Sandbox Reserved 819: Difference between revisions

The trimeric structure functions as a light-driven proton pump thanks to a retinal molecule, called <scene name='56/568017/New_scene_ret_2/1'>RET</scene>, which changes its conformation when absorbing a photon, resulting in a conformational change of the surrounding protein and the proton pumping action. Others ligands are linked with each subunit of the trimeric structure like the bacterioruberin (<scene name='56/568017/22b/1'>22B</scene>). Several saccharides are also linked to the trimeric structure. The bacterioruberin is a 50 carbon carotenoid pigment which give a red color to the membrane . The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as an antioxidant, rather than directly blocking UV light. It is able to protect the cell from reactive oxygen species produced from exposure to UV by acting as a target. Furthermore, the bacterioruberin is essential because it plays a structural role for the trimerization of aR2.  

Archaerhodopsin-2 consists of the protein moiety rhodopsin and a reversibly covalently bound cofactor, retinal. The protein <scene name='56/568017/Rhodopsin/1'>rhodopsin</scene>  has 7 transmembrane alpha helices, embedded  in the plasma membrane, whose helices are connected  each other by protein loops. It binds retinal, C20 H28 O , a photoreactive chromophore, located in a central pocket on the seventh helix at the <scene name='56/568017/Lysine_221/1'>lysine residue 221</scene> by covalent bond. Retinal is a polyene chromophore and allows  to convert light into metabolic energy. It absorbs visible light maximally at 550-570 nm.  

It catches a photon, leading to a conformational change of the rhodopsin. This is an isomerization of 11-cis-retinal into all-trans-retinal. Retinal binds covalently to the lysine 221 on the transmembrane helix nearest the C-terminus of the protein through a Schiff base linkage. Formation of the Schiff base linkage involves removing the oxygen atom from retinal and two hydrogen atoms from the free amino group of lysine, giving H2O. Retinylidene is the divalent group formed by removing the oxygen atom from retinal, and so opsins is called retinylidene proteins. A Schiff base is a compound with a functional group made up of a carbon-nitrogen double bond with a nitrogen atom connected to an aryl or alkyl group, not hydrogen. Schiff bases in a broad sense have the general formula R1-R2-C=N-R3, where R is an organic side chain. In this definition, Schiff base is synonymous with azomethine. The chain on the nitrogen makes the Schiff base a stable imine. A Schiff base derived from an aniline, where R3 is a phenyl or a substituted phenyl.