https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&feed=atom&action=historyNormal Mode Analysis Hemochromatosis - Revision history2024-03-28T23:43:07ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=28571&oldid=prevBernhoferm: /* Transferrin receptor protein 1 (TFR) */2012-08-31T19:44:01Z<p><span dir="auto"><span class="autocomment">Transferrin receptor protein 1 (TFR)</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In addition to the NMA performed on HFE we also wanted to take a brief look at the effects of HFE on the normal modes of TFR. We computed the normal modes for the chains A (HFE), B (B2M), and C (TFR) of 1de4 and for the C chain only. The atomic fluctuations (computed by WEBnm@) for TFR are shown in <xr id="tfr_fluctuations"/>. In order to be able to compare the values we cut out the fluctuations for TFR from the complex (A+B+C chain) and re-normalized them to sum up to 100 (like the ones for the C chain do). The plot shows a decrease in the whole end region (610-756), the ligand binding region<ref name="tfr-ligand">http://www.uniprot.org/uniprot/P02786</ref>. Due to the reduced mobility in this region after binding to HFE the complex should be pretty stable. As<del class="diffchange diffchange-inline"> one of</del> HFE<del class="diffchange diffchange-inline">'s</del> <del class="diffchange diffchange-inline">functions is</del> to <del class="diffchange diffchange-inline">compete with other ligands that</del> <del class="diffchange diffchange-inline">bind</del> to TFR in order to reduce the iron <del class="diffchange diffchange-inline">transport</del>, this induced stability might come in handy.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In addition to the NMA performed on HFE we also wanted to take a brief look at the effects of HFE on the normal modes of TFR. We computed the normal modes for the chains A (HFE), B (B2M), and C (TFR) of 1de4 and for the C chain only. The atomic fluctuations (computed by WEBnm@) for TFR are shown in <xr id="tfr_fluctuations"/>. In order to be able to compare the values we cut out the fluctuations for TFR from the complex (A+B+C chain) and re-normalized them to sum up to 100 (like the ones for the C chain do). The plot shows a decrease in the whole end region (610-756), the ligand binding region<ref name="tfr-ligand">http://www.uniprot.org/uniprot/P02786</ref>. Due to the reduced mobility in this region after binding to HFE the complex should be pretty stable. As HFE <ins class="diffchange diffchange-inline">needs</ins> to <ins class="diffchange diffchange-inline">remain</ins> <ins class="diffchange diffchange-inline">bound</ins> to TFR in order to reduce the iron <ins class="diffchange diffchange-inline">uptake</ins>, this induced stability might come in handy.</div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=28529&oldid=prevBernhoferm: /* Short task description */2012-08-31T18:51:45Z<p><span dir="auto"><span class="autocomment">Short task description</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Detailed description: [[Task_9_-_Normal_Mode_Analysis|Normal mode analysis]]</div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=28269&oldid=prevBernhoferm: /* Modes */ removed done todo2012-08-31T10:01:20Z<p><span dir="auto"><span class="autocomment">Modes: </span> removed done todo</span></p>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>TODO: Describe motions... [http://www.youtube.com/watch?v=vY_Ry8J_jdw&t=8s or watch this.]</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27335&oldid=prevBernhoferm: /* Modes */2012-07-30T19:46:29Z<p><span dir="auto"><span class="autocomment">Modes</span></span></p>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Mode 7 shows completely different movements as it did before. Instead of the almost uniform rotation of both domains it now exhibits a hinge-motion between both of them. Mode 8 is also slightly different in that the C1 domain lost most of its rotational movement and shows more a "flapping" one. In contrast to the previous two modes there is almost no difference for mode 9 (e.g. only a minor change in the excursion of the C1 domain's rotation) and the modes 10 to 12 are more or less identical to the ones calculated with WEBnm@.</div></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27333&oldid=prevBernhoferm: /* Modes */2012-07-30T19:31:45Z<p><span dir="auto"><span class="autocomment">Modes</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The lack of an active site makes it hard to give the movements a meaningful function such as cleaving of the substrate or openening of a pocket. Nevertheless the ability of both domains to move independently should be beneficial for HFE to bind both its complex-partners, TFR and Beta-2-Microglobulin, as <del class="diffchange diffchange-inline">each</del> <del class="diffchange diffchange-inline">of them</del> binds to <del class="diffchange diffchange-inline">one domain (TFR to</del> MHC I domain<del class="diffchange diffchange-inline">;</del> <del class="diffchange diffchange-inline">B2M</del> to C1 domain<del class="diffchange diffchange-inline">)</del>.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The lack of an active site makes it hard to give the movements a meaningful function such as cleaving of the substrate or openening of a pocket. Nevertheless the ability of both domains to move independently should be beneficial for HFE to bind both its complex-partners, TFR and Beta-2-Microglobulin, as <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">first</ins> binds to <ins class="diffchange diffchange-inline">the</ins> MHC I domain <ins class="diffchange diffchange-inline">and the second</ins> to<ins class="diffchange diffchange-inline"> the</ins> C1 domain.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
</tr>
</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27332&oldid=prevBernhoferm: /* Modes */2012-07-30T19:30:56Z<p><span dir="auto"><span class="autocomment">Modes</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:30, 30 July 2012</td>
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<td colspan="2" class="diff-lineno">Line 98:</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The lack of an active site makes it hard to give the movements a meaningful function such as cleaving of the substrate or openening of a pocket. Nevertheless the ability of both domains to move independently should be beneficial for HFE to bind both its complex-partners, TFR and Beta-2-Microglobulin, as each of them binds to one domain (TFR to MHC I domain; B2M to C1 domain).</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
</tr>
</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27331&oldid=prevBernhoferm: /* Modes */2012-07-30T19:22:15Z<p><span dir="auto"><span class="autocomment">Modes</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
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<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:22, 30 July 2012</td>
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<td colspan="2" class="diff-lineno">Line 96:</td>
<td colspan="2" class="diff-lineno">Line 96:</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>TODO: Describe motions... [http://www.youtube.com/watch?v=vY_Ry8J_jdw&t=8s or watch this.]</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>TODO: Describe motions... [http://www.youtube.com/watch?v=vY_Ry8J_jdw&t=8s or watch this.]</div></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td colspan="2" class="diff-empty"> </td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The most notable thing about the normal modes' motions is that the lowest ones (7-10) have almost no intra-domain movements (i.e. the MHC I and C1 domains move as a whole). Only mode 11 and 12 start bending the domains (e.g. the folding of the C1 domain in mode 11). The domains also do not seem to share any of their rotational axes and thus there is no classic hinge movement. These independent domain movements are probably caused by the lack of a strong inter-domain connection as there is only a single loop between them. Mode 7 is the only exception to this as both domains seem to rotate around almost the same axis.</div></td>
</tr>
<tr>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figtable id="webnma_modes7to12"></div></td>
</tr>
</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27302&oldid=prevBernhoferm: /* Transferrin receptor protein 1 (TFR) */2012-07-30T13:32:13Z<p><span dir="auto"><span class="autocomment">Transferrin receptor protein 1 (TFR)</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:32, 30 July 2012</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
</tr>
<tr>
<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In addition to the NMA performed on HFE we also wanted to take a brief look at the effects of HFE on the normal modes of TFR. We computed the normal modes for the chains A (HFE), B (B2M), and C (TFR) of 1de4 and for the C chain only. The atomic fluctuations (computed by WEBnm@) for TFR are shown in <xr id="tfr_fluctuations"/>. In order to be able to compare the values we cut out the fluctuations for TFR from the complex (A+B+C chain) and re-normalized them to sum up to 100 (like the ones for the C chain do). The plot shows a decrease in the whole end region (610-756), the ligand binding region<ref name="tfr-ligand">http://www.uniprot.org/uniprot/P02786</ref>. Due to the reduced mobility in this region after binding to HFE the complex should be pretty stable. <del class="diffchange diffchange-inline">This demonstrates</del> one of <del class="diffchange diffchange-inline">the</del> functions <del class="diffchange diffchange-inline">of</del> <del class="diffchange diffchange-inline">HFE:</del> <del class="diffchange diffchange-inline">competing</del> with other ligands that bind to TFR in order to reduce the iron transport.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In addition to the NMA performed on HFE we also wanted to take a brief look at the effects of HFE on the normal modes of TFR. We computed the normal modes for the chains A (HFE), B (B2M), and C (TFR) of 1de4 and for the C chain only. The atomic fluctuations (computed by WEBnm@) for TFR are shown in <xr id="tfr_fluctuations"/>. In order to be able to compare the values we cut out the fluctuations for TFR from the complex (A+B+C chain) and re-normalized them to sum up to 100 (like the ones for the C chain do). The plot shows a decrease in the whole end region (610-756), the ligand binding region<ref name="tfr-ligand">http://www.uniprot.org/uniprot/P02786</ref>. Due to the reduced mobility in this region after binding to HFE the complex should be pretty stable. <ins class="diffchange diffchange-inline">As</ins> one of <ins class="diffchange diffchange-inline">HFE's</ins> functions <ins class="diffchange diffchange-inline">is</ins> <ins class="diffchange diffchange-inline">to</ins> <ins class="diffchange diffchange-inline">compete</ins> with other ligands that bind to TFR in order to reduce the iron transport<ins class="diffchange diffchange-inline">, this induced stability might come in handy</ins>.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br style="clear:both;"></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br style="clear:both;"></div></td>
</tr>
</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27301&oldid=prevBernhoferm: /* Transferrin receptor protein 1 (TFR) */2012-07-30T13:27:18Z<p><span dir="auto"><span class="autocomment">Transferrin receptor protein 1 (TFR)</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:27, 30 July 2012</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="tfr_fluctuations"></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><figure id="tfr_fluctuations"></div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[File:Hemo_webnma_tfr_fluctuations.png|thumb|250px|<font size=1>'''Figure:''' <del class="diffchange diffchange-inline">TODO</del>.]]</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[File:Hemo_webnma_tfr_fluctuations.png|thumb|250px|<font size=1>'''Figure<ins class="diffchange diffchange-inline"> 2</ins>:''' <ins class="diffchange diffchange-inline">Comparison between the atomic fluctuations of TFR (1de4C) when in complex with HFE/B2M (green) and when unbound (red)</ins>.]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figure></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figure></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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</table>Bernhofermhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Normal_Mode_Analysis_Hemochromatosis&diff=27300&oldid=prevBernhoferm: /* B-factors */2012-07-30T13:25:12Z<p><span dir="auto"><span class="autocomment">B-factors</span></span></p>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>| align="right" | [[File:hemo_elnemo_1a6zC_bfactors.png|thumb|200px]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>| align="right" | [[File:hemo_elnemo_1a6zC_bfactors.png|thumb|200px]]</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|+ style="caption-side: bottom; text-align: left" |<font size=1>'''Table <del class="diffchange diffchange-inline">X</del>:''' <del class="diffchange diffchange-inline">TODO</del>.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|+ style="caption-side: bottom; text-align: left" |<font size=1>'''Table <ins class="diffchange diffchange-inline">9</ins>:''' <ins class="diffchange diffchange-inline">Comparison between the predicted and observed B-factors based on the first 100 normal modes computed by ElNemo (right) and mapping of the predicted B-factors onto HFE's structure (left). Color codes: red (150 and higher), orange (100 to 149), yellow (50 to 99), and green (below 50)</ins>.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figtable></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></figtable></div></td>
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</table>Bernhoferm