Gramicidin Channel in Lipid Bilayer: Difference between revisions

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scene='38/388981/Protein_only/2'  oldscene='User:Eric_Martz/Sandbox_10/Gramicidin/4' />
scene='38/388981/Protein_only/2'  oldscene='User:Eric_Martz/Sandbox_10/Gramicidin/4' />


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The scenes on this page have been repaired. [[User:Eric Martz|Eric Martz]] 00:37, 30 September 2014 (IST)
The scenes on this page have been repaired. [[User:Eric Martz|Eric Martz]] 00:37, 30 September 2014 (IST)
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</td></tr></table>
<!--TEST FOR DEVELOPMENT: <scene name='38/388981/Gramicidin_redo/1'>Bad scene with translucency not in mode -1.</scene>-->
TEST FOR DEVELOPMENT: <scene name='38/388981/Gramicidin_redo/1'>Bad scene with translucency not in mode -1.</scene>-->


Two copies of the 15-amino-acid gramicidin peptide are shown here (<scene name='38/388981/Protein_only/2' oldname='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 name="crouzy">PMID: 7529578</ref>. The shape of the protein is shown with tiny dots, inside of which is a ribbon [[backbone]] trace connecting the alpha carbon atoms of each amino acid chain.
Two copies of the 15-amino-acid gramicidin peptide are shown here (<scene name='38/388981/Protein_only/2' oldname='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 name="crouzy">PMID: 7529578</ref>. The shape of the protein is shown with tiny dots, inside of which is a ribbon [[backbone]] trace connecting the alpha carbon atoms of each amino acid chain.


<ul>
<ul>
<li>Show <scene name='38/388981/Protein_only/4' oldname='User:Eric_Martz/Sandbox_10/Gramicidin/2'>only the backbone</scene> of the gramicidin protein chains. The chains are covalently linked with dioxane in this experiment ({{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}),
<li>Show <scene name='38/388981/Protein_only/4' oldname='User:Eric_Martz/Sandbox_10/Gramicidin/2'>only the backbone</scene> of the gramicidin protein chains. The chains are covalently linked with dioxolane in this experiment ({{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}})
 
</li>
<li><scene name='38/388981/Gramicidin_redo/3' oldname='User:Eric_Martz/Sandbox_10/Gramicidin_with_bilayer/3'>Show a slice of the lipid bilayer.</scene>
{{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_P}}
<br>(Most hydrogen atoms are omitted.)
</li>
</li>
<li><scene name='38/388981/Gramicidin_redo/3' oldname='User:Eric_Martz/Sandbox_10/Gramicidin_with_bilayer/3'>Show a slice of the lipid bilayer.</scene> (Most hydrogen atoms are omitted.)
<li>Show <scene name='38/388981/Gramicidin_redo/4' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/1'>water</scene>. Notice how the hydrophobic lipid &quot;tails&quot; exclude water.
</li><li>Show <scene name='38/388981/Gramicidin_redo/4' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/1'>water</scene>. Notice how the hydrophobic lipid &quot;tails&quot; exclude water.
</li>
</li>
<li>Water passes  
<li>Water passes  
<scene name='38/388981/Gramicidin_redo/6' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/3'>through the channel</scene>.
<scene name='38/388981/Gramicidin_redo/6' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/3'>through the channel</scene>.
</li><li>
</li>
Show <scene name='38/388981/Gramicidin_redo/7' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/4'>only water</scene>.
<li>Show <scene name='38/388981/Gramicidin_redo/7' oldname='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/4'>only water</scene>.
</li><li>
</li>
Show only
<li>Show only
<scene name='Gramicidin_Channel_in_Lipid_Bilayer/Two_pes_two_waters/1'>2 phospholipids and 2 waters</scene>. For an explanation of their structure, see the [http://biomodel.uah.es/en/model2/bilayer detailed tutorial], also  [http://biomodel.uah.es/model2/bicapa_j/inicio.htm disponible en espa&ntilde;ol].
<scene name='38/388981/Two_phospholipids_2_waters/1' oldname='Gramicidin_Channel_in_Lipid_Bilayer/Two_pes_two_waters/1'>2 phospholipids and 2 waters</scene>. {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_P}}.
<br>For an explanation of their structure, see the [http://biomodel.uah.es/en/model2/bilayer detailed tutorial], also  [http://biomodel.uah.es/model2/bicapa/inicio.htm disponible en espa&ntilde;ol].
</li>
</li>
</ul>
</ul>
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==See Also==
==See Also==
* A detailed explanation and tutorial about [http://biomodel.uah.es/en/model2/bilayer Lipid Bilayers and the Gramicidin Channel].
* A detailed explanation and tutorial about [http://biomodel.uah.es/en/model2/bilayer Lipid Bilayers and the Gramicidin Channel].
* [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!
* [http://firstglance.jmol.org/fg.htm?mol=bilagram.pdb.gz This model in FirstGlance in Jmol]. Be sure to click the ''Ligands+'' and ''Water'' buttons!
* [[Lipids: structure and classification]]
* [http://bme3d.molviz.org/ BioMolecular Explorer 3D], a resource for high school teachers that includes a section on gramicidin in a lipid bilayer.
* [http://bme3d.molviz.org/ BioMolecular Explorer 3D], a resource for high school teachers that includes a section on gramicidin in a lipid bilayer.
* [[High school teachers' resources]]
* [[High school teachers' resources]]
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==Notes==
==Notes==
* The [[PDB file]] shown here, [[Image:Gramicidin in bilayer.pdb.gz]], was kindly provided by Serge Crouzy<ref name="crouzy" />.
* The [[PDB file]] shown here, [[Image:Gramicidin in bilayer.pdb.gz]], was kindly provided by Serge Crouzy<ref name="crouzy" />.
* To load the scenes on this page into the [[SAT]], change the page name to [[User:Eric_Martz/Sandbox_10]], where these scenes were developed.


==References==
==References==
<references />
<references />


[[es:Canal_de_gramicidina_en_bicapa_lipídica_(Spanish)]]
[[es:Gramicidin Channel in Lipid Bilayer (Spanish)]]

Latest revision as of 21:52, 28 June 2017

Theoretical Model: The structure described on this page was determined theoretically (in 1994[1]), and hence should be interpreted with caution.

Theoretical model of gramicidin in a lipid bilayer (phosphatidyl ethanolamine).

Drag the structure with the mouse to rotate


Two copies of the 15-amino-acid gramicidin peptide are shown here () arranged as they are believed to be when they form a channel through a lipid bilayer membrane[1]. The shape of the protein is shown with tiny dots, inside of which is a ribbon backbone trace connecting the alpha carbon atoms of each amino acid chain.

  • Show of the gramicidin protein chains. The chains are covalently linked with dioxolane in this experiment (C, O)
  • C, H, O, N, P
    (Most hydrogen atoms are omitted.)
  • Show . Notice how the hydrophobic lipid "tails" exclude water.
  • Water passes .
  • Show .
  • Show only . C, H, O, N, P.
    For an explanation of their structure, see the detailed tutorial, also disponible en español.
Remember to use the popup button and then resize the popup window to enlarge the molecular scenes.

See AlsoSee Also

NotesNotes

ReferencesReferences

  1. ↑ 1.0 1.1 1.2 Crouzy S, Woolf TB, Roux B. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys J. 1994 Oct;67(4):1370-86. PMID:7529578 doi:http://dx.doi.org/10.1016/S0006-3495(94)80618-6

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

Eric Martz, Angel Herraez, Jaime Prilusky, David Canner
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