Sandbox Reserved 1852: Difference between revisions

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After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/1'>scaffold</scene> was found in the 6-bladed [https://en.wikipedia.org/wiki/Beta-propeller beta-propeller] of ''Loligo vulgalis,'' or the European Squid. <ref name="Siegel"/><ref name="Scharff">PMID:11435114</ref> The protein is relatively simple, with only one chain, one unit, 324 residues, and no extra ligands, metal ions, or small molecules bound.

[[Image:Diels-AlderaseSurfaces.png|300px|~~right~~|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the diene is in yellow and the dienophile is in green. The reaction proceeds via attack of the C6 on the C5, shifting electron density to C2, which attacks C1.]]

[[Image:Diels-AlderaseSurfaces.png|300px|left|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the diene is in yellow and the dienophile is in green. The reaction proceeds via attack of the C6 on the C5, shifting electron density to C2, which attacks C1.]]

====Active Site====

In the active state, there are <scene name='10/1075254/Active_site/3'>two catalytic residues</scene> that aim to stabilize the transition state of the Diels-Alder reaction. The Y134 acts as a <scene name='10/1075253/Y134_h_donation/1'>hydrogen bond donor</scene> to the oxygen on the <scene name='10/1075253/Ligand/6'>ligand</scene>. Q208 acts as a <scene name='10/1075254/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the ligand. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed, outlined in HOMO/LUMO.

Sandbox Reserved 1852: Difference between revisions

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@@ Line 14: / Line 14: @@
 After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/1'>scaffold</scene> was found in the 6-bladed [https://en.wikipedia.org/wiki/Beta-propeller beta-propeller] of ''Loligo vulgalis,'' or the European Squid. <ref name="Siegel"/><ref name="Scharff">PMID:11435114</ref> The protein is relatively simple, with only one chain, one unit, 324 residues, and no extra ligands, metal ions, or small molecules bound.
-[[Image:Diels-AlderaseSurfaces.png|300px|right|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the diene is in yellow and the dienophile is in green. The reaction proceeds via attack of the C6 on the C5, shifting electron density to C2, which attacks C1.]]
+[[Image:Diels-AlderaseSurfaces.png|300px|left|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the diene is in yellow and the dienophile is in green. The reaction proceeds via attack of the C6 on the C5, shifting electron density to C2, which attacks C1.]]
 ====Active Site====
 In the active state, there are <scene name='10/1075254/Active_site/3'>two catalytic residues</scene> that aim to stabilize the transition state of the Diels-Alder reaction. The Y134 acts as a <scene name='10/1075253/Y134_h_donation/1'>hydrogen bond donor</scene> to the oxygen on the <scene name='10/1075253/Ligand/6'>ligand</scene>. Q208 acts as a <scene name='10/1075254/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the ligand. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed, outlined in HOMO/LUMO.