Sandbox Reserved 1849: Difference between revisions

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The goal of designing these minibinders was to create a molecule with a higher binding affinity with the RBD than ACE2, meaning they had to be designed with specific residues that form stronger connections with the same binding pockets that ACE2 would bind to <ref name="Longxing">PMID:32907861</ref>. This section highlights some important residue differences between the minibinders and ACE2 that give the minibinders a higher affinity.

The glutamine-493 (Q493) residue is an important residue in showing the differences in strength between ACE2 and the minibinders <ref name="Longxing">PMID:32907861</ref>. ACE2 doesn’t make use of this residue when binding to the RBD, the nearest residues, Glu-35 and Lys-31 <scene name='10/1075250/Q493_ace2/5'>don’t form any interaction with Q493</scene>. Comparing this to the AHB2 minibinder, which <scene name='10/1075250/Q493-ahb2/3'>forms a Hydrogen bond with the Q493 residue</scene>, the AHB2 minibinder makes better use of the RBD’s residue than ACE2, helping it have a higher affinity to the spike protein. LCB1 makes even better use of the Q493 residue, forming two hydrogen bonds with two different residues, giving it the highest affinity based on the Q493 residue.

The glutamine-493 (Q493) residue is an important residue in showing the differences in strength between ACE2 and the minibinders <ref name="Longxing">PMID:32907861</ref>. ACE2 doesn’t make use of this residue when binding to the RBD, the nearest residues, Glu-35 and Lys-31 <scene name='10/1075250/Q493_ace2/5'>don’t form any interaction with Q493</scene>. Comparing this to the AHB2 minibinder, which <scene name='10/1075250/Q493-ahb2/3'>forms a Hydrogen bond with the Q493 residue</scene>, the AHB2 minibinder makes better use of the RBD’s residue than ACE2, helping it have a higher affinity to the spike protein. LCB1 makes even better use of the Q493 residue, <scene name='10/1075250/Q493_lcb1/4'>forming two hydrogen bonds with two different residues</scene>, giving it the highest affinity based on the Q493 residue.

Another important binding site on the RBD includes the Lysine-417 (K417) and Arginine-403 (R403) residues. While ACE2 does form a hydrogen bond interaction with the K417 residue using its own D30 residue, LCB1 forms H bond interactions with both of them, using its own D30 residue, forming a very strong interaction that is hard to break.

Sandbox Reserved 1849: Difference between revisions

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 The goal of designing these minibinders was to create a molecule with a higher binding affinity with the RBD than ACE2, meaning they had to be designed with specific residues that form stronger connections with the same binding pockets that ACE2 would bind to <ref name="Longxing">PMID:32907861</ref>. This section highlights some important residue differences between the minibinders and ACE2 that give the minibinders a higher affinity.
-The glutamine-493 (Q493) residue is an important residue in showing the differences in strength between ACE2 and the minibinders <ref name="Longxing">PMID:32907861</ref>. ACE2 doesn’t make use of this residue when binding to the RBD, the nearest residues, Glu-35 and Lys-31 <scene name='10/1075250/Q493_ace2/5'>don’t form any interaction with Q493</scene>. Comparing this to the AHB2 minibinder, which <scene name='10/1075250/Q493-ahb2/3'>forms a Hydrogen bond with the Q493 residue</scene>, the AHB2 minibinder makes better use of the RBD’s residue than ACE2, helping it have a higher affinity to the spike protein. LCB1 makes even better use of the Q493 residue, forming two hydrogen bonds with two different residues, giving it the highest affinity based on the Q493 residue.
+The glutamine-493 (Q493) residue is an important residue in showing the differences in strength between ACE2 and the minibinders <ref name="Longxing">PMID:32907861</ref>. ACE2 doesn’t make use of this residue when binding to the RBD, the nearest residues, Glu-35 and Lys-31 <scene name='10/1075250/Q493_ace2/5'>don’t form any interaction with Q493</scene>. Comparing this to the AHB2 minibinder, which <scene name='10/1075250/Q493-ahb2/3'>forms a Hydrogen bond with the Q493 residue</scene>, the AHB2 minibinder makes better use of the RBD’s residue than ACE2, helping it have a higher affinity to the spike protein. LCB1 makes even better use of the Q493 residue, <scene name='10/1075250/Q493_lcb1/4'>forming two hydrogen bonds with two different residues</scene>, giving it the highest affinity based on the Q493 residue.
 Another important binding site on the RBD includes the Lysine-417 (K417) and Arginine-403 (R403) residues. While ACE2 does form a hydrogen bond interaction with the K417 residue using its own D30 residue, LCB1 forms H bond interactions with both of them, using its own D30 residue, forming a very strong interaction that is hard to break.