User:Daniel Schemenauer/Sandbox 1: Difference between revisions

<StructureSection load='4oo9' size='340' side='right' caption='metabotropic Glutamate Receptor 5 PDB:[http://www.rcsb.org/pdb/explore/explore.do?structureId=4oo9 4oo9]' scene='72/726409/Overview/5'>

G-coupled protein receptors [https://en.wikipedia.org/wiki/G_protein–coupled_receptor GPCR's] are helical trans-membrane proteins that bind to an extracellular signal and activate a cellular response.  The human genome encodes for approximately 750 GPCR's, 350 of which are known to respond to extracellular ligands<ref name="GPCRRep">PMID: 12679517 </ref>.  GPCR's are divided into four major classes based on sequence similarity and transduction mechanism: Class A,B,C, and F<ref name="MSGPCR">PMID:23407534</ref>. Metabotropic Glutamate Receptor 5 (<scene name='72/726409/Overview/5'>mGlu₅</scene>) is a class C GPCR that is involved in the G_q pathway<ref name="CCGPCR">PMID:12782243</ref>. In this pathway, the G-protein disassociates and the alpha subunit activates [https://en.wikipedia.org/wiki/Phospholipase_C Phospholipase C].  Phospholipase C in turn cleaves [https://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate PIP2] to [https://en.wikipedia.org/wiki/Diglyceride DA] and [https://en.wikipedia.org/wiki/Inositol_trisphosphate IP3].  IP3 then binds to calcium channels on the [https://en.wikipedia.org/wiki/Endoplasmic_reticulum Endoplasmic reticulum] creating an increased cellular concentration of calcium.  Increased calcium concentrations thus leads to increased neuronal activity<ref name="MSGPCR">PMID:23407534</ref>.  mGlu₅ is highly expressed in neuronal and glial cells in the central nervous system, where glutamate serves as the major neurotransmitter.  When glutamate binds to the extracellular domain of mGlu₅ consisting of the Venus Fly Trap motif<ref name="Primary">PMID: 25042998 </ref>, a conformational change through the trans-membrane domains activates the coupled [http://proteopedia.org/wiki/index.php/GTP-binding_protein G-protein].   

<scene name='72/726409/Overview/5'>mGlu₅</scene> is seen as a [https://en.wikipedia.org/wiki/Protein_dimer homodimer] ''in vivo,'' with each subunit being comprised of three domains: extracellular, trans-membrane and cysteine-rich.  mGlu₅ is centered on the trans-membrane domain, comprised of seven α-helices all roughly parallel to one another<ref name="Primary">PMID: 25042998 </ref>. Also displayed is the Intracellular Loop (ICL) 1 which forms a short α-helix.  Additionally, ICL3 and Extracellular Loops (ECL) 1 and 3 all lack secondary structure, and ECL2 interacts with trans-membrane (TM) helices 1, 2, and 3 as well as ECL 1<ref name="Primary">PMID: 25042998 </ref>.

A number of intramolecular interactions within the trans-membrane domain stabilize the inactive conformation of mGlu₅, and demonstrated by <scene name='72/726409/Overview/5'>mGlu₅</scene> being represented in the inactivate state, the capacity for glutamate to bind to the mGlu₅ receptor is critically hindered, thus decreasing the aforementioned [https://en.wikipedia.org/wiki/Gq_alpha_subunit G_q pathway].  The first of these interactions is an ionic interaction, termed the <scene name='72/726409/Ionic_lock2/2'>Ionic Lock</scene>, between Lysine 665 of TM3 and Glutamate 770 of TM6.  Evidence for the importance of this interaction came through a kinetic study of mutant proteins where both residues were separately substituted with alanine, resulting in constitutive activity of the GPCR and its coupled pathway<ref name="Primary">PMID: 25042998 </ref>.  A second critical interaction that stabilizes the inactive conformer is a <scene name='72/726409/Hydrogen_bond_614-668/2'>Hydrogen Bond </scene> between Serine 614 of ICL1 and Arginine 668 of TM3. Similarly, when Serine 614 was mutated to alanine, high levels of activity were seen in the mutant GPCR<ref name="Primary">PMID: 25042998 </ref>.

A <scene name='72/726404/Scene_6/8'>Disulfide Bond </scene> between Cysteine 644 of TM3 and Cysteine 733 of <scene name='72/726409/Mavoglurant_overview2/3'>ECL2</scene> is critical at anchoring ECL2 and is highly conserved across Class C GPCR’s<ref name="Primary">PMID: 25042998 </ref>.  The ECL2's presence combined with the helical bundle of the trans-membrane domain creates a <scene name='72/726409/Electrogradient2/6'>Binding Cap</scene> that restricts entrance to the allosteric binding site within the seven trans-membrane α-helices.  This restricted entrance has no effect on the natural ligand, glutamate, as it binds to the extracellular domain, but this entrance dictates potential drug targets that act through allosteric modulation<ref name="Primary">PMID: 25042998 </ref>.

 

[[Image:Mav_HB_2.png|300 px|left|thumb|Figure 2. Hydrogen Bonding between mGlu₅ and Mavoglurant. Blue coloration represents Hydrogen Bond donor whereas red coloration represents Hydrogen Bond acceptor.]]