targeting. Our work raises new questions regarding a potential mechanistic role of dimerization in rhodopsin signaling.

Retinal Attachment Instability Is Diversified among Mammalian Melanopsins.

Melanopsins play a key role in non-visual photoreception in mammals. Their close phylogenetic relationship to the photopigments in invertebrate visual cells suggests they have evolved to acquire molecular characteristics that are more suited for their non-visual functions. Here we set out to identify such characteristics by comparing the molecular properties of mammalian melanopsin to those of invertebrate melanopsin and visual pigment. Our data show that the Schiff base linking the chromophore retinal to the protein is more susceptive to spontaneous cleavage in mammalian melanopsins. We also find this stability is highly diversified between mammalian species, being particularly unstable for human melanopsin. Through mutagenesis analyses, we find that this diversified stability is mainly due to parallel amino acid substitutions in extracellular regions. We propose that the different stability of the retinal attachment in melanopsins may contribute to functional tuning of non-visual photoreception in mammals.

Structure and Conformation of the Carotenoids in Human Retinal Macular Pigment.

Human retinal macular pigment (MP) is formed by the carotenoids lutein and zeaxanthin (including the isomer meso-zeaxanthin). MP has several functions in improving visual performance and protecting against the damaging effects of light, and MP levels are used as a proxy for macular health-specifically, to predict the likelihood of developing age-related macular degeneration. While the roles of these carotenoids in retinal health have been the object of intense study in recent years, precise mechanistic details of their protective action remain elusive. We have measured the Raman signals originating from MP carotenoids in ex vivo human retinal tissue, in order to assess their structure and conformation. We show that it is possible to distinguish between lutein and zeaxanthin, by their excitation profile (related to their absorption spectra) and the position of their ν1 Raman mode. In addition, analysis of the ν4 Raman band indicates that these carotenoids are present in a specific, constrained conformation in situ, consistent with their binding to specific proteins as postulated in the literature. We discuss how these conclusions relate to the function of these pigments in macular protection. We also address the possibilities for a more accurate, consistent measurement of MP levels by Raman spectroscopy.

Identical Hydrogen-Bonding Strength of the Retinal Schiff Base between Primate Green- and Red-Sensitive Pigments: New Insight into Color Tuning Mechanism.

Three aspects are generally considered in the color-tuning mechanism of vision: (I) chromophore distortion, (II) electrostatic interaction between the protonated Schiff base and counterion, and (III) polarity around the ß-ionone ring and polyene chain. Primate green- and red-sensitive proteins are highly homologous but display maximum absorption at 530 and 560 nm, respectively. In the present study, the N-D stretching frequency of monkey green-sensitive protein was identified by using C15-D retinal. The hydrogen-bonding strength between monkey green and red was identical. Together with a previous resonance Raman study, we conclude that the 30 nm difference originates exclusively from the polarity around the ß-ionone ring and polyene chain. Three amino acids (Ala, Phe, and Ala in monkey green and Ser, Tyr, and Thr in monkey red, respectively) may be responsible for color tuning together with protein-bound water molecules around the ß-ionone ring and polyene chain but not at the Schiff base region.

Retinal Development and Ommin Pigment in the Cranchiid Squid Teuthowenia pellucida (Cephalopoda: Oegopsida).

The cranchiid Teuthowenia pellucida, like many deep-sea squid species, possesses large eyes that maximise light sensitivity in a nearly aphotic environment. To assess ontogenetic changes in the visual system, we conducted morphometric and histological analyses of the eyes using specimens from New Zealand collections. While the ratio between eye diameter and mantle length maintained a linear relationship throughout development, histological sections of the retina revealed that the outer photoreceptor layer became proportionally longer as the animal aged, coincident with a habitat shift into deeper, darker ocean strata. Other retinal layers maintained the same absolute thickness as was observed in paralarvae. Granules of the pigment ommin, normally located in the screening layer positioned at the base of the photoreceptors, were also observed at the outer end of the photoreceptor segments throughout the retina in young and mid-sized specimens. Early developmental stages of this species, dwelling in shallow waters, may therefore rely on migratory ommin to help shield photoreceptors from excess light and prevent over-stimulation. The oldest, deeper-dwelling specimens of T. pellucida examined had longer photoreceptors, and little or no migrated ommin was observed; we suggest therefore that short-term adaptive mechanisms for bright light conditions may be used primarily during epipelagic, early life stages in this species.

Spectral tuning in the eyes of deep-sea lanternfishes (Myctophidae): a novel sexually dimorphic intra-ocular filter.

Deep-sea fishes possess several adaptations to facilitate vision where light detection is pushed to its limit. Lanternfishes (Myctophidae), one of the world's most abundant groups of mesopelagic fishes, possess a novel and unique visual specialisation, a sexually dimorphic photostable yellow pigmentation, constituting the first record of a visual sexual dimorphism in any non-primate vertebrate. The topographic distribution of the yellow pigmentation across the retina is species specific, varying in location, shape and size. Spectrophotometric analyses reveal that this new retinal specialisation differs between species in terms of composition and acts as a filter, absorbing maximally between 356 and 443 nm. Microspectrophotometry and molecular analyses indicate that the species containing this pigmentation also possess at least 2 spectrally distinct rod visual pigments as a result of a duplication of the Rh1 opsin gene. After modelling the effect of the yellow pigmentation on photoreceptor spectral sensitivity, we suggest that this unique specialisation acts as a filter to enhance contrast, thereby improving the detection of bioluminescent emissions and possibly fluorescence in the extreme environment of the deep sea. The fact that this yellow pigmentation is species specific, sexually dimorphic and isolated within specific parts of the retina indicates an evolutionary pressure to visualise prey/predators/mates in a particular part of each species' visual field.

Pigment Deposition in the Rat Retina.

Incidental findings in the rat eye are not uncommon in acute and long-term toxicological studies. These findings can be associated with a number of causes unrelated to treatment with the test article, including congenital malformation, trauma, infection, metabolic disease, genetic predisposition, and age-related changes. The occurrence of pigment deposition in the retina of Wistar Hannover (Crl:WI (Han)) rats in a 4-week toxicity study is reported in this communication. The microscopic examination of the eyes in the 4-week toxicity study revealed focal yellow-brown pigment deposits in the retina, mainly located in the ganglion cell layer. The retinal pigment deposits were randomly distributed in the control and treated groups and were considered incidental. The deposits were clearly positive for ferric iron in the Perls' stain but not for lipofuscin by the Schmorl's and Long Ziehl-Neelsen methods. The iron-containing pigment is likely to represent hemosiderin accumulation after retinal micro-hemorrhage or could be indicative of the normal intraretinal iron transport and turnover.

Functional characterisation of the chromatically antagonistic photosensitive mechanism of erythrophores in the tilapia Oreochromis niloticus.

Non-visual photoreceptors with diverse photopigments allow organisms to adapt to changing light conditions. Whereas visual photoreceptors are involved in image formation, non-visual photoreceptors mainly undertake various non-image-forming tasks. They form specialised photosensory systems that measure the quality and quantity of light and enable appropriate behavioural and physiological responses. Chromatophores are dermal non-visual photoreceptors directly exposed to light and they not only receive ambient photic input but also respond to it. These specialised photosensitive pigment cells enable animals to adjust body coloration to fit environments, and play an important role in mate choice, camouflage and ultraviolet (UV) protection. However, the signalling pathway underlying chromatophore photoresponses and the physiological importance of chromatophore colour change remain under-investigated. Here, we characterised the intrinsic photosensitive system of red chromatophores (erythrophores) in tilapia. Like some non-visual photoreceptors, tilapia erythrophores showed wavelength-dependent photoresponses in two spectral regions: aggregations of inner pigment granules under UV and short-wavelengths and dispersions under middle- and long-wavelengths. The action spectra curve suggested that two primary photopigments exert opposite effects on these light-driven processes: SWS1 (short-wavelength sensitive 1) for aggregations and RH2b (rhodopsin-like) for dispersions. Both western blot and immunohistochemistry showed SWS1 expression in integumentary tissues and erythrophores. The membrane potential of erythrophores depolarised under UV illumination, suggesting that changes in membrane potential are required for photoresponses. These results suggest that SWS1 and RH2b play key roles in mediating intrinsic erythrophore photoresponses in different spectral ranges and this chromatically dependent antagonistic photosensitive mechanism may provide an advantage to detect subtle environmental photic change.