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| | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> | | <!-- INSERT YOUR SCENES AND TEXT BELOW THIS LINE --> |
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| - | =='''Phosphatase Inhibitor complexes: pdb 1nny'''== | + | =='''YourMacromolecule'''== |
| - | <Structure load='1nny' size='500' frame='true' align='right' caption='PTP1B inhibitor' scene='Insert optional scene name here' />
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| | ===Introduction=== | | ===Introduction=== |
| - | <scene name='Sandbox_Reserved_431/Monomer/1'>Monomer</scene>
| + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
| - | | + | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> |
| - | Diabetes is a quickly growing disease that is affecting more and more people every day. Diabetes is caused when the body either does not produce enough insulin, or has a resistance to insulin. Insulin resistance occurs when an increase in the concentration of insulin in the cells leads to a decrease in the cell’s uptake of insulin.
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| - | When insulin binds to a normal insulin receptor, three specific tyrosine residues are phosphorylated and this serves as the first step in insulin signaling. The insulin receptor is bound to the cell by a beta strand that extends through the membrane into the interior of the cell. The insulin binds to the two different binding sites on the receptor and is used to move the glucose in the blood stream to different tissues in order to use as energy.
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| - | In a person with type 2 diabetes, the cells are unable to uptake glucose due to decreased insulin receptor signaling. This decrease in signaling can be caused by the protein tyrosine phosphatase (PTP1B). PTP1B is responsible for the dephosphorylation of the insulin receptor, and therefore responsible for the down regulation of insulin signaling and the cause of diabetes.
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| - | As explained below in the section labelled 'Binding Interactions,' recent efforts have been made to develop new drugs that would inhibit the effects of the PTP1B protein. A small, potent and selective inhibitor was developed that competitively and reversibly binds to the binding sites on the insulin receptor and selectively inhibits PTP1B. This PTP1B inhibitor increases the half-life of the phosphorylated insulin receptor, which in turn enhances the effects of insulin in patients with type 2 diabetes.
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| - | <ref>Szczepankiewicz BG, Liu G, Hajduk PJ, Abad-Zapatero C, Pei Z, Xin Z, Lubben TH, Trevillyan JM, Stashko MA, Ballaron SJ, Liang H, Huang F, Hutchins CW, Fesik SW, Jirousek MR. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J Am Chem Soc. 2003 Apr 9;125(14):4087-96. PMID:12670229 doi:10.1021/ja0296733</ref>
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| - | <Structure load='1nny' size='500' frame='true' align='left' caption='PTP1B catalytic loop' scene='Insert optional scene name here' /> | + | |
| - | <br><br> | + | |
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| | ===Overall Structure=== | | ===Overall Structure=== |
| - | | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, insert caption here' scene='Sandbox_Reserved_430/Intra-strand_phosphate/1' /> |
| - | The secondary structure of the monomer includes 8 <font color='magenta'>alpha </font>
| + | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> |
| - | <scene name='Sandbox_Reserved_431/Alpha_helix/3'>helices</scene> and 10 beta strands, 8 <font color='deepskyblue'>beta strands</font> make up the main <scene name='Sandbox_Reserved_431/Beta_sheet/3'>beta sheet</scene>. The beta sheet adopts a highly twisted configuration.
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| - | The <font color = 'mediumspringgreen'>C-terminal </font> <scene name='Sandbox_Reserved_431/C_terminus/1'>35 residues</scene> are predominantly hydrophobic in nature and function in targeting the enzyme to the cytoplasmic face of membranes of the endoplasmic reticulum (ER).
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| - | A structural feature that is highly conserved among PTPs is the catalytic, or <font color = 'limegreen'>PTP </font> <scene name='Sandbox_Reserved_431/Catalytic_site/1'>loop</scene>. The phosphate recognition site is created from a loop that is located at the amino-terminus of an alpha helix. PTP loop is made up of the following residues (I/V)HCXAGXGR(S/T)G that includes the <scene name='Sandbox_Reserved_431/Catalytic_site/2'>active site</scene> <font color = 'red'>Cys215 </font>. <ref> PMID:12829250 </ref> Another conserved loop, the recognition loop, plays an important role in substrate recognition. The pTyr loop contains Tyr 46 (tyrosine), which defines the depth of the cleft and contributes to the specificity for phosphotyrosine-containing substrates. The <scene name='Sandbox_Reserved_431/Tyr_46_and_val_49/7'>residues</scene> <font color = 'yellow'> Tyr 46 </font> and <font color = 'darkorange'> Val 49 </font> assist the substrate's insertion into catalytic site.
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| - | <scene name='Sandbox_Reserved_431/Ser216/1'>Ser</scene> <font color ='navy'> 216 </font> of the PTP loop forms a hydrogen bond with the the recognition loop, stabilizing the active site cleft. A third conserved loop is the <font color = 'blue'> WPD </font> | + | |
| - | <scene name='Sandbox_Reserved_431/Wpd_loop/1'>loop</scene>. For this specific inhibitor of the enzyme, once the substrate binds there is no conformational change in the structure of the loop.<sup>[1]</sup> | + | |
| - | For other inhibitors of this enzyme, once the substrate binds to the binding site, there is a conformational change in which the WPD loop closes around the side chain of the pTyr residue of the substrate. This causes Phe 282 to stack against the phenyl side chain of of the substrate pTyr, stabilizing the closed loop.<sup>[1]</sup> This conformation positions the <font color = 'teal'>Asp </font> <scene name='Sandbox_Reserved_431/Asp_181/2'>181</scene> to function as a general acid in the initial part of the phosphorylation transfer step.
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| - | PTP1B represents an example of the concept of an induced fit, which means that the binding of the substrate induces a conformational change that creates a form of the enzyme that is catalytic.
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| - | <br> <br><br><br> | + | |
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| | ===Binding Interactions=== | | ===Binding Interactions=== |
| - | | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
| - | PTP1B is thought to primarily be responsible for the dephosphorylation of the insulin receptor and, therefore, acts to downregulate insulin signaling. Inhibiting PTP1B is linked to improved insulin response and activation of the insulin pathway. PTP1B deficient mice showed a resistance to diet induced diabetes.
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| - | <Structure load='1nny' size='500' frame='true' align='right' caption='Enzyme active site' scene='Insert optional scene name here' /> | + | |
| - | Overall the <scene name='Sandbox_Reserved_431/Working_ligand/1'>ligand</scene> is a competitive inhibitor which reversibly binds to two sites simultaneously and has a high selectivity for PTP1B over other phosphatases. This ligand was engineered by a research group from Abbot labs and the steps they took in its design revolve around many important binding interactions. The group designed the drug in <scene name='Sandbox_Reserved_431/Ligand_design/1'>three different stages</scene>. In order to identify this inhibiting ligand, the research group of interest first used a computer to scan a library of 10,000 organic compounds based on there NMR spectra, searching for those who have an affinity for the enzymes active site. The best match produced by the screen was diaryloxamic acid which the group then modified to <font color = 'dodgerblue'>naphthyloxamic acid</font> , reasoning that an inhibitor that took up more space would be a more potent inhibitor. When the group mixed this molecule with enzyme, NMR data showed a chemical shift in <scene name='Sandbox_Reserved_431/1st_binding/4'>Val49, Gly220, and Gly 218</scene>, part of the active site of the enzyme. The observed kinetics indicated competitive and reversible inhibition.
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| - | After their initial success, the group then reasoned that since the active domain of PTP1B is somewhat conserved by many other phosphatases and extremely similar in some ( TCPTP), incorporation of binding to a second and nonactive site would dramatically increase selectivity. Based off of naphthyloxamic acid, the group then created what they called <font color = 'darkorange'>compound 12</font> hoping that it would satisfy these conditions. Mixing the new ligand and enzyme then screening with NMR N-15 and C-13 resonance yielded data showing that in addition to binding to Val49, Gly220, and Gly 218, the new ligand bound to additional active sites, those being <scene name='Sandbox_Reserved_431/Active_site_2/5'>Gln262 and Arg221</scene> The new ligand also forms hydrogen bonds to the backbone of residues <font color = 'darkorange'> Ser216-Gly220</font> as well as forming a hydrophobic interaction with Tyr46. The group improved the site two ligand creating <font color = 'magenta'>compound 23</font> compound 23, which primarily adds interactions with <scene name='Sandbox_Reserved_431/Active_site_2/6'>Met258, Arg24, and Arg254</scene>. It is not yet know whether <font color = 'magenta'> Arg 24, Arg 254,</font> or both residues are interacting with the ligand, but it is believed that they are either forming hydrogen bonds to the ligand or forming a salt bridge. The groups final ligand shows excellent potency for PTP1B while also showing high seletivity against other phosphatases.
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| | ===Additional Features=== | | ===Additional Features=== |
| - | <Structure load='1nny' size='500' frame='true' align='right' caption='Dephosphorylation reaction' scene='Insert optional scene name here' /> | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| - | '''Dephosphorylation of the Tyrosine-Phosphate Residue''' | + | ===Quiz Question 1=== |
| | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| - | A phosphorylated residue enters the active site of the protein, facilitated by the recognition loop residues <scene name='Sandbox_Reserved_431/Tyr_46_and_val_49/5'>Tyr 46 and Val 49</scene>. The base of the entrance through which it is brought is known as the PTP loop. The phosphotyrosine entering is amphipathic, thus requiring a non-polar pocket for its phenol ring while the polar end is positioned in the catalytic site. Once inside, the substrate causes a conformational change in the WPD loop, causing the substrate to be held in place for a nucleophilic attack. Also, the residue, <scene name='Sandbox_Reserved_431/Asp_181/1'>Asp 181</scene>, is shifted, so that it can act as an acid. The first step of the reaction involves Asp 181 attaching a hydrogen atom to the oxygen of tyrosine, thus neutralizing it and allowing it to diffuse from the site. Binding in the PTP loop occurs, so the connection between Arg 221 and the phosphate of the substrate is maximized. The WPD loop now has a very stable conformation, as binding has increased with multiple surrounding residues, <scene name='Sandbox_Reserved_431/Pro_180_trp_179_and_phe_182/2'>Pro 180, Trp 179, and Phe 182</scene>. The tyrosine residue is now positioned in close proximity to the <scene name='Sandbox_Reserved_431/Initial_view/2'>sulfur of Cys 215</scene>, allowing Cys 215 to remove the phosphate as an intermediate step in the reaction. Now, the phosphate binds to the <scene name='Sandbox_Reserved_431/Cys_215_and_asp_181/2'>Cys 215</scene>, forming the cysteinyl-phosphate intermediate. This intermediate will then be dephosphorylated again, creating a water phosphate complex. Afterwards, the enzyme will return to its resting conformation and will be able to accept another tyrosine for dephosphorylation.[3]
| + | ===Quiz Question 2=== |
| | + | <Structure load='1a84' size='300' frame='true' align='right' caption='pdbcode, Insert caption here' scene='Insert optional scene name here' /> |
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| | ===Credits=== | | ===Credits=== |
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| - | Introduction - Jill Carlson | + | Introduction - name of team member |
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| - | Overall Structure - Polina Berdnikova | + | Overall Structure - name of team member |
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| - | Drug Binding Site - Brett Clinton | + | Drug Binding Site - name of team member |
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| - | Additional Features - James Hamblin | + | Additional Features - name of team member |
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| - | ===References===
| + | Quiz Question 1 - name of team member |
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| | + | Quiz Question 2 - name of team member |
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| | + | ===References=== |
| | <references/> | | <references/> |
| - | 3. Edwards, K., T. Davis, D. Marcey, J. Kurihara, D. Yamamoto. 2001. Comparative Analysis of the Band 4.1/ezrin-related Protein Tyrosine Phosphatase Pez from Two Drosophila Species: Implication for Structure and Function. Gene 275: 195-205. | |
