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		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587840</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587840"/>
		<updated>2016-04-19T08:14:15Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] to the extracellular side of GCGR leads to the activation of the receptor. On the intracellular side, upon this activation, a guanine diphosphate (GDP) is exchanged for a guanine triphosphate (GTP) - which, in turn, activates adenylate cyclase. Converting adenosine triphosphate (ATP) into cyclic adenosine monophosphate (cAMP), adenylate cyclase initiates protein kinase A (PKA) activity, which releases glucose into the blood stream. Overall, activation of the GCGR elevates blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;)&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref name=&#039;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref name=&#039;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587838</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587838"/>
		<updated>2016-04-19T07:58:42Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;)&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref name=&#039;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref name=&#039;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587837</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587837"/>
		<updated>2016-04-19T07:57:17Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;)&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref name=&amp;quot;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref name=&amp;quot;other_article&#039;&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587836</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587836"/>
		<updated>2016-04-19T07:52:52Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;)&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref&amp;gt;PMID:22908259 &amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587835</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587835"/>
		<updated>2016-04-19T07:51:56Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref&amp;gt;PMID:22908259 &amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor&amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587834</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587834"/>
		<updated>2016-04-19T07:50:59Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref name=&#039;therapeutic_article&#039;&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref&amp;gt;PMID:22908259 &amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor &#039;&#039;&#039;citation needed&#039;&#039;&#039;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587833</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587833"/>
		<updated>2016-04-19T07:49:10Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref&amp;gt;PMID:22908259 &amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
As GCGR holds great promise as a therapeutic target, there are currently three drugs under development that are designed to treat Type 2 Diabetes by targeting the human glucagon receptor &#039;&#039;&#039;citation needed&#039;&#039;&#039;. Although they are still in phase I of their clinical trials, preliminary research has shown promising results&amp;lt;ref&amp;gt;DOI 10.2174/1573399810666141224121927&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587831</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587831"/>
		<updated>2016-04-19T07:32:03Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &amp;lt;ref&amp;gt;PMID:22908259 &amp;lt;/ref&amp;gt;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587830</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587830"/>
		<updated>2016-04-19T07:30:30Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &amp;lt;ref&amp;gt;DOI 10.1016/j.tips.2013.11.001&amp;lt;/ref&amp;gt;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587829</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587829"/>
		<updated>2016-04-19T07:27:02Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587828</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587828"/>
		<updated>2016-04-19T07:25:42Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref name =&#039;conformation_article&#039;&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587827</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587827"/>
		<updated>2016-04-19T07:23:58Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &amp;lt;ref&amp;gt;PMID:26227798 &amp;lt;/ref&amp;gt;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587826</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587826"/>
		<updated>2016-04-19T07:18:05Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &amp;lt;ref&amp;gt;DOI 10.1039/C6CP00798H&amp;lt;/ref&amp;gt; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587825</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587825"/>
		<updated>2016-04-19T07:14:27Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:ECD_bound_to_glucagon.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587824</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587824"/>
		<updated>2016-04-19T07:13:40Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 2. Bound Molecule of Glucagon.&#039;&#039;&#039; A molecule of glucagon is shown bound to the GCGR&#039;s ECD (shown in magenta)]]Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:ECD_bound_to_glucagon.png&amp;diff=2587823</id>
		<title>File:ECD bound to glucagon.png</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:ECD_bound_to_glucagon.png&amp;diff=2587823"/>
		<updated>2016-04-19T07:10:52Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587819</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587819"/>
		<updated>2016-04-19T07:03:46Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587818</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587818"/>
		<updated>2016-04-19T07:01:56Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the receptor, meaning glucagon binds much closer to the cell membrane. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587815</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587815"/>
		<updated>2016-04-19T07:00:33Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt; of all other classes of GPCRs. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587813</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587813"/>
		<updated>2016-04-19T06:59:24Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;&#039;&#039;Figure 1. GCGR Binding Pocket.&#039;&#039;&#039; A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587812</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587812"/>
		<updated>2016-04-19T06:58:30Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png|200 px|left|thumb|&#039;Figure 1. GCGR Binding Pocket. A cross-section of the GCGR binding pocket shows its width and depth]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587811</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587811"/>
		<updated>2016-04-19T06:55:56Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
[[Image:Labeled_Binding_Pocket.png]]The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Labeled_Binding_Pocket.png&amp;diff=2587809</id>
		<title>File:Labeled Binding Pocket.png</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Labeled_Binding_Pocket.png&amp;diff=2587809"/>
		<updated>2016-04-19T06:53:57Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587798</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587798"/>
		<updated>2016-04-19T06:27:15Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (&amp;lt;scene name=&#039;72/721538/Ecls/1&#039;&amp;gt;ECL1, ECL2, and ECL3&amp;lt;/scene&amp;gt;) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Among experimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587792</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587792"/>
		<updated>2016-04-19T06:11:09Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of &amp;lt;scene name=&#039;72/721538/Helix_v_and_vi/1&#039;&amp;gt;helicies V and VI&amp;lt;/scene&amp;gt; (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587790</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587790"/>
		<updated>2016-04-19T06:04:48Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas produces glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
Like all classes of glucagon receptors, which include class A ([https://en.wikipedia.org/wiki/Rhodopsin-like_receptors rhodopsin-like]), B (secretin-like), and [https://en.wikipedia.org/wiki/Class_C_GPCR C] ([https://en.wikipedia.org/wiki/Metabotropic_glutamate_receptor metabotropic glutamate]), GCGR has a 7tm domain. While class B receptors do share characteristics with class C receptors, they are more similar to class A receptors. Class B receptors and class A receptors share less than 15% sequence [https://en.wikipedia.org/wiki/Homology_(biology) homology]; however, they do share similar [https://en.wikipedia.org/wiki/Signal_transduction signal transduction] mechanisms as well as the 7tm domain. The orientations and positions of the 7tm helices are also conserved between both classes of glucagon receptors. &lt;br /&gt;
&lt;br /&gt;
However, one particular difference between class A receptors and class B receptors is an inward shift of the intracellular component of Helix VII. In class A receptors this inward shift is instrumental in receptor activation, yet in class B receptors it remains unclear what role this shift plays. &lt;br /&gt;
  &lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors.&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of helicies V and VI (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/2&#039;&amp;gt;Glu245-Thr351&amp;lt;/scene&amp;gt;) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587787</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587787"/>
		<updated>2016-04-19T05:59:23Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of helicies V and VI (breaking hydrogen bonds between &amp;lt;scene name=&#039;72/721538/Arg173-ser350_h_bond/1&#039;&amp;gt;Arg173-Ser350&amp;lt;/scene&amp;gt; and Glu245-Thr351) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587786</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587786"/>
		<updated>2016-04-19T05:44:24Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest &amp;lt;scene name=&#039;72/721538/Binding_pocket/1&#039;&amp;gt;binding pocket&amp;lt;/scene&amp;gt;. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of helicies V and VI (breaking hydrogen bonds between Arg173-Ser305 and Glu245-Thr351) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587782</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587782"/>
		<updated>2016-04-19T05:12:15Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of helicies V and VI (breaking hydrogen bonds between Arg173-Ser305 and Glu245-Thr351) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587781</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2587781"/>
		<updated>2016-04-19T05:09:58Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (ECD).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges are a distinct feature of class B receptors only because their interaction results in the distinct stalk found only in class B receptors&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.  &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface &amp;lt;scene name=&#039;72/721537/Helical_interactions_vi-v-iii/2&#039;&amp;gt;stabilization&amp;lt;/scene&amp;gt; between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends three α-helical turns above the plane of the membrane. It is proposed that the stalk helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation] differentiating between the receptor&#039;s active and inactive states. The active, or open conformation, is characterized by an intracellular outward movement of helicies V and VI (breaking hydrogen bonds between Arg173-Ser305 and Glu245-Thr351) &#039;&#039;citation needed&#039;&#039; and an extracellular rotation of the ECD until it is almost perpendicular to the membrane surface &#039;&#039;citation needed&#039;&#039;. While the stalk region of Helix I helps to facilitate the motion of the ECD, intracellular G-protein coupling and extracellular glucagon binding stabilized this active state. In the abscence of glucagon, however, the GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD &#039;&#039;citation needed&#039;&#039;. In this closed state, the ECD covers the extracellular surface of the 7tm.  To transition between states, the ECD rotates and moves down towards the 7tm domain. This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein &#039;&#039;citation needed&#039;&#039;.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, GCGRis a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Amongstexperimental treatments, two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. While the entire cleft of the ECD is blocked by mAb1, mAb3 blocks glucagon binding by stabilizing a conformation of the ECD that promotes receptor inactivation &#039;&#039;citation needed&#039;&#039;. Another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. Disrupting the normal interactions between the ECD and the 7tm domains, these antibodies inhibit the receptor&#039;s function and help to lower blood glucose level.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586766</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586766"/>
		<updated>2016-04-12T13:35:25Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586764</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586764"/>
		<updated>2016-04-12T13:34:33Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;structure_article&amp;quot; /&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586762</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586762"/>
		<updated>2016-04-12T13:33:33Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name =&#039;structure_article&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586758</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586758"/>
		<updated>2016-04-12T13:32:16Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586754</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586754"/>
		<updated>2016-04-12T13:29:26Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name=&#039;structure&#039;&amp;gt;PMID:23863937/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;1&amp;quot;/&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;1&amp;quot;/&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586749</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586749"/>
		<updated>2016-04-12T13:28:17Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref name=&#039;1&#039;&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref name=&amp;quot;1&amp;quot;/&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref name=&amp;quot;1&amp;quot;/&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:7tm.pdb&amp;diff=2586658</id>
		<title>File:7tm.pdb</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:7tm.pdb&amp;diff=2586658"/>
		<updated>2016-04-12T12:33:49Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586636</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2586636"/>
		<updated>2016-04-12T12:20:56Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/2&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The &#039;&#039;&#039;human glucagon receptor&#039;&#039;&#039; (&#039;&#039;&#039;GCGR&#039;&#039;&#039;) is one of 15 secretin-like, or Class B, [https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor G-protein coupled receptors] (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of [https://en.wikipedia.org/wiki/Alpha_helix alpha helices] that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel [https://en.wikipedia.org/wiki/Beta_sheet β-sheets] and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The glucagon receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates [https://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], through [https://en.wikipedia.org/wiki/Adenylyl_cyclase adenylate cyclase] that initiates [https://en.wikipedia.org/wiki/Protein_kinase_A protein kinase A] (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
In contrast to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 250 px|right|thumb|Glu 406 Salt Bridges]]. These salt bridges appear to be distinct feature of class B receptors only, however, because there is no conservation of these residues seen in class A receptors. &lt;br /&gt;
&lt;br /&gt;
A conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] can be found in 7tm region at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both class A and class B receptors. Additionally, the ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B-specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine Asn] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine Leu] 242 of Helix III. [[Image:Conserved Class B Residues.png | 250 px|left|thumb|Helical Interactions VI-V-III]]&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in class A receptors are turned toward the membrane&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between Helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for [https://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 Type 2 diabetes]. Specifically, molecules that antagonize the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupting glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. By disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Through binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2585006</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2585006"/>
		<updated>2016-03-30T04:26:59Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in Class A receptors are turned toward the membrane&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. Although researchers are not entirely sure of its function, this helix is completely conserved in Class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs&amp;lt;ref&amp;gt;PMID:23863937&amp;lt;/ref&amp;gt;. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of the GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupt glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. Disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2585003</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2585003"/>
		<updated>2016-03-30T04:22:19Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in Class A receptors are turned toward the membrane. Although researchers are not entirely sure of its function, this helix is completely conserved in Class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of the GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGR&#039;s role in glucose homeostasis, it is a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. Studies have shown that two antibodies, mAb1 and mAb23, target the ECD domain of the GCGR interrupt glucagon binding&amp;lt;ref&amp;gt;PMID:22908259&amp;lt;/ref&amp;gt;. Disrupting the normal interactions between the ECD and the 7tm domains, these antibiotics inhibit the receptor&#039;s function and help to lower blood glucose level. Additional research has shown that another antibody, mAb7, inhibits GCGR allosterically&amp;lt;ref&amp;gt;PMID:24189067&amp;lt;/ref&amp;gt;. Binding to a site outside of the binding pocket, mAb7 inhibits the receptor without interacting with essential glucagon binding residues. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584990</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584990"/>
		<updated>2016-03-30T03:50:28Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]&lt;br /&gt;
The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in Class A receptors are turned toward the membrane. Although researchers are not entirely sure of its function, this helix is completely conserved in Class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of the GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584987</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584987"/>
		<updated>2016-03-30T03:48:58Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in Class A receptors are turned toward the membrane. Although researchers are not entirely sure of its function, this helix is completely conserved in Class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of the GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584985</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584985"/>
		<updated>2016-03-30T03:46:52Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
The GCGR also contains an intracellular Helix VIII that is comprised of roughly 20 amino acids at the C-terminal end. This helix tilts approximately 25 degrees away from the membrane - the corresponding position in Class A receptors are turned toward the membrane. Although researchers are not entirely sure of its function, this helix is completely conserved in Class B structures. &lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the widest and longest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips of Helicies III and VII are some of the largest among the GPCRs. As a result, the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/bin/nihms495648f2.jpg binding cavity] of the GCGR is located deeper inside the molecule. &lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584978</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584978"/>
		<updated>2016-03-30T03:29:13Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:25674162&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584976</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584976"/>
		<updated>2016-03-30T03:21:46Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I Stalk Region ====&lt;br /&gt;
The tip of Helix I extends above the cell membrane into the extracellular space creating a &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt; stalk region&amp;lt;/scene&amp;gt;. This region is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584973</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584973"/>
		<updated>2016-03-30T03:17:31Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain has an α-β-β structure that consists of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to Class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. No conservation of these residues are seen in Class A receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a Class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I &amp;quot;Stalk&amp;quot; Region ====&lt;br /&gt;
The &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt;&amp;quot;Stalk&amp;quot; Region&amp;lt;/scene&amp;gt; of Helix I is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which stabilizes the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. To transition between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of GCGR, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCGR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584964</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584964"/>
		<updated>2016-03-30T03:07:40Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain  has a α-β-β structure consisting of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine and therefore this helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. &lt;br /&gt;
Since there is no conservation of these residues in class A receptors these salt bridges are likely an important feature of secretin-like class B receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I &amp;quot;Stalk&amp;quot; Region ====&lt;br /&gt;
The &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt;&amp;quot;Stalk&amp;quot; Region&amp;lt;/scene&amp;gt; of Helix I is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which serves to stabilize the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. Transitioning between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of the human glucagon receptor, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCPR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584962</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584962"/>
		<updated>2016-03-30T03:04:36Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The extracellular domain  has a α-β-β structure consisting of two antiparallel β-sheets and a N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine and therefore this helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. &lt;br /&gt;
Since there is no conservation of these residues in class A receptors these salt bridges are likely an important feature of secretin-like class B receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I &amp;quot;Stalk&amp;quot; Region ====&lt;br /&gt;
The &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt;&amp;quot;Stalk&amp;quot; Region&amp;lt;/scene&amp;gt; of Helix I is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which serves to stabilize the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. Transitioning between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of the human glucagon receptor, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCPR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of GCGRs role in glucose homeostasis, it is  a potential drug target for Type 2 diabetes. Specifically, molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584960</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584960"/>
		<updated>2016-03-30T03:00:26Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
&lt;br /&gt;
== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The Extracellular Domain  has a α-β-β structure which consists of two antiparallel β-sheets and an N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
== Function ==&lt;br /&gt;
&lt;br /&gt;
The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Structure ==&lt;br /&gt;
&lt;br /&gt;
=== Class B vs. Class A ===&lt;br /&gt;
&lt;br /&gt;
As opposed to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine and therefore this helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
&lt;br /&gt;
Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. &lt;br /&gt;
Since there is no conservation of these residues in class A receptors these salt bridges are likely an important feature of secretin-like class B receptors. &lt;br /&gt;
&lt;br /&gt;
The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As a part of the interface stabilization between helices VI, V, and III, a class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== GCGR-Specific Traits ===&lt;br /&gt;
&lt;br /&gt;
==== Helix I &amp;quot;Stalk&amp;quot; Region ====&lt;br /&gt;
The &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt;&amp;quot;Stalk&amp;quot; Region&amp;lt;/scene&amp;gt; of Helix I is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
&lt;br /&gt;
==== Intracellular Helix VIII ====&lt;br /&gt;
&lt;br /&gt;
==== Binding Pocket ====&lt;br /&gt;
&lt;br /&gt;
The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
&lt;br /&gt;
====Other Unique Structural Features ====&lt;br /&gt;
&lt;br /&gt;
An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which serves to stabilize the structure of GCGR. &lt;br /&gt;
&lt;br /&gt;
== Glucagon Binding == &lt;br /&gt;
&lt;br /&gt;
Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. Transitioning between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
&lt;br /&gt;
In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of the human glucagon receptor, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCPR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
&lt;br /&gt;
This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
&lt;br /&gt;
== Clinical Relevance ==&lt;br /&gt;
&lt;br /&gt;
Because of this, it is being looked as a potential drug target for Type 2 diabetes. Molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584959</id>
		<title>Sandbox Reserved 1167</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_1167&amp;diff=2584959"/>
		<updated>2016-03-30T02:59:52Z</updated>

		<summary type="html">&lt;p&gt;Alexis Coulis: &lt;/p&gt;
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&lt;div&gt;{{Sandbox_Reserved_CH462_Central_Metabolism}}&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
==Class B Human Glucagon G-Protein Coupled Receptor==&lt;br /&gt;
&amp;lt;StructureSection load=&#039;4l6r&#039; size=&#039;340&#039; side=&#039;right&#039; caption=&#039;Human Glucagon Class B GPCR ( 7tm PDB: [[4l6r]], ECD PDB: [[4ers]])&#039; scene=&#039;72/721538/Glucagon_receptor/1&#039;&amp;gt;&lt;br /&gt;
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This is a default text for your page &#039;&#039;&#039;&#039;&#039;&#039;. Click above on &#039;&#039;&#039;edit this page&#039;&#039;&#039; to modify. Be careful with the &amp;amp;lt; and &amp;amp;gt; signs.&lt;br /&gt;
You may include any references to papers as in: the use of JSmol in Proteopedia &amp;lt;ref&amp;gt;DOI 10.1002/ijch.201300024&amp;lt;/ref&amp;gt; or to the article describing Jmol &amp;lt;ref&amp;gt;PMID:21638687&amp;lt;/ref&amp;gt; to the rescue.&lt;br /&gt;
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== Background ==&lt;br /&gt;
[[Image:7tm_labeled_with_membrane.png|200 px|left|thumb|The 7tm spans the cell&#039;s membrane]]The human glucagon receptor (GCGR) is one of 15 secretin-like, or Class B, G-protein-coupled receptors (GPCRs). Like other GPCRs, it has a &amp;lt;scene name=&#039;72/721538/7tm_labeled_helicies/3&#039;&amp;gt;7 trans-membrane &amp;lt;/scene&amp;gt; helical domain (shown in blue) and a globular N-terminus &amp;lt;scene name=&#039;72/721538/Ecd/2&#039;&amp;gt;extracellular domain&amp;lt;/scene&amp;gt; (shown in magenta). As its name suggests, the 7tm is made up of alpha helices that pass through the membrane seven times. The Extracellular Domain  has a α-β-β structure which consists of two antiparallel β-sheets and an N-terminal α-helix&amp;lt;ref&amp;gt;PMID:26227798&amp;lt;/ref&amp;gt;. &lt;br /&gt;
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== Function ==&lt;br /&gt;
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The Glucagon Receptor plays an important role in glucose homeostasis. During times of fasting (or low blood sugar) the pancreas dispatches glucagon to activate the GCGR in the liver. The [http://www.nature.com/nature/journal/v499/n7459/fig_tab/nature12393_F5.html binding of glucagon] stimulates gluconeogenesis, through adenylate cyclase that initiates protein kinase A (PKA) activity&amp;lt;ref&amp;gt;PMID:PMC4321206&amp;lt;/ref&amp;gt;. This pathway synthesizes glucose, elevating blood sugar levels. &lt;br /&gt;
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== Structure ==&lt;br /&gt;
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=== Class B vs. Class A ===&lt;br /&gt;
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As opposed to class A glucagon receptors which have a [https://en.wikipedia.org/wiki/Proline proline] kink, in all  [https://en.wikipedia.org/wiki/Secretin_receptor_family secretin-like class B glucagon receptors] there is a [https://en.wikipedia.org/wiki/Glycine Glycine] at position 393 in Helix VII which allows for a &amp;lt;scene name=&#039;72/721537/Gly_393_helical_bend/1&#039;&amp;gt;helical bend&amp;lt;/scene&amp;gt;. This Glycine and therefore this helical bend is fully [https://en.wikipedia.org/wiki/Conserved_sequence conserved] in all secretin-like class B receptors and is an important part of the FQGxxVxxYCF [https://en.wikipedia.org/wiki/Sequence_motif motif].&lt;br /&gt;
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Another important structural component found in all secretin-like class B receptors are the two conserved [https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 salt bridges] found between [https://en.wikipedia.org/wiki/Arginine Arg] 346 and [https://en.wikipedia.org/wiki/Glutamic_acid Glu] 406 and Arg 173 and Glu 406 [[Image:Salt Bridge Interactions.png | 300 px|left|thumb|Glu 406 Salt Bridges]]. &lt;br /&gt;
Since there is no conservation of these residues in class A receptors these salt bridges are likely an important feature of secretin-like class B receptors. &lt;br /&gt;
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The 7tm region has a conserved [https://en.wikipedia.org/wiki/Disulfide disulfide bond] at &amp;lt;scene name=&#039;72/721538/7tm_disulfide_bond/2&#039;&amp;gt;Cys224-Cys294&amp;lt;/scene&amp;gt; which helps to stabilize the 7tm fold. This bond is conserved among both Class A and Class B receptors.The ECD region of Class B GCPRs is defined by three conserved disulfide bonds. These bonds occur at &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_1/4&#039;&amp;gt;Cys62-Cys104&amp;lt;/scene&amp;gt;, &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_2/1&#039;&amp;gt;Cys46-Cys71&amp;lt;/scene&amp;gt;, and &amp;lt;scene name=&#039;72/721538/Ecd_disulfide_bond_3/1&#039;&amp;gt;Cys85-Cys126&amp;lt;/scene&amp;gt;.&lt;br /&gt;
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As a part of the interface stabilization between helices VI, V, and III, a class B specific [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bond] occurs between [https://en.wikipedia.org/wiki/Asparagine N] 318 of Helix V and [https://en.wikipedia.org/wiki/Leucine L] 242 of Helix III. &lt;br /&gt;
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=== GCGR-Specific Traits ===&lt;br /&gt;
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==== Helix I &amp;quot;Stalk&amp;quot; Region ====&lt;br /&gt;
The &amp;lt;scene name=&#039;72/721538/Helix_i/14&#039;&amp;gt;&amp;quot;Stalk&amp;quot; Region&amp;lt;/scene&amp;gt; of Helix I is longer than any other class of GPCR and extends 3 α-helical turns above the plane of the membrane. It helps to capture the glucagon peptide and facilitates it&#039;s insertion into the 7tm. &lt;br /&gt;
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==== Intracellular Helix VIII ====&lt;br /&gt;
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==== Binding Pocket ====&lt;br /&gt;
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The Class B GPCR has the longest and deepest binding pocket. The distance between the EC tips of Helicies II and VI  as well as between the tips between Helicies III and VII are some of the largest among the GPCRs.&lt;br /&gt;
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====Other Unique Structural Features ====&lt;br /&gt;
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An important interface stabilization interaction between helices I and VII occurs between [https://en.wikipedia.org/wiki/Serine Ser] 152 of Helix I and Ser 390 of Helix VII. Due to their close proximity to one another, they form an important &amp;lt;scene name=&#039;72/721537/Ser-ser_hydrogen_bond/2&#039;&amp;gt;hydrogen bond&amp;lt;/scene&amp;gt; which serves to stabilize the structure of GCGR. &lt;br /&gt;
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== Glucagon Binding == &lt;br /&gt;
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Research has shown that Class B GCPRs exist in either an [http://www.nature.com/ncomms/2015/150731/ncomms8859/fig_tab/ncomms8859_F3.html open or closed conformation]. Transitioning between states, the ECD rotates and moves down towards the 7tm domain. The stalk region of Helix I helps to facilitate this motion of the ECD. &lt;br /&gt;
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In its open state, the ECD and the stalk region of Helix 1 are almost perpendicular to the membrane surface. In the case of the human glucagon receptor, this open confirmation is stabilized by glucagon binding. In the absence of glucagon, however, the  GCPR adopts a closed conformation in which all three of the extracellular loops of the 7tm (ECL1, ECL2, and ECL3) can interact with the ECD. In this closed state, the ECD covers the extracellular surface of the 7tm. &lt;br /&gt;
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This transition mechanism is consistent with the &amp;quot;two-domain&amp;quot; binding mechanism of Class B GCPRs in which (1) the C-terminus of the ligand first binds to the ECD allowing (2) the N-terminus of the ligand to interact with the 7tm and activate the protein.​&lt;br /&gt;
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== Clinical Relevance ==&lt;br /&gt;
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Because of this, it is being looked as a potential drug target for Type 2 diabetes. Molecules that antagoinze the glucagon receptor may be able to lower blood sugar levels. &lt;br /&gt;
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&amp;lt;/StructureSection&amp;gt;&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;/div&gt;</summary>
		<author><name>Alexis Coulis</name></author>
	</entry>
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