Sandbox Reserved 1165: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 19: Line 19:




[[Image:Screen_Shot_2016-03-22_at_5.28.03_PM.png|(|):|425 px|center|thumb|'''Figure 4: Binding Pocket Residues:''' Residues with side chains of carbon(utilizing the [https://en.wikipedia.org/wiki/Hydrophobic_effect hydrophobic effect]) are shown in green and side chains containing oxygen ([https://en.wikipedia.org/wiki/Hydrophile hydrophilic]) are shown in red. The properties of hydrophobicity and hydrophilicity of the residues create the [https://en.wikipedia.org/wiki/Ligand_%28biochemistry%29#Receptor.2Fligand_binding_affinity binding affinity] of glucagon.]]  
[[Image:Screen_Shot_2016-03-22_at_5.28.03_PM.png|(|):|425 px|center|thumb|'''Figure 4: Binding Pocket Residues:''' Residues with side chains of carbon(utilizing the [https://en.wikipedia.org/wiki/Hydrophobic_effect hydrophobic effect]) are shown in green and side chains containing oxygen ([https://en.wikipedia.org/wiki/Hydrophile hydrophilic]) are shown in red. The properties of hydrophobicity and hydrophilicity of the residues create the [https://en.wikipedia.org/wiki/Ligand_%28biochemistry%29#Receptor.2Fligand_binding_affinity binding affinity] of glucagon.<ref name="Ligands">PMID: 21542831</ref>]]  


Many of the [https://en.wikipedia.org/wiki/Residue_(chemistry) residues] in the binding pocket that are in direct contact with the glucagon molecule are [https://en.wikipedia.org/wiki/Ion charged] or are [https://en.wikipedia.org/wiki/Chemical_polarity polar]. The [https://en.wikipedia.org/wiki/Active_site binding site] location of the hormone peptide ligand has been identified, and the N-terminus of glucagon is known to bind partly with the ECD while the rest of glucagon binds deep into the <scene name='72/721535/Binding_pocket_orange/1'>binding pocket</scene>. The [https://en.wikipedia.org/wiki/Amino_acid amino acids] at the N-terminus of the class B 7TM have the ability to form [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonds] and [https://en.wikipedia.org/wiki/Ionic_bonding ionic interactions], which can be seen in the [https://en.wikipedia.org/wiki/Peptide_sequence amino acid sequence] of glucagon (Figure 2). <ref name="Sequence">PMID: 11946536</ref>
Many of the [https://en.wikipedia.org/wiki/Residue_(chemistry) residues] in the binding pocket that are in direct contact with the glucagon molecule are [https://en.wikipedia.org/wiki/Ion charged] or are [https://en.wikipedia.org/wiki/Chemical_polarity polar]. The [https://en.wikipedia.org/wiki/Active_site binding site] location of the hormone peptide ligand has been identified, and the N-terminus of glucagon is known to bind partly with the ECD while the rest of glucagon binds deep into the <scene name='72/721535/Binding_pocket_orange/1'>binding pocket</scene>. The [https://en.wikipedia.org/wiki/Amino_acid amino acids] at the N-terminus of the class B 7TM have the ability to form [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonds] and [https://en.wikipedia.org/wiki/Ionic_bonding ionic interactions], which can be seen in the [https://en.wikipedia.org/wiki/Peptide_sequence amino acid sequence] of glucagon (Figure 2). <ref name="Sequence">PMID: 11946536</ref>
Line 27: Line 27:




 
There are specific amino acid interactions that hold the helices of the 7TM in the conformation that maximizes [http://www.chemicool.com/definition/affinity.html affinity]. <ref name="Ligands">PMID: 21542831</ref> This includes the [https://en.wikipedia.org/wiki/Disulfide disulfide bond] between <scene name='72/721535/Disulfide_bond_notspin/1'> Cys 294 and Cys 224</scene> that serves to hold the helices in the proper orientation for binding. Additionally, the [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] between Glu 406, Arg 173, and Arg 346, also mentioned earlier, hold the conformation together for higher affinity (Figure 3). <ref name="Ligands">PMID: 21542831</ref> Finally, alpha helical structure of the stalk is imperative to the affinity and binding of the glucagon. <ref name="Tips">PMID: 23863937</ref>  
There are also many smaller residues on glucagon that support the bulky residues on the GCGR. These residues are located within the binding pocket of the 7TM (Figure 4). <ref name="Ligands">PMID: 21542831</ref> There are specific amino acid interactions that hold the helices of the 7TM in the closed conformation that maximizes [http://www.chemicool.com/definition/affinity.html affinity]. <ref name="Ligands">PMID: 21542831</ref> This includes the [https://en.wikipedia.org/wiki/Disulfide disulfide bond] between Cys 294 and Cys 224 that was mentioned earlier that serves to hold the ECL1 and ECL2 in the proper orientation. Additionally, the [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] between Glu 406, Arg 173, and Arg 346, also mentioned earlier, hold the conformation together for higher affinity (Figure 3). <ref name="Ligands">PMID: 21542831</ref> Finally, alpha helical structure of the stalk is imperative to the affinity and binding of the glucagon. <ref name="Tips">PMID: 23863937</ref>  




Retrieved from "https://proteopedia.org/Sandbox_Reserved_1165"