Sandbox323: Difference between revisions

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SwissDock analysis showed a preference for larger molecules, specifically fatty acids. Lactide, Ethyl Butyrate, and Triethylene Glycol exhibited noticeably weak binding affinities to the theorized active site of 4Q7Q. <ref name="SwissDockOne">Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res. 2024, 52 (W1), W324-W332. DOI: 10.1093/nar/gkae300.</ref><ref name="SwissDockTwo">

Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011, 39 (Web Server issue), W270-W277. DOI: 10.1093/nar/gkr366</ref><ref name="SwissDockThree">

Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011, 39 (Web Server issue), W270-W277. DOI: 10.1093/nar/gkr366</ref><ref name="SwissDockThree"> Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model., 2021, 61 (8), 3891–3898, DOI: 10.1021/acs.jcim.1c00203</ref><ref name="SwissDockFour">Trott O, Olson AJ. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem., 2010, 31 (2), 455–461, DOI: 10.1002/jcc.21334</ref> These ligands may be ill-suited to act as substrates for 4Q7Q as they are remarkably polar, and lipids—one of the potential categories of substrates for 4Q7Q—are mostly non-polar.<ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />

Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model., 2021, 61 (8), 3891–3898, DOI: 10.1021/acs.jcim.1c00203</ref><ref name="SwissDockFour">Trott O, Olson AJ. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem., 2010, 31 (2), 455–461, DOI: 10.1002/jcc.21334</ref> These ligands may be ill-suited to act as substrates for 4Q7Q as they are remarkably polar, and lipids—one of the potential categories of substrates for 4Q7Q—are mostly non-polar.<ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />

[[Image:DecanoateDocking.png|300px|right|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />]]

[[Image:DecanoateDocking.png|300px|right|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />]]

Despite this, these ligands show noticeable hydrophobic interactions with the active site. This implies 4Q7Q uses hydrophobic regions to help guide substrates into the right orientation for enzymatic processes. This also further supports the possibility that 4Q7Q primarily operates with hydrophobic lipid-based substrates. This also explains why Methyl Acetate exhibited a relatively weaker affinity for 4Q7Q, as its smaller structure prevented hydrophobic interactions.

[[Image:4Q7QDockingEnergies.png|300px|left|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />]]

[[Image:4Q7QDockingEnergies.png|300px|left|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />]]

=== Hypothetical Function ===

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 SwissDock analysis showed a preference for larger molecules, specifically fatty acids. Lactide, Ethyl Butyrate, and Triethylene Glycol exhibited noticeably weak binding affinities to the theorized active site of 4Q7Q. <ref name="SwissDockOne">Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res. 2024, 52 (W1), W324-W332. DOI: 10.1093/nar/gkae300.</ref><ref name="SwissDockTwo">
-Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011, 39 (Web Server issue), W270-W277. DOI: 10.1093/nar/gkr366</ref><ref name="SwissDockThree">
+Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011, 39 (Web Server issue), W270-W277. DOI: 10.1093/nar/gkr366</ref><ref name="SwissDockThree"> Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model., 2021, 61 (8), 3891–3898, DOI: 10.1021/acs.jcim.1c00203</ref><ref name="SwissDockFour">Trott O, Olson AJ. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem., 2010, 31 (2), 455–461, DOI: 10.1002/jcc.21334</ref> These ligands may be ill-suited to act as substrates for 4Q7Q as they are remarkably polar, and lipids—one of the potential categories of substrates for 4Q7Q—are mostly non-polar.<ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />
-Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model., 2021, 61 (8), 3891–3898, DOI: 10.1021/acs.jcim.1c00203</ref><ref name="SwissDockFour">Trott O, Olson AJ. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem., 2010, 31 (2), 455–461, DOI: 10.1002/jcc.21334</ref> These ligands may be ill-suited to act as substrates for 4Q7Q as they are remarkably polar, and lipids—one of the potential categories of substrates for 4Q7Q—are mostly non-polar.<ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />
-[[Image:DecanoateDocking.png|300px|right|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />]]
+[[Image:DecanoateDocking.png|300px|right|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />]]
 Despite this, these ligands show noticeable hydrophobic interactions with the active site. This implies 4Q7Q uses hydrophobic regions to help guide substrates into the right orientation for enzymatic processes. This also further supports the possibility that 4Q7Q primarily operates with hydrophobic lipid-based substrates. This also explains why Methyl Acetate exhibited a relatively weaker affinity for 4Q7Q, as its smaller structure prevented hydrophobic interactions.
-[[Image:4Q7QDockingEnergies.png|300px|left|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour />]]
+[[Image:4Q7QDockingEnergies.png|300px|left|thumb|SwissDock-based analysis of the intermolecular interactions between Decanoate and 4Q7Q's proposed active site <ref name="SwissDockOne" /><ref name="SwissDockTwo" /><ref name="SwissDockThree" /><ref name="SwissDockFour" />]]
 === Hypothetical Function ===