User:Eric Martz/Sandbox 10

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Proposed Title: Gramicidin Channel in Lipid Bilayer
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<applet load='3hyd' size='400' frame='true' align='right' />
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<!--{{Theoretical_model}} says "protein"-->
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<scene name='User:Eric_Martz/Sandbox_10/Whole_peptide/1'>Heptapeptide as balls/sticks</scene>.
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<table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td valign='top'>[[Image:Note.gif|left]] '''Theoretical Model:'''
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The structure described on this page was determined [[theoretical_models|theoretically]], and hence should be interpreted with caution.</td></tr></table>
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<applet size='400' frame='true' align='right' caption='Theoretical model of gramicidin in a lipid bilayer (phosphatidyl ethanolamine).'
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<scene name='User:Eric_Martz/Sandbox_10/Hbond_angles_to_n-term/1'>Show putative hbonds between N-terminus and water</scene>.
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scene='User:Eric_Martz/Sandbox_10/Gramicidin/4' />
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Two copies of the gramicidin protein are shown here (<scene name='User:Eric_Martz/Sandbox_10/Gramicidin/4'>restore initial scene</scene>) arranged as they are believed to be when they form a channel through a lipid bilayer membrane<ref>PMID: 7529578</ref>. The shape of the protein is shown transparent (ghostly), and a backbone trace connecting the alpha carbon atoms of each amino acid chain is opaque (solid).
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<ul>
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<li>Show <scene name='User:Eric_Martz/Sandbox_10/Gramicidin/2'>only the backbone</scene> of the gramicidin protein chains.
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</li>
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<li><scene name='User:Eric_Martz/Sandbox_10/Gramicidin_with_bilayer/3'>Show a slice of the lipid bilayer.</scene> (Most hydrogen atoms are omitted.)
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</li>
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<li>Show <scene name='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/1'>water</scene>. Notice how the hydrophobic lipid &quot;tails&quot; exclude water.
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</li>
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<li>Water passes
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<scene name='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/3'>through the channel</scene>.
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</li><li>
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Show <scene name='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/4'>only water</scene>.
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</li>
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</ul>
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<table style="background-color:pink;padding:6px;" width="30%" border="0"><tr><td>Remember to use the '''popup''' button and then resize the popup window to enlarge the molecular scenes.</td></tr></table>
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{{Clear}}
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==See Also==
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* A detailed explanation and tutorial about [http://www2.uah.es/biomodel/en/model2/bilayer/inicio.htm Lipid Bilayers and the Gramicidin Channel].
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* [http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/f/fd/Gramicidin_in_bilayer.pdb.gz This model in FirstGlance in Jmol]. Be sure to click the ''Ligands+'' and ''Water'' buttons!
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* [http://bme3d.molviz.org/ BioMolecular Explorer 3D], a resource for high school teachers that includes a section on gramicidin in a lipid bilayer.
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* [[High school teachers' resources]]
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==Notes==
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* The [[PDB file]] shown here, [[Image:Gramicidin in bilayer.pdb.gz]], was kindly provided by Serge Crouzy.
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==References==
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<references />
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Current revision

PDB ID 3hyd

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Eric Martz

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