Gramicidin Channel in Lipid Bilayer
From Proteopedia
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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:''' | <table style="background-color:#ffffc0" cellpadding="8" width="95%" border="0"><tr><td valign='top'>[[Image:Note.gif|left]] '''Theoretical Model:''' | ||
| - | The structure described on this page was determined [[theoretical_models|theoretically]], and hence should be interpreted with caution.</td></tr></table> | + | The structure described on this page was determined [[theoretical_models|theoretically]] (in 1994<ref name="crouzy" />), and hence should be interpreted with caution.</td></tr></table> |
<applet size='400' frame='true' align='right' caption='Theoretical model of gramicidin in a lipid bilayer (phosphatidyl ethanolamine).' | <applet size='400' frame='true' align='right' caption='Theoretical model of gramicidin in a lipid bilayer (phosphatidyl ethanolamine).' | ||
| - | scene='User:Eric_Martz/Sandbox_10/Gramicidin/4' /> | + | scene='38/388981/Protein_only/2' oldscene='User:Eric_Martz/Sandbox_10/Gramicidin/4' /> |
| - | Two copies of the gramicidin | + | <!--<table style="background-color:#d0ffd0;padding:6px;"><tr><td> |
| + | The scenes on this page have been repaired. [[User:Eric Martz|Eric Martz]] 00:37, 30 September 2014 (IST) | ||
| + | </td></tr></table> | ||
| + | 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. | ||
<ul> | <ul> | ||
| - | <li>Show <scene name='User:Eric_Martz/Sandbox_10/Gramicidin/2'>only the backbone</scene> of the gramicidin protein chains. | + | <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> | ||
| - | <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.) | + | <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> |
| - | </li><li>Show <scene name='User:Eric_Martz/Sandbox_10/Hydrated_bilayer_w_gramicidin/1'>water</scene>. Notice how the hydrophobic lipid "tails" exclude water. | + | {{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>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 "tails" exclude water. | ||
</li> | </li> | ||
<li>Water passes | <li>Water passes | ||
| - | <scene name='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='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/ | + | <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 español]. | ||
</li> | </li> | ||
</ul> | </ul> | ||
| - | <table style="background-color: | + | <table style="background-color:#ffd0d0;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> |
{{Clear}} | {{Clear}} | ||
==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://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]] | ||
| + | * The Spanish version of this page: [[Canal de gramicidina en bicapa lipídica (Spanish)]] | ||
| + | * For additional information, see: [[Membrane Channels & Pumps]] | ||
==Notes== | ==Notes== | ||
| - | * The [[PDB file]] shown here, [[Image:Gramicidin in bilayer.pdb.gz]], was kindly provided by Serge Crouzy | + | * The [[PDB file]] shown here, [[Image:Gramicidin in bilayer.pdb.gz]], was kindly provided by Serge Crouzy<ref name="crouzy" />. |
| - | + | ||
==References== | ==References== | ||
<references /> | <references /> | ||
| + | |||
| + | [[es:Gramicidin Channel in Lipid Bilayer (Spanish)]] | ||
Current revision
 |
|
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 Also
- A detailed explanation and tutorial about Lipid Bilayers and the Gramicidin Channel.
- This model in FirstGlance in Jmol. Be sure to click the Ligands+ and Water buttons!
- Lipids: structure and classification
- BioMolecular Explorer 3D, a resource for high school teachers that includes a section on gramicidin in a lipid bilayer.
- High school teachers' resources
- The Spanish version of this page: Canal de gramicidina en bicapa lipídica (Spanish)
- For additional information, see: Membrane Channels & Pumps
Notes
- The PDB file shown here, Image:Gramicidin in bilayer.pdb.gz, was kindly provided by Serge Crouzy[1].
References
- ↑ 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
