Bacteriorhodopsin

Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by Haloarchaea, 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.

Function

Bacteriorhodopsin is a light-driven H+ ion transporter found in some Haloarchaea, most notably Halobacterium salinarum (formerly known as syn. H. halobium). The proton-motive force generated by the protein is used by ATP synthase to generate adenosine triphosphate (ATP). By expressing Bacteriorhodopsin, the archaea cells are able to synthesise ATP in the absence of a carbon source.

Structure

thumb|A bacteriorhodopsin [[Protein trimer|trimer, showing the approximate positions of the extracellular and cytoplasmic sides of the membrane (red and blue lines respectively)]]

Bacteriorhodopsin is a 27 kDa integral membrane protein 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.

Bacteriorhodopsin is synthesized as a protein precursor, 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, to create the retinylidene chromophore.
Cleavage of the signal peptide, the first 13 amino acids at the N-terminus, and the conversion of residue Gln14 to pyroglutamate
Removal of residue Asp262 at the C-terminus

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 changes (collectively known as the photocycle). The conformational changes alter the pKa 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.

Alt text

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. The nine stages are:

: bR + photon → K L M1 M2 M2' N N' O bR on the extracellular face of the protein.

Homologs and other similar proteins

Bacteriorhodopsin belongs to the microbial rhodopsin family. Its homologs include the archaerhodopsins, the light-driven chloride pump halorhodopsin (for which the crystal structure is also known), and some directly light-activated channels such as channelrhodopsin.

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 sequences. Both rhodopsin and bacteriorhodopsin belong to the 7TM receptor family of proteins, but rhodopsin is a G protein-coupled receptor and bacteriorhodopsin is not. In the first use of electron crystallography to obtain an atomic-level protein structure, 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 and Femtosecond crystallography.

All other phototrophic systems in bacteria, algae, and plants use chlorophylls or bacteriochlorophylls rather than bacteriorhodopsin. These also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain 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 helixes (PDB ID: 1X0S ). One more small helix is light blue, beta sheet 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 )

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Literature

External links

Bacteriorhodopsin: Molecule of the Month, by David Goodsell, RCSB Protein Data Bank
Protein-Based Artificial Retina Manufacturing: Characterization of the Function and Stability of Bacteriorhodopsin Following Exposure to a Microgravity Environment, by Nicole Wagner and Jordan Greco