Sandbox Reserved 1852: Difference between revisions

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[[Image:DielsAlderasecomboinfo Large.jpeg|540px|left|thumb|Figure 1. A) Example mechanism of a simple Diels-Alder reaction. B) Diels-Alderase substrates. Diene is 4-carboxybenzyl trans-1,3-butadiene-1-carbamate; dienophile is N,N- dimethylacrylamide. C) Illustration of 3R, 4S endo stereoisomerism, which the Diels-Alderase is selective for.]]

The binding pocket of 4o5t is selective for two substrates, 4-carboxybenzyl trans-1,3-butadiene-1-carbamate (~~[https://en.wikipedia.org/wiki/Diene~~ diene]) and N,N- dimethylacrylamide (dienophile). These substrates are shown as a single, combined ligand, 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate, in the protein model. The binding site contains a [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] donor (Tyr134) which lowers the LUMO energy and stabilizes the negative charge on the dienophile.<ref name="Siegel"/> It also contains a hydrogen bond acceptor (Glu208) that increases the HOMO energy and stabilizes the positive charge on the diene.<ref name="Siegel"/> Both of these H-bonding interactions work to stabilize the transition state while also orienting the substrates in optimal conformations for reacting.

The binding pocket of 4o5t is selective for two substrates, 4-carboxybenzyl trans-1,3-butadiene-1-carbamate (diene) and N,N- dimethylacrylamide (dienophile). These substrates are shown as a single, combined ligand, 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate, in the protein model. The binding site contains a [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] donor (Tyr134) which lowers the LUMO energy and stabilizes the negative charge on the dienophile.<ref name="Siegel"/> It also contains a hydrogen bond acceptor (Glu208) that increases the HOMO energy and stabilizes the positive charge on the diene.<ref name="Siegel"/> Both of these H-bonding interactions work to stabilize the transition state while also orienting the substrates in optimal conformations for reacting.

Overall, the Diels-Alderase stimulates improvement in synthetic laboratories and demonstrates early success in the now-prominent world of [https://www.nobelprize.org/prizes/chemistry/2024/press-release/ computational enzyme design.]

Sandbox Reserved 1852: Difference between revisions

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@@ Line 10: / Line 10: @@
 [[Image:DielsAlderasecomboinfo Large.jpeg|540px|left|thumb|Figure 1. A) Example mechanism of a simple Diels-Alder reaction. B) Diels-Alderase substrates. Diene is 4-carboxybenzyl trans-1,3-butadiene-1-carbamate; dienophile is N,N- dimethylacrylamide. C) Illustration of 3R, 4S endo stereoisomerism, which the Diels-Alderase is selective for.]]
-The binding pocket of 4o5t is selective for two substrates, 4-carboxybenzyl trans-1,3-butadiene-1-carbamate ([https://en.wikipedia.org/wiki/Diene diene]) and N,N- dimethylacrylamide (dienophile). These substrates are shown as a single, combined ligand, 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate, in the protein model. The binding site contains a [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] donor (Tyr134)  which lowers the LUMO energy and stabilizes the negative charge on the dienophile.<ref name="Siegel"/> It also contains a hydrogen bond acceptor (Glu208)  that increases the HOMO energy and stabilizes the positive charge on the diene.<ref name="Siegel"/> Both of these H-bonding interactions work to stabilize the transition state while also orienting the substrates in optimal conformations for reacting.
+The binding pocket of 4o5t is selective for two substrates, 4-carboxybenzyl trans-1,3-butadiene-1-carbamate (diene) and N,N- dimethylacrylamide (dienophile). These substrates are shown as a single, combined ligand, 4-{[2-(phosphonooxy)ethyl]carbamoyl}benzyl [(1R,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamate, in the protein model. The binding site contains a [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] donor (Tyr134)  which lowers the LUMO energy and stabilizes the negative charge on the dienophile.<ref name="Siegel"/> It also contains a hydrogen bond acceptor (Glu208)  that increases the HOMO energy and stabilizes the positive charge on the diene.<ref name="Siegel"/> Both of these H-bonding interactions work to stabilize the transition state while also orienting the substrates in optimal conformations for reacting.
 Overall, the Diels-Alderase stimulates improvement in synthetic laboratories and demonstrates early success in the now-prominent world of [https://www.nobelprize.org/prizes/chemistry/2024/press-release/ computational enzyme design.]