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==The trimeric structure of Archaerhodopsin-2==

Archaerhodopsin-2 is a retinal protein–carotenoid complex found in the claret membrane of Halorubrum sp. aus-2 and it represents a real adaptation to life at high salt concentrations. In these membranes, three Archaerhodopsin-2 chains form a trimeric structure [http://www.pdb.org/pdb/explore/jmol.do?structureId=2Z55&view=symmetry&bionumber=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 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 conformation. Thus, a larger pH gradient can be generated across the membrane, leading to an increased efficiency of the proton pumping. Therefore the trimeric structure is more efficient than the monomeric structure.

Archaerhodopsin-2 consists of the protein moiety rhodopsin and a reversibly covalently bound cofactor, the retinal.

The trimeric structure functions as a light-driven proton pump thanks to this 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>). The bacterioruberin plays a structural role for the trimerization of aR2.  

Several saccharides and some lipids and glycolipids also interact with the trimeric structure like the 2,3-di-phytanyl-glycerol (<scene name='56/568017/New_scene_3/1'>L2P</scene>). The lipids and the glycolipids fill the intratrimer hydrophobic space and they are required to the complex activity. Others lipids surround the trimeric structure and are essential to preserve it.<ref>PMID:18082767</ref>

   

===Structure and functioning of the Retinal (RET)===

The retinal (C20 H28 O) is a photoreactive chromophore.

==Ligands==

===The bacterioruberin (22B)===

It interacts with the aR2 surface and the carbohydrate <scene name='56/568017/Glc/1'>GLC</scene>. It binds to: the A chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the <scene name='56/568017/Tyr_85/1'>Tyrosine 85</scene>; the B chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the Tyrosine 85; the D chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 281 (GLC) and thanks to a hydrogen bond with the Tyrosine 85; the E chain thanks to a covalent bond with the carbohydrate alpha-D-glucose 284 (GLC) and thanks to a hydrogen bond with the Tyrosine 85. Others bonds exist like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=L2P].

===Saccharides===

Several saccharides can interact with the trimeric structure: β-D-galactose (<scene name='56/568017/Gal/1'>GAL</scene>) [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/GAL], α-D-glucose (<scene name='56/568017/Glc/1'>GLC</scene>) [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/GLC] and α-D-mannose (<scene name='56/568017/Man/1'>MAN</scene>) [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/MAN].

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=2z55

== 3D structures of Archaerhodopsin-2 and others ==

[[2ei4]]-Trimeric structure of Archaerhodopsin-2