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| | {{Template:Sandbox Reserved Lynmarie Thompson}} | | {{Template:Sandbox Reserved Lynmarie Thompson}} |
| | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> | | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> |
| - | <Structure load=' | |
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| - | =='''Glycogen Synthase Kinase 3 Beta'''== | + | =='''Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)<ref>PMID: 21885279 </ref>'''== |
| - | <StructureSection load='1q3d' size='350' side='right' caption='A look at GSK-3β. pdbcode: 1q3d.' scene='Insert optional scene name here'>
| + | by Benjamin Homyak, Soo Lim Park, Marissa Burgess |
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| | + | [[Student Projects for UMass Chemistry 423 Spring 2016]] |
| | + | <StructureSection load='2yly' size='350' side='right' caption='p-hydroxybenzenesulphonamides ERb receptor (PDB entry [[2yly]])' scene=''> |
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| | ==Introduction== | | ==Introduction== |
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| - | '''Glycogen synthase kinase-3''', or '''GSK-3''', is one of the main proteins that controls the activation of glycogen synthase. GSK-3 is serine/threonine protein kinase which regulates the phosphorylation of serine and threonine molecules. Serine/threonine kinase is important for the regulation of cell proliferation, cell death, cell differentiation, and embryonic development<ref>PMID: 16912193</ref>. GSK-3 is found in two forms, GSK-3β and GSK-3α. The two forms have different functions with GSK-3 β involved in energy metabolism, neuronal cell development, and body pattern formation, while GSK-3α has more function with WNT signaling pathways, which controls cell fate. This proteopedia page will be focused on GSK-3β. The GSK-3β is found in most mammals, all with similar structure and function. In experiments when GSK-3β was perturbed in mice, embryonic lethality during gestation was demonstrated<ref>PMID: 20599907</ref>. Recent research in regards to GSK-3β includes type II diabetes, Alzheimer's Disease, inflammation, cancer, and neurological disorders such as strokes and bipolar disorder.
| + | Estrogen receptors are proteins found on and inside of the cell. When activated by estrogen these receptors are important in sexual maturation and gestation. There are two types of estrogen receptors that exist which include nuclear estrogen receptors (ERα and ERβ), which are included in the nuclear receptor family of intracellular receptors, and membrane estrogen receptors. |
| - | GSK-3β has been shown to interact with various enzymes including: TGF- β1, Smad3, AKAP11, AXIN1, AXIN2, AR, CTNNB1, DNM1L, MACF1 MUC1, SMAD3, NOTCH1,NOTCH2, P53, PRKAR2A, SGK3, and TSC2. This page focuses on a GSK-3β complex with a Staurosporine inhibitor. Since ATP has a stronger affinity to binding to staurosporine than to protein kinases, the molecule acts a competitive inhibitor in regards to GSK-3β<ref name="paper">PMID: 14529625</ref>.
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| - | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the complex.
| + | A series of p-hydroxybenzenesulphonamides ERβ receptor agonists discovered along with various compounds listed showed selectivity over the ERα receptor. Overall, they found that compound 11 showed better binding conformation determined by X-ray, and presents a better starting point for the journey to find a more selective ERβ agonist. |
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| - | ==Overall Structure==
| + | Looking at the gonadal steroid hormone estradiol,1, action is performed through estrogen subtypes, ERα and ERβ. The detrimental effects of ERβ in comparison to the proliferative effects ERα are found to inhibit breast and endometrial tissue compared to ERα and could potentially be responsible for the immunomodulatory and neuropharmacalogical behavior of estradiol 1,2. The interest in the therapeutic benefits of selective ERβ agonists to combatant various conditions including endometriosis and inflammatory bowel disease. |
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| - | The overall structure of GSK-3β has two phosphorylation sites that are involved in catalysis. One of these sites is Ser 9, resulting in the inactivation of GSK-3β. The second phosphorylation site is Tyr 216, located on the activation loop (<span style="color:green">'''green'''</span> ), and is responsible for the increase in catalytic activity. GSK-3β has the characteristic two-domain kinase fold, containing a N-terminal β-strand domain (<span style="color:Blue">'''light blue, residues 25-138'''</span>) and a C-terminal α-helical domain (<span style="color:red">'''red, residues 139-343'''</span>). There is an interface between the α and β domains, at which the ATP-binding site is located, encircled by the hinge and the glycine-rich loop. The activation loop (<span style="color:green">'''green'''</span>) runs along the surface of the substrate-binding groove. There are 39 residues in the C-terminus end that are outside the main kinase fold. These residues form a small domain that closely packs next to the α-helical domain. The β-strand domain is formed by seven β-strands that run in an antiparallel formation. Strands 2-6 form a β-barrel, through which a short α helix (<span style="color:orange">'''yellow, residues 96-102'''</span>) aligns against the β-barrel <ref name="overall">PMID: 11427888</ref>.
| + | This is an overall scene with the beta sheets in purple and the alpha helices in ball and stick figures <scene name='48/483890/Ben_homyak_overall_structure/1'>Overall Structure</scene> |
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| - | <scene name='48/483890/Overall_structure_of_gsk-3beta/3'>Green Scene for Overall Structure</scene> | + | Here is another scene with a rainbow diagram description of the whole molecule |
| - | ==Binding Interactions==
| + | <scene name='48/483890/2yly_overall_diagram/3'>Rainbow diagram</scene> |
| - | Before GSK-3β can phosphorylate a substrate, the β and α domains of the protein must align. To ensure alignment of the domains, which can either promote or decrease catalysis, GSK-3β utilizes phosphorylated residues. As mentioned in overall structure, phosphorylation of Ser 9 inhibits the catalytic ability of GSK-3β, while phosphorylation of Tyr 216 promotes catalysis by 200 fold. When Ser 9 is phosphorylated, the N-terminus of the protein acts as a pseudo-substrate, binding to the active site and preventing any catalytic activity from occurring. The inhibitor staurosporine, prevents catalytic activity by binding slightly above the active site of GSK-3β while rotating the N-terminal domain of the protein back in order to occupy a prefered binding mode. More details on the binding of staurosporine can be read in the Additional Features section. When Tyr 216 is phosphorylated, the polar residues Arg 96, Arg 180, and Lys 205 all rearranged, due to electrostatic interactions to point towards the phosphorylated molecule, allowing for the protein to fold into its active form <ref name="overall"/>.
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| - | To influence binding of substrates, a salt bridge must form between Glu 97 and Lys 85 located in the active site. GSK-3β recognizes a sequence on the substrate containing two serine molecules separated by three residues (SXXXS). If the last serine in the sequence is phosphorylated prior to its encounter with GSK-3β, also known as primed phosphorylation, then the catalytic rate increases by 100-1000 fold. Catalytic activity of primed phosphorylated substrates increases catalytic activity by replacing the phosphate ion that aligns the Arg 96, Arg 180, and Lys 205 residues. Although not all substrates that GSK-3β phosphorylated require primed phosphorylation, substrates that do have a primed serine increase catalytic activity by utilizing electrostatic interactions to hold the protein in its active form <ref name="overall"/>.
| + | ==Overall Structure== |
| | + | The assembly composition of the 2yly protein is a homodimer. (Quaternary structure) |
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| - | <scene name='48/483890/Binding_interactions/1'> Alignment of Arg 96, Arg 180, and Lys 205</scene> when Tyr 216 is phosphorylated, due to the electrostatic interactions between the residues and the phosphate ion.<span style="color:Blue">'''Blue atoms'''</span> - cationic side chains <span style="color:Grey">'''White atoms'''</span> - amino acid backbone
| + | The DNA Binding domain is located in the C region, which is highly conserved. The ligand binding domain is located at the C terminus in the E and F regions. The ligand binding domain is often called the “three-layered anti-parallel α helical sandwich” because it contains 12 alpha helices along with one beta hairpin. Sites for dimerization and nuclear localization are located in the the D region, which is poorly conserved. Both ERα and ERβ have several splice variants, with ERα having over 20 and ERβ having 5. |
| - | ==Additional Features==
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| - | There are three kinds of interactions in the GSK-3β and staurosporine complex, including: direct H-bonds, water-mediated polar interactions and hydrophobic interactions .The GSK-3β and <span style="color: orange">'''staurosporine'''</span> complex shows <scene name='48/483890/Additional_feature_v6/5'>distinct hydrogen bonding (H-bond) interaction</scene>.
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| - | There are only two direct H-bonds, and they are observed between
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| - | * The <span style="color:red">'''carbonyl oxygen'''</span> of Asp 133 and <span style="color:blue">'''N<sup>1</sup> (nitrogen)'''</span> of staurosporine. The length of this hydrogen bond is 2.93 Å.
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| - | * The backbone <span style="color:blue">'''nitrogen'''</span> of Val 135 and <span style="color:red">'''O<sup>5</sup> (oxygen)'''</span> of staurosporine. The length of this hydrogen bond is 2.76 Å.
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| - | Besides direct H-bond, the water-mediated polar interactions are observed between the <span style="color:red">'''carbonyl oxygen'''</span> of Gln 185 and <span style="color:blue">'''N<sup>4</sup> (nitrogen)'''</span> of the glycosidic ring.
| + | The 2yly protein's secondary structure consists of mostly alpha helices (148 residues) and only two beta strands (6 residues) on the outside of the receptor shown below with the alpha helices showing polar and non-polar parts of the chain. The beta sheets are shown in yellow in the second green scene. |
| - | The typical hydrogen bond (H-bond) is categorized to be between 2.2 and 4.0 Å <ref name="book">Jeffrey, George A. An introduction to hydrogen bonding; Oxford University Press: Oxford, 1997</ref>.
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| - | Since many pdb files lack hydrogen atoms, a significant H-bond can be considered when donor-acceptor distance are probably 3.5 Å <ref name="book" />.
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| - | However, the length between between Gln 185 and Strauroporine is 4.47 Å which surpasses typical H-bond distance; therefore, it forms a water mediated polar interaction between these atoms instead of direct H-bond<ref name="paper"/>.
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| - | This is a unique interaction to the GSK-3β and staurosporine complex, since other protein kinase (e.g. CDK2, Chk1, LCK, PKA) -staurosporine complexes show direct H-bond interaction between two moieties.
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| - | There is a significant number of <scene name='48/483890/Additional_feature_v4/2'>hydrophobic interaction</scene> in the GSK-3β and staurosporine complex; to be more specific, this complex buries 891 Å<sup>2</sup> surface area<ref name="paper" />. The <span style="color:pink">'''hydrophobic residues'''</span> significantly interact with the fuzed carbazole moiety of saurosporine.
| + | - <scene name='48/483890/2yly_alpha_helicies/1'>Alpha Helices</scene>, and <scene name='48/483890/2yly_beta_sheets/1'>Beta Sheets</scene> |
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| - | ==Quiz Question 1==
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| - | GSK-3β has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3β complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3β complex. This is because, in a GSK-3β complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding<ref name="paper" />.
| + | - Tertiary Structure |
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| - | What type of bonding does GSK-3β exhibit with staurosporine, and which of its residues form this type of bond? If needed, a green screen of the complex can be found below.
| + | - Polar- Pink, Hydrophobic- Grey <scene name='48/483890/2yly_polar_hydrophobic/1'>Polar and Nonpolar Groups</scene> |
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| - | <scene name='48/483890/Ligand_bonding_type/1'>View Complex</scene> | + | - Surface groups (orange) vs. Buried groups (blue) <scene name='48/483890/2yly_surface_buried/1'>Check it out</scene> |
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| - | ==Quiz Question 2== | + | ==Binding Interactions== |
| - | What are the locations of the active sites on each isoform?
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| - | These green screens may help you. Remember to zoom and rotate each scene to better understand the structures. The first scene displays the two isoforms. The second screen shows the Amino and Carboxy chain termini with a provided color key to use when viewing. The third scene shows the locations of the α-helices and β-sheets on the protein as well as the complexed staurosporene molecule.
| + | Among the series of p-hydroxybenzene sulfonamide ERβ receptor agonists discovered, protein 2yly has been identified for great selectivity over the related ERα receptor. Protein 2yly was originally designed to form an interaction with the His 475 through the tertiary hydroxyl group. However, the hydroxyl group serves as a conformational lock to form an internal hydrogen bond with the <scene name='48/483890/Soolim_binding/1'>sulphonamide oxygen </scene> about 2.3 Å apart.<sup>[1]</sup> |
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| - | 1) <scene name='48/483890/Isophorms/2'>Color representation of the two isoforms complexed with the staurosporine ligands</scene>
| + | Internally packed against the phenyl group is the cyclopropyl group with large <scene name='48/483890/Soolim_hydrophobic/1'>hydrophobic interactions</scene> (shown in gray) between Ile 373 and both the benzyl and chiral methyl groups. The sulphonamide oxygens come in close contact with Met 336 and the benzyl group of the ligand comes near His 475 but there are no coulombic interactions formed. Depending on the functional group placed either next to the tertiary hydroxyl group or on the benzyl ring, further Van der Waals interactions can be seen within the lipophilic pocket. In other words, depending on the polarity of the group attached to the sulphonamide, interactions with His 475 will be varied. |
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| - | 2) <scene name='48/483890/N_to_c_chain_rainbow/4'>Amino and carboxy chain termini</scene>
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| - | {{Template:ColorKey_Amino2CarboxyRainbow}}
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| - | 3) <scene name='48/483890/Alpha_helices_and_beta_sheets/4'>Beta sheets in green, alpha helices in blue</scene>
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| | ==See Also== | | ==See Also== |
| - | *[[UvrABC]] | + | *[[http://www.proteopedia.org/wiki/index.php/Estrogen_receptor Estrogen Receptor]] |
| - | *[http://www.proteopedia.org/wiki/index.php/GSK-3 Glycogen Synthase Kinase 3]
| + | *[[http://www.proteopedia.org/wiki/index.php/1yy4 1yy4]] |
| - | *[http://proteopedia.org/wiki/index.php/Serine/threonine_protein_kinase Serine/Threonie Protein Kinase] | + | *[[http://www.proteopedia.org/wiki/index.php/1u3s 1u3s]] |
| - | *[http://proteopedia.org/wiki/index.php/3zdi Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Inhibitor 7d] | + | *[[http://www.proteopedia.org/wiki/index.php/1x78 1x78]] |
| - | *[http://proteopedia.org/wiki/index.php/1pyx Glycogen Synthase Kinase 3 Beta complexed with AMP-PNP] | + | *[[http://www.proteopedia.org/wiki/index.php/1qkm 1qkn]] |
| - | *[http://proteopedia.org/wiki/index.php/4b7t Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Leucettine L4]
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| - | *[http://www.proteopedia.org/wiki/index.php/3pup Glycogen Synthase Kinase 3 beta (GSK3B) complexed with a ruthenium octasporine ligand (OS1)] | + | |
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| | ==Credits== | | ==Credits== |
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| - | Introduction - Zachary Plourde | + | Introduction - Benjamin Homyak |
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| - | Overall Structure - Sarah Johnson
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| - | Binding Interactions - Christina Lincoln
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| - | Additional Features - Bach Pham & Elvan Cevac
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| - | Quiz Question 1 - Nerses Haroutunian
| + | Overall Structure - Marissa Burgess |
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| - | Quiz Question 2 - Nick H-K
| + | Drug Binding Site - Soo Lim Park |
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| | ==References== | | ==References== |
| | <references/> | | <references/> |
