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.  
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.  
====Active Site====
====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.
In the designed active site, <scene name='10/1075254/Active_site/3'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 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'>dienophile</scene>. Q208 acts as a <scene name='10/1075254/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the diene. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed.
====Helix Cap====
====Helix Cap====
In the evolution process, researchers added a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] motif 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 Km 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] motif 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>


== Mechanism ==
== Mechanism ==
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