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 reti ...

as a chromophore 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 Phototaxis is a kind of taxis, or locomotory movement, that occurs when a whole organism moves towards or away from a stimulus of light. This is advantageous for phototrophic organisms as they can orient themselves most efficiently to receive ...

in flagellates to

eyesight Visual perception is the ability to interpret the surrounding environment through photopic vision (daytime vision), color vision, scotopic vision (night vision), and mesopic vision (twilight vision), using light in the visible spectrum reflect ...

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 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 In chemistry, isomers are molecules or polyatomic ions with identical molecular formulae – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers. Is ...

, 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, respo ...

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 atoms ...

ly bound non-protein cofactor,

(retinaldehyde). The protein structure of rhodopsin consists of a bundle of seven

transmembrane helices A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs generally adopt an alpha helix topological conformation, although some TMDs such as those in porins can adopt a different conformation. Because the interior of the lipid bi ...

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 and

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

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 elec ...

s like their relatives, rhodopsins contain retinal which changes conformation in reaction to light via

photoisomerization In chemistry, photoisomerization is a form of isomerization induced by photoexcitation. Both reversible and irreversible photoisomerizations are known for photoswitchable compounds. The term "photoisomerization" usually, however, refers to a re ...

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 In chemistry, photoisomerization is a form of isomerization induced by photoexcitation. Both reversible and irreversible photoisomerizations are known for photoswitchable compounds. The term "photoisomerization" usually, however, refers to a re ...

(

-dependent

isomerization In chemistry, isomerization or isomerisation is the process in which a molecule, polyatomic ion or molecular fragment is transformed into an isomer with a different chemical structure. Enolization is an example of isomerization, as is tautomeriz ...

) 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 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 io ...

(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 a ...

and triggers a second messenger 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 transmembra ...

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,

channelrhodopsin Channelrhodopsins are a subfamily of retinylidene proteins ( rhodopsins) that function as light-gated ion channels. They serve as sensory photoreceptors in unicellular green algae, controlling phototaxis: movement in response to light. Express ...

s, bacteriorhodopsins,

halorhodopsin 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 (but not primary se ...

proteorhodopsin Proteorhodopsin (also known as pRhodopsin) is a family of transmembrane proteins that use retinal as a chromophore for light-mediated functionality, in this case, a proton pump. pRhodopsin is found in marine planktonic bacteria, archaea and euka ...

s, archaerhodopsins,

heliorhodopsin Heliorhodopsin is a family of rhodopsins discovered in 2018 by Alina Pushkarev in the laboratory of Professor Oded Beja. The new family of heliorhodopsins has a distinct protein sequence from known Type 1 (microbial) and Type 2 (animal) rhodopsi ...

s and xanthorhodopsins to carry out

phototrophy Phototrophs () are organisms that carry out photon capture to produce complex organic compounds (e.g. carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconcep ...

. 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 A proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane A biological membrane, biomembrane or cell membrane is a selectively permeable membrane that separates the interior of a cell f ...

, 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

(channelrhodopsins in flagellates). 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

s 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 Guanylate cyclase (EC 4.6.1.2, also known as guanyl cyclase, guanylyl cyclase, or GC; systematic name GTP diphosphate-lyase (cyclizing; 3′,5′-cyclic-GMP-forming)) is a lyase enzyme that converts guanosine triphosphate (GTP) to cyclic guanos ...

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 spe ...

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 (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 taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...

s contain five subfamilies of (rhod)opsins and

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

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 cells 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 animal coverings, such as the arthropod exoskeleton, have different de ...

of amphibians, the pineal glands 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 hypothalamu ...

of toads, and the human

brain A brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a ve ...

. They can be categorized into several distinct classes including: *visual opsins (classical rhodopsin and relatives), * melanopsins * peropsins * neuropsins * encephalopsins

Visual perception

The "visual purple" rhodopsin (opsin-2) of the rod cells in the vertebrate retina absorbs green-blue light. The

photopsin Vertebrate visual opsins are a subclass of ciliary opsins and mediate vision in vertebrates. They include the opsins in human rod and cone cells. They are often abbreviated to ''opsin'', as they were the first opsins discovered and are still t ...

s of the cone cells 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 a ...

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 Transducin (Gt) is a protein naturally expressed in vertebrate retina rods and cones and it is very important in vertebrate phototransduction. It is a type of heterotrimeric G-protein with different α subunits in rod and cone photoreceptors. L ...

), cGMP phosphodiesterase, closure of a cation channel and ultimately hyperpolarization of the visual photoreceptor cell. The visual rhodopsins of

s and molluscs differ from the vertebrate proteins in their signal transduction cascade involving G-proteins, phospholipase C, 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 is involved in the light entrainment of the circadian clock 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 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