Three-dimensional structure of bovine rhodopsin. The seven transmembrane domains are shown in varying colors. The chromophore is shown in red.
The retinal molecule inside an opsin protein absorbs a photon of light. Absorption of the photon causes retinal to change from its 11-cis-retinal isomer into its all-trans-retinal isomer. This change in shape of retinal pushes against the outer opsin protein to begin a signal cascade, which may eventually result in chemical signaling being sent to the brain as visual perception. The retinal is re-loaded by the body so that signaling can happen again.
Opsins are a group of proteins, made light-sensitive, via the chromophore retinal found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal, the first step in the visual transduction cascade. Another opsin found in the mammalian retina, melanopsin, is involved in circadian rhythms and pupillary reflex but not in vision.
A chromophore is the part of a molecule responsible for its color. The color that is seen by our eyes is the one not absorbed within a certain wavelength spectrum of visible light. The chromophore is a region in the molecule where the energy difference between two separate molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state. In biological molecules that serve to capture or detect light energy, the chromophore is the moiety that causes a conformational change of the molecule when hit by light.
Retinal is also known as retinaldehyde. It was originally called retinene, and renamed after it was discovered to be vitamin A aldehyde. Retinal is one of the many forms of vitamin A. Retinal is a polyene chromophore, bound to proteins called opsins, and is the chemical basis of animal vision. Retinal allows certain microorganisms to convert light into metabolic energy.
A photoreceptor cell is a specialized type of neuroepithelial cell found in the retina that is capable of visual phototransduction. The great biological importance of photoreceptors is that they convert light into signals that can stimulate biological processes. To be more specific, photoreceptor proteins in the cell absorb photons, triggering a change in the cell's membrane potential.
Bilins, bilanes or bile pigments are biological pigments formed in many organisms as a metabolic product of certain porphyrins. Bilin was named as a bile pigment of mammals, but can also be found in lower vertebrates, invertebrates, as well as red algae, green plants and cyanobacteria. Bilins can range in color from red, orange, yellow or brown to blue or green.
Microbial rhodopsins, also known as bacterial rhodopsins are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point for retinal.
Cryptochromes are a class of flavoproteins that are sensitive to blue light. They are found in plants and animals. Cryptochromes are involved in the circadian rhythms of plants and animals, and possibly also in the sensing of magnetic fields in a number of species. The name cryptochrome was proposed as a portmanteau combining the cryptic nature of the photoreceptor, and the cryptogamic organisms on which many blue-light studies were carried out.
Bacteriorhodopsin is a protein used by Archaea, most notably by halobacteria, a class of the Euryarchaeota. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.
Halorhodopsin is a light-gated ion pump, specific for chloride ions, found in archaea, known as halobacteria. It is a seven-transmembrane retinylidene protein from microbial rhodopsin family. It is similar in tertiary structure to vertebrate rhodopsins, the pigments that sense light in the retina. Halorhodopsin also shares sequence similarity to channelrhodopsin, another light-driven ion channel. Halorhodopsin contains the essential light-isomerizable vitamin A derivative all-trans-retinal. Due to the intense attention on solving the structure and function of this molecule, halorhodopsin is one of the few membrane proteins whose crystal structure is known.
Sensory rhodopsin II (SRII), also known as pharaonis phoborhodopsin (ppR), is a membrane protein of archaea, responsible generating the phototaxis signal. Sensory rhodopsin II is found in Halobacterium salinarum and Natronomonas pharaonis.
Long-wave sensitive LWS Cone 500–570 nm Green, yellow, red OPN1LW "red" / OPN1MW "green"
Middle-wavelength sensitive (OPN1MW) Opsin –λmax of 530 nm, in the green region of the electromagnetic spectrum.  May be called the "green opsin," "chlorolabe," "M opsin" or "MWS opsin."
Short-wavelength sensitive (OPN1SW) Opsin –λmax of 430 nm, in the blue region of the electromagnetic spectrum.  May be called the "blue opsin," "cyanolabe," "S opsin" or "SWS opsin."
The panopsins of teleost fish are called: Teleost multiple tissue (TMT) opsins.
The identification of the crystal structure of squid rhodopsin  is likely to further our understanding of its function in this group.
Involved in circadian rhythms, pupillary reflex, and color correction in high-brightness situations. Phylogenetically a member of the R-opsin (rhabdomeric) group, functionally and structurally an r-opsin, but does not occur in rhabdomeres.
Go/RGR opsins include Go-opsins, RGR-opsins, neuropsins, and peropsins.
Opsin proteins covalently bind to a vitamin A-based retinaldehyde chromophore through a Schiff base linkage to a lysine residue in the seventh transmembrane alpha helix. In vertebrates, the chromophore is either 11- cis -retinal (A1) or 11-cis-3,4-didehydroretinal (A2) and is found in the retinal binding pocket of the opsin. The absorption of a photon of light results in the photoisomerization of the chromophore from the 11-cis to an all-trans conformation. The photoisomerization induces a conformational change in the opsin protein, causing the activation of the phototransduction cascade. The opsin remains insensitive to light in the trans form. It is regenerated by the replacement of the all-trans retinal by a newly synthesized 11-cis-retinal provided from the retinal epithelial cells. Opsins are functional while bound to either chromophore, with A2-bound opsin λmax being at a longer wavelength than A1-bound opsin.
Opsins contain seven transmembrane α-helical domains connected by three extra-cellular and three cytoplasmic loops. Many amino acid residues, termed functionally conserved residues, are highly conserved between all opsin groups, indicative of important functional roles. All residue positions discussed henceforth are relative to the 348 amino acid bovine rhodopsin crystallized by Palczewski et al.  Lys296 is conserved in all known opsins and serves as the site for the Schiff base linkage with the chromophore. Cys138 and Cys110 form a highly conserved disulfide bridge. Glu113 serves as the counterion, stabilizing the protonation of the Schiff linkage between Lys296 and the chromophore. The Glu134-Arg135-Tyr136 is another highly conserved motif, involved in the propagation of the transduction signal once a photon has been absorbed.
Certain amino acid residues, termed spectral tuning sites, have a strong effect on λmax values. Using site-directed mutagenesis, it is possible to selectively mutate these residues and investigate the resulting changes in light absorption properties of the opsin. It is important to differentiate spectral tuning sites, residues that affect the wavelength at which the opsin absorbs light, from functionally conserved sites, residues important for the proper functioning of the opsin. They are not mutually exclusive, but, for practical reasons, it is easier to investigate spectral tuning sites that do not affect opsin functionality. For a comprehensive review of spectral tuning sites see Yokoyama  and Deeb.  The impact of spectral tuning sites on λmax differs between different opsin groups and between opsin groups of different species.
Review of opsins and current research: Shichida, Y.; Matsuyama, T. (2009). "Evolution of opsins and phototransduction". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364 (1531): 2881–2895. doi:10.1098/rstb.2009.0051. PMC 2781858 . PMID 19720651.
Rhodopsin is a light-sensitive receptor protein involved in visual phototransduction. It is named after ancient Greek ῥόδον (rhódon) for rose, due to its pinkish color, and ὄψις (ópsis) for sight. Rhodopsin is a biological pigment found in the rods of the retina and is a G-protein-coupled receptor (GPCR). It belongs to opsins. Rhodopsin is extremely sensitive to light, and thus enables vision in low-light conditions. When rhodopsin is exposed to light, it immediately photobleaches. In humans, it is regenerated fully in about 30 minutes, after which rods are more sensitive.
In ocular physiology, adaptation is the ability of the eye to adjust to various levels of light. Natural night vision, or scotopic vision, is the ability to see under low-light conditions. In humans, rod cells are exclusively responsible for night vision as cone cells are only able to function at higher illumination levels. Night vision is of much poorer quality than day vision because it is limited by a reduced resolution and therefore provides the ability to only discriminate between shades of black and white. In order for humans to transition from day to night vision they must undergo a dark adaptation period in which each eye adjusts from a high luminescence setting to a low luminescence setting. This adaptation period is different for both rod and cone cells and results from the regeneration of photopigments to restore retinal sensitivity.
Photopsins are the photoreceptor proteins found in the cone cells of the retina that are the basis of color vision. Iodopsin, the cone pigment system in chicken retina, is a close analog of the visual purple rhodopsin that is used in night vision. Iodopsin consists of the protein component and a bound chromophore, retinal.
Melanopsin is a type of photopigment belonging to a larger family of light-sensitive retinal proteins called opsins and encoded by the gene Opn4. In the mammalian retina, there are two additional categories of opsins, both involved in the formation of visual images: rhodopsin and photopsin in the rod and cone photoreceptor cells, respectively.
Photopigments are unstable pigments that undergo a chemical change when they absorb light. The term is generally applied to the non-protein chromophore moiety of photosensitive chromoproteins, such as the pigments involved in photosynthesis and photoreception. In medical terminology, "photopigment" commonly refers to the photoreceptor proteins of the retina.
Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. They mediate light responses as varied as visual perception, phototropism and phototaxis, as well as responses to light-dark cycles such as circadian rhythm and other photoperiodisms including control of flowering times in plants and mating seasons in animals.
Retinylidene protein, is a family of proteins that use retinal as a chromophore for light reception. It is the molecular basis for a variety of light-sensing systems from phototaxis in flagellates to eyesight in animals. Retinylidene proteins include all forms of opsin and rhodopsin. While rhodopsin in the narrow sense refers to a dim-light visual pigment found in vertebrates, usually on rod cells, rhodopsin in the broad sense refers any molecule consisting of an opsin and a retinal chromophore in the ground state. When activated by light, the chromophore is isomerized, at which point the molecule as a whole is no longer rhodopsin, but a related molecule such as metarhodopsin. However, it remains a retinylidene protein. The chromophore then separates from the opsin, at which point the bare opsin is a retinylidene protein. Thus, the molecule remains a retinylidene protein throughout the phototransduction cycle.
The bleach and recycle process is used within the retina to ensure that the chromophore 11-cis retinal is present within opsin molecules in sufficient quantities to allow phototransduction to occur. It uses vitamin A (retinol) derivatives.
Peropsin, a visual pigment-like receptor, is a protein that in humans is encoded by the RRH gene.
Neuropsin is a protein that in humans is encoded by the OPN5 gene. It is a photoreceptor protein sensitive to ultraviolet (UV) light. The OPN5 gene was discovered in mouse and human genomes and its mRNA expression was also found in neural tissues. Neuropsin is bistable at 0 °C and activates a UV-sensitive, heterotrimeric G protein Gi-mediated pathway in mammalian and avian tissues.
OPN1LW is a gene on the X chromosome that encodes for long wave sensitive (LWS) opsin, or red cone photopigment. It is responsible for perception of visible light in the yellow-green range on the visible spectrum. The gene contains 6 exons with variability that induces shifts in the spectral range. OPN1LW is subject to homologous recombination with OPN1MW, as the two have very similar genomes. These recombinations can lead to various vision problems, such as red-green colourblindness and blue monochromacy. The protein encoded is a G-protein coupled receptor with embedded 11-cis-retinal, whose light excitation causes a cis-trans conformational change that begins the process of chemical signalling to the brain.
RPE-retinal G protein-coupled receptor also known as RGR-opsin is a protein that in humans is encoded by the RGR gene.
Platynereis dumerilii is a species of annelid. It was originally placed into the genus Nereis and later reassigned to Platynereis. Platynereis dumerilii lives in coastal marine waters from temperate to tropical zones. It can be found in a wide range from the Azores, the Mediterranean, in the North Sea, the English Channel, and the Atlantic down to the Cape of Good Hope, in the Black Sea, the Red Sea, the Persian Gulf, the Sea of Japan, the Pacific, and the Kerguelen Islands. Platynereis dumerilii is today an important lab animal, it is considered as a living fossil, and it is used in many phylogenetic studies as a model organism. Platynereis dumerilii reaches an age of 3 to 18 month and males reach a length of 2 to 3 cm, while females reach a length of 3 to 4 cm.
Evolution of human colour vision over time: humans have developed a trichromatic view of the world in comparison to a majority of other mammals that only see the world from a dichromatic view. Early human ancestors are believed to have viewed the world using UV vision as far back as 90 million years ago. It is thought that the shift to trichromatic vision capabilities and the ability to see blue light have evolved as an adaptive trait over time.
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