Sandbox 173: Difference between revisions
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==Structure== | ==Structure== | ||
<applet load='1u19' size='300' color='black' frame='true' align='right' caption='Structure of Rhodopsin. The generated structures are from Chain A.'/> | |||
===Rhodopsin Architecture=== | ===Rhodopsin Architecture=== | ||
Rhodopsin consists of seven mostly α-helical transmembrane domains (H1-H7) linked sequentially by extracellular and cytoplasmic loops (E1-E3 and C1-C3 respectively), with the extracellular amino-terminal tail and the cytoplasmic carboxyl-terminal tail<ref>Article 12</ref>. Four of the helices are tilted and three of the helices are approximately perpendicular to the membrane plane<ref>Article 4</ref>. There is notable interaction between the four extracellular domains, but only a few associations are observed with the cytoplasmic domains<ref>Article 9</ref>. Helix 7 is close to being elongated around the Lysine 296 retinal attachment site, and also contains the residues Proline 291 and Proline 303, with Proline 303 being part of a conserved motif<ref>Article 9</ref>. Near the retinal region, there is a <scene name='Sandbox_173/Beta_4_strand_and_retinal/2'>β4 strand (Serine 186-Cysteine 187-Glycine 188-Isoleucine 189)</scene> within the Extracellular Helix 2 that runs almost parallel to the chromophore held in place, and is stabilized by the essential conserved | Rhodopsin consists of seven mostly α-helical transmembrane domains (H1-H7) linked sequentially by extracellular and cytoplasmic loops (E1-E3 and C1-C3 respectively), with the extracellular amino-terminal tail and the cytoplasmic carboxyl-terminal tail<ref>Article 12</ref>. Four of the helices are tilted and three of the helices are approximately perpendicular to the membrane plane<ref>Article 4</ref>. There is notable interaction between the four extracellular domains, but only a few associations are observed with the cytoplasmic domains<ref>Article 9</ref>. Helix 7 is close to being elongated around the Lysine 296 retinal attachment site, and also contains the residues Proline 291 and Proline 303, with Proline 303 being part of a conserved motif<ref>Article 9</ref>. Near the retinal region, there is a <scene name='Sandbox_173/Beta_4_strand_and_retinal/2'>β4 strand (Serine 186-Cysteine 187-Glycine 188-Isoleucine 189)</scene> within the Extracellular Helix 2 that runs almost parallel to the chromophore held in place, and is stabilized by the essential conserved | ||
<scene name='Sandbox_173/Disulfide_bond/4'>disulfide bond between Cysteine 110 and Cysteine 187</scene>. This loop also potentially contacts the chromophore through Glutamine 181 and Tyrosine 191<ref>Article 12</ref>. | <scene name='Sandbox_173/Disulfide_bond/4'>disulfide bond between Cysteine 110 and Cysteine 187</scene>. This loop also potentially contacts the chromophore through Glutamine 181 and Tyrosine 191<ref>Article 12</ref>. | ||
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As this ligand is bound in the 12-s-''trans'' conformation, there arises the non-bonding interactions between the C-13 methyl group and C-10 hydrogen that contribute to non-planarity. This leads to the ability of the chromophore polyene tail to undergo fast photoisomerization around the C-11=C-12 double bond during light-induced activation<ref>Article 2</ref>. Also, it is found that the C-11=C-12 double bond is pre-twisted in the ground state of rhodopsin, which is partly attributed to the C20 methyl group attached to C13 through interaction with Tryptophan 265. This pre-twist may give insight on the features of isomerization about this bond upon light activation <ref>Original article</ref>. | As this ligand is bound in the 12-s-''trans'' conformation, there arises the non-bonding interactions between the C-13 methyl group and C-10 hydrogen that contribute to non-planarity. This leads to the ability of the chromophore polyene tail to undergo fast photoisomerization around the C-11=C-12 double bond during light-induced activation<ref>Article 2</ref>. Also, it is found that the C-11=C-12 double bond is pre-twisted in the ground state of rhodopsin, which is partly attributed to the C20 methyl group attached to C13 through interaction with Tryptophan 265. This pre-twist may give insight on the features of isomerization about this bond upon light activation <ref>Original article</ref>. | ||
Somewhat enclosing this chromophore is a retinal binding pocket partially formed by the N-terminal domain overlaying the extracellular turns including Extracellular Helix 2, which folds into the molecular center<ref>Article 6</ref>. | Somewhat enclosing this chromophore is a retinal binding pocket partially formed by the N-terminal domain overlaying the extracellular turns including Extracellular Helix 2, which folds into the molecular center<ref>Article 6</ref>. | ||
==Function== | ==Function== | ||
