Sandbox Reserved 819: Difference between revisions

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


The rhodopsin belongs to the CATH Superfamily 1.20.1070.10[http://www.cathdb.info/version/3.5.0/superfamily/1.20.1070.10]   


It binds retinal [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/RET], 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 (others bonds exist like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=RET]). Retinal is a polyene chromophore and allows to convert light into metabolic energy. It absorbs visible light maximally at 550-570 nm.
The protein <scene name='56/568017/Rhodopsin/1'>rhodopsin</scene>  has 7 transmembrane alpha helices, embedded  in the plasma membrane. These helices are connected to each other by protein loops.
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 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 rhodopsin===


The rhodopsin belongs to the CATH Superfamily 1.20.1070.10[http://www.cathdb.info/version/3.5.0/superfamily/1.20.1070.10]   
===Structure and functioning of the Retinal (RET)===


The protein <scene name='56/568017/Rhodopsin/1'>rhodopsin</scene>  has 7 transmembrane alpha helices, embedded  in the plasma membrane. These helices are connected to each other by protein loops.


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 rhodopsin binds retinal [http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/RET], 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 (others bonds exist like van-der-waals bonds [http://www.ebi.ac.uk/pdbe-site/pdbemotif/?tab=boundmolecule&pdb=2z55&ligandCode3letter=RET]). 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.




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