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) | ||
</td></tr></table> | </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. | 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 | <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>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='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='38/388981/Two_phospholipids_2_waters/1' oldname='Gramicidin_Channel_in_Lipid_Bilayer/Two_pes_two_waters/1'>2 phospholipids and 2 waters</scene>. | <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]. | |||
<br>For an explanation of their structure, see the [http://biomodel.uah.es/en/model2/bilayer detailed tutorial], also [http://biomodel.uah.es/model2/ | |||
</li> | </li> | ||
</ul> | </ul> | ||
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* 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=bilagram.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" />. | ||
==References== | ==References== | ||
<references /> | <references /> | ||
[[es: | [[es:Gramicidin Channel in Lipid Bilayer (Spanish)]] | ||