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.

<scene name='User:Anat_Levit/Sandbox_1/~~Pkr1_2rh1_residues~~/1'>~~TextToBeDisplayed~~</scene>

The TM cavity of PKR1 and PKR2 is quite a narrow cleft, similar to the epinephrine binding site of β2-Adrenergic receptor. It is a narrow and deep cleft that is largely concealed from solvent, which may enable ligand interaction with both walls. Based on the comparison to 2RH1, we can see that the residues lining the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_based_residues/2'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.

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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='400' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>
+<applet load='PKR1_model1.pdb' size='300' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>
-<scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_residues/1'>TextToBeDisplayed</scene>
+The TM cavity of PKR1 and PKR2 is quite a narrow cleft, similar to the epinephrine binding site of β2-Adrenergic receptor. It is a narrow and deep cleft that is largely concealed from solvent, which may enable ligand interaction with both walls. Based on the comparison to 2RH1, we can see that the residues lining the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_based_residues/2'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.