User:Anat Levit/Sandbox 1: Difference between revisions

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To determine the location of a potential TM binding cavity for each receptor, we structurally aligned and superimposed each of the models onto the structures of bovine Rhodopsin ([[1l9h]], [[1f88]]), human β2-Adrenergic receptor ([[2rh1]]) and human A2-Adenosine receptor ([[3eml]]). The Prokineticin receptors binding sites were determined based on homology to the known binding site-composing residues of the templates.

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The ligand binding pocket of bovine Rhodopsin is similar in position to the β2-Adrenergic receptor binding site, and also involves TMs II, III, V and VI. The position does not vary considerably with alternate ligands or between different subtypes of different species. The retinal binding pocket relies mainly on hydrophobic interactions in addition to a covalent linkage with TM VII. In both, PROKR1 and PROKR2, Trp288 is part of the binding pocket. This position is homologues to Trp265 of Rhodopsin which interacts with retinal (a tryptophan is in general conserved at this position in class A receptors and is thought to be involved in receptor signaling).

The ligand binding pocket of bovine Rhodopsin is similar in position to the β2-Adrenergic receptor binding site, and also involves TMs II, III, V and VI. The position does not vary considerably with alternate ligands or between different subtypes of different species. The retinal binding pocket relies mainly on hydrophobic interactions in addition to a covalent linkage with TM VII. In both, <scene name='User:Anat_Levit/Sandbox_1/Pkr1_1l9h_based_residues/1' target='PROKR1'>PROKR1</scene> and PROKR2, Trp288 is part of the binding pocket. This position is homologues to Trp265 of Rhodopsin which interacts with retinal (a tryptophan is in general conserved at this position in class A receptors and is thought to be involved in receptor signaling).

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 To determine the location of a potential TM binding cavity for each receptor, we structurally aligned and superimposed each of the models onto the structures of bovine Rhodopsin ([[1l9h]], [[1f88]]), human β2-Adrenergic receptor ([[2rh1]]) and human A2-Adenosine receptor ([[3eml]]). The Prokineticin receptors binding sites were determined based on homology to the known binding site-composing residues of the templates.
-<applet load='PKR1_model1.pdb' size='300' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>
+<applet load='PKR1_model1.pdb' size='300' name='PROKR1' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>
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-The ligand binding pocket of bovine Rhodopsin is similar in position to the β2-Adrenergic receptor binding site, and also involves TMs II, III, V and VI. The position does not vary considerably with alternate ligands or between different subtypes of different species. The retinal binding pocket relies mainly on hydrophobic interactions in addition to a covalent linkage with TM VII. In both, PROKR1 and PROKR2, Trp288 is part of the binding pocket. This position is homologues to Trp265 of Rhodopsin which interacts with retinal (a tryptophan is in general conserved at this position in class A receptors and is thought to be involved in receptor signaling).
+The ligand binding pocket of bovine Rhodopsin is similar in position to the β2-Adrenergic receptor binding site, and also involves TMs II, III, V and VI. The position does not vary considerably with alternate ligands or between different subtypes of different species. The retinal binding pocket relies mainly on hydrophobic interactions in addition to a covalent linkage with TM VII. In both, <scene name='User:Anat_Levit/Sandbox_1/Pkr1_1l9h_based_residues/1' target='PROKR1'>PROKR1</scene> and PROKR2, Trp288 is part of the binding pocket. This position is homologues to Trp265 of Rhodopsin which interacts with retinal (a tryptophan is in general conserved at this position in class A receptors and is thought to be involved in receptor signaling).