Activation of rhodopsin: new insights from structural and biochemical studies

Deprotonation of retinal Schiff base and structural dynamics in the early photoreaction of primate blue cone visual pigment

Animal rhodopsin is a photoreceptive protein crucial for vision, with activation triggered by the cis-trans isomerization of a retinal chromophore upon light absorption. This activation involves a series of thermal intermediates, ultimately leading to G protein-mediated signal transduction. The retinal chromophore is covalently bound to the protein through a protonated Schiff base, and its deprotonation during the formation of the active intermediate is believed to induce structural changes in α-helices that facilitate G-protein interactions. Using low-temperature UV-visible absorption and Fourier transform infrared spectroscopy, we investigated the early photoreaction of the primate blue cone visual pigment (MB). Our results demonstrate that Schiff base deprotonation in the early photoreaction is coupled with local perturbations in α-helices, promoting the formation of the Lumi intermediate. Using site-directed mutagenesis, we identified the proton acceptor involved in Schiff base deprotonation and mapped the regions of α-helical structural changes during the formation of the Lumi intermediate. We discovered that the proton released from the Schiff base is transferred to the counterion Glu113. Systematic mutagenesis revealed that structural perturbations in transmembrane helix 7 bring Glu113 and the lysine residue forming the Schiff base into proximity, facilitating efficient proton transfer during the early photoreaction. Additionally, the Lumi intermediate formed at low temperatures was found to revert to the original state through thermally driven reverse proton transfer, coupled with retinal reisomerization. From an evolutionary perspective, MB is part of a group of UV-sensitive cone visual pigments characterized by a deprotonated retinal Schiff base in the ground state. The observed propensity for MB to undergo Schiff base deprotonation is consistent with this evolutionary trait.

OPN3-mediated positive regulation of angiogenesis in HUVECs through VEGFR2 interaction

Many rhodopsin-like G-protein-coupled receptors (Rh-GPCRs) are known to either promote or inhibit angiogenesis. Among these, Opsin 4 and Opsin 5 are specifically involved in vascular development within the eye. Opsin 3 (OPN3), another member of Rh-GPCRs, performs a variety of light-dependent and light-independent functions in extraocular tissue. However, its role in endothelial cells and angiogenesis remains unclear. Here, we found that OPN3 knockdown or knockout in zebrafish impairs embryonic angiogenesis and vascular development. Similarly, silencing OPN3 in human umbilical vein endothelial cells (HUVECs) inhibits cellular proliferation, migration, sprouting, and tube formation, while OPN3 overexpression promotes these cellular processes. Moreover, OPN3 regulates angiogenesis in HUVECs through the VEGFR2-AKT pathway, with OPN3 and VEGFR2 co-localizing at the plasma membrane and forming a physical complex. These findings provide new insights into the non-light-dependent functions of OPN3 in angiogenesis, expanding our understanding of its physiological roles and offering potential therapeutic strategies for angiogenesis-related diseases.

Dysregulation of Retinal Melatonin Biosynthetic Pathway and Differential Expression of Retina-Specific Genes Following Blast-Induced Ocular Injury in Ferrets

BACKGROUND/OBJECTIVES

Blast-induced traumatic ocular injuries (bTOI) pose a significant risk to military and civilian populations, often leading to visual impairment or blindness. Retina, the innermost layer of ocular tissue consisting of photoreceptor and glial cells, is highly susceptible to blast injuries. Despite its prevalence, the molecular mechanisms underlying retinal damage following bTOI remain poorly understood, hindering the development of targeted therapies. Melatonin, a neuroprotective indoleamine with antioxidant, anti-inflammatory, and circadian regulatory properties, is synthesized in the retina and plays a crucial role in retinal health. Similarly, retina-specific genes, such as Rhodopsin, Melanopsin, and RPE65, are essential for photoreceptor function, visual signaling, and the visual cycle. However, their responses to blast exposure have not been thoroughly investigated.

METHODS

In this study, we utilized a ferret model of bTOI to evaluate the temporal expression of melatonin-synthesizing enzymes, such as tryptophan hydroxylase 1 and 2 (TPH1 and TPH2), Aralkylamine N-acetyltransferase (AANAT), and Acetylserotonin-O-methyltransferase (ASMT), and retina-specific genes (Rhodopsin, Melanopsin) and retinal pigment epithelium-specific 65 kDa protein (RPE65) at 4 h, 24 h, 7 days, and 28 days post-blast. Ferrets were exposed to tightly coupled blast overpressure waves using an advanced blast simulator, and retinal tissues were collected for quantitative polymerase chain reaction (qPCR) analysis.

RESULTS

The results revealed dynamic and multiphasic transcriptional responses. TPH1 and TPH2 exhibited significant upregulation at 24 h, followed by downregulation at 28 days, indicating blast-induced dysregulation of tryptophan metabolism, including melatonin synthesis. Similarly, AANAT and ASMT showed acute downregulation post-blast, with late-phase disruptions. Rhodopsin expression increased at 24 h but declined at 28 days, while Melanopsin and RPE65 demonstrated early upregulation followed by downregulation, reflecting potential disruptions in circadian regulation and the visual cycle.

CONCLUSIONS

These findings highlight the complex regulatory mechanisms underlying retinal responses to bTOI, involving neuroinflammation, oxidative stress, and disruptions in melatonin synthesis and photoreceptor cell functions. The results emphasize the therapeutic potential of melatonin in mitigating retinal damage and preserving visual function.

Trichromacy and ultraviolet vision in a nocturnal marsupial

Color vision among mammals is diverse and complex, with many physiological and genetic factors affecting spectral sensitivity, the ability to perceive different wavelengths of light. In this study, the color vision of the sugar glider (Petaurus breviceps), a nocturnal, gliding mammal, was examined through a series of behavioral tests, genetic analyses, and immunohistochemistry. This is the first study to classify the color vision capabilities of this species. Sugar gliders demonstrated trichromacy and ultraviolet (UV) sensitivity, the latter of which was further supported by genetic analysis. Visualization of the sugar glider retina exhibited a rod-dominant retina that expresses rhodopsin, short-wavelength sensitive 1 opsin, and long/medium-wavelength sensitive opsin. Diurnal primates were thought to be the only mammals able to visualize trichromatically, however the results of this examination and evidence from a few other marsupial studies provide support for nocturnal trichromacy in Metatheria. Intriguingly, the genetic basis for the medium-wavelength sensitivity in marsupials has yet to be discovered. Our results are evidence of a fourth Australian marsupial that is UV-trichromatic, supporting complex spectral sensitivity and UV vision as benefits to survival in nocturnal environments. Given that Rh1 sensitivity at 501 nm explains the green sensitivity behaviorally, question arises how many other nocturnal 'dichromatic' species use rods for trichromatic vision in mesopic light.

Investigating the Origin of Automatic Rhodopsin Modeling Outliers Using the Microbial Gloeobacter Rhodopsin as Testbed

The automatic rhodopsin modeling (ARM) approach is a computational workflow devised for the automatic buildup of hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild-type rhodopsins and mutants, with the purpose of establishing trends in their photophysical and photochemical properties. Despite the success of ARM in accurately describing the visible light absorption maxima of many rhodopsins, for a few cases, called outliers, it might lead to large deviations with respect to experiments. Applying ARM toGloeobacter rhodopsin (GR), a microbial rhodopsin with important applications in optogenetics, we analyze the origin of such outliers in the absorption energies obtained for GR wild-type and mutants at neutral pH, with a total root-mean-square deviation (RMSD) of 0.42 eV with respect to the experimental GR excitation energies. Having discussed the importance and the uncertainty of one particular amino-acid pKa, namely histidine at position 87, we propose and test several modifications to the standard ARM protocol: (i) improved pKa predictions along with the consideration of several protonation microstates, (ii) attenuation of the opsin electrostatic potential at short-range, (iii) substitution of the state-average complete active space (CAS) electronic structure method by its state-specific approach, and (iv) complete replacement of CAS with mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT). The best RMSD result we obtain is 0.2 eV combining the protonation of H87 and using MRSF/CAMH-B3LYP.

Functional characterization of optic photoreception in Lymnaea stagnalis

Optic photoreception is a critical function for animal survival. Across the evolutionary spectrum, diverse animal models have been used to investigate visual system function and potential mechanisms under physiological or pathophysiological states. However less is known on photoreceptive behaviors and retinal processing in invertebrates, especially molluscs. This study focuses on the freshwater pond snail, Lymnaea stagnalis (L. stagnalis), to explore its visual function and underlying mechanisms. Using anatomical and histological approaches we characterized the L. stagnalis eye structure and demonstrated structural connections and retinal rhodopsin-positive sensory cells potentially critical for phototransduction. To assess the snail phototactic responses, we developed a new neurobehavioral protocol and employed DeepLabCut to track and quantify animal locomotion. We demonstrated that L. stagnalis exhibits a positive locomotory response to intense focal light and has diverse photo-locomotory responses. Further, we conducted phylogenetic and protein structure analyses and demonstrated that L. stagnalis has a unique repertoire of both vertebrate and invertebrate phototransduction genes. Further characterization of a rhodopsin-like gene identified unique characteristics compared to other mollusks and vertebrates, suggesting different mechanisms of phototransduction. Taken together, our work establishes L. stagnalis as a model organism for studying optic photoreception, offering new insights into the evolution and diversity of visual function across animal species.

Channelrhodopsins with distinct chromophores and binding patterns

Channelrhodopsins are popular optogenetic tools in neuroscience, but remain poorly understood mechanistically. Here we report the cryo-EM structures of channelrhodopsin-2 (ChR2) from Chlamydomonas reinhardtii and H. catenoides kalium channelrhodopsin (KCR1). We show that ChR2 recruits an endogenous N-retinylidene-PE-like molecule to a previously unidentified lateral retinal binding pocket, exhibiting a reduced light response in HEK293 cells. In contrast, H. catenoides kalium channelrhodopsin (KCR1) binds an endogenous retinal in its canonical retinal binding pocket under identical condition. However, exogenous ATR reduces the photocurrent magnitude of wild type KCR1 and also inhibits its leaky mutant C110T. Our results uncover diverse retinal chromophores with distinct binding patterns for channelrhodopsins in mammalian cells, which may further inspire next generation optogenetics for complex tasks such as cell fate control.

In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling

Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic tool. Here, we aim to utilize mouse melanopsin to trigger macrophage migration by its subcellular optical activation with localized blue light, while simultaneously imaging the migration with red light. To reduce melanopsin's red light sensitivity, we employ a combination of in silico structure prediction and automated quantum mechanics/molecular mechanics modeling to predict minimally invasive mutations to shift its absorption spectrum towards the shorter wavelength region of the visible spectrum without compromising the signaling efficiency. The results demonstrate that it is possible to achieve melanopsin mutants that resist red light-induced activation but are activated by blue light and display properties indicating preserved bistability. Using the A333T mutant, we show that the blue light-induced subcellular melanopsin activation triggers localized PIP3 generation and macrophage migration, which we imaged using red light, demonstrating the optogenetic utility of minimally engineered melanopsins.

Interactions between electromagnetic radiation and biological systems

Even though the bioeffects of electromagnetic radiation (EMR) have been extensively investigated during the past several decades, our understandings of the bioeffects of EMR and the mechanisms of the interactions between the biological systems and the EMRs are still far from satisfactory. In this article, we introduce and summarize the consensus, controversy, limitations, and unsolved issues. The published works have investigated the EMR effects on different biological systems including humans, animals, cells, and biochemical reactions. Alternative methodologies also include dielectric spectroscopy, detection of bioelectromagnetic emissions, and theoretical predictions. In many studies, the thermal effects of the EMR are not properly controlled or considered. The frequency of the EMR investigated is limited to the commonly used bands, particularly the frequencies of the power line and the wireless communications; far fewer studies were performed for other EMR frequencies. In addition, the bioeffects of the complex EM environment were rarely discussed. In summary, our understanding of the bioeffects of the EMR is quite restrictive and further investigations are needed to answer the unsolved questions.

Honeybee as a food nutrition analysis model of neural development and gut microbiota

Research on the relationships between the gut microbiota and the neurophysiology and behavior of animals has grown exponentially in just a few years. Insect behavior may be controlled by molecular mechanisms that are partially homologous to those in mammals, and swarming insects may be suitable as experiment models in these types of investigations. All core gut bacteria in honeybees can be cultivated in vitro. Certain gut microflora of bees can be genetically engineered or sterilized and colonized. The bee gut bacteria model is established more rapidly and has a higher flux than other sterile animal models. It may help elucidate the pathogenesis of intestinal diseases and identify effective molecular therapeutic targets against them. In the present review, we focused on the contributions of the honeybee model in learning cognition and microbiome research. We explored the relationship between honeybee behavior and neurodevelopment and the factors determining the mechanisms by which the gut microbiota affects the host. In particular, we concentrated on the correlation between gut microbiota and brain development. Finally, we examined strategies for the effective use of simple animal models in animal cognition and microbiome research.

Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain

Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six - a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.

Cones and cone pathways remain functional in advanced retinal degeneration

Most defects causing retinal degeneration in retinitis pigmentosa (RP) are rod-specific mutations, but the subsequent degeneration of cones, which produces loss of daylight vision and high-acuity perception, is the most debilitating feature of the disease. To understand better why cones degenerate and how cone vision might be restored, we have made the first single-cell recordings of light responses from degenerating cones and retinal interneurons after most rods have died and cones have lost their outer-segment disk membranes and synaptic pedicles. We show that degenerating cones have functional cyclic-nucleotide-gated channels and can continue to give light responses, apparently produced by opsin localized either to small areas of organized membrane near the ciliary axoneme or distributed throughout the inner segment. Light responses of second-order horizontal and bipolar cells are less sensitive but otherwise resemble those of normal retina. Furthermore, retinal output as reflected in responses of ganglion cells is less sensitive but maintains spatiotemporal receptive fields at cone-mediated light levels. Together, these findings show that cones and their retinal pathways can remain functional even as degeneration is progressing, an encouraging result for future research aimed at enhancing the light sensitivity of residual cones to restore vision in patients with genetically inherited retinal degeneration.

Rhodopsin, light-sensor of vision

The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.

Convergent evolution of animal and microbial rhodopsins

Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.

Structural view of G protein-coupled receptor signaling in the retinal rod outer segment

Visual phototransduction is the most extensively studied G protein-coupled receptor (GPCR) signaling pathway because of its quantifiable stimulus, non-redundancy of genes, and immense importance in vision. We summarize recent discoveries that have advanced our understanding of rod outer segment (ROS) morphology and the pathological basis of retinal diseases. We have combined recently published cryo-electron tomography (cryo-ET) data on the ROS with structural knowledge on individual proteins to define the precise spatial limitations under which phototransduction occurs. Although hypothetical, the reconstruction of the rod phototransduction system highlights the potential roles of phosphodiesterase 6 (PDE6) and guanylate cyclases (GCs) in maintaining the spacing between ROS discs, suggesting a plausible mechanism by which intrinsic optical signals are generated in the retina.

The evolutionary history and spectral tuning of vertebrate visual opsins

Many animals depend on the sense of vision for survival. In eumetazoans, vision requires specialized, light-sensitive cells called photoreceptors. Light reaches the photoreceptors and triggers the excitation of light-detecting proteins called opsins. Here, we describe the story of visual opsin evolution from the ancestral bilaterian to the extant vertebrate lineages. We explain the mechanisms determining color vision of extant vertebrates, focusing on opsin gene losses, duplications, and the expression regulation of vertebrate opsins. We describe the sequence variation both within and between species that has tweaked the sensitivities of opsin proteins towards different wavelengths of light. We provide an extensive resource of wavelength sensitivities and mutations that have diverged light sensitivity in many vertebrate species and predict how these mutations were accumulated in each lineage based on parsimony. We suggest possible natural and sexual selection mechanisms underlying these spectral differences. Understanding how molecular changes allow for functional adaptation of animals to different environments is a major goal in the field, and therefore identifying mutations affecting vision and their relationship to photic selection pressures is imperative. The goal of this review is to provide a comprehensive overview of our current understanding of opsin evolution in vertebrates.

Hydration-mediated G-protein-coupled receptor activation

Although G-protein–coupled receptors (GPCRs) control vast physiological pathways, their activation remains chemically and physically enigmatic. Our osmotic stress studies of the visual receptor rhodopsin have redefined the standard model of GPCR signaling by revealing the essential role of bulk water. We show results consistent with a large number of water molecules flooding the rhodopsin interior during activation to stabilize the effector binding conformation. These results suggest a model of GPCR activation in which the receptor becomes solvent-swollen upon formation of the active state. We thus demonstrate the mechanism whereby water acts as a powerful allosteric modulator of a pharmacologically important membrane protein family.

The Rhodopsin family of G-protein–coupled receptors (GPCRs) comprises the targets of nearly a third of all pharmaceuticals. Despite structural water present in GPCR X-ray structures, the physiological relevance of these solvent molecules to rhodopsin signaling remains unknown. Here, we show experimental results consistent with the idea that rhodopsin activation in lipid membranes is coupled to bulk water movements into the protein. To quantify hydration changes, we measured reversible shifting of the metarhodopsin equilibrium due to osmotic stress using an extensive series of polyethylene glycol (PEG) osmolytes. We discovered clear evidence that light activation entails a large influx of bulk water (∼80–100 molecules) into the protein, giving insight into GPCR activation mechanisms. Various size polymer osmolytes directly control rhodopsin activation, in which large solutes are excluded from rhodopsin and dehydrate the protein, favoring the inactive state. In contrast, small osmolytes initially forward shift the activation equilibrium until a quantifiable saturation point is reached, similar to gain-of-function protein mutations. For the limit of increasing osmolyte size, a universal response of rhodopsin to osmotic stress is observed, suggesting it adopts a dynamic, hydrated sponge-like state upon photoactivation. Our results demand a rethinking of the role of water dynamics in modulating various intermediates in the GPCR energy landscape. We propose that besides bound water, an influx of bulk water plays a necessary role in establishing the active GPCR conformation that mediates signaling.

Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action

Failure of a protein to achieve its functional structural state and normal cellular location contributes to the etiology and pathology of heritable human conformational diseases. The autosomal dominant form of retinitis pigmentosa (adRP) is an incurable blindness largely linked to mutations of the membrane protein rod opsin. While the mechanisms underlying the noxious effects of the mutated protein are not completely understood, a common feature is the functional protein conformational loss. Here, the wild type and 39 adRP rod opsin mutants were subjected to mechanical unfolding simulations coupled to the graph theory-based protein structure network analysis.

A robust computational model was inferred and in vitro validated in its ability to predict endoplasmic reticulum retention of adRP mutants, a feature linked to the mutation-caused misfolding. The structure-based approach could also infer the structural determinants of small chaperone action on misfolded protein mutants with therapeutic implications.

The approach is exportable to conformational diseases linked to missense mutations in any membrane protein.

The rhodopsin-retinochrome system for retinal re-isomerization predates the origin of cephalopod eyes

Background

The process of photoreception in most animals depends on the light induced isomerization of the chromophore retinal, bound to rhodopsin. To re-use retinal, the all-trans-retinal form needs to be re-isomerized to 11-cis-retinal, which can be achieved in different ways. In vertebrates, this mostly includes a stepwise enzymatic process called the visual cycle. The best studied re-isomerization system in protostomes is the rhodopsin-retinochrome system of cephalopods, which consists of rhodopsin, the photoisomerase retinochrome and the protein RALBP functioning as shuttle for retinal. In this study we investigate the expression of the rhodopsin-retinochrome system and functional components of the vertebrate visual cycle in a polyplacophoran mollusk, Leptochiton asellus, and examine the phylogenetic distribution of the individual components in other protostome animals.

Results

Tree-based orthology assignments revealed that orthologs of the cephalopod retinochrome and RALBP are present in mollusks outside of cephalopods. By mining our dataset for vertebrate visual cycle components, we also found orthologs of the retinoid binding protein RLBP1, in polyplacophoran mollusks, cephalopods and a phoronid. In situ hybridization and antibody staining revealed that L. asellus retinochrome is co-expressed in the larval chiton photoreceptor cells (PRCs) with the visual rhodopsin, RALBP and RLBP1. In addition, multiple retinal dehydrogenases are expressed in the PRCs, which might also contribute to the rhodopsin-retinochrome system.

Conclusions

We conclude that the rhodopsin-retinochrome system is a common feature of mollusk PRCs and predates the origin of cephalopod eyes. Our results show that this system has to be extended by adding further components, which surprisingly, are shared with vertebrates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01939-x.

Conformational insights into the C-terminal mutations of human rhodopsin in retinitispigmentosa

Rhodopsin is a light-sensitive transmembrane receptor involved in the visual transduction cascade. Among the several rhodopsin mutations related to retinitis pigmentosa (RP), those affecting the C-terminal VAPA-COOH motif that is implicated in rhodopsin trafficking from the Golgi to the rod outer segment are notably associated with more aggressive RP forms. However, molecular reasons for defective rhodopsin signaling due to VAPA-COOH mutations, which might include steric hindrance, physicochemical features and structural determinants, are yet unknown, thus limiting further drug design approaches. In this work, clinically relevant rhodopsin mutations at the P347 site within the VAPA-COOH motif were investigated by molecular dynamics (MD) simulations and compared to the wild-type (WT) system. In agreement with experimental evidence, conformational fluctuations of the intrinsically disordered C-terminal tail of WT and mutant rhodopsin were found not to affect the overall structure of the transmembrane domain, including binding to the retinal cofactor. The WT VAPA-COOH motif adopts a unique conformation that is not found in pathological mutants, suggesting that structural features could better explain the pathogenicity of P347 rhodopsin mutants than physicochemical or steric determinants. These results were confirmed by MD simulations in both membrane-embedded full-length opsin and membrane-free C-terminal deca-peptides, these latter becoming very useful and small-size model systems for further investigations of rhodopsin C-terminal mutations. Structural details elucidated in this work might facilitate the understanding of the pathological mechanisms of this class of rhodopsin mutants, which will be instrumental to the development of new therapeutic strategies.

Principles of odor coding in vertebrates and artificial chemosensory systems

The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.

Positive selection drives the evolution of a primate bitter taste receptor gene

Bitter taste perception is important in food choice of animals, and it is mediated by bitter taste receptor (T2R) containing three regions: extracellular regions (ECs), transmembrane regions (TMs), and intracellular regions (ICs). It is hypothesized that ECs, TMs, and ICs are under different selective pressures, with ECs being unstable while TMs and ICs being constrained. To test this hypothesis, we examined the selective pressures on one of the bitter taste receptor genes-T2R1 and its different areas from 35 primates and found that T2R1 was under neutral evolution but with some positively selected sites in it. Further analyses suggested that TMs, ICs, and the concatenated transmembrane region TM1237 were under purifying selection; in contrast, extracellular regions, the first and second extracellular loop (EL1, EL2), were subject to positive selection with several positively selected sites in them. Therefore, this study supported the above-mentioned hypothesis. The reason why EL1 and EL2 of T2R1 have positively selected sites is probably due to their participation in forming the cap-like structure involved in ligand binding. Positive selection acts as a driving force of the T2R1 functional differentiation and confers the ability to discern various bitter substances for primates, which could help them to adapt to the changing environment during the evolutionary course.

Behavior of Chemokine Receptor 6 (CXCR6) in Complex with CXCL16 Soluble form Chemokine by Molecular Dynamic Simulations: General Protein‒Ligand Interaction Model and 3D-QSAR Studies of Synthetic Antagonists

The CXCR6‒CXCL16 axis is involved in several pathological processes, and its overexpression has been detected in different types of cancer, such as prostate, breast, ovary, and lung cancer, along with schwannomas, in which it promotes invasion and metastasis. Moreover, this axis is involved in atherosclerosis, type 1 diabetes, primary immune thrombocytopenia, vitiligo, and other autoimmune diseases, in which it is responsible for the infiltration of different immune system cells. The 3D structure of CXCR6 and CXCL16 has not been experimentally resolved; therefore, homology modeling and molecular dynamics simulations could be useful for the study of this signaling axis. In this work, a homology model of CXCR6 and a soluble form of CXCL16 (CXCR6‒CXCL16s) are reported to study the interactions between CXCR6 and CXCL16s through coarse-grained molecular dynamics (CG-MD) simulations. CG-MD simulations showed the two activation steps of CXCR6 through a decrease in the distance between the chemokine and the transmembrane region (TM) of CXCR6 and transmembrane rotational changes and polar interactions between transmembrane segments. The polar interactions between TM3, TM5, and TM6 are fundamental to functional conformation and the meta-active state of CXCR6. The interactions between D77-R280 and T243-TM7 could be related to the functional conformation of CXCR6; alternatively, the interaction between Q195-Q244 and N248 could be related to an inactive state due to the loss of this interaction, and an arginine cage broken in the presence of CXCL16s allows the meta-active state of CXCR6. A general protein‒ligand interaction supports the relevance of TM3‒TM5‒TM6 interactions, presenting three relevant pharmacophoric features: HAc (H-bond acceptor), HDn (H-bond donator), and Hph (hydrophobic), distributed around the space between extracellular loops (ECLs) and TMs. The HDn feature is close to TM3 and TM6; likewise, the HAc and Hph features are close to ECL1 and ECL2 and could block the rotation and interactions between TM3‒TM6 and the interactions of CXCL16s with the ECLs. Tridimensional quantitative structure-activity relationships (3D-QSAR) models show that the positive steric (VdW) and electrostatic fields coincide with the steric and positive electrostatic region of the exo-azabicyclo[3.3.1]nonane scaffold in the best pIC50 ligands. This substructure is close to the E274 residue and therefore relevant to the activity of CXCR6. These data could help with the design of new molecules that inhibit chemokine binding or antagonize the receptor based on the activation mechanism of CXCR6 and provoke a decrease in chemotaxis caused by the CXCR6‒CXCL16 axis.

Structural aspects of rod opsin and their implication in genetic diseases

Vision in dim-light conditions is triggered by photoactivation of rhodopsin, the visual pigment of rod photoreceptor cells. Rhodopsin is made of a protein, the G protein coupled receptor (GPCR) opsin, and the chromophore 11-cis-retinal. Vertebrate rod opsin is the GPCR best characterized at the atomic level of detail. Since the release of the first crystal structure 20 years ago, a huge number of structures have been released that, in combination with valuable spectroscopic determinations, unveiled most aspects of the photobleaching process. A number of spontaneous mutations of rod opsin have been found linked to vision-impairing diseases like autosomal dominant or autosomal recessive retinitis pigmentosa (adRP or arRP, respectively) and autosomal congenital stationary night blindness (adCSNB). While adCSNB is mainly caused by constitutive activation of rod opsin, RP shows more variegate determinants affecting different aspects of rod opsin function. The vast majority of missense rod opsin mutations affects folding and trafficking and is linked to adRP, an incurable disease that awaits light on its molecular structure determinants. This review article summarizes all major structural information available on vertebrate rod opsin conformational states and the insights gained so far into the structural determinants of adCSNB and adRP linked to rod opsin mutations. Strategies to design small chaperones with therapeutic potential for selected adRP rod opsin mutants will be discussed as well.

Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein-ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding

Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.

Common activation mechanism of class A GPCRs

Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.

Elucidating the Molecular Mechanism of Ultrafast Pfr-State Photoisomerization in Bathy Bacteriophytochrome PaBphP

Bacteriophytochromes are photoreceptors that regulate various physiological processes induced by photoisomerization in a linear tetrapyrrole chromophore upon red/far-red light absorption. Here, we investigate the photoinduced Pfr-state isomerization mechanism of a bathy bacteriophytochrome from Pseudomonas aeruginosa combining femtosecond-resolved fluorescence and absorption methods. We observed initial coherent oscillation motions in the first 1 ps with low-frequency modes below 60 cm^-1, then a bifurcation of the wavepacket with the distinct excited-state lifetimes in a few picoseconds, and finally chromophore-protein coupled ground-state conformational evolution on nanosecond time scales. Together with systematic mutational studies, we revealed the critical roles of hydrogen bonds in tuning the photoisomerization dynamics. These results provide a clear molecular picture of the Pfr-state photoisomerization, a mechanism likely applicable to the other phytochromes.

G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity

The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures reveal a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. This binding site contains a sodium ion in those GPCRs that are crystallized in their inactive conformations but does not in those GPCRs that are trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction have until now remained obscure. Here, by modeling the available experimental data, we show that the sodium gradient over the cell membrane increases the sensitivity of GPCRs if their activation is thermodynamically coupled to the sodium ion translocation into the cytoplasm but decreases it if the sodium ion retreats into the extracellular space upon receptor activation. The model quantitatively describes the available data on both activation and suppression of distinct GPCRs by membrane voltage. The model also predicts selective amplification of the signal from (endogenous) agonists if only they, but not their (partial) analogs, induce sodium translocation. Comparative structure and sequence analyses of sodium-binding GPCRs indicate a key role for the conserved leucine residue in the second transmembrane helix (Leu2.46) in coupling sodium translocation to receptor activation. Hence, class A GPCRs appear to harness the energy of the transmembrane sodium potential to increase their sensitivity and selectivity.

A light in the dark: state of the art and perspectives in optogenetics and optopharmacology for restoring vision

In the last decade, innovative therapeutic strategies against inherited retinal degenerations (IRDs) have emerged. In particular, chemical- and opto-genetics approaches or a combination of them have been identified for modulating neuronal/optical activity in order to restore vision in blinding diseases. The ‘chemical-genetics approach’ (optopharmacology) uses small molecules (exogenous photoswitches) for restoring light sensitivity by activating ion channels. The ‘opto-genetics approach’ employs light-activated photosensitive proteins (exogenous opsins), introduced by viral vectors in injured tissues, to restore light response. These approaches offer control of neuronal activities with spatial precision and limited invasiveness, although with some drawbacks. Currently, a combined therapeutic strategy (optogenetic pharmacology) is emerging. This review describes the state of the art and provides an overview of the future perspectives in vision restoration.

Functional characterisation of naturally occurring mutations in human melanopsin

Melanopsin is a blue light-sensitive opsin photopigment involved in a range of non-image forming behaviours, including circadian photoentrainment and the pupil light response. Many naturally occurring genetic variants exist within the human melanopsin gene (OPN4), yet it remains unclear how these variants affect melanopsin protein function and downstream physiological responses to light. Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants. From 1242 human OPN4 variants collated in the NCBI Short Genetic Variation database (dbSNP), we identified 96 that lead to non-synonymous amino acid substitutions. These 96 missense mutations were screened using sequence alignment and comparative approaches to select 16 potentially deleterious variants for functional characterisation using calcium imaging of melanopsin-driven light responses in HEK293T cells. We identify several previously uncharacterised OPN4 mutations with altered functional properties, including attenuated or abolished light responses, as well as variants demonstrating abnormal response kinetics. These data provide valuable insight into the structure-function relationships of human melanopsin, including several key functional residues of the melanopsin protein. The identification of melanopsin variants with significantly altered function may serve to detect individuals with disrupted melanopsin-based light perception, and potentially highlight those at increased risk of sleep disturbance, circadian dysfunction, and visual abnormalities.

Photoreceptors Take Charge: Emerging Principles for Light Sensing

The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.

Removal of the blue component of light significantly decreases retinal damage after high intensity exposure

Light causes damage to the retina (phototoxicity) and decreases photoreceptor responses to light. The most harmful component of visible light is the blue wavelength (400–500 nm). Different filters have been tested, but so far all of them allow passing a lot of this wavelength (70%). The aim of this work has been to prove that a filter that removes 94% of the blue component may protect the function and morphology of the retina significantly. Three experimental groups were designed. The first group was unexposed to light, the second one was exposed and the third one was exposed and protected by a blue-blocking filter. Light damage was induced in young albino mice (p30) by exposing them to white light of high intensity (5,000 lux) continuously for 7 days. Short wavelength light filters were used for light protection. The blue component was removed (94%) from the light source by our filter. Electroretinographical recordings were performed before and after light damage. Changes in retinal structure were studied using immunohistochemistry, and TUNEL labeling. Also, cells in the outer nuclear layer were counted and compared among the three different groups. Functional visual responses were significantly more conserved in protected animals (with the blue-blocking filter) than in unprotected animals. Also, retinal structure was better kept and photoreceptor survival was greater in protected animals, these differences were significant in central areas of the retina. Still, functional and morphological responses were significantly lower in protected than in unexposed groups. In conclusion, this blue-blocking filter decreases significantly photoreceptor damage after exposure to high intensity light. Actually, our eyes are exposed for a very long time to high levels of blue light (screens, artificial light LED, neons…). The potential damage caused by blue light can be palliated.

Ligand-induced action of the W2866.48 rotamer toggle switch in the β2-adrenergic receptor

Studies focused on GPCRs, particularly on the β₂-adrenergic receptor (β₂-AR), have demonstrated the relationship between ligand structure, receptor conformational changes and the corresponding pharmacological outcomes. Herein, we studied the molecular details of the rotameric flip of the W286^6.48 sidechain, i.e. a presumed action switch that has not been reported in native β₂-AR thus far. It is believed that although both the 'active' and 'inactive' conformers of β₂-AR exhibit similar conformations of this switch, it may still play a substantial role in the ligand-induced activation of the receptor. By using both experimental methods (time-resolved fluorescence spectroscopy) and molecular modeling techniques (enhanced-sampling molecular dynamics), we characterized the conformational rearrangements of W286^6.48 in relation to the type of ligand present in the binding cavity and to the conformation of the receptor ('active' vs. 'inactive' β₂-AR). We found that the conformational behaviour of W286^6.48 is correlated with the pharmacological character of the ligand present in the binding cavity but not with the instantaneous conformation of the receptor. Namely, agonists promote the W286^6.48 conformations that facilitate the increase of the solvation within the inner receptor channel. In contrast, antagonists and inverse agonists act toward the decrease of the solvation in the inner channel. This creates an opportunity for using computational methodologies in determining the pharmacological properties of various ligands. The combination of the time-resolved fluorescence spectroscopy technique with the enhanced-sampling molecular dynamics simulations is shown to be a powerful tool for studying the ligand-induced conformational rearrangements in GPCRs.

REEP6 deficiency leads to retinal degeneration through disruption of ER homeostasis and protein trafficking

Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy. We recently identified mutations in REEP6, which encodes the receptor expression enhancing protein 6, in several families with autosomal recessive RP. REEP6 is related to the REEP and Yop1p family of ER shaping proteins and potential receptor accessory proteins, but the role of REEP6 in the retina is unknown. Here we characterize the disease mechanisms associated with loss of REEP6 function using a Reep6 knockout mouse generated by CRISPR/Cas9 gene editing. In control mice REEP6 was localized to the inner segment and outer plexiform layer of rod photoreceptors. The Reep6-/- mice exhibited progressive photoreceptor degeneration from P20 onwards. Ultrastructural analyses at P20 by transmission electron microscopy and 3View serial block face scanning EM revealed an expansion of the distal ER in the Reep6-/- rods and an increase in their number of mitochondria. Electroretinograms revealed photoreceptor dysfunction preceded degeneration, suggesting potential defects in phototransduction. There was no effect on the traffic of rhodopsin, Rom1 or peripherin/rds; however, the retinal guanylate cyclases GC1 and GC2 were severely affected in the Reep6 knockout animals, with almost undetectable expression. These changes correlated with an increase in C/EBP homologous protein (CHOP) expression and the activation of caspase 12, suggesting that ER stress contributes to cell death. Collectively, these data suggest that REEP6 plays an essential role in maintaining cGMP homeostasis though facilitating the stability and/or trafficking of guanylate cyclases and maintaining ER and mitochondrial homeostasis.

A G Protein-Coupled Receptor Dimerization Interface in Human Cone Opsins

G protein-coupled receptors (GPCRs) detect a wide variety of physical and chemical signals and transmit that information across the cellular plasma membrane. Dimerization is a proposed modulator of GPCR signaling, but the structure and stability of class A GPCR dimerization have been difficult to establish. Here we investigated the dimerization affinity and binding interface of human cone opsins, which initiate and sustain daytime color vision. Using a time-resolved fluorescence approach, we found that human red cone opsin exhibits a strong propensity for dimerization, whereas the green and blue cone opsins do not. Through mutagenesis experiments, we identified a dimerization interface in the fifth transmembrane helix of human red cone opsin involving amino acids I230, A233, and M236. Insights into this dimerization interface of red cone opsin should aid ongoing investigations of the structure and function of GPCR quaternary interactions in cell signaling. Finally, we demonstrated that the same residues needed for dimerization are also partially responsible for the spectral tuning of red cone opsin. This last observation has the potential to open up new lines of inquiry regarding the functional role of dimerization for red cone opsin.

Principles of Ocular Pharmacology

Recently, in a poll by Research America, a significant number of individuals placed losing their eyesight as having the greatest impact on their lives more so than other conditions, such as limb loss or memory loss. When they were also asked to rank which is the worst disease that could happen to them, blindness was ranked first by African-Americans and second by Caucasians, Hispanics, and Asians. Therefore, understanding the mechanisms of disease progression in the eye is extremely important if we want to make a difference in people's lives. In addition, developing treatment programs for these various diseases that could affect our eyesight is also critical. One of the most effective treatments we have is in the development of specific drugs that can be used to target various components of the mechanisms that lead to ocular disease. Understanding basic principles of the pharmacology of the eye is important if one seeks to develop effective treatments. As our population ages, the incidence of devastating eye diseases increases. It has been estimated that more than 65 million people suffer from glaucoma worldwide (Quigley and Broman. Br J Ophthalmol 90:262-267, 2006). Add to this the debilitating eye diseases of age-related macular degeneration, diabetic retinopathy, and cataract, the number of people effected exceeds 100 million. This chapter focuses on ocular pharmacology with specific emphasis on basic principles and outlining where in the various ocular sites are drug targets currently in use with effective drugs but also on future drug targets.

Powdered G-Protein-Coupled Receptors

Preparation and storage of functional membrane proteins such as G-protein-coupled receptors (GPCRs) are crucial to the processes of drug delivery and discovery. Here, we describe a method of preparing powdered GPCRs using rhodopsin as the prototype. We purified rhodopsin in CHAPS detergent with low detergent to protein ratio so the bulk of the sample represented protein (ca. 72% w/w). Our new method for generating powders of membrane proteins followed by rehydration paves the way for conducting functional and biophysical experiments. As an illustrative application, powdered rhodopsin was prepared with and without the cofactor 11-cis-retinal to enable partial rehydration of the protein with D₂O in a controlled manner. Quasi-elastic neutron scattering studies using both spatial motion and energy landscape models form the basis for crucial insights into structural fluctuations and thermodynamics of GPCR activation.

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor

Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, crucial for protein function, as only observed for globular proteins previously. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, an idea of the generic free-energy landscape is used to explain the GPCR dynamics of ligand-binding and ligand-free protein conformations, which can be further applied to other GPCR systems.

Transmembrane Helices Tilt, Bend, Slide, Torque, and Unwind between Functional States of Rhodopsin

The seven-helical bundle of rhodopsin and other G-protein coupled receptors undergoes structural rearrangements as the transmembrane receptor protein is activated. These structural changes are known to involve tilting and bending of various transmembrane helices. However, the cause and effect relationship among structural events leading to a cytoplasmic crevasse for G-protein binding is less well defined. Here we present a mathematical model of the protein helix and a simple procedure to determine multiple parameters that offer precise depiction of a helical conformation. A comprehensive survey of bovine rhodopsin structures shows that the helical rearrangements during the activation of rhodopsin involve a variety of angular and linear motions such as torsion, unwinding, and sliding in addition to the previously reported tilting and bending. These hitherto undefined motion components unify the results obtained from different experimental approaches, and demonstrate conformational similarity between the active opsin structure and the photoactivated structures in crystallo near the retinal anchor despite their marked differences.

Functional genomics identifies regulators of the phototransduction machinery in the Drosophila larval eye and adult ocelli

Sensory perception of light is mediated by specialized Photoreceptor neurons (PRs) in the eye. During development all PRs are genetically determined to express a specific Rhodopsin (Rh) gene and genes mediating a functional phototransduction pathway. While the genetic and molecular mechanisms of PR development is well described in the adult compound eye, it remains unclear how the expression of Rhodopsins and the phototransduction cascade is regulated in other visual organs in Drosophila, such as the larval eye and adult ocelli. Using transcriptome analysis of larval PR-subtypes and ocellar PRs we identify and study new regulators required during PR differentiation or necessary for the expression of specific signaling molecules of the functional phototransduction pathway. We found that the transcription factor Krüppel (Kr) is enriched in the larval eye and controls PR differentiation by promoting Rh5 and Rh6 expression. We also identified Camta, Lola, Dve and Hazy as key genes acting during ocellar PR differentiation. Further we show that these transcriptional regulators control gene expression of the phototransduction cascade in both larval eye and adult ocelli. Our results show that PR cell type-specific transcriptome profiling is a powerful tool to identify key transcriptional regulators involved during several aspects of PR development and differentiation. Our findings greatly contribute to the understanding of how combinatorial action of key transcriptional regulators control PR development and the regulation of a functional phototransduction pathway in both larval eye and adult ocelli.

Conditional Ablation of Retinol Dehydrogenase 10 in the Retinal Pigmented Epithelium Causes Delayed Dark Adaption in Mice

Regeneration of the visual chromophore, 11-cis-retinal, is a crucial step in the visual cycle required to sustain vision. This cycle consists of sequential biochemical reactions that occur in photoreceptor cells and the retinal pigmented epithelium (RPE). Oxidation of 11-cis-retinol to 11-cis-retinal is accomplished by a family of enzymes termed 11-cis-retinol dehydrogenases, including RDH5 and RDH11. Double deletion of Rdh5 and Rdh11 does not limit the production of 11-cis-retinal in mice. Here we describe a third retinol dehydrogenase in the RPE, RDH10, which can produce 11-cis-retinal. Mice with a conditional knock-out of Rdh10 in RPE cells (Rdh10 cKO) displayed delayed 11-cis-retinal regeneration and dark adaption after bright light illumination. Retinal function measured by electroretinogram after light exposure was also delayed in Rdh10 cKO mice as compared with controls. Double deletion of Rdh5 and Rdh10 (cDKO) in mice caused elevated 11/13-cis-retinyl ester content also seen in Rdh5(-/-)Rdh11(-/-) mice as compared with Rdh5(-/-) mice. Normal retinal morphology was observed in 6-month-old Rdh10 cKO and cDKO mice, suggesting that loss of Rdh10 in the RPE does not negatively affect the health of the retina. Compensatory expression of other retinol dehydrogenases was observed in both Rdh5(-/-) and Rdh10 cKO mice. These results indicate that RDH10 acts in cooperation with other RDH isoforms to produce the 11-cis-retinal chromophore needed for vision.

Retinoid Processing in Induced Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cultures

Stem cell therapy for retinal degenerative diseases such as age-related macular degeneration is a promising clinical option for the replacement of photoreceptors and retinal pigment epithelium (RPE). Induced pluripotent stem cell technology has emerged as a viable potential source of cells for transplantation in retinal degenerative disorders. Induced pluripotent stem cells have been used to derive RPE and have been tested for their functional behavior. These cells have the ability to express RPE-specific proteins and morphologically resemble native RPE. Induced pluripotent stem cell-derived RPE are also able to contribute to the visual cycle by their ability to metabolize all-trans retinol, a critical function of RPE in maintaining visual function. Advances in induced pluripotent stem cell technology will contribute to the development of clinical therapies for retinal degenerative diseases as well as provide a tool to understand the pathology of these disorders.

Structural dynamics and energetics underlying allosteric inactivation of the cannabinoid receptor CB1

G protein-coupled receptors (GPCRs) are surprisingly flexible molecules that can do much more than simply turn on G proteins. Some even exhibit biased signaling, wherein the same receptor preferentially activates different G-protein or arrestin signaling pathways depending on the type of ligand bound. Why this behavior occurs is still unclear, but it can happen with both traditional ligands and ligands that bind allosterically outside the orthosteric receptor binding pocket. Here, we looked for structural mechanisms underlying these phenomena in the marijuana receptor CB1. Our work focused on the allosteric ligand Org 27569, which has an unusual effect on CB1-it simultaneously increases agonist binding, decreases G--protein activation, and induces biased signaling. Using classical pharmacological binding studies, we find that Org 27569 binds to a unique allosteric site on CB1 and show that it can act alone (without need for agonist cobinding). Through mutagenesis studies, we find that the ability of Org 27569 to bind is related to how much receptor is in an active conformation that can couple with G protein. Using these data, we estimated the energy differences between the inactive and active states. Finally, site-directed fluorescence labeling studies show the CB1 structure stabilized by Org 27569 is different and unique from that stabilized by antagonist or agonist. Specifically, transmembrane helix 6 (TM6) movements associated with G-protein activation are blocked, but at the same time, helix 8/TM7 movements are enhanced, suggesting a possible mechanism for the ability of Org 27569 to induce biased signaling.

Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling

G-protein-coupled receptors (GPCRs) transduce signals from the extracellular environment to intracellular proteins. To gain structural insight into the regulation of receptor cytoplasmic conformations by extracellular ligands during signaling, we examine the structural dynamics of the cytoplasmic domain of the β2-adrenergic receptor (β2AR) using (19)F-fluorine NMR and double electron-electron resonance spectroscopy. These studies show that unliganded and inverse-agonist-bound β2AR exists predominantly in two inactive conformations that exchange within hundreds of microseconds. Although agonists shift the equilibrium toward a conformation capable of engaging cytoplasmic G proteins, they do so incompletely, resulting in increased conformational heterogeneity and the coexistence of inactive, intermediate, and active states. Complete transition to the active conformation requires subsequent interaction with a G protein or an intracellular G protein mimetic. These studies demonstrate a loose allosteric coupling of the agonist-binding site and G-protein-coupling interface that may generally be responsible for the complex signaling behavior observed for many GPCRs.

Kinetics of thermal activation of an ultraviolet cone pigment

Visual pigments can be thermally activated via isomerization of the retinyl chromophore and hydrolysis of the Schiff base (SB) through which the retinyl chromophore is bound to the opsin protein. Here, we present the first combined experimental and theoretical study of the thermal activation of a Siberian hamster ultraviolet (SHUV) pigment. We measured the rates of thermal isomerization and hydrolysis in the SHUV pigment and bovine rhodopsin. We found that these rates were significantly faster in the UV pigment than in rhodopsin due to the difference in the structural and electrostatic effects surrounding the unprotonated Schiff base (USB) retinyl chromophore in the UV pigment. Theoretical (DFT-QM/MM) calculations of the cis-trans thermal isomerization revealed a barrier of ∼23 kcal/mol for the USB retinyl chromophore in SHUV compared to ∼40 kcal/mol for protonated Schiff base (PSB) chromophore in rhodopsin. The lower barrier for thermal isomerization in the SHUV pigment is attributed to the (i) lessening of the steric restraints near the β-ionone ring and SB ends of the chromophore, (ii) displacement of the transmembrane helix 6 (TM6) away from the binding pocket toward TM5 due to absence of the salt bridge between the USB and the protonated E113 residue, and (iii) change in orientation of the hydrogen-bonding networks (HBNs) in the extracellular loop 2 (EII). The results in comparing thermal stability of UV cone pigment and rhodopsin provide insight into molecular evolution of vertebrate visual pigments in achieving low discrete dark noise and high photosensitivity in rod pigments for dim-light vision.

Functions of the DRY motif and intracellular loop 2 of human melanocortin 3 receptor

The melanocortin 3 receptor (MC3R) regulates several physiological functions, including feed efficiency, nutrient partitioning, fasting response, natriuresis, and immune reactions. Naturally occurring mutations in the MC3R gene have been shown to be associated with increased adiposity and lung diseases such as tuberculosis and cystic fibrosis. The DRY motif at the cytoplasmic end of transmembrane domain 3 (TM3) and the second intracellular loop 2 (ICL2) are known to be important for receptor function in several G protein-coupled receptors (GPCRs). To gain a better understanding of the functions of this domain in MC3R, we performed alanine-scanning mutagenesis on 18 residues. We showed that alanine mutation of 11 residues reduced the maximal binding and maximal cAMP production stimulated by agonists. Mutation of two residues did not change maximal binding but resulted in impaired signaling in the Gs-cAMP pathway. Mutation of five residues impaired signaling in the ERK1/2 pathway. We have also shown that alanine mutants of seven residues that were defective in the cAMP pathway were not defective in the ERK1/2 pathway, demonstrating biased signaling. In summary, we demonstrated that the cytoplasmic end of TM3 and the ICL2 were critical for MC3R function. We also reported for the first time biased signaling in MC3R.