Bacteriorhodopsin is a protein used by Archaea, most notably by

haloarchaea Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of ...

, a

class Class or The Class may refer to: Common uses not otherwise categorized * Class (biology), a taxonomic rank * Class (knowledge representation), a collection of individuals or objects * Class (philosophy), an analytical concept used differently ...

of the

Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extre ...

. 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 An electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the chemical gradient, or difference in solute concentration across a membrane, and th ...

is subsequently converted into chemical energy.

Function

Bacteriorhodopsin is a light-driven H⁺ ion transporter found in some haloarchaea, most notably ''

Halobacterium salinarum ''Halobacterium salinarum'', formerly known as ''Halobacterium cutirubrum'' or ''Halobacterium halobium'', is an extremely halophilic marine obligate aerobic archaeon. Despite its name, this is not a bacterium, but a member of the domain Archaea. ...

'' (formerly known as syn. ''H. halobium''). The

proton-motive force Chemiosmosis is the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. An important example is the formation of adenosine triphosphate (ATP) by the movement of hydrogen ions (H+) across a membra ...

generated by the protein is used by

ATP synthase ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (Pi). It is classified under ligases as it changes ADP by the formation ...

to generate adenosine triphosphate (ATP). By expressing bacteriorhodopsin, the archaea cells are able to synthesise ATP in the absence of a carbon source.

Structure

Bacteriorhodopsin is a 27

kDa The dalton or unified atomic mass unit (symbols: Da or u) is a non-SI unit of mass widely used in physics and chemistry. It is defined as of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at r ...

integral membrane protein An integral, or intrinsic, membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All ''transmembrane proteins'' are IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a signif ...

usually found in two-dimensional crystalline patches known as "purple membrane", which can occupy almost 50% of the surface area of the archaeal cell. The repeating element of the hexagonal lattice is composed of three identical protein chains, each rotated by 120 degrees relative to the others. Each monomer has seven transmembrane alpha helices and an extracellular-facing, two-stranded

beta sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a ge ...

. Bacteriorhodopsin is synthesized as a

protein precursor A protein precursor, also called a pro-protein or pro-peptide, is an inactive protein (or peptide) that can be turned into an active form by post-translational modification, such as breaking off a piece of the molecule or adding on another molecul ...

, known as bacterio-opsin, which is extensively modified after translation. The modifications are: * Covalent conjugation of a retinal molecule to residue Lys216, via a

Schiff base In organic chemistry, a Schiff base (named after Hugo Schiff) is a compound with the general structure ( = alkyl or aryl, but not hydrogen). They can be considered a sub-class of imines, being either secondary ketimines or secondary aldim ...

, to create the retinylidene chromophore. * Cleavage of the

signal peptide A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16-30 amino acids long) present at the N-ter ...

, the first 13 amino acids at the N-terminus, and the conversion of residue Gln14 to

pyroglutamate Pyroglutamic acid (also known as PCA, 5-oxoproline, pidolic acid) is a ubiquitous but little studied natural amino acid derivative in which the free amino group of glutamic acid or glutamine cyclizes to form a lactam. The names of pyroglutamic ...

* Removal of residue Asp262 at the C-terminus

Spectral properties

Bacteriorhodopsin molecule is purple and is most efficient at absorbing green light (in the wavelength range 500-650 nm). In the native membrane, the protein has a maximum absorbance at 553 nm, however addition of detergent disrupts the trimeric form, leading a loss of exciton coupling between the chromophores, and the monomeric form consequently has an absorption maximum of 568 nm. Bacteriorhodopsin has a broad excitation spectrum. For a detection wavelength between 700 and 800 nm, it has an appreciable detected emission for excitation wavelengths between 470 nm and 650 nm (with a peak at 570 nm). When pumped at 633 nm, the emission spectrum has appreciable intensity between 650 nm and 850 nm.

Mechanism

Photocycle overview

Bacteriorhodopsin is a light-driven proton pump. It is the retinal molecule that changes its isomerization state from all-''trans'' to 13-''cis'' when it absorbs a photon. The surrounding protein responds to the change in the chromophore shape, by undergoing an ordered sequence of

conformational change In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or othe ...

s (collectively known as the photocycle). The conformational changes alter the p''K''_a values of conserved amino acids in the core of the protein, including Asp85, Asp96 and the Schiff base N atom (Lys216). These sequential changes in acid dissociation constant, result in the transfer of one proton from the intracellular side to the extracellular side of the membrane for each photon absorbed by the chromophore. Bacteriorhodopsin retinal

The bacteriorhodopsin photocycle consists of nine distinct stages, starting from the ground or resting state, which is denoted 'bR'. The intermediates are identified by single letters and may be distinguished by their

absorption spectra Absorption spectroscopy refers to spectroscopic techniques that measure the absorption of radiation, as a function of frequency or wavelength, due to its interaction with a sample. The sample absorbs energy, i.e., photons, from the radiating fi ...

. The nine stages are: : bR + photon → K L M₁ M₂ M₂' N N' O bR

Ground state + photon → K state → L state

Bacteriorhodopsin in the ground state absorbs a photon and the retinal changes isomerization from all-''trans'' 15-''anti'' to the strained 13-''cis'' 15-''anti'' in the K state. The isomerisation reaction is fast and occurs in less than 1 ps. The retinal adopts a less strained conformation to form the L intermediate.

L state → M₁ state

Asp85 accepts a proton from the Schiff base N atom. In the M₁ intermediate, neither the Schiff base nor Asp85 are charged.

M₁ state → M₂ state

The Schiff base rotates away from the extracelluar side of the protein towards the cytoplasmic side, in preparation to accept a new proton.

M₂ state → M₂' state

A proton is released from Glu204 and Glu194 to the extracellular medium.

M₂' state → N state

The retinal Schiff base accepts a proton from Asp96. In the N state, both Asp96 and the Schiff base are charged.

N state → N' state

Asp96 accepts a proton from the cytoplasmic side of the membrane and becomes uncharged.

N' state → O state

Retinal reisomerizes to the all-''trans'' state.

O state → ground state

Asp85 transfers a proton to Glu194 and Glu204 on the extracellular face of the protein.

Homologs and other similar proteins

Bacteriorhodopsin belongs to the

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 ...

family. Its homologs include the

archaerhodopsin Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genera ''Halobacterium'' and '' Halorubrum''. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pum ...

s, the light-driven chloride pump

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 ...

(for which the crystal structure is also known), and some directly light-activated channels such as

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. Expressed ...

. Bacteriorhodopsin is similar to vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal; however, the functions of rhodopsin and bacteriorhodopsin are different, and there is limited similarity in their

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 am ...

sequences. Both rhodopsin and bacteriorhodopsin belong to the

7TM 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 ...

family of proteins, but rhodopsin is a G protein-coupled receptor and bacteriorhodopsin is not. In the first use of

electron crystallography Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM). Comparison with X-ray crystallography It can complement X-ray crystallography for studies of very small crystals ...

to obtain an atomic-level

protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer ma ...

, the structure of bacteriorhodopsin was resolved in 1990. It was then used as a template to build models of G protein-coupled receptors before crystallographic structures were also available for these proteins. It has been excessively studied on both mica and glass substrates using

Atomic force microscopy Atomic force microscopy (AFM) or scanning force microscopy (SFM) is a very-high-resolution type of scanning probe microscopy (SPM), with demonstrated resolution on the order of fractions of a nanometer, more than 1000 times better than the opti ...

and Femtosecond crystallography. All other phototrophic systems in bacteria, algae, and plants use

chlorophyll Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to ...

s or

bacteriochlorophyll Bacteriochlorophylls (BChl) are photosynthetic pigments that occur in various phototrophic bacteria. They were discovered by C. B. van Niel in 1932. They are related to chlorophylls, which are the primary pigments in plants, algae, and cyanobacter ...

s rather than bacteriorhodopsin. These also produce a proton gradient, but in a quite different and more indirect way involving an

electron transfer chain An electron transport chain (ETC) is a series of protein complexes and other molecules that transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples th ...

consisting of several other proteins. Furthermore, chlorophylls are aided in capturing light energy by other pigments known as "antennas"; these are not present in bacteriorhodopsin-based systems. It is possible that phototrophy independently evolved at least twice, once in bacteria and once in archaea.

Gallery

File:Bacteriorhodopsin subunit 1X0S.gif, link=File:Bacteriorhodopsin subunit 1X0S large.gif, Bacteriorhodopsin single monomer with retinal molecule between 7 vertical

alpha helix The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ea ...

es ( PDB ID: 1X0S Image created wit
RasTop
(Molecular Visualization Software).). One more small helix is light blue,

yellow. File:Bacteriorhodopsin trimer 1X0S.png, link=File:Bacteriorhodopsin trimer 1X0S large.gif, Bacteriorhodopsin trimer with one retinal molecule in each subunit seen from the extracellular side EC ( PDB ID: 1X0S ).

Literature

External links

Bacteriorhodopsin: Molecule of the Month
by David Goodsell, RCSB Protein Data Bank

by Nicole Wagner & Jordan Greco {{Proton pumps 7TM receptors Photosynthesis Integral membrane proteins Archaea proteins