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The trimeric structure of Archaerhodopsin-2 and the bacterioruberin
Archaerhodopsin-2 (aR2) is a light-driven proton pump. It is a retinal protein–carotenoid complex found in the claret membrane of Halorubrum sp. aus-2 and represents a real adaptation to life at high salt concentrations . In these membranes, three Archaerhodopsin-2 or chains form a trimeric structure [1], capturing light energy and using it to move protons across the membrane out of the cell. It exists four different chains with different structures: A,B,D,E (They are not represented here). The resulting proton gradient is subsequently converted into chemical energy. The trimerization increases the thermal stability of the protein aR2 in the claret membrane of Halorubrum sp. aus-2 and enlarges the pH range where the protein can keep its neutral purple conformation.The trimerization also increases the efficiency of the proton pumping power, which is defined by the largest pH gradient that the proton pump can generate across the membrane. So, the trimeric structure is more efficient than the monomeric structure.
The trimeric structure functions as a light-driven proton pump thanks to a retinal molecule, called , 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 (). 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.
Some lipids and glycolipids interact with the trimeric structure like the 2,3-di-phytanyl-glycerol () . They fill the intratrimer hydrophobic space and they are required to the complex activity. Others lipids surround the trimeric structure, which is essential to preserve it.[1]
Structure and functioning of the Retinal (RET)
Archaerhodopsin-2 consists of the protein moiety rhodopsin and a reversibly covalently bound cofactor, retinal. The protein has 7 transmembrane alpha helices, embedded in the plasma membrane, whose helices are connected each other by protein loops. It binds retinal [2], C20 H28 O , a photoreactive chromophore, located in a central pocket on the seventh helix at the by covalent bond (others bonds exist like van-der-waals bonds [3]). 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.
The rhodopsin
The rhodopsin belongs to the CATH Superfamily 1.20.1070.10[4]
The rhodopsin harvests energy from light to carry out metabolic processes using a non-chlorophyll-based pathway.The light induces a phototactic response, thanks to the retinal, by interacting with transducer membrane-embedded proteins that have no relation to G proteins. There are four different rhodopsin with different structures: A, B, D, E.
The bacterioruberin (22B)
The bacterioruberin [5], C50 H76 O4, is a 50 carbon carotenoid pigment which give a red color to the membrane . It binds to: the B chain thanks a hydrogen bond with the , the and the HOH 304 thanks an electrosatic bond; the D chain thanks a hydrogen bond with the Tyrosine 156; the E chain thanks a hydrogen bond with the Tyrosine 156.(others bonds exist like van-der-waals bonds [6])
The 2,3-di-phytanyl-glycerol (L2P)
The 2,3-di-phytanyl-glycerol [7], C43 H88 O3, is an archaeol (di-O-phytanylglycerol). This is a double ether of sn-1-glycerol where positions 2 and 3 are bound to phytanyl residues.The archaeols are Archaea homologs of diacylglycerols (DAGs). It interacts with the aR2 surface and the carbohydrate . It binds to: the A chain thanks a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks a hydrogen bond with the ; the B chain thanks a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks a hydrogen bond with the Tyrosine 85; the D chain thanks a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks a hydrogen bond with the Tyrosine 85; the E chain thanks a covalent bond with the carbohydrate alpha-D-glucose 284 (GLC) and thanks a hydrogen bond with the Tyrosine 85.(others bonds exist like van-der-waals bonds [8])
External ressources
References
- ↑ Yoshimura K, Kouyama T. Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2. J Mol Biol. 2008 Feb 1;375(5):1267-81. Epub 2007 Nov 22. PMID:18082767 doi:10.1016/j.jmb.2007.11.039
