Retinylidene proteins, are proteins that use

retinal Retinal (also known as retinaldehyde) is a polyene chromophore. Retinal, bound to proteins called opsins, is the chemical basis of visual phototransduction, the light-detection stage of visual perception (vision). Some microorganisms use re ...

as a

chromophore 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 by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molec ...

for

light Light or visible light is electromagnetic radiation that can be perceived by the human eye. Visible light is usually defined as having wavelengths in the range of 400–700 nanometres (nm), corresponding to frequencies of 750–420 te ...

reception. They are the molecular basis for a variety of light-sensing systems from phototaxis in

flagellate A flagellate is a cell or organism with one or more whip-like appendages called flagella. The word ''flagellate'' also describes a particular construction (or level of organization) characteristic of many prokaryotes and eukaryotes and the ...

s to eyesight in

animal Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...

s. Retinylidene proteins include all forms of opsin and rhodopsin (in the broad sense). While

rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the RHO gene and a G-protein-coupled receptor (GPCR). It is the opsin of the rod cells in the retina and a light-sensitive receptor protein that triggers visual phototransduct ...

in the narrow sense refers to a dim-light visual pigment found in vertebrates, usually on rod cells, ''rhodopsin'' in the broad sense (as used here) refers to 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.

Structure

All rhodopsins consist of two building blocks, a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

moiety and a reversibly

covalent A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atom ...

ly bound non-protein cofactor,

(retinaldehyde). The protein structure of rhodopsin consists of a bundle of seven transmembrane helices that form an internal pocket binding the photoreactive chromophore. They form a superfamily with other membrane-bound receptors containing seven transmembrane domains, for example

odor An odor (American English) or odour (Commonwealth English; see spelling differences) is caused by one or more volatilized chemical compounds that are generally found in low concentrations that humans and animals can perceive via their sense ...

and

chemokine Chemokines (), or chemotactic cytokines, are a family of small cytokines or Cell signaling, signaling proteins secreted by Cell (biology), cells that induce directional movement of leukocytes, as well as other cell types, including endothelial a ...

receptors.

Mechanism of light reception

Instead of being activated by binding chemical

ligand In coordination chemistry, a ligand is an ion or molecule ( functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's ele ...

s like their relatives, rhodopsins contain retinal which changes conformation in reaction to light via photoisomerization and thus are activated by light. The retinal molecule can take on several different cis-trans isomeric forms, such as all-''trans'', 11-''cis'' and 13-''cis''. Photoisomerization (

-dependent isomerization) of retinal from ''cis'' to ''trans'' or vice versa induces a conformational change in the receptor protein. This change acts as a molecular switch to activate a

signal transduction Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular ...

mechanism within the cell. Depending on the type of rhodopsin, it either opens an

ion channel Ion channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ...

(for example in bacteria) or activates an associated

G protein G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their ...

and triggers a

second messenger Second messengers are intracellular signaling molecules released by the cell in response to exposure to extracellular signaling molecules—the first messengers. (Intercellular signals, a non-local form or cell signaling, encompassing both first m ...

cascade (for example in animal eyes).

Types of rhodopsins

Retinylidene proteins or rhodopsins exist in many species from bacteria to algae and animals. They can be divided into two distinct types based on their sequence as well as the retinal isomer they contain at the ground state and their signal transduction mechanisms.

Microbial rhodopsins

Like animal rhodopsins,

microbial rhodopsin 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 transmembr ...

s (found in prokaryotes and algae) contain a retinal chromophore and have seven transmembrane alpha helices; however, they are not coupled to a G protein. The retinal chromophore differs from the animal 11-''cis'' form) and is an all-''trans'' retinal isomer at the ground state, which isomerizes to 13-''cis'' upon light activation; the chromophore is also known as microbial-type chromophore. Examples are bacterial sensory rhodopsins, channelrhodopsins, bacteriorhodopsins, halorhodopsins, proteorhodopsins, archaerhodopsins, heliorhodopsins and xanthorhodopsins to carry out phototrophy. They act as light-gated ion channels and can be further distinguished by the type of ion they channel. Bacteriorhodopsin functions as a proton pump, whereas halorhodopsin act as a chloride pump. Their functions range from bacterial

photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...

(bacteriorhodopsin) to driving phototaxis (channelrhodopsins in

s). Signal transduction in phototaxis involves

depolarization In biology, depolarization or hypopolarization is a change within a cell, during which the cell undergoes a shift in electric charge distribution, resulting in less negative charge inside the cell compared to the outside. Depolarization is ess ...

of the cell membrane. Unicellular flagellate algae contain channelrhodopsins that act as light-gated cation channels when expressed in heterologous systems. Many other pro- and eukaryotic organisms (in particular, fungi such as ''Neurospora'') express rhodopsin ion pumps or sensory rhodopsins of yet-unknown function. Very recently, microbial rhodopsins with guanylyl cyclase activity have been discovered. While all microbial rhodopsins have significant

sequence homology Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...

to one another, they have no detectable sequence homology to the

G-protein-coupled receptor G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily-related p ...

(GPCR) family to which animal visual rhodopsins belong. Nevertheless, microbial rhodopsins and GPCRs are possibly evolutionarily related, based on the similarity of their three-dimensional structures. Therefore, they have been assigned to the same superfamily in

Structural Classification of Proteins The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine t ...

(SCOP).

G protein-coupled receptors

The retinylidene proteins of the animal kingdom are also referred to as

opsin Animal opsins are G-protein-coupled receptors and a group of proteins made light-sensitive via a chromophore, typically retinal. When bound to retinal, opsins become Retinylidene proteins, but are usually still called opsins regardless. Most pro ...

Vertebrate Vertebrates () comprise all animal taxon, taxa within the subphylum Vertebrata () (chordates with vertebral column, backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the ...

s contain five subfamilies of (rhod)opsins and

arthropod Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a Segmentation (biology), segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and Arth ...

s three subfamilies.G Protein-Coupled Receptor Data Base
/ref> Opsins belong to the class of

G protein-coupled receptor G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily-related p ...

s and bind an 11-''cis'' isomer of retinal at the ground state that photoisomerizes to an all-''trans'' retinal upon light activation. They are commonly found in the light-sensing organs, for example in the

photoreceptor cell 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 (visible electromagnetic radiati ...

s of vertebrate

retina The retina (from la, rete "net") is the innermost, light-sensitive layer of tissue of the eye of most vertebrates and some molluscs. The optics of the eye create a focused two-dimensional image of the visual world on the retina, which then ...

where they facilitate eyesight. Animal opsins can also be found in the

skin Skin is the layer of usually soft, flexible outer tissue covering the body of a vertebrate animal, with three main functions: protection, regulation, and sensation. Other cuticle, animal coverings, such as the arthropod exoskeleton, have diffe ...

of amphibians, the

pineal gland The pineal gland, conarium, or epiphysis cerebri, is a small endocrine gland in the brain of most vertebrates. The pineal gland produces melatonin, a serotonin-derived hormone which modulates sleep patterns in both circadian and seasonal ...

s of lizards and birds, the

hypothalamus The hypothalamus () is a part of the brain that contains a number of small nuclei with a variety of functions. One of the most important functions is to link the nervous system to the endocrine system via the pituitary gland. The hypothalamus ...

of toads, and the human

brain The brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It consists of nervous tissue and is typically located in the head ( cephalization), usually near organs for special ...

. They can be categorized into several distinct classes including: *visual opsins (classical

and relatives), *

melanopsin 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 fo ...

s * peropsins * neuropsins * encephalopsins

Visual perception

The "visual purple"

(opsin-2) of the

rod cell Rod cells are photoreceptor cells in the retina of the eye that can function in lower light better than the other type of visual photoreceptor, cone cells. Rods are usually found concentrated at the outer edges of the retina and are used in p ...

s in the vertebrate retina absorbs green-blue light. The photopsins of the

cone cell Cone cells, or cones, are photoreceptor cells in the retinas of vertebrate eyes including the human eye. They respond differently to light of different wavelengths, and the combination of their responses is responsible for color vision. Con ...

s of the retina differ in a few

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...

s resulting in a shift of their light absorption spectra. The three human photopsins absorb yellowish-green (photopsin I), green (photopsin II), and bluish-violet (photopsin III) light and are the basis of

color vision Color vision, a feature of visual perception, is an ability to perceive differences between light composed of different wavelengths (i.e., different spectral power distributions) independently of light intensity. Color perception is a part of ...

, whereas the more light-sensitive "visual purple" is responsible for the monochromatic vision in the dark. Light signal transduction involves an enzyme cascade of G-proteins ( transducin), cGMP phosphodiesterase, closure of a

cation An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conve ...

channel and ultimately hyperpolarization of the visual

. The visual rhodopsins of

s and molluscs differ from the vertebrate proteins in their signal transduction cascade involving G-proteins,

phospholipase C Phospholipase C (PLC) is a class of membrane-associated enzymes that cleave phospholipids just before the phosphate group (see figure). It is most commonly taken to be synonymous with the human forms of this enzyme, which play an important role i ...

, and ultimately

of the visual photoreceptor cell.

Others

Other

s found in humans include encephalopsin (or panopsin, opsin-3), melanopsin (opsin-4), neuropsin (opsin-5) and peropsin.

Melanopsin 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 fo ...

is involved in the light entrainment of the

circadian clock A circadian clock, or circadian oscillator, is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time. Such a clock's ''in vivo'' period is necessarily almost exactly 24 hours (the earth's current solar day) ...

in vertebrates. Encephalopsins and neuropsins are highly expressed in nerve cells and brain tissue, but so far their function is unknown. Peropsin binds all-''trans'' retinal (microbial-type chromophore) and might function as a

photoisomerase Retinal isomerase () is an enzyme that catalyzes the isomerisation of all-trans-retinal in the eye into 11-cis-retinal which is the form that most opsins bind. :all-trans-retinal \rightleftharpoons 11-cis-retinal Hence, this enzyme has one subs ...

to return retinal to the 11-''cis'' isomer form needed in visual perception.

References

External links

Calculated positions of retinylidene proteins in the lipid bilayer
{{Eye proteins Sensory receptors Biological pigments 7TM receptors