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/~~1075253~~/Y134_h_donation/3'>~~hydrogen bond donor~~</scene> to the oxygen on the dienophile (see Fig. 2). Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene. 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'>TextToBeDisplayed</scene> to the oxygen on the dienophile (see Fig. 2). Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>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====

In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/~~1075252~~/Alpha_helix_highlighted/4'>~~motif~~</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'>TextToBeDisplayed</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>

== Mechanism ==

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='10/1075253/Y134_h_donation/3'>hydrogen bond donor</scene> to the oxygen on the dienophile (see Fig. 2). Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>hydrogen bond acceptor</scene> to the nitrogen on the diene. 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'>TextToBeDisplayed</scene> to the oxygen on the dienophile (see Fig. 2). Q208 acts as a <scene name='10/1075254/208_bond_donor/3'>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====
-In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075252/Alpha_helix_highlighted/4'>motif</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'>TextToBeDisplayed</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>
 == Mechanism ==