Sandbox 250: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman, Allison Granberry, Jaime Prilusky

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-<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td>Please do NOT make changes to this Sandbox until after September 15, 2010. Sandboxes 250-265 are reserved until then for use by students in Hostos-Lincoln Academy, NYC, in a class taught by Ms. Allison Granberry  (algran2@gmail.com).</td></tr>
+==='''Designing a Physical Model to Tell the Story of Acetylcholinesterase'''===
+Reflected in our design are two key concepts of AChE: the biochemistry of how the ACh overcomes the depth of the active site gorge before hydrolysis can occur, and how a toxin inhibits the substrate from finding the active site.Two physical models were designed and made by 3-dimensional printing technology: ''Torpedo californica (Tc)'' AChE in complex with a modeled ACh ligand, and ''Tc'' AChE in complex with FAS-II. Both models were based on protein data bank (PDB) files, and Rasmol computer modeling program. PDB files included PDB entry code 2ace for the ''Tc''AChE/ACh complex, and PDB entry code 1fss for the ''Tc'' AChE/FAS-II complex.
-{{STRUCTURE_1a6m |  PDB=1a6m  |  SCENE=Sandbox_85/Myoglobin_overview/3 }}
+<applet load='2ace' size='300' frame='true' align='left' caption='AChE/ACh' />
-<scene name='Sandbox_85/Myoglobin_overview/3'>Original View</scene><br>
-<scene name='Sandbox_90/Leut_with_labelled_residues/2'>LeuT labelled residues</scene><br>
+===='''Features of the Substrate Traffic Story: AChE/ACh'''====
-<scene name='Sandbox_90/Inhibition_binding_site/1'>Competetive inhibition site</scene><br>
+AChE is an alpha/beta hydrolase fold with an amino acid sequence of 4-535. The <scene name='Sandbox/2ace/3'>alpha carbon backbone</scene> of AChE has ? alpha helices and ? beta sheets.
-<scene name='Sandbox_90/Leut_wh20_interactions/1'>LeuT wH20 Interactions</scene>
+The <scene name='Sandbox/Ache_ach/15'>14 aromatic residues</scene> that line the active site gorge are tyr70, trp84, trp120, tyr121, tyr130, trp233, trp279, phe288, phe290, phe330, phe331, tyr334, trp432 and tyr442.
+The <scene name='Sandbox/Ache_ach/14'>Catalytic Triad</scene> or active site includes glu327, his440 and ser200. Here is where Acetylcholine is hydrolyzed.
+Three of the aromatic residues that line the gorge attract the quaternary ammonium ion of ACh. These 3 aromatic residues, trp279, tyr70, and tyr121, sit at the entrance of the gorge and make up the <scene name='Sandbox/Ache_ach/13'>Peripheral Anionic Site</scene>.
+Two of the 14 aromatic residues lining the active site gorge that are considered significant for holding ACh in an optimal position for hydrolysis are trp84 and phe330. These residues form the <scene name='Sandbox/Ache_ach/16'>Catalytic Anionic Site</scene>.