Sandbox Reserved 969: Difference between revisions

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In the closed conformation, inner helices are near and straight. There is a subsequent '''bundle crossing''' formed by interactions between C-terminal residues. In the region just above the bundle crossing, <scene name='60/604488/Phe_92/1'>Phe92</scene> from each inner helix forms contacts with a '''hydrophobic patch''' on the opposite face of Phe92 from the neighboring inner helix formed by Val91, Phe94, Ile95 and Leu98. <ref> PMID: 19098917</ref>
In the closed conformation, inner helices are near and straight. There is a subsequent '''bundle crossing''' formed by interactions between C-terminal residues. In the region just above the bundle crossing, <scene name='60/604488/Phe_92/1'>Phe92</scene> from each inner helix forms contacts with a '''hydrophobic patch''' on the opposite face of Phe92 from the neighboring inner helix formed by Val91, Phe94, Ile95 and Leu98. <ref> PMID: 19098917</ref>


[[Image:Close_structure.jpg|left|100px|The structure of the closed complex]]




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Channel opening is a '''conserved mechanism'''.The inner helix '''twist''' and '''bend''' thanks to a<scene name='60/604488/Glycine_conserved/1'> conserved glycine residue Gly87</scene> which is considered as the '''gating hinge'''. After this bending, the inner helices twist of 45° around their helical helix and the outer helix tilt tangentially in the same direction by 11° without any twisting motion. As all of helix twist or move inside of a subunit, intra-subunit interactions between inner and outer helix don’t differ a lot. On the contrary, inter-subunit interactions between neighboring inner helix change. In fact, Phe92 swings away and points its side chain towards the central ion conduction pathway due to inner helix bending and the hydrophobic patch slides along the neighboring inner helix by two helical turns and forms new Van der Waals contacts with <scene name='60/604488/Phe85/1'>Phe 85 </scene>. This resulted in a '''disruption of the bundle crossing''' and so intra- and inter- subunits interactions in the open state become less important than in the close state. <ref>PMID: 19098917</ref>
Channel opening is a '''conserved mechanism'''.The inner helix '''twist''' and '''bend''' thanks to a<scene name='60/604488/Glycine_conserved/1'> conserved glycine residue Gly87</scene> which is considered as the '''gating hinge'''. After this bending, the inner helices twist of 45° around their helical helix and the outer helix tilt tangentially in the same direction by 11° without any twisting motion. As all of helix twist or move inside of a subunit, intra-subunit interactions between inner and outer helix don’t differ a lot. On the contrary, inter-subunit interactions between neighboring inner helix change. In fact, Phe92 swings away and points its side chain towards the central ion conduction pathway due to inner helix bending and the hydrophobic patch slides along the neighboring inner helix by two helical turns and forms new Van der Waals contacts with <scene name='60/604488/Phe85/1'>Phe 85 </scene>. This resulted in a '''disruption of the bundle crossing''' and so intra- and inter- subunits interactions in the open state become less important than in the close state. <ref>PMID: 19098917</ref>


[[Image:open_structure.jpg|right|100px|The structure of the open complex]]


== '''Active Site & Ions Passage''' ==
== '''Active Site & Ions Passage''' ==


There are '''4 ions binding sites''' in the NaK channel <ref> PMID: 16467789</ref>. This diversity allows by different mechanisms to conduit <scene name='60/604488/Ion_binding_sites/1'>several cations</scene>. They have similar chemical environments but they have '''different ion selectivity'''. Two of them (sites S3 and S4) are conserved, that is to say they are the same than in the high selective K+ channel while S1 and S2 become a vestibular structure where K+ and Na+ ions can diffuse<ref> PMID: 19098915 </ref> .[[Image:biding_sites.jpg|center|00px|The different ions binding site]]
There are '''4 ions binding sites''' in the NaK channel <ref> PMID: 16467789</ref>. This diversity allows by different mechanisms to conduit <scene name='60/604488/Ion_binding_sites/1'>several cations</scene>. They have similar chemical environments but they have '''different ion selectivity'''. Two of them (sites S3 and S4) are conserved, that is to say they are the same than in the high selective K+ channel while S1 and S2 become a vestibular structure where K+ and Na+ ions can diffuse<ref> PMID: 19098915 </ref> .[[Image:biding_sites_lola.jpg|center|00px|The different ions binding site]]


We will see for every binding site how his structure allows the passage of one or several ions.
We will see for every binding site how his structure allows the passage of one or several ions.
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=== Site 3 ===
=== Site 3 ===
[[Image:Proteopedia_superposition.jpg|right|200px|Structures of the channel with different channels]]


He is the most non selective ion binding site which let pass mono and divalent cations, so a contamination can occur : presence of unkonwn species of ion at this site.  
He is the most non selective ion binding site which let pass mono and divalent cations, so a contamination can occur : presence of unkonwn species of ion at this site.  
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