Sandbox Reserved 1852: Difference between revisions

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After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/2'>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.

====Active Site====

In the designed active site, <scene name='10/1075254/Active_site/6'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 acts as a <scene name='10/1075254/Y134_h_donation/3'>hydrogen bond donor</scene> to the oxygen on the dienophile [Fig. 2]. Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene [Fig. 2]. These interactions help reduce the energetic gap between orbitals, allowing the reaction to proceed.

In the designed active site, <scene name='10/1075254/Active_site/6'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 acts as a <scene name='10/1075254/Y134_h_donation/3'>hydrogen bond donor</scene> to the oxygen on the dienophile [Fig. 2]. Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene [Fig. 2]. These interactions help reduce the energetic gap between orbitals, allowing the reaction to proceed. The active site geometry also plays a large role in the binding of the substrates and how they react on a stereochemical level. By making small changes in the active site, changes can be made to the selectivity.

====Helix Cap====

In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075254/Alpha_helix_highlighted/1'>cap</scene> to the top of the binding site. The hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref>

In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075254/Alpha_helix_highlighted/1'>cap</scene> to the top of the binding site. The original hypothesis was that including a steric group near to the top of the active site would increase the binding affinity of the enzyme and improve the reaction kinetics. It was experimentally shown that he hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref>

Sandbox Reserved 1852: Difference between revisions

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@@ Line 25: / Line 25: @@
 After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/2'>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.
 ====Active Site====
-In the designed active site, <scene name='10/1075254/Active_site/6'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 acts as a <scene name='10/1075254/Y134_h_donation/3'>hydrogen bond donor</scene> to the oxygen on the dienophile [Fig. 2]. Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene [Fig. 2]. These interactions help reduce the energetic gap between orbitals, allowing the reaction to proceed.
+In the designed active site, <scene name='10/1075254/Active_site/6'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 acts as a <scene name='10/1075254/Y134_h_donation/3'>hydrogen bond donor</scene> to the oxygen on the dienophile [Fig. 2]. Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene [Fig. 2]. These interactions help reduce the energetic gap between orbitals, allowing the reaction to proceed. The active site geometry also plays a large role in the binding of the substrates and how they react on a stereochemical level. By making small changes in the active site, changes can be made to the selectivity.
 ====Helix Cap====
-In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075254/Alpha_helix_highlighted/1'>cap</scene> to the top of the binding site. The hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref>
+In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075254/Alpha_helix_highlighted/1'>cap</scene> to the top of the binding site. The original hypothesis was that including a steric group near to the top of the active site would increase the binding affinity of the enzyme and improve the reaction kinetics. It was experimentally shown that he hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref>