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=== Charge Network ===
=== Charge Network ===
[[Image:charge network residues.png|250 px|right|thumb|Figure 3. TAK-875 with key binding residues]]hGPR40 has a distinct binding pocket that is established by seven key residues. The importance of these residues for agonist binding was determined by [https://www.neb.com/applications/cloning-and-synthetic-biology/site-directed-mutagenesis mutagenesis] studies. Each of these residues have either a [http://www.proteinstructures.com/Structure/Structure/amino-acids.html charged or polar R-group] that allows them to develop a charge network. This network keeps the residues in a stable, unbound state until exposed to a substrate. When the substrate (an agonist) enters the binding pocket, four of the seven <scene name='72/721541/Hydrogen_binding_1/6'>key binding residues</scene> interact directly with the carboxylate moiety of the agonist. In 2007 and 2009, researchers showed the presence of Arg 183 and Arg 258 in the binding pocket <ref name="Sum">PMID: 17699519</ref><ref name="Sum, C.">PMID:19068482</ref> Along with the two Arginine residues, the charge network incorporates two Tyrosine residues.These residues (Tyr 91 and Tyr 240) also stabilize the carboxylate of the agonists. It was further determined that Tyr 240 is epecially important for binding. Mutation of Tyr 240 caused a reduction in the binding affinity of TAK-875 by eight fold and had a significant effect on the [https://en.wikipedia.org/wiki/Dissociation_constant K<sub>D</sub>] of the protein.<ref name="Srivastava"/>  
[[Image:charge network residues.png|250 px|right|thumb|Figure 3. TAK-875 with key binding residues]]hGPR40 has a distinct binding pocket that is established by seven key residues. The importance of these residues for agonist binding was determined by [https://www.neb.com/applications/cloning-and-synthetic-biology/site-directed-mutagenesis mutagenesis] studies. Each of these residues have either a [http://www.proteinstructures.com/Structure/Structure/amino-acids.html charged or polar R-group] that allows them to develop a charge network. This network keeps the residues in a stable, unbound state until exposed to a substrate. When the substrate (an agonist) enters the binding pocket, four of the seven <scene name='72/721541/Hydrogen_binding_1/6'>key binding residues</scene> interact directly with the carboxylate moiety of the agonist. In 2007 and 2009, researchers showed the presence of Arg183 and Arg258 in the binding pocket <ref name="Sum">PMID: 17699519</ref><ref name="Sum, C.">PMID:19068482</ref> Along with the two arginine residues, the charge network incorporates two tyrosine residues. These residues (Tyr91 and Tyr240) also stabilize the carboxylate group on the agonists. It was further determined that Tyr240 is especially important for binding. Mutation of Tyr240 caused a reduction in the binding affinity of TAK-875 by eight fold and had a significant effect on the [https://en.wikipedia.org/wiki/Dissociation_constant K<sub>D</sub>] of the protein.<ref name="Srivastava"/>  


=== ECL2 ===
=== ECL2 ===
Although it may be different in many ways, hGPR40 is similar to most G protein coupled receptors because it contains a highly conserved hairpin loop. This extracellular loop (<scene name='72/721541/Ecl2/3'>ECL2</scene>), is accompanied by a [https://en.wikibooks.org/wiki/Structural_Biochemistry/Chemical_Bonding/_Disulfide_bonds disulfide bond] and serves an important role in the protein. In hGPR40, ECL2 has two sections: a beta sheet and an auxiliary loop. The [https://en.wikipedia.org/wiki/Beta_sheet beta sheet] (shown in cyan) spans helices 4 and 5. The ECL2 of hGPR40 differs from that of other proteins because it contains an auxiliary loop (magenta) of 13 extra residues. The entire extracellular loop has low mobility and flexibility which allows it to act as a cap for the binding pocket. The only exception to the low flexibility is the tip of the auxiliary loop, which corresponds to residues Asp 152-Asn 155. This area of greater mobility allows for substrates to enter the binding site.<ref name="Srivastava"/>
Although it may be different in many ways, hGPR40 is similar to most G protein coupled receptors because it contains a highly conserved hairpin loop. This extracellular loop (<scene name='72/721541/Ecl2/3'>ECL2</scene>), is accompanied by a [https://en.wikibooks.org/wiki/Structural_Biochemistry/Chemical_Bonding/_Disulfide_bonds disulfide bond] and serves an important role in the protein. In hGPR40, ECL2 has two sections: a beta sheet and an auxiliary loop. The [https://en.wikipedia.org/wiki/Beta_sheet beta sheet] (shown in cyan) spans helices 4 and 5. The ECL2 of hGPR40 differs from that of other proteins because it contains an auxiliary loop (magenta) of 13 extra residues. The entire extracellular loop has low mobility and flexibility which allows it to act as a cap for the binding pocket. The only exception to the low flexibility is the tip of the auxiliary loop, which corresponds to residues Asp152-Asn155. This area of greater mobility allows for substrates to enter the binding site.<ref name="Srivastava"/>


== Function ==
== Function ==

Revision as of 13:36, 12 April 2016

Human GPR40 (hGPR40), also known as Free Fatty Acid Receptor 1 (FFAR1)

hGPR40

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References