Proton Channels

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The M2 protein of influenza A virus is a proton channel. Its function is essential for productive infection by the virus.
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<StructureSection load='' size='450' side='right' scene='Proton_Channels/Cartoon/2' caption='Linear interpolation morph from [[3bkd]] to model 1 of [[2rlf]]. '>
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In January, 2008, crystallographic and NMR structures were published side by side in ''Nature'' for the transmembrane domains of the M2 protein: [[3bkd]] and [[2rlf]]. The former appeared to be in an open conformation blocked by amantadine, while the latter appeared to be in a closed conformation stabilized by rimantadine.
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The M2 protein of influenza A virus is a proton channel. Its function is essential for productive infection by the virus.
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<applet load='3bkd2rlf.pdb' size='300' frame='true' align='right' caption='Linear interpolation morph from [[3bkd]] to [[2rlf| 2rlf model 1]]' />
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See [[:Category:Proton_channel]] for a list of all proton channel structures.
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At right is a linear-interpolation morph between 3BKD and 2RLF, showing the proposed opening and closing of this channel.
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Controls for animating this morph in the ''Scene Authoring Tools'' are under development. For now, click on "Jmol" to open the menu, and click on "Console". Enter these two commands into the bottom box of the console:
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In January, 2008, crystallographic and NMR structures were published side by side in ''Nature'' for the transmembrane domains of the M2 protein: [[3bkd]] to [[2rlf]]. The former appeared to be in an open conformation blocked by amantadine, while the latter appeared to be in a closed conformation stabilized by rimantadine. (Neither drug is shown in the morph at right.)
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<pre>
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animation mode palindrome
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<!-- THESE LINKS DO NOT WORK IN THE CAPTION; NEITHER DOES THE FORM [[3bkd]]
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frame play
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caption='Linear interpolation morph from [http://proteopedia.org/wiki/index.php/3bkd 3bkd] to [http://proteopedia.org/wiki/index.php/2rlf 2rlf model 1] ' />
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</pre>
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-->
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To stop, then resume the animation, use these two commands one at a time:
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At right is a [[Morphs|linear-interpolation morph]] between 3BKD and 2RLF, showing the proposed opening and closing of this channel. {{Button_Toggle_Animation2}}
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<pre>
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frame pause
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In addition to watching the animation as alpha-helical ribbons, it is useful to watch it <scene name='Proton_Channels/Spacefilled/1'>spacefilled</scene>. '''Be sure to rotate the molecule with your mouse to watch the animation from different perspectives!'''
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frame play
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</pre>
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<scene name='Proton_Channels/Gating/1'>His37 and Trp41</scene> are believed to be crucial for pH-dependent gating.
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In addition to watching the animation as alpha-helical ribbons, it is useful to watch it
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(The apparent collapse and re-expansion of their sidechains is an artifact due to the [[Morphs|linear interpolation method of morphing]].) Here are His and Trp <scene name='Proton_Channels/Gating/2'>spacefilled</scene>.
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To be explained in a later revision, along with new scenes:
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[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b505428-6008 Morph from Yale]
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{{Clear}}
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==3D structures of ion channels==
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[[Ion channels]]
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==Additional Resources==
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For additional information, see: [[Influenza]] <br />
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For additional information, see: [[Membrane Channels & Pumps]]
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<br />
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<br />
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</StructureSection>

Current revision

Linear interpolation morph from 3bkd to model 1 of 2rlf.

Drag the structure with the mouse to rotate
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