User:Anat Levit/Sandbox 1: Difference between revisions

Line 56:

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 (via van der Waals contacts). 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/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.

The TM cavity of PKR1 and PKR2 is 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 (via van der Waals contacts). 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/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.

The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/5' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.

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).

@@ Line 56: / Line 56: @@
-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 (via van der Waals contacts). 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/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.
+The TM cavity of PKR1 and PKR2 is 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 (via van der Waals contacts). 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/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.
 The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/5' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.
+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).