https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Allie+PatonProteopedia - User contributions [en]2026-09-21T05:32:12ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2588148Sandbox Reserved 11802016-04-22T02:46:25Z<p>Allie Paton: </p>
<hr />
<div>=Glucagon G protein-coupled receptor=<br />
<br />
<StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene='72/721552/The_right_one/1'><br />
<br />
==Class B GPCRs==<br />
G protein coupled receptors (GPCRs) are the largest class of integral membrane proteins. GPCRs are divided into five families; the rhodopsin family (class A), the secretin family (class B), the glutamate family (class C), the frizzled/taste family (class F), and the adhesion family.<ref name= "Zhang 2006"/> Roughly 5% of the human genome encodes g protein-coupled receptors, which are responsible for the transduction of endogenous signals and the instigation of cellular responses. All GPCRs contain a similar seven α-helical transmembrane domain <scene name='72/727091/Full_Structure_with_Labels/1'>(TMD or 7TMD)</scene> that once bound to its ligand, undergoes a conformational change and tranduces a signal to coupled, heterotrimeric G proteins. The initiation of intracellular signal pathways occur in response to stimuli such as light, Ca2+, amino acids, nucleotides, odorants, peptides, and other proteins, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor#Physiological_roles and accomplishes many interesting physiological roles]. <ref name= "Zhang 2006">DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases the intracellular concentration of cAMP, inositol phosphate, and calcium levels. <ref>DOI 10.1111/bph.12689</ref> These secondary messengers are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest as disease targets. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structural approaches to the development of agonists and antagonists have however been hampered by the lack of accurate Class B TMD visualizations. Recent crystal structure images of corticoptropin-releasing factor receptor 1 (PDB: 4K5Y) and human glucagon receptor (PDB: 4L6R) were accomplished through x-ray crystallography. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
<br />
<br />
==Glucagon Receptor (GCGR)==<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon. See also [http://sbkb.org/fs/glucagon-receptor PSI Structural Biology Database] Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates.<ref name = 'Lehninger'/> Once the peptide hormone is released, it binds to GCGR, a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> GCGR can regulate additional signal pathways, including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
Glucagon is also a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA.<ref name = 'Lehninger'/> HMG-CoA is inactivated by phosphorylation and moderates cholesterol production to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
<br />
===Structure===<br />
<br />
The class B GPCRs, including GCGR, are different from other GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is <scene name='72/721552/The_right_one/3'>essential to ligand binding affinity.</scene> A135P mutations impact stalk stability by removing an important salt bridge between Glu133 - Lys136. A second difference between class B and other GPCRs is that the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity.<ref name= "Siu 2013"/> Most notably, class B GPCRs contain a <scene name='72/727091/Corticotropin_glucagon_aligned/1'>prominent central splay</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>from other GPCRs</scene>, and represents a tantalizing target for agonists/antagonists.<ref name= "Hollenstein 2014"/><br />
<br />
Because of the difficulty in stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. GCGR is known to regulate additional signal pathways through the adoption of differing receptor conformations and to interact with receptor activity-modifying proteins (RAMPs) altering the signaling bias of the receptor.<ref name= "Xu 2009"/><br />
<br />
<br />
===Glucagon Binding===<br />
<br />
The large, soluble N-terminal extracellular domains (ECD) of GCGR provide initial ligand selectivity with the deep, ligand pocket (Fig. 2) of the TMD providing secondary recognition.<ref name= "Yang 2015"/> <br />
[[Image:Protter GLR HUMAN.png |400 px|left|thumb|Fig. 1: Snake Plot of GCGR TMD. Residues of particular importance in glucagon binding affinity are found in green, yellow, and black. Residues in red are the location of critical disulfide bonds, while blue residues were found to be highly conserved across all class B GPCRs.<ref name= "Siu 2013"/>]]<br />
<br />
In a comprehensive mutagenesis and glucagon-binding study, a total of 129 mutations of GCGR were tested. 41 of these covering 28 different locations in the GCGR TMD were found to have at least a fourfold decrease in glucagon binding affinity<ref name= "Siu 2013"/>. (see Fig. 1) It is the face of the central cavity that harbors the majority of the residues which play an important role in glucagon binding.<ref name= "Siu 2013"/> The binding site was shown to be a dynamic area traveling from the middle of the stalk region (Tyr 138) to deep within the 7TM core (Glu 362), encompassing positions along ECL1, ECL2 and ECL3 and helices I, II, III, V, VI and VII.[[Image:Movie Frame 6.png |200 px|center|thumb|Fig. 2: <scene name='72/721552/Glucagon_binding/3'>Deep, central cavity</scene> functioning as anchoring site for glucagon's n-terminal residues.]][[Image:Glucagon with Q3 and N-terminus.png |200 px|right|thumb|Fig. 3: Surface visualization of glucagon visualizing the three dimensional shape of the N-terminal tail that interacts with the binding site of GCGR central cavity.]]<br />
<br />
Mutagenesis and photo cross-linking studies determined essential, conserved residues in glucagon and have been <scene name='72/727091/Glucagon_important_residues/2'>labeled and colored</scene> in red.<ref name= "Siu 2013"/> Glucagon residues His 1, Gln 3, Phe 6, and Tyr 10 are critical to successful binding interaction with the GCGR while others are important for structural rigidity. The n-terminus of glucagon (Fig. 3) leads to a protuberance that fits into the deep, interior cavity of the GCGR 7TMD (Fig. 2) where four residues reside that play strong roles in ligand binding affinity. There is a <scene name='72/721552/Glucagon_binding_zoomed_in/1'>narrow neck</scene> to the entrance of the cavity, providing a firm anchor during peptide docking. <br />
<br />
<br />
<br />
<br />
<br />
<br />
==Clinical relevance ==<br />
<br />
Because GCGR can interact with multiple types of G protein subfamilies, discovering small molecule inhibitors could lead to a wide range of focused therapies.<ref name= "Weston 2015"/> Blocking conformations that favor interaction with specific G proteins could allow the knockdown of targeted signal pathways. For example, GCGR is known to interact with inhibitory Gαi proteins that antagonize cAMP production.<ref name= "Weston 2015"/> The finding of an agonist for this pathway could lead to breakthroughs in the treatment of diabetes mellitus. Recently some fundamental work has been done with RAMPs which were shown to alter ligand preference in class B GPCRs.<ref name= "Wootten 2013">DOI:10.1111/j.1476-5381.2012.02202.x</ref> Specifically, RAMP2 association has been shown to alter the pharmacology of all GCGR ligands (glucagon and oxyntomodulin). RAMP2 association altered cAMP production, indicating an effect on signaling bias and g protein coupling.<br />
<br />
Attempts to target the GCGR have proven relatively unsuccessful. Three small molecule modulators were reported with the hope of enhanced pharmaceutical regulation.<ref name= "Kazda 2015">DOI: 10.1021/jm058026u</ref> (Fig. 4) No further progress was reported. Modest gains have been made in targeting glucagon-like peptide-1 receptors (a GPCR closely related to GCGR) but with the caveat of severe, adverse side-effects.<ref name= "Weston 2015">DOI 10.1074/jbc.M114.624601</ref> Encouraging results have recently come from Eli Lilly and Company who have been testing a small molecule antagonist of the GCGR (LY2409021) in phase two trials with some success.<ref name= "Kazda 2015">DOI: 10.2337/dc15-1643</ref><br />
<br />
CHANGE THIS FIGURE TO SMALL MOLECULE INHIBITORS 9, 10, AND 11 FROM YANG 2015 - USE THE CITATION FROM THE IMAGE BELOW FOR THAT FIGURE. TITLE THE FIGURE: "Figure 4: Three small molecule antagonists reported in 2007.<ref name= "Kazda 2015"/>"<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Kazda 2015"/>.]]<br />
<br />
<br />
==See Also==<br />
[http://sbkb.org/fs/glucagon-receptor PSI Structural Biology Database]<br />
[https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G protein-coupled receptors] Wikipedia page<br />
<br />
<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2588146Sandbox Reserved 11802016-04-22T02:43:18Z<p>Allie Paton: </p>
<hr />
<div>=Glucagon G protein-coupled receptor=<br />
<br />
<StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene='72/721552/The_right_one/1'><br />
<br />
==Class B GPCRs==<br />
G protein coupled receptors (GPCRs) are the largest class of integral membrane proteins. GPCRs are divided into five families; the rhodopsin family (class A), the secretin family (class B), the glutamate family (class C), the frizzled/taste family (class F), and the adhesion family.<ref name= "Zhang 2006"/> Roughly 5% of the human genome encodes g protein-coupled receptors, which are responsible for the transduction of endogenous signals and the instigation of cellular responses. All GPCRs contain a similar seven α-helical transmembrane domain <scene name='72/727091/Full_Structure_with_Labels/1'>(TMD or 7TMD)</scene> that once bound to its ligand, undergoes a conformational change and tranduces a signal to coupled, heterotrimeric G proteins. The initiation of intracellular signal pathways occur in response to stimuli such as light, Ca2+, amino acids, nucleotides, odorants, peptides, and other proteins, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor#Physiological_roles and accomplishes many interesting physiological roles]. <ref name= "Zhang 2006">DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases the intracellular concentration of cAMP, inositol phosphate, and calcium levels. <ref>DOI 10.1111/bph.12689</ref> These secondary messengers are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest as disease targets. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structural approaches to the development of agonists and antagonists have however been hampered by the lack of accurate Class B TMD visualizations. Recent crystal structure images of corticoptropin-releasing factor receptor 1 (PDB: 4K5Y) and human glucagon receptor (PDB: 4L6R) were accomplished through x-ray crystallography. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
<br />
<br />
==Glucagon Receptor (GCGR)==<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon. See also [http://sbkb.org/fs/glucagon-receptor PSI Structural Biology Database] Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates.<ref name = 'Lehninger'/> Once the peptide hormone is released, it binds to GCGR, a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> GCGR can regulate additional signal pathways, including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
Glucagon is also a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA.<ref name = 'Lehninger'/> HMG-CoA is inactivated by phosphorylation and moderates cholesterol production to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
<br />
===Structure===<br />
<br />
The class B GPCRs, including GCGR, are different from other GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is <scene name='72/721552/Ligand_binding_interactions/1'>essential to ligand binding affinity</scene>. A135P mutations impact stalk stability by removing an important salt bridge between Glu133 - Lys136. A second difference between class B and other GPCRs is that the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity.<ref name= "Siu 2013"/> Most notably, class B GPCRs contain a <scene name='72/727091/Corticotropin_glucagon_aligned/1'>prominent central splay</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>from other GPCRs</scene>, and represents a tantalizing target for agonists/antagonists.<ref name= "Hollenstein 2014"/><br />
<br />
Because of the difficulty in stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. GCGR is known to regulate additional signal pathways through the adoption of differing receptor conformations and to interact with receptor activity-modifying proteins (RAMPs) altering the signaling bias of the receptor.<ref name= "Xu 2009"/><br />
<br />
<br />
===Glucagon Binding===<br />
<br />
The large, soluble N-terminal extracellular domains (ECD) of GCGR provide initial ligand selectivity with the deep, ligand pocket (Fig. 2) of the TMD providing secondary recognition.<ref name= "Yang 2015"/> <br />
[[Image:Protter GLR HUMAN.png |400 px|left|thumb|Fig. 1: Snake Plot of GCGR TMD. Residues of particular importance in glucagon binding affinity are found in green, yellow, and black. Residues in red are the location of critical disulfide bonds, while blue residues were found to be highly conserved across all class B GPCRs.<ref name= "Siu 2013"/>]]<br />
<br />
In a comprehensive mutagenesis and glucagon-binding study, a total of 129 mutations of GCGR were tested. 41 of these covering 28 different locations in the GCGR TMD were found to have at least a fourfold decrease in glucagon binding affinity<ref name= "Siu 2013"/>. (see Fig. 1) It is the face of the central cavity that harbors the majority of the residues which play an important role in glucagon binding.<ref name= "Siu 2013"/> The binding site was shown to be a dynamic area traveling from the middle of the stalk region (Tyr 138) to deep within the 7TM core (Glu 362), encompassing positions along ECL1, ECL2 and ECL3 and helices I, II, III, V, VI and VII.[[Image:Movie Frame 6.png |200 px|center|thumb|Fig. 2: <scene name='72/721552/Glucagon_binding/3'>Deep, central cavity</scene> functioning as anchoring site for glucagon's n-terminal residues.]][[Image:Glucagon with Q3 and N-terminus.png |200 px|right|thumb|Fig. 3: Surface visualization of glucagon visualizing the three dimensional shape of the N-terminal tail that interacts with the binding site of GCGR central cavity.]]<br />
<br />
Mutagenesis and photo cross-linking studies determined essential, conserved residues in glucagon and have been <scene name='72/727091/Glucagon_important_residues/2'>labeled and colored</scene> in red.<ref name= "Siu 2013"/> Glucagon residues His 1, Gln 3, Phe 6, and Tyr 10 are critical to successful binding interaction with the GCGR while others are important for structural rigidity. The n-terminus of glucagon (Fig. 3) leads to a protuberance that fits into the deep, interior cavity of the GCGR 7TMD (Fig. 2) where four residues reside that play strong roles in ligand binding affinity. There is a <scene name='72/721552/Glucagon_binding_zoomed_in/1'>narrow neck</scene> to the entrance of the cavity, providing a firm anchor during peptide docking. <br />
<br />
<br />
<br />
<br />
<br />
<br />
==Clinical relevance ==<br />
<br />
Because GCGR can interact with multiple types of G protein subfamilies, discovering small molecule inhibitors could lead to a wide range of focused therapies.<ref name= "Weston 2015"/> Blocking conformations that favor interaction with specific G proteins could allow the knockdown of targeted signal pathways. For example, GCGR is known to interact with inhibitory Gαi proteins that antagonize cAMP production.<ref name= "Weston 2015"/> The finding of an agonist for this pathway could lead to breakthroughs in the treatment of diabetes mellitus. Recently some fundamental work has been done with RAMPs which were shown to alter ligand preference in class B GPCRs.<ref name= "Wootten 2013">DOI:10.1111/j.1476-5381.2012.02202.x</ref> Specifically, RAMP2 association has been shown to alter the pharmacology of all GCGR ligands (glucagon and oxyntomodulin). RAMP2 association altered cAMP production, indicating an effect on signaling bias and g protein coupling.<br />
<br />
Attempts to target the GCGR have proven relatively unsuccessful. Three small molecule modulators were reported with the hope of enhanced pharmaceutical regulation.<ref name= "Kazda 2015">DOI: 10.1021/jm058026u</ref> (Fig. 4) No further progress was reported. Modest gains have been made in targeting glucagon-like peptide-1 receptors (a GPCR closely related to GCGR) but with the caveat of severe, adverse side-effects.<ref name= "Weston 2015">DOI 10.1074/jbc.M114.624601</ref> Encouraging results have recently come from Eli Lilly and Company who have been testing a small molecule antagonist of the GCGR (LY2409021) in phase two trials with some success.<ref name= "Kazda 2015">DOI: 10.2337/dc15-1643</ref><br />
<br />
CHANGE THIS FIGURE TO SMALL MOLECULE INHIBITORS 9, 10, AND 11 FROM YANG 2015 - USE THE CITATION FROM THE IMAGE BELOW FOR THAT FIGURE. TITLE THE FIGURE: "Figure 4: Three small molecule antagonists reported in 2007.<ref name= "Kazda 2015"/>"<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Kazda 2015"/>.]]<br />
<br />
<br />
==See Also==<br />
[http://sbkb.org/fs/glucagon-receptor PSI Structural Biology Database]<br />
[https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G protein-coupled receptors] Wikipedia page<br />
<br />
<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587963Sandbox Reserved 11812016-04-20T22:08:31Z<p>Allie Paton: </p>
<hr />
<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
<br />
<scene name='72/727091/Full_Structure_with_Labels/1'>Labels</scene><br />
<br />
<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
Old Stuff:<br />
<br />
[[Image:ALA135PRO stalk unwinding.png|150 px|left|thumb|Fig. 1: A135P Mutation and effect on stalk stability <ref name= "Siu 2013"/>. ]] [[Image:Gln142 Tyr138 Glucagon interaction.png|150 px|right|thumb|Fig. 2: Stalk stabilized by salt bridge between Glu133-Lys136. Residues in yellow are demonstrated to have an effect on ligand binding affinity.<ref name= "Siu 2013"/>]] <br />
<br />
[[Image:Asn_298__Trp_295.png|150 px|left|thumb|Fig. 3: Active sites linked to glucagon binding affinity located on ECL1 are labeled<ref name= "Siu 2013"/>.]]<br />
<br />
[[Image:Corticotropin class B and Glucagon class B receptors aligned.png |150 px|left|thumb|Fig. 4: Corticotropin-releasing factor 1 and glucagon receptors; Class B GPCRs with notable central splay]] [[Image:Beta2 class A and Glucagon class B receptors aligned.png |150 px|right|thumb|Fig. 5: Beta 2-adrenergic (class A) and glucagon receptors; showing an absence of central splay in Class A GPCRs.]]<br />
<br />
[[Image:Movie_Frame_2.png|100 px|left|thumb|Fig. 7: Active site buried deep in 7TMD of glucagon receptor.]]<br />
<br />
[[Image:Movie_Frame_7.png|175 px|left|thumb|Fig. 14: Distance measurement of GCGR 7TMD Y138-D362 of 19-20 angstroms and labeled with complimentary glucagon interaction residues.]]<br />
[[Image:H1___Y10_with_measurement.png|175 px|right|thumb|Fig. 15: Distance measurement of H1-Y10 of 22-24 angstroms and labeled with complimentary GCGR 7TMD residue interactions.]]<br />
<br />
===Future research direction=== <br />
Research for Class A GPCRs is much more extensive than for its secretin, class B counterparts, although class B is proving to be a worthwhile to invest researching. The challenge of class B stabilization, expression, and molecular size , has made class B GPCRs particularly hard to assay. Biochemical research has increased in the class B specifications, because it has been realized that receptors can be modulated by more than the agonist and antagonists present in vivo. Leading research consists of a complex interwoven scheme of equilibria manipulation in multi-receptor conformations. <ref name="Salon 2011"/></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587962Sandbox Reserved 11802016-04-20T22:01:50Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
<scene name='72/727091/Full_Structure_with_Labels/1'>Labels</scene><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |500 px|center|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
<br />
[[Image:Movie Frame 8.png |275 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
[[Image:Glucagon with Q3 and N-terminus.png |275 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|275 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587961Sandbox Reserved 11802016-04-20T21:58:59Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
<scene name='72/727091/Full_Structure_with_Labels/1'>Labels</scene><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |500 px|center|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
<br />
[[Image:Movie Frame 8.png |275 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
[[Image:Glucagon with Q3 and N-terminus.png |275 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|275 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587960Sandbox Reserved 11802016-04-20T21:52:19Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |500 px|center|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
<br />
[[Image:Movie Frame 8.png |275 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
[[Image:Glucagon with Q3 and N-terminus.png |275 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|275 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587959Sandbox Reserved 11802016-04-20T21:40:24Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |500 px|center|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
<br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
<br />
[[Image:Movie Frame 8.png |275 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
[[Image:Glucagon with Q3 and N-terminus.png |275 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|275 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|275 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587958Sandbox Reserved 11802016-04-20T21:03:56Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='420' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |500 px|center|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
<br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
<br />
[[Image:Movie Frame 8.png |275 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
[[Image:Glucagon with Q3 and N-terminus.png |275 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|150 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|150 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587957Sandbox Reserved 11812016-04-20T20:45:32Z<p>Allie Paton: </p>
<hr />
<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
<br />
<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/2'>Glucagon Binding Zoomed Out</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
Old Stuff:<br />
<br />
[[Image:ALA135PRO stalk unwinding.png|150 px|left|thumb|Fig. 1: A135P Mutation and effect on stalk stability <ref name= "Siu 2013"/>. ]] [[Image:Gln142 Tyr138 Glucagon interaction.png|150 px|right|thumb|Fig. 2: Stalk stabilized by salt bridge between Glu133-Lys136. Residues in yellow are demonstrated to have an effect on ligand binding affinity.<ref name= "Siu 2013"/>]] <br />
<br />
[[Image:Asn_298__Trp_295.png|150 px|left|thumb|Fig. 3: Active sites linked to glucagon binding affinity located on ECL1 are labeled<ref name= "Siu 2013"/>.]]<br />
<br />
[[Image:Corticotropin class B and Glucagon class B receptors aligned.png |150 px|left|thumb|Fig. 4: Corticotropin-releasing factor 1 and glucagon receptors; Class B GPCRs with notable central splay]] [[Image:Beta2 class A and Glucagon class B receptors aligned.png |150 px|right|thumb|Fig. 5: Beta 2-adrenergic (class A) and glucagon receptors; showing an absence of central splay in Class A GPCRs.]]<br />
<br />
[[Image:Movie_Frame_2.png|100 px|left|thumb|Fig. 7: Active site buried deep in 7TMD of glucagon receptor.]]<br />
<br />
[[Image:Movie Frame 3.png |200 px|right|thumb|Fig. 9: Location of anchoring pocket within central cavity.<ref name= "Siu 2013"/>]]<br />
<br />
[[Image:Movie Frame 6.png |100 px|left|thumb|Fig. 10: Ballooned pocket functioning as anchoring site for glucagon residues 1-4.]]<br />
<br />
[[Image:Movie_Frame_7.png|175 px|left|thumb|Fig. 14: Distance measurement of GCGR 7TMD Y138-D362 of 19-20 angstroms and labeled with complimentary glucagon interaction residues.]]<br />
[[Image:H1___Y10_with_measurement.png|175 px|right|thumb|Fig. 15: Distance measurement of H1-Y10 of 22-24 angstroms and labeled with complimentary GCGR 7TMD residue interactions.]]<br />
<br />
===Future research direction=== <br />
Research for Class A GPCRs is much more extensive than for its secretin, class B counterparts, although class B is proving to be a worthwhile to invest researching. The challenge of class B stabilization, expression, and molecular size , has made class B GPCRs particularly hard to assay. Biochemical research has increased in the class B specifications, because it has been realized that receptors can be modulated by more than the agonist and antagonists present in vivo. Leading research consists of a complex interwoven scheme of equilibria manipulation in multi-receptor conformations. <ref name="Salon 2011"/></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587945Sandbox Reserved 11802016-04-20T18:03:40Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='340' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |400 px|left|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
[[Image:Movie Frame 8.png |150 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
<br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
[[Image:Glucagon with Q3 and N-terminus.png |200 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|150 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|150 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
== References ==<br />
<references/><br />
</StructureSection></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587944Sandbox Reserved 11802016-04-20T17:59:16Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='340' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
[[Image:Protter GLR HUMAN.png |400 px|left|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
[[Image:Movie Frame 8.png |150 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
<br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
[[Image:Glucagon with Q3 and N-terminus.png |200 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|150 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|150 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
</StructureSection><br />
<br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587942Sandbox Reserved 11812016-04-20T17:54:50Z<p>Allie Paton: </p>
<hr />
<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
<br />
<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/2'>Glucagon Binding Zoomed Out</scene><br />
<br />
<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
<br />
<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene><br />
<br />
Old Stuff:<br />
<br />
[[Image:ALA135PRO stalk unwinding.png|150 px|left|thumb|Fig. 1: A135P Mutation and effect on stalk stability <ref name= "Siu 2013"/>. ]] [[Image:Gln142 Tyr138 Glucagon interaction.png|150 px|right|thumb|Fig. 2: Stalk stabilized by salt bridge between Glu133-Lys136. Residues in yellow are demonstrated to have an effect on ligand binding affinity.<ref name= "Siu 2013"/>]] <br />
<br />
[[Image:Asn_298__Trp_295.png|150 px|left|thumb|Fig. 3: Active sites linked to glucagon binding affinity located on ECL1 are labeled<ref name= "Siu 2013"/>.]]<br />
<br />
[[Image:Corticotropin class B and Glucagon class B receptors aligned.png |150 px|left|thumb|Fig. 4: Corticotropin-releasing factor 1 and glucagon receptors; Class B GPCRs with notable central splay]] [[Image:Beta2 class A and Glucagon class B receptors aligned.png |150 px|right|thumb|Fig. 5: Beta 2-adrenergic (class A) and glucagon receptors; showing an absence of central splay in Class A GPCRs.]]<br />
<br />
[[Image:Movie_Frame_2.png|100 px|left|thumb|Fig. 7: Active site buried deep in 7TMD of glucagon receptor.]]<br />
<br />
[[Image:Movie Frame 3.png |200 px|right|thumb|Fig. 9: Location of anchoring pocket within central cavity.<ref name= "Siu 2013"/>]]<br />
<br />
[[Image:Movie Frame 6.png |100 px|left|thumb|Fig. 10: Ballooned pocket functioning as anchoring site for glucagon residues 1-4.]]</div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1180&diff=2587941Sandbox Reserved 11802016-04-20T17:54:17Z<p>Allie Paton: </p>
<hr />
<div><StructureSection load='4L6R' size='340' side='right' caption='7TM structure of human class B GPCR 4L6R', [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
G protein coupled receptors (GPCRs) are recognized as the largest known class of integral membrane proteins and are divided into five families; the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F). Roughly 5% of the human genome encodes g-protein-coupled receptors which are responsible for the transduction of endogenous signals and the instigation of cellular response. The variants all contain a similar seven α-helical transmembrane domain (TMD or 7TMD) that, once bound to its peptide ligand, undergoes conformational change and tranduces a signal to coupled, heterotrimeric G proteins which initiate intracellular signal pathways and generate physiological and pathological processes. <ref>DOI 10.1371/journal.pcbi.0020013</ref><br />
<br />
Class B GPCRs contain 15 distinct receptors for peptide hormones and generate their signal pathway through the activation of adenylate cyclase (AC) which increases concentration of cAMP, inositol phosphate, and calcium levels in cyto. <ref>DOI 10.1111/bph.12689</ref> These signals are essential elements of intracellular signal cascades for human diseases including type II diabetes mellitus, osteoporosis, obesity, cancer, neurological degeneration, cardiovascular diseases, headaches, and psychiatric disorders; making their regulation through drug targeting of particular interest to companies developing novel molecules. <ref name= "Hollenstein 2014">DOI 10.1016/j.tips.2013.11.001</ref> Structurally based approaches to the development of small-molecule agonists and antagonists have been hampered by the lack of accurate Class B TMD visualizations until recent crystal structures of corticoptropin-releasing factor receptor 1 and human glucagon were realized. <ref name= "Hollenstein 2013">DOI 10.1038/nature12357</ref> <ref name= "Siu 2013">DOI 10.1038/nature12393</ref><br />
<br />
The glucagon class B GPCR (GCGR) is involved in glucose homeostasis through the binding of the signal peptide glucagon.<br />
<br />
==Glucagon Receptor==<br />
Glucagon is released from pancreatic α-cells when blood glucose levels fall after a period of fasting or several hours following intake of dietary carbohydrates. Once the peptide hormone is released, it binds to GCGR which is a 485 amino acid protein found in the liver, kidney, intestinal smooth muscle, brain, and adipose tissues. <ref name= "Yang 2015">DOI 10.1038/aps.2015.78</ref> Upon binding, signaling is initiated to heterotrimeric G-proteins containing Gαs. <ref name= "Ahren 2009">DOI 10.1038/nrd2782</ref> Additionally, GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. <ref name= "Xu 2009">DOI 10.3109/10799890903295150</ref><br />
<br />
==Structural Considerations==<br />
===Comparison between Class A and Class B GPCRs===<br />
The class B GPCRs, of which GCGR is a member, are different from other Class A GPCRs in several ways. The first is that class B GPCRs contain a protrusion known as a 'stalk,' which is a three α-helical turn elongation of the N-terminus that protrudes past the extracellular (EC) membrane. Structural integrity of this domain in GCGR is essential to ligand binding affinity. (Fig's 1 and 2) <br />
<br />
Secondly, the extracellular loop 1 (ECL1) is 3-4 times longer than comparable loops in class A GPCRs, and also affects ligand binding affinity. (Fig. 3)<ref name= "Siu 2013"/> <br />
<br />
Most notably, class B GPCRs contain a prominent central splay (Fig. 4) <scene name='72/727091/Corticotropin_glucagon_aligned/1'>(two Class B protein receptors demonstrating central splay)</scene> which is solvent filled and accessible from the extracellular side. This central splay is notably absent from class A GPCRs (Fig. 5) <scene name='72/727091/B2-adrenergic_glucagon_aligned/9'>(Class A vs. Class B GPCRs)</scene>, represents a tantalizing target for agonists/antagonists, and is the focus of much current research into GCGR signal regulation. <ref name= "Hollenstein 2014"/><br />
<br />
===Structurally Significant GCGR 7TDM Residues===<br />
[[Image:Protter GLR HUMAN.png |400 px|left|thumb|Fig. 6: Snake Plot of GCGR TMD<ref name= "Siu 2013"/>]]<br />
<br />
The snake plot (Fig. 6) shows the conservation and effects of mutagenesis in the 7TMD structure of class B human GPCR. The highly conserved amino acids imply an importance to that functioning of the individual residues and their interactions. The amino acids which have a great impact on the function of the receptor are highlighted in teal, yellow, and black, and offer evidence that the position and interaction of the amino acid is crucial for protein function. Most of the residues that play an important role in glucagon binding face the main cavity of the 7TM structure. Mutagenesis in these positions highly compromises the functioning of the glucagon binding.<br />
<br />
==Functions of Glucagon receptor (GCGR)==<br />
<br />
It has been discovered that the large, soluble N-terminal extracellular domains (ECD) of GCGR are primary in ligand selectivity with the deep, ligand pocket (Fig. 7) of the TMD providing secondary recognition. <ref name= "Yang 2015"/> <br />
<br />
Because of the difficulty of stabilizing and crystallizing Class B TMDs, very little is known about the conformational changes that transduce cell signals endogenously. It is known that GCGR can regulate additional signal pathways including G-proteins of the Gαi family through the adoption of differing receptor conformations. Research is ongoing. <ref name= "Xu 2009"/><br />
<br />
GCGR generates downstream signals predominantly through the increase of intracellular cAMP, however there are other pathways being uncovered that are the result of GCGR adopting multiple, active conformations. Researchers are currently investigating how receptor activity-modifying proteins (RAMPs) interact with the ligand and GCGR in which the signaling bias of the receptor is altered. <ref>DOI 10.1074/jbc.M114.624601</ref><br />
<br />
GPCR activity is regularly quantified by ligand binding affinity, potency, efficacy, and kinetics. These measurement are used to measure drug ligand interactions in vivo. Recently, GPCRs have been crystallized and catalogued, which tend to include a need to stabilize the receptor, emphasizing the instability of the G coupled protein receptor. Zhang et. al. imply the importance of receptor folding in the cell membrane, in the human class B GPCR the 7TM portion, for receptor stability and function. <ref>DOI 10.1016/j.tibs.2014.12.005</ref><br />
<br />
==The Signal Peptide: Glucagon==<br />
<br />
Glucagon, a signaling ligand in the metabolic pathway, has three main biological functions. <br />
<br />
Glucagon is a regulator of the production of cholesterol, which is an energetically intensive process. When energy resources are low, downregulation of cholesterol production begins with glucagon binding to GCGR, which stimulates the phosphorylation of HMG-CoA. Once HMG-CoA has been phosphorylated, it is inactivated and cholesterol production is moderated to conserve energy. <br />
<br />
Glucagon also takes part in fatty acid mobilization by affecting levels of adipose tissue in the organism. Activation of GCGR by glucagon initiates triacylglycerol breakdown and the phosphorylation of perilipin and lipases via cAMP signal pathways. This allows the body to export fatty acids to the liver and other crucial tissues for energy use and makes more glucose available for use in brain functioning. <br />
<br />
Glucagon's main role is the regulation of blood glucose levels. Glucagon lowers the concentration of fructose 2,6-bisphosphate which is an allosteric inhibitor of the gluconeogenic enzyme fructose 1,6-bisphosphotase and activates phosphofructose kinase 1, which increases glucose levels via glycolysis.<br />
<br />
<ref name = 'Lehninger'>'Lehninger A., Nelson D.N, & Cox M.M. (2008) Lehninger Principles of Biochemistry. W. H. Freeman, fifth edition.' </ref><br />
<br />
Essential, conserved residues of glucagon, as discovered through mutagenesis and photo cross-linking studies have been labeled and colored in red. <ref name= "Siu 2013"/> <scene name='72/727091/Glucagon_important_residues/2'>Important stability/active sites</scene><br />
<br />
Through mutagenesis and photo-crosslinking studies, several residues deep within the central cavity of the GCGR 7TMD were discovered neighboring Glu362, which is approximately 19 angstroms from the base of the EC stalk and the location of Tyr138. (Fig. 8) <br />
[[Image:Movie Frame 8.png |150 px|left|thumb|Fig.8: Relationship between Tyr138 and Glu362 - residues found to have direct relationship to glucagon binding affinity.]]<br />
<br />
Four essential residues exist deep within the central cavity which all play strong roles in ligand binding affinity. (Fig. 9)<br />
<br />
A narrow entry gives way to a large, anchoring site for residues 1-4 of glucagon. (Fig. 10)<br />
<br />
Essential to glucagon's binding, a long, N-terminal tail winds to a clump of 4 residues, culminating in bulge that fits into the central, anchoring site of the 7TMD. (Fig. 11)<br />
[[Image:Glucagon with Q3 and N-terminus.png |200 px|right|thumb|Fig. 11: Surface visualization of glucagon demonstrating three dimensional fit of N-terminal tail into binding site of GCGR central cavity active site]]<br />
<br />
==Clinical relevance==<br />
Class B secretin-like receptors have gained relevance in therapeutics and drug targets. Maintaining information about the class B GPCRs conformational flexibility, allows for a better understanding of the receptor-ligand binding and its pharmaceutical relevance. The 7TM structure offers a direct connect between the extracellular and intracellular region, which offers a mechanism for signal transduction within the cell. GPCRs regulate cellular processes as required by the organs in which they are located. GPCR’s are used in the functioning of neuron synapses, ion transport regulation, homeostasis, cell division, and cell morphology. Mutations in the GPCR have been linked with retinitis pigmentosa, female infertility, nephrogenic diabetes insipidus, and familial exudative vitreoretinopathy. <ref name= "Salon 2011">DOI 10.1124/pr.110.003350</ref><br />
<br />
===Future research direction=== <br />
Research for Class A GPCRs is much more extensive than for its secretin, class B counterparts, although class B is proving to be a worthwhile to invest researching. The challenge of class B stabilization, expression, and molecular size , has made class B GPCRs particularly hard to assay. Biochemical research has increased in the class B specifications, because it has been realized that receptors can be modulated by more than the agonist and antagonists present in vivo. Leading research consists of a complex interwoven scheme of equilibria manipulation in multi-receptor conformations. <ref name="Salon 2011"/><br />
<br />
===Current drug targets===<br />
A variety of small molecule modulators have been developed over the past several years providing the promise of enhanced pharmaceutical regulation of GCGR. <ref name= "Yang 2015"/>(Fig's. 12 and 13)<br />
<br />
[[Image:Small molecule modulators Page 1.jpg|150 px|left|thumb|Fig. 12: Small molecule regulators of GCGR, part 1<ref name= "Yang 2015"/>.]]<br />
[[Image:Small molecule modulators Page 2.jpg|150 px|right|thumb|Fig. 13: Small molecule regulators of GCGR, part 2<ref name= "Yang 2015"/>.]]<br />
<br />
===Possible structural considerations for large molecule agonists/antagonists===<br />
Utilizing the visualizations of the GCGR 7TMD and glucagon peptide ligand, dimensional/structural analyses can be performed to develop models for novel molecules of increasing specificity for GCGR binding/regulation. Performing a dimensional analysis between the binding pocket and the base of the EC stalk, a large pseudopeptide molecule of 17-24 angstroms in size could be utilized to mimic the characteristics of GCGR's natural ligand, glucagon. (Fig's. 14 and 15)<br />
<br />
[[Image:Movie_Frame_7.png|175 px|left|thumb|Fig. 14: Distance measurement of GCGR 7TMD Y138-D362 of 19-20 angstroms and labeled with complimentary glucagon interaction residues.]]<br />
[[Image:H1___Y10_with_measurement.png|175 px|right|thumb|Fig. 15: Distance measurement of H1-Y10 of 22-24 angstroms and labeled with complimentary GCGR 7TMD residue interactions.]]<br />
<br />
==See Also==<br />
*[[]]<br />
__TOC__<br />
</StructureSection><br />
<br />
<br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587414Sandbox Reserved 11812016-04-15T18:52:18Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
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<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
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<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene><br />
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<scene name='72/721552/Glucagon_binding/2'>Glucagon Binding Zoomed Out</scene><br />
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<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene><br />
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<scene name='72/721552/Glucagon_binding_zoomed_in/1'>Glucagon Binding Zoomed in</scene></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587406Sandbox Reserved 11812016-04-15T18:32:30Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
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<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
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<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene><br />
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<scene name='72/721552/Glucagon_binding/2'>Glucagon Binding Zoomed Out</scene><br />
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<scene name='72/721552/Glucagon_binding/3'>Glucagon Binding Full Rendering</scene></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587405Sandbox Reserved 11812016-04-15T18:29:21Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
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<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
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<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene><br />
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<scene name='72/721552/Glucagon_binding/2'>Glucagon Binding Zoomed Out</scene></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587403Sandbox Reserved 11812016-04-15T18:26:42Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
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<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene><br />
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<scene name='72/721552/Glucagon_binding/1'>Glucagon Binding Zoomed Out</scene></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587395Sandbox Reserved 11812016-04-15T18:02:36Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/><br />
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<scene name='72/721552/Ligand_binding_interactions/1'>Ligand Binding Interactions and Crucial Disulfide Bond</scene></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587374Sandbox Reserved 11812016-04-15T17:22:31Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='7TM structure of human class B GPCR 4L6R' scene='72/727091/Full_structure_with_labels/1'/></div>Allie Patonhttps://proteopedia.org/index.php?title=Sandbox_Reserved_1181&diff=2587370Sandbox Reserved 11812016-04-15T17:16:27Z<p>Allie Paton: </p>
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<div><Structure load='4L6R' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /></div>Allie Patonhttps://proteopedia.org/index.php?title=Phosphoglycerate_Mutase&diff=2585168Phosphoglycerate Mutase2016-03-31T04:29:05Z<p>Allie Paton: </p>
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<div>{{STRUCTURE_1eqj| PDB=1eqj | SIZE=350| SCENE= |right|CAPTION=Phosphoglycerate mutase complex with phosphoglyceric acid and Mn+2 ion (purple) [[1eqj]] }}<br />
<br />
== Background ==<br />
[[Glycolysis]] is a 10-step process that invests energy in the initial stages only to recover greater amounts of energy in the final steps. Every step in this metabolic pathway is essential to the ultimate production of energy. Every step is catalyzed by one or more enzymes that enhance the rate of the given reaction. '''Phosphoglycerate mutase''' (PGM) is the specific homotetramer enzyme that catalyzes step 8 of glycolysis transfering the phosphate from 3-phosphoglyceric acid (3PG) to the second carbon to form 2-phosphoglyceric acid (2PG), having the Protein Data Bank ID [[1qhf]]<ref>PMID:10531478</ref>. PGM is found in organisms from yeast to humans because it plays a significant role in glycolysis, which is a highly conserved process across many taxa. A deficiency of this enzyme causes CNS symptoms, muscle weakness, cramps and fatigue with exercise. '''2,3-bisphosphoglycerate-independent phosphoglycerate mutase''' (BIPGM) is found in archaea and eubacteria. It catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate<ref>http://disability.ucdavis.edu/disease_deatails.php?id=45</ref>. See [[Glycolysis Enzymes]].<br />
<br />
== Structure ==<br />
In terms of the <scene name='Christopher_Vachon_Sandbox/Secondary_structures/1'>secondary structure</scene>, this protein is classified as an alpha/beta protein. Further, the fold is classified as “phosphoglycerate mutase-like”, having 3 main layers of alpha/beta/alpha. PGM contains a mixed beta sheet of 6 strands, with strand 5 existing as an anti-parallel strand to the rest. The quaternary structure usually is comprised of two identical subunits, thus this enzyme can be classified as a homodimer. The dimers have a relative molecular mass of 56,000-60,000 kDa. <ref name="winn">S., Winn I., Fothergill A. L., Harkins N. R., and Watson C. H. "Structure and Activity of Phosphoglycerate Mutase." Sciences 293.1063 (1981): 121-30. Print.</ref><br />
One exception includes the PGM enzyme of yeast which is a <scene name='Christopher_Vachon_Sandbox/Tetrameric/1'>homotetramer</scene> of mass 110,000 kDa. <ref name="winn" /> Though the quaternary structure is the same in terms of the active site, several variations exist, called isozymes, which depend on the tissue in which the enzyme is active. Mm-type, mb-type, and bb-type are isozymes that catalyze glycolysis in smooth muscle, cardiac and skeletal muscle, and the remaining tissues, respectively.<ref>"Phosphoglycerate mutase -." Wikipedia, the free encyclopedia. Web. 27 Feb. 2010. <http://en.wikipedia.org/wiki/Phosphoglycerate_mutase>.</ref> <br />
<br />
== Reaction and Mechanism ==<br />
PGM is an integral step in the process of glycolysis. Since this enzyme is a mutase, it will catalyze the transfer of a functional group from one position to another on a given substrate makin this an isomerization reaction. It is responsible for the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG), having 2,3-bisphosphoglycerate as an intermediate. <ref name="voet">Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. Print.</ref> With a Gibbs free energy of about 1.1 KJ/mol, this reaction is nearly energetically neutral. Despite this, it is absolutely necessary in order to generate the proper molecule needed to continue in the glycolytic pathway. The reaction that PGM catalyzes is shown below:<br />
<br />
3PG + P-Enzyme → 2,3BPG + Enzyme → 2PG + P-Enzyme<br /><br />
3-phosphoglycerate -> intermediate -> 2-phosphoglycerate<br />
<br />
[[Image:120px-Glycerate_3-phosphate_svg.png]] <br />
[[Image:94px-2,3-Bisphosphoglycerate_svg.png]] <br />
[[Image:120px-2-phospho-D-glycerate_wpmp.png]] <br />
<br />
It is important to note that the phosphate group that is placed on C2 is not the same phosphate group that was initially on C3. <br />
In order to understand how PGM catalyzes this reaction, an explanation of its active site is imperative. The most important residues in this enzyme include <scene name='Christopher_Vachon_Sandbox/His_8_good/2'>His 8 and 179</scene> with imidazole groups which are in close proximity to carbons 2 and 3 in the substrate. His-8 is phosphorylated during during catalysis, and it is likely that His-179 acts as the proton donor/acceptor <ref>Rose, Z.B. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, <scene name='Phosphoglycerate_Mutase/First_try/1'>TextToBeDisplayed</scene>211-253</ref>. Based on crystallography experiments, the active site where these histidine residues reside lies at the bottom of a deep groove in each subunit. <ref name="winn" /> The sites in each subunit, whether the enzyme is a homodimer or homotetramer, are well separated. The active enzyme contains a phosphoryl group attached to His 8. This phosphoryl group is what is transferred to C2 of the substrate, resulting in an intermediate 2,3-bisphosphoglycerate-enzyme complex. Thus there is a <scene name='Christopher_Vachon_Sandbox/Good_active_site_scene/6'>covalently attached phosphate</scene> in the active monomer. <ref name="voet" /> The phosphate group on C3 of the substrate is then transferred back onto His 8, thus regenerating the active form of the enzyme. <br />
<br />
In addition to the importance of the two histidine residues in the active site, the amino acids that line the <scene name='Christopher_Vachon_Sandbox/Good_active_site_scene/5'>active site</scene> are also functionally important. These residues include H179, H8, E15, S11, T20, R59, and E86.<ref name="voet" /> Several positively charged residues line the active site pocket. These residues usually tend to be <scene name='Christopher_Vachon_Sandbox/Arginine_residues/1'>arginine residues</scene>, which are important for the optimal activity of the enzyme. <ref name="winn" /> This structure is logical for its function because the enzyme binds a negatively charged substrate, thus a positively charged groove fosters tight binding with a negative substrate. The third and final important aspect of the active site is the presence of <scene name='Christopher_Vachon_Sandbox/Glutamate_residues_2/1'>glutamate residues 15 and 86</scene>.<ref name="winn" /> It is suggested that the carboxyl groups of these amino acid residues act as proton-withdrawing groups as they flank both sides of the substrate. <br />
<br />
== Kinetics ==<br />
According to kinetics studies, both cofactor independent and dependent phophoglycerate mutases were found to follow Michaelis-Menten kinetics. Km values were found to be from about 100-200 μM. Other studies reveal how salt concentration and pH influence the kinetics of phosphoglycerate mutase. At low ionic concentrations Km values were around 1 μM, but increased to about 40 μM with the addition of 400 mM KCl. The presence of negatively charged ions in solution could possibly compete with the negatively charged substrate, thus increasing the Km. Additionally, the pH optimum for the enzyme from all species has been found to be 5.9. <ref name="winn" /> <br />
<br />
== Regulation ==<br />
In terms of regulation, competitive inhibitors resemble the negatively charged substrate and bind to the active site. Such inhibitors include inositol hexakisphosphate and benzene hexacarboxylate. <ref>Rigden, D. J.; Walter, R. A.; Phillips, S. E. V.; Fothergill-Gilmore, L. A.Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis J. Mol. Biol. 1999, 289, 691– 699</ref> Additionally, the phosphomethyl analogue of 3-phosphoglycerate (2-hydroxy-4-phosphonobutanoate) is a potent inhibitor of phosphoglycerate mutase. <ref>McAleese, S.M., Fothergill-Gilmore, L.A.&Dixon, H.B.F. (1985) Biochem. J. 230, 535-542 </ref> These along with many other polyanions, including EDTA, have been reported to act as competitive inhibitors of phosphoglycerate mutase due to their anionic resemblance. As mentioned before, phosphoglycerate mutase has a rather small positive Gibbs free energy. Thus, this reaction proceeds easily in both directions. Overall, this reaction is not the site of major regulation because it is a reversible reaction. <br />
<br />
== Phosphoglycerate Mutase Deficiency ==<br />
When phosphoglycerate mutase has a genetic defect, it results in a muscle disease that interferes with the processing of carbohydrates. The onset can occur anywhere from childhood to adulthood. The inheritance pattern is autosomal recessive. <ref>http://www.mda.org/disease/pgam.html</ref> Phosphoglycerate mutase deficicncy patients may experience CNS symptoms such as mental retardation and seizures. Certain individuals may experience a purely myopathic syndrome with progressive proximal muscle weakness and incidents of myoglobinuria, exercise intolerance, may become easy fatigued with cramps and urine discoloration. Diagnosing this deficiency can be done with Laboratory tests that demonstrate and increased serum CK level. Or there are diagnostic tests available that test for the absence of the enzyme. Also, muscle pathology of this deficiency shows subsarcolemmal glycogen ± tubular combinations. <ref>http://disability.ucdavis.edu/disease_deatails.php?id=45</ref><br />
<br />
==3D structures of phosphoglycerate mutase==<br />
<br />
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}<br />
{{#tree:id=OrganizedByTopic|openlevels=0|<br />
<br />
*Phosphoglycerate mutase<br />
<br />
**[[3o0t]], [[3mxo]] – hPGM5 residues 90-289 – human<br /><br />
**[[1yfk]], [[1yjx]], [[4gpi]], [[4gpz]] – hPGM1<br /><br />
**[[3ezn]] – BpPGM – ''Burkholderia pseudomallei''<br /><br />
**[[3d8h]] – PGM – ''Cryptosporidium parvum''<br /><br />
**[[1v7q]], [[1v37]] – PGM – ''Thermus thermophilus''<br /><br />
**[[1xq9]] - PfPGM – ''Plasmodium falciparum''<br /><br />
**[[3kkk]] - PfPGM (mutant) <br /><br />
**[[1rii]] – PGM – ''Mycobacteriumtuberculosis''<br /><br />
**[[1e58]] – EcPGM – ''Escherichia coli''<br /><br />
**[[1fzt]] – PGM – Fission yeast – NMR<br /><br />
**[[5pgm]], [[4pgm]], [[3pgm]] – yPGM – yeast<br /><br />
<br />
*Phosphoglycerate mutase binary complexes<br />
<br />
**[[3lnt]] – BpPGM + malonic acid <br /><br />
**[[3gw8]] – BpPGM + glycerol + VO4<BR /><br />
**[[3gp5]] - BpPGM + PGA + VO4<BR /><br />
**[[3fdz]] - BpPGM + PGA + di-PGA<br /><br />
**[[3gp3]] – BpPGM + phosphoserine<br /><br />
**[[1eqj]], [[1ejj]] – BsPGM + PGA – ''Bacillus stearothermophilus''<br /><br />
**[[1e59]] – EcPGM + VO4<BR /> <br />
**[[1qhf]] – yPGM + PGA <br /><br />
**[[1bq3]] – yPGM + inositol hexakisphosphate<br /><br />
**[[1bq4]] – yPGM + benzene hexacarboxylate<br />
<br />
*2,3-bisphosphoglycerate-independent phosphoglycerate mutase<br />
<br />
**[[1t8p]], [[3nfy]] – hPGM <br /> <br />
**[[4emb]] – PGM – ''Borrelia burgdorferi''<br /><br />
**[[4eo9]] – PGM – ''Mycobacterium leprae''<br /><br />
**[[4my4]] – SaPGM – ''Staphylococcus aureus''<br /><br />
**[[4nwj]] – SaPGM + 3PG<br /><br />
**[[4nwx]], [[4qax]] – SaPGM + 2PG<br /><br />
**[[2a9j]], [[2h4x]], [[2h52]] – hPGM + 3PG<br /><br />
**[[2f90]] - hPGM + 3PG + AlF4<br /><br />
**[[2h4z]], [[2hhj]] – hPGM + 2,3-BGP<br /><br />
**[[1ejj]] - GsPGM + 3PG – ''Geobacillus stearothermophilus''<br /><br />
**[[1eqj]] - GsPGM + 2PG<br /><br />
**[[3idd]], [[3kd8]] – TaBIPGM – ''Thermoplasma acidophilum''<br /><br />
**[[3nvl]] – BIPGM - ''Trypanosoma brucei''<br /><br />
**[[2ify]] – BIPGM – ''Bacillus anthracis''<br /><br />
**[[2zkt]] – BIPGM – ''Pyrococcus horikoshii''<br /><br />
**[[3igy]], [[3igz]] – BIPGM + Co + PGA – ''Leishmania mexicana''<br /><br />
**[[1o98]] – BsBIPGM + PGA<br /><br />
**[[1o99]] - BsBIPGM (mutant) + PGA<br />
}}<br />
==Additional Resources==<br />
For additional information, please see: [[Carbohydrate Metabolism]]<br />
<br /><br />
<br />
==References==<br />
<references/><br />
<br />
[[Category:Topic Page]]</div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2583020User:Allie Paton/Sandbox 11812016-03-18T18:51:50Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene='72/727084/Scene_1/2'><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
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<br />
<scene name='72/727084/Scene_1/2'>Nucleotide 200-205</scene><br />
<scene name='72/727084/Temp_map/1'>Temp Map</scene><br />
<br />
== Function of Glucagon Receptor ==<br />
<br />
<br />
== Disease ==<br />
=== Diabetes Mellitus ===<br />
=== Biological Function of Glucagon ===<br />
<br />
== Biochemical Significance ==<br />
=== Kinetics ===<br />
=== Ligand Binding ===<br />
=== Sequence Conservation and Homology ===<br />
=== Conformational Change ===<br />
<br />
== Structural highlights ==<br />
=== Crucial Structural Interactions ===<br />
=== Peptide Sequence ===<br />
=== Active Binding Sites ===<br />
<br />
<br />
== Relevance ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
==== Structural Similarities ====<br />
==== Sequential Similarities ====<br />
=== Current Drug Targets ===<br />
<br />
== Future Direction ==<br />
=== Drug Development ===<br />
=== Possible Structures for Agonists ===<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2583013User:Allie Paton/Sandbox 11812016-03-18T17:56:00Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene='72/727084/Scene_1/2'><br />
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<br />
<scene name='72/727084/Scene_1/2'>Nucleotide 200-205</scene><br />
<scene name='72/727084/Temp_map/1'>Temp Map</scene><br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
=== Diabetes Mellitus ===<br />
<br />
== Biochemical Significance ==<br />
=== Kinetics ===<br />
=== Ligand Binding ===<br />
=== Sequence Conservation and Homology ===<br />
<br />
== Structural highlights ==<br />
=== Crucial Structural Interactions ===<br />
<br />
== Relevance ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Future Direction ==<br />
=== Drug Development ===<br />
<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580194User:Allie Paton/Sandbox 11812016-03-04T19:29:40Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene='72/727084/Scene_1/2'><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
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<br />
<scene name='72/727084/Scene_1/2'>Nucleotide 200-205</scene><br />
<scene name='72/727084/Temp_map/1'>Temp Map</scene><br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580192User:Allie Paton/Sandbox 11812016-03-04T19:24:20Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene='72/727084/Scene_1/2'><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='72/727084/Scene_1/2'>TextToBeDisplayed</scene><br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580190User:Allie Paton/Sandbox 11812016-03-04T19:17:55Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene='(Scene 1)'><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580167User:Allie Paton/Sandbox 11812016-03-04T18:53:21Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='4L6R' size='340' side='right' caption='7TM Helical Structure of 4L6R GPCR' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580162User:Allie Paton/Sandbox 11812016-03-04T18:47:16Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png |100 px|left|thumb|Figure Legend]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580157User:Allie Paton/Sandbox 11812016-03-04T18:45:21Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
[[Image:Class B.png]]<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580156User:Allie Paton/Sandbox 11812016-03-04T18:44:18Z<p>Allie Paton: </p>
<hr />
<div>==Structure of Class B Human Glucagon G-Protein Coupled Receptors==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
=== Class B in Comparison to Class A ===<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
=== Future Direction ===<br />
<br />
== Structural highlights ==<br />
=== Ligand Binding Site ===<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580148User:Allie Paton/Sandbox 11812016-03-04T18:40:54Z<p>Allie Paton: </p>
<hr />
<div>[[Image:Example.jpg]]==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=File:Class_B.png&diff=2580142File:Class B.png2016-03-04T18:38:08Z<p>Allie Paton: </p>
<hr />
<div></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1181&diff=2580126User:Allie Paton/Sandbox 11812016-03-04T18:28:03Z<p>Allie Paton: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...</p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1181'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton&diff=2580125User:Allie Paton2016-03-04T18:27:43Z<p>Allie Paton: </p>
<hr />
<div>[[User:Allie Paton/Sandbox 1181]]<br />
<br />
* Full Real Name:<br />
Alexandra Paton<br />
* Position:<br />
Undergraduate Student<br />
* Institution (NO ABBREVIATIONS):<br />
Butler University<br />
* City, State/Province, Country:<br />
Indianapolis, IN, USA<br />
* Field of Expertise or Study:<br />
CH 462/Spring 2016</div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton/Sandbox_1&diff=2580124User:Allie Paton/Sandbox 12016-03-04T18:26:08Z<p>Allie Paton: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...</p>
<hr />
<div>==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page '''Allie Paton/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Allie Patonhttps://proteopedia.org/index.php?title=User:Allie_Paton&diff=2580123User:Allie Paton2016-03-04T18:24:17Z<p>Allie Paton: </p>
<hr />
<div>[[User:Allie Paton/Sandbox 1]]<br />
<br />
* Full Real Name:<br />
Alexandra Paton<br />
* Position:<br />
Undergraduate Student<br />
* Institution (NO ABBREVIATIONS):<br />
Butler University<br />
* City, State/Province, Country:<br />
Indianapolis, IN, USA<br />
* Field of Expertise or Study:<br />
CH 462/Spring 2016</div>Allie Paton