Retinoid and chemistry of vision 
Retinoids and carotenoids are molecules whose chemistry and metabolism in conjunction with specific processing proteins, help explain the chemical basis of vision. Since both retinoids and carotenoids are classified as isoprenoids, they have limited chemical transformation possibilities. Interestingly, because these genes have found to be highly conserved in the formation of insect and vertebrate vision and are involved in chromophore production and recycling, the concept of a common ancestral origin for the chemistry of vision has been proposed and developed.
Chromophore isomerization 
Cycles of cis to trans isomerization of the visual chromophore is an intrinsic mechanism for animal vision.
G protein signaling is a signal transduction pathway where heptahelical transmembrane receptors such as rhodopsin respond to a variety of chemical signals (hormones, neurotransmitters, etc.), activate the heterotrimeric G proteins, and help carry out a cascade of events that are responsible for many physiological processes throughout the body.
It has been discovered that visual pigments make up one class of G protein-coupled receptors and have components such as opsin (integral transmembrane protein) and a covalently attached retinylidene chromophore that is involved in the process of phototransduction.
Visual GPCR signaling requires a diet-derived chromophore that is generated naturally through an oxidative cleavage of carotenoids (C40) to retinoids (C20). The retinoid then is converted to 11-cis-retinal derivatives (2-dehydro-retinal for vertebrates, 3-hydroxy-retinal for insects). These retinal derivatives would then form a Schiff-base linkage with a Lys residue in opsin to create functional visual pigments. When light is absorbed, all the cis chromophores would isomerize to the trans isomers, which subsequently transforms rhodopsin into an activated state called Meta II. Meta II binds transducin (photoreceptor specific G protein), initiating a cascade that results in the hyperpolarization of the plasma membrane.
In order to regenerate the cis-chromophores, an enzymatic pathway called the retinoid cycle has been studied. This cycle involves the rod photoreceptors and cone photoreceptors. Rod photoreceptors consume the cis isomers despite being saturated by cone photoreceptors under bright light. Thus, a cone specific regeneration pathway has been proposed to avoid this competition between the two receptors. If mutations occur at the genes that code for important components such as proteins that facilitate the absorption, transportation, metabolism, and storage pathway of dietary precursors for chromophore (carotenoids and retinoids), blinding diseases and more fatal diseases such as Matthew-Wood syndrome may develop.
Recycling Visual Chromophore 
The first step of the recycling process is carried out by retinol dehydrogenases (RDHs), where all the trans-retinal is reduced to trans-retinol. The main RDHs are the RDH8 in outer segments (OS) photoreceptor and RDH12 in photoreceptor inner segments (there are other RDHs). All the trans-retinol is transported from the OS to the RPE, where they are esterified. This process is facilitated by two retinoid-binding proteins called the interphotoreceptor retinoid-binding protein (IRBP) and cellular retinol-binding protein-1 (CRBP1). These trans-retinyl esters form a stable storage form for vitamin A and oil droplet structures called retinosomes. Then, the enzyme RPE65 catalyzes the endothermic reaction that converts all trans-retinoids to 11-cis-retinols. In the final step, enzymes such as RDH5, RDH10, and RDH11 catalytically oxidize the 11-cis-retinols to the original 11-cis-retinals that are needed to sustain vision. These 11-cis-retinals then bind to cellular retinaldehyde-binding protein (CRALBP), which mediates its transport back to the photoreceptor OS and opsin.
In the cone regeneration pathway, all the trans-retinol released from cone OS is transported to Muller cells rather than RPEs. There, they are isomerized to 11-cis isomeric form and esterify to 11-cis-retinyl esters by acyl-CoA: retinol acyltransferase (ARAT). These esters are converted to 11-cis-retinol with the aid of 11-cis-retinyl ester hydrolase (REH), then they bind to CRALBP and taken back to cone receptors. In the final step, NADP+/NADPH dependent 11-cis-RDH activity facilitates the regeneration of visual chromophore.
Structures of Visual Cycle Enzymes and Retinal/Retinol-binding Proteins 
Visual cycle enzymes are the series of microsomal enzymes that facilitate the conversion of trans-retinol to cis-retinal. They are typically membrane-bound enzymes, which makes them harder to study because detergent is needed before X-ray crystallography could proceed. Apocarotenoid oxygenase (ACO), a water-soluble homolog of the RPE65 enzyme, belongs to the carotenoid cleavage oxygenase (CCO) family. The structure of ACO demonstrates that the CCOs contain a 7-bladed β-propeller general fold and that the ferrous ion cofactor is coordinated by four highly conserved His residues. Structure of native RPE65 from Bos Taurus shows that there is only one way of inserting the protein into the active site. This is identified by the discovery of a single tunnel in RPE65 that allows both the entry of substrates and the release of products. Deducing from this structure, scientists have proposed that retinoid substrates enter the active site from the membrane and the products leave the active site into another component in the membrane (RDH5) for further processing. These processes happen to take place in the endoplasmic reticulum membranes without involvement of retinoid-binding proteins.
There are four main retinol/retinal binding proteins; they are the RBP, CRBP, IRBP, and CRALBP. RBP and CRBP are cup shape proteins with a single domain. The active site where ligands are bound is comprised of hydrophobic anti-parallel β-barrel folds that have an affinity for only the trans-retinol molecules. The orientations of the bounded retinols are different in RBP and CRBP. When found in RBP, they tend to cluster around the cavity entrance. In contrast, they are found in the cavity base in CRBP.
IRBP is a soluble lipoglycoprotein made by photoreceptor neurons. Its major function is thought to be facilitating the transport of retinoids between the cell layers of photoreceptors and RPE. In contrast to the single domain observed in RBP and CRBP, the protein contains approximately three to four retinoid binding sites. The protein adopts a rod-shape structure and upon ligand binding, conformational changes to a bent molecular structure. Upon further structural analysis, two hydrophobic cavities are revealed to be potential ligand binding sites.
CRALBP belongs to a family of proteins that in their natural state, bind hydrophobic ligands and is consisted of a cluster of highly basic amino acid residues. High-resolution structural analysis has revealed that the 11-cis-Retinal binds deeply in the cavity of the protein, with the center of the ligand closest to the cavity entrance. In contrast to its cis double bond being twisted in rhodopsin (which converts to trans when triggered by light), the retinal molecule adopts a perfect cis configuration when bound to CRALBP. This makes cis-to-trans isomerization highly unfavorable. Thus, the retinal can preserve its cis configuration while being transported to opsin and photoreceptor OS.
Photochemical and chemical retinoid isomerization 
The conjugated double bond in retinoids, when triggered by light, proceeds to isomerize. Under light perception, 11-cis-retinylidene is converted to all-trans-retinylidene. In this reaction mechanism, the double bond is transiently broken by the energy supplied by the photon. In order to regenerate the light-sensitive chromophore, a process called isomerohydrolase (so called retinoid isomerase) activity is required. The enzyme catalyzes the reaction of water with a carbocation. In the case of photochemical pathway, this enzyme catalyzes the process of regenerating the cis conformation retinylidene. However, from a theoretical chemical mechanism perspective, isomerization and hydrolysis of this molecule by water does not seem to be plausible. Although many reaction mechanisms have been proposed, Sn1 nucleophilic substitution seems to be the most plausible mechanism. In this reaction, a very stable double-bond-conjugated carbocation is generated after the alkyl-cleavage of the ester group by a ferric/ferrous ion cofactor and RPE65. The addition of a nucleophile completes the transformation of all-trans-retinyl esters to 11-cis-retinol.
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