https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&feed=atom&action=historyMolecular Dynamcis analysis - Revision history2024-03-28T10:59:00ZRevision history for this page on the wikiMediaWiki 1.31.16https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15838&oldid=prevLanderer: /* Discussion */2011-10-03T16:55:11Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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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 16:55, 3 October 2011</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</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 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>'''The flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsd) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the <del class="diffchange diffchange-inline">transferrin</del> protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure also a cystein is placed which can form a disulfide bond. In case of 282a, the cystein is replaced by an tyrosin, in the case of 282b, the cystein is replaced by an serin. In both cases, the mutated residues can form a hydrogen bond with the cystein to replace the disulfide bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref>. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the tyrosin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible amino acids at this position should be calculated.</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>'''The flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsd) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the <ins class="diffchange diffchange-inline">TFR</ins> protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure also a cystein is placed which can form a disulfide bond. In case of 282a, the cystein is replaced by an tyrosin, in the case of 282b, the cystein is replaced by an serin. In both cases, the mutated residues can form a hydrogen bond with the cystein to replace the disulfide bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref>. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the tyrosin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible amino acids at this position should be calculated.</div></td>
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</table>Landererhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15837&oldid=prevLanderer: /* Discussion */2011-10-03T13:10:18Z<p><span dir="auto"><span class="autocomment">Discussion</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;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:10, 3 October 2011</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</div></td>
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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;"></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 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>'''The flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsd) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a <del class="diffchange diffchange-inline">tyrosine</del> is placed. In case of 282a, the <del class="diffchange diffchange-inline">tyrosine</del> is replaced by an <del class="diffchange diffchange-inline">serin</del>, <del class="diffchange diffchange-inline">which</del> <del class="diffchange diffchange-inline">are</del> <del class="diffchange diffchange-inline">both</del> <del class="diffchange diffchange-inline">polar</del> <del class="diffchange diffchange-inline">and neutral</del>, <del class="diffchange diffchange-inline">and</del> <del class="diffchange diffchange-inline">both</del> <del class="diffchange diffchange-inline">have</del> <del class="diffchange diffchange-inline">an</del> <del class="diffchange diffchange-inline">OH-group</del> <del class="diffchange diffchange-inline">to</del> <del class="diffchange diffchange-inline">form</del> <del class="diffchange diffchange-inline">a</del> <del class="diffchange diffchange-inline">hydrogen</del> <del class="diffchange diffchange-inline">bond. In</del> the <del class="diffchange diffchange-inline">case</del> <del class="diffchange diffchange-inline">of</del> <del class="diffchange diffchange-inline">282b,</del> <del class="diffchange diffchange-inline">the</del> <del class="diffchange diffchange-inline">thyronine</del> <del class="diffchange diffchange-inline">is</del> <del class="diffchange diffchange-inline">replaced</del> <del class="diffchange diffchange-inline">by</del> <del class="diffchange diffchange-inline">an</del> cystein<del class="diffchange diffchange-inline">,</del> <del class="diffchange diffchange-inline">which</del> <del class="diffchange diffchange-inline">also</del> <del class="diffchange diffchange-inline">could</del> <del class="diffchange diffchange-inline">form a hydrogen</del> bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref><del class="diffchange diffchange-inline"> but as on the other site also a cystein is placed, so a disulfide bond can be formed</del>. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the <del class="diffchange diffchange-inline">serin</del> in structure 282a. To get a better idea what happened here exactly, the<del class="diffchange diffchange-inline"> </del> flexibility for all other possible <del class="diffchange diffchange-inline">mutations</del> should be calculated.</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>'''The flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsd) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure<ins class="diffchange diffchange-inline"> also</ins> a <ins class="diffchange diffchange-inline">cystein</ins> is placed<ins class="diffchange diffchange-inline"> which can form a disulfide bond</ins>. In case of 282a, the <ins class="diffchange diffchange-inline">cystein</ins> is replaced by an <ins class="diffchange diffchange-inline">tyrosin</ins>, <ins class="diffchange diffchange-inline">in</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">case</ins> <ins class="diffchange diffchange-inline">of</ins> <ins class="diffchange diffchange-inline">282b</ins>, <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">cystein</ins> <ins class="diffchange diffchange-inline">is</ins> <ins class="diffchange diffchange-inline">replaced</ins> <ins class="diffchange diffchange-inline">by</ins> <ins class="diffchange diffchange-inline">an</ins> <ins class="diffchange diffchange-inline">serin.</ins> <ins class="diffchange diffchange-inline">In</ins> <ins class="diffchange diffchange-inline">both</ins> <ins class="diffchange diffchange-inline">cases,</ins> the <ins class="diffchange diffchange-inline">mutated</ins> <ins class="diffchange diffchange-inline">residues</ins> <ins class="diffchange diffchange-inline">can</ins> <ins class="diffchange diffchange-inline">form</ins> <ins class="diffchange diffchange-inline">a</ins> <ins class="diffchange diffchange-inline">hydrogen</ins> <ins class="diffchange diffchange-inline">bond</ins> <ins class="diffchange diffchange-inline">with</ins> <ins class="diffchange diffchange-inline">the</ins> cystein <ins class="diffchange diffchange-inline">to</ins> <ins class="diffchange diffchange-inline">replace</ins> <ins class="diffchange diffchange-inline">the</ins> <ins class="diffchange diffchange-inline">disulfide</ins> bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref>. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the <ins class="diffchange diffchange-inline">tyrosin</ins> in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible <ins class="diffchange diffchange-inline">amino acids at this position</ins> should be calculated.</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;"></td>
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<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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties <del class="diffchange diffchange-inline">if</del> the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors movement like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very interesting to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this<del class="diffchange diffchange-inline"> an analyze the</del> effect.</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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties <ins class="diffchange diffchange-inline">of</ins> the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors movement like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very interesting to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this effect.</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>== References ==</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>== References ==</div></td>
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</table>Landererhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15325&oldid=prevGreil: /* Discussion */2011-09-21T15:54:07Z<p><span dir="auto"><span class="autocomment">Discussion</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 15:54, 21 September 2011</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</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="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 flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the <del class="diffchange diffchange-inline">rmsf</del>) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the thyronine is replaced by an cystein, which also could form a hydrogen bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfide bond can be formed. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the serin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible mutations should be calculated.</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>'''The flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the <ins class="diffchange diffchange-inline">rmsd</ins>) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the thyronine is replaced by an cystein, which also could form a hydrogen bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfide bond can be formed. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the serin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible mutations should be calculated.</div></td>
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</table>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15324&oldid=prevGreil: /* Discussion */2011-09-21T15:43:46Z<p><span dir="auto"><span class="autocomment">Discussion</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="center"</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>|[[File:disc_compared_flexibility.png|thumb|center|400px|Figure 4.1: Comparison of the flexibility per residue in nm. Also the difference of the mutated structures compared to the wild-type is shown. a value close to zero indicates no change in flexibility while a value larger zero indicate a higher flexibility in the wild-type structure and a value smaller zero a higher flexibility in the mutated structure.]]</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>|[[File:disc_compared_flexibility.png|thumb|center|400px|Figure 4.1: Comparison of the flexibility per residue in nm. Also the difference of the mutated structures compared to the wild-type is shown. a value close to zero indicates no change in flexibility while a value larger zero indicate a higher flexibility in the wild-type structure and a value smaller zero a higher flexibility in the mutated structure.]]</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:1a6z_all_superim_bfactors.png|thumb|center|400px|Figure 4.2: Superimposed structures of the wild-type and the two mutated structures colored according to <del class="diffchange diffchange-inline">there</del> b-factors. Blue colored regions are stable ones, while red regions are the flexible ones. The marked regions corresponds in <del class="diffchange diffchange-inline">there</del> numbering to the boxes numbered in Figure 4.1.]]</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>|[[File:1a6z_all_superim_bfactors.png|thumb|center|400px|Figure 4.2: Superimposed structures of the wild-type and the two mutated structures colored according to <ins class="diffchange diffchange-inline">their</ins> b-factors. Blue colored regions are stable ones, while red regions are the flexible ones. The marked regions corresponds in <ins class="diffchange diffchange-inline">their</ins> numbering to the boxes numbered in Figure 4.1.]]</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>|[[File:1a6z_all_superim_bfactors_detail_4.png|thumb|center|400px|Figure 4.3: Detailed look at the mutated side. For each structure, the residue at position 282 is visible, also the interacting cysteine.]]</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>|[[File:1a6z_all_superim_bfactors_detail_4.png|thumb|center|400px|Figure 4.3: Detailed look at the mutated side. For each structure, the residue at position 282 is visible, also the interacting cysteine.]]</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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</table>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15323&oldid=prevGreil: /* Discussion */2011-09-21T15:41:48Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:41, 21 September 2011</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>==Discussion ==</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>==Discussion ==</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>In all cases, the simulation parameter, like temperature, pressure and so on behave the same. So, we assume that all simulation reached the same state and are comparable.<del class="diffchange diffchange-inline"> </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>In all cases, the simulation parameter, like temperature, pressure and so on behave the same. So, we assume that all simulation reached the same state and are comparable.</div></td>
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<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>
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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 Solvent''' accessible surface remains the same in all simulations, just in the case of 282a, we see a slightly change towards the hydrophobix residues on the surface. For the wild-type and the 282b structure, an equal amount of hydrophilic and hydrophobic residues are accessible. The high hydrophilic fraction of the surface is probably due to the fact that the HFE protein is located in the plasmamembrane, whereat the membrane region is not part of the simulated structure. '''The Ramachandran''' plots of the simulations show, that the wild-type is more diverse than the two mutated structures. A larger difference is specialy in the positive phi range observable (Figures 1.25 2.25 3.25). Here, many angle compinations present in the wild-type are missing in the mutated structures. The two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimansional counterpart. For the wild-type and the 282b structure, we see a slowe divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactliy what one can observe in the flexibility analysis. '''The flexibility''' is the most interessting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsf) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connectiing two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whitin a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole princible can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows thze wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a differents at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connnected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the tyronine is replaced by an cystein, which also could form a hydrogen bondy<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfid bond can be formed. This disulfid bond is more stabile as the hydrogen bonds since no water nach attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibilty is decreased by the serin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible mutations should be calculated.</div></td>
<td colspan="2" class="diff-empty"> </td>
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<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 Solvent''' accessible surface remains the same in all simulations, just in the case of 282a, we see a slightly change towards the hydrophobic residues on the surface. For the wild-type and the 282b structure, an equal amount of hydrophilic and hydrophobic residues are accessible. The high hydrophilic fraction of the surface is probably due to the fact that the HFE protein is located in the plasma membrane, whereat the membrane region is not part of the simulated structure.</div></td>
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<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>
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<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 Ramachandran''' plots of the simulations show, that the wild-type is more diverse than the two mutated structures. A larger difference is specially in the positive phi range observable (Figures 1.25 2.25 3.25). Here, many angle combinations present in the wild-type are missing in the mutated structures.</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;"></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 two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimensional counterpart. For the wild-type and the 282b structure, we see a slow divergence than in the case of 282a. WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactly what one can observe in the flexibility analysis.</div></td>
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<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 flexibility''' is the most interesting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsf) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connecting two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whiting a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole principle can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows the wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a difference at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the thyronine is replaced by an cystein, which also could form a hydrogen bond<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfide bond can be formed. This disulfide bond is more stable as the hydrogen bonds since no water can attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibility is decreased by the serin in structure 282a. To get a better idea what happened here exactly, the flexibility for all other possible mutations should be calculated.</div></td>
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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;"></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>
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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;"></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>{|align="center"</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>{|align="center"</div></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>|[[File:disc_compared_flexibility.png|thumb|center|400px|Figure 4.1: <del class="diffchange diffchange-inline">Comparisson</del> of the flexibility per residue in nm. Also the difference of the mutated structures compared to the wild-type is shown. a value close to zero indicates no change in flexibility while a value larger zero indicate a higher flexibility in the wild-type structure and a value smaller zero a higher flexibility in the mutated structure.]]</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:disc_compared_flexibility.png|thumb|center|400px|Figure 4.1: <ins class="diffchange diffchange-inline">Comparison</ins> of the flexibility per residue in nm. Also the difference of the mutated structures compared to the wild-type is shown. a value close to zero indicates no change in flexibility while a value larger zero indicate a higher flexibility in the wild-type structure and a value smaller zero a higher flexibility in the mutated structure.]]</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;"><div>|[[File:1a6z_all_superim_bfactors.png|thumb|center|400px|Figure 4.2: Superimposed structures of the wild-type and the two mutated structures colored according to there b-factors. Blue colored regions are stable ones, while red regions are the flexible ones. The marked regions corresponds in there numbering to the boxes numbered in Figure 4.1.]]</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>|[[File:1a6z_all_superim_bfactors.png|thumb|center|400px|Figure 4.2: Superimposed structures of the wild-type and the two mutated structures colored according to there b-factors. Blue colored regions are stable ones, while red regions are the flexible ones. The marked regions corresponds in there numbering to the boxes numbered in Figure 4.1.]]</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;"><div>|[[File:1a6z_all_superim_bfactors_detail_4.png|thumb|center|400px|Figure 4.3: Detailed look at the mutated side. For each structure, the residue at position 282 is visible, also the interacting cysteine.]]</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>|[[File:1a6z_all_superim_bfactors_detail_4.png|thumb|center|400px|Figure 4.3: Detailed look at the mutated side. For each structure, the residue at position 282 is visible, also the interacting cysteine.]]</div></td>
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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;"></td>
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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;"></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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties if the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors <del class="diffchange diffchange-inline">movment</del> like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very <del class="diffchange diffchange-inline">intersting</del> to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this an analyze the effect.</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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties if the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors <ins class="diffchange diffchange-inline">movement</ins> like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very <ins class="diffchange diffchange-inline">interesting</ins> to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this an analyze the effect.</div></td>
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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;"></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>
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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>== References ==</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>== References ==</div></td>
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</table>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15322&oldid=prevGreil at 15:38, 21 September 20112011-09-21T15:38:25Z<p></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15322&oldid=15321">Show changes</a>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15321&oldid=prevGreil: /* Wildtype */2011-09-21T15:28:00Z<p><span dir="auto"><span class="autocomment">Wildtype</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 15:28, 21 September 2011</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> Box 2001 5</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> Box 2001 5</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>
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<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>The Simulation took ''6h33:50'' <del class="diffchange diffchange-inline">ans</del> the simulation speed was ''36.564 ns/day''. So, to reach 1 second of simulation, we had to wait around ''75061'' years. But this is a bit to long for this Project, so we just used the results we got. The potential energy was fluctuating about ''-9.185e+05 kJ/mol'' with a range of about ''0.15e+04 kJ/mol''. These information are given in the different log-files provided by the simulation. To create the pdb file for the visualization, we used the command <code>trjconv -s ref_md.tpr -f ref_md.tpr.xtc -o protein.pdb -pbc nojump -dt 10</code>.</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>The Simulation took ''6h33:50'' <ins class="diffchange diffchange-inline">and</ins> the simulation speed was ''36.564 ns/day''. So, to reach 1 second of simulation, we had to wait around ''75061'' years. But this is a bit to long for this Project, so we just used the results we got. The potential energy was fluctuating about ''-9.185e+05 kJ/mol'' with a range of about ''0.15e+04 kJ/mol''. These information are given in the different log-files provided by the simulation. To create the pdb file for the visualization, we used the command <code>trjconv -s ref_md.tpr -f ref_md.tpr.xtc -o protein.pdb -pbc nojump -dt 10</code>.</div></td>
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<td class="diff-marker"> </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>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15320&oldid=prevGreil: /* Wildtype */2011-09-21T15:26:28Z<p><span dir="auto"><span class="autocomment">Wildtype</span></span></p>
<a href="https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15320&oldid=15231">Show changes</a>Greilhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15231&oldid=prevLanderer: /* Discussion */2011-09-19T21:21:47Z<p><span dir="auto"><span class="autocomment">Discussion</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;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:21, 19 September 2011</td>
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<td colspan="2" class="diff-lineno">Line 751:</td>
<td colspan="2" class="diff-lineno">Line 751:</td>
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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;"></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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties if the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors movment like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very intersting to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this an analyze the effect.</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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties if the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors movment like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very intersting to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this an analyze the effect.</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;"></td>
<td colspan="2" class="diff-empty"> </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;"></td>
<td colspan="2" class="diff-empty"> </td>
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<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;"></td>
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<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>As both mutations are at the same position and change the properties of the protein different, the loss in function is probaly more due to the specific residue than due to the spesific position at this position is not interacting directly with the known interaction partners. Also we are sure that the reason for the loss in function is in both cases a diffrent one. In the case of 282a, the loss in function is most likely due to a loss in flexibility and a change in the properties of the surface while the functional loss for the other mutation (282b) is more due to</div></td>
<td colspan="2" class="diff-empty"> </td>
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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;"></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>
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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>== References ==</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>== References ==</div></td>
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</table>Landererhttps://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Molecular_Dynamcis_analysis&diff=15230&oldid=prevLanderer: /* Discussion */2011-09-19T21:21:32Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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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 21:21, 19 September 2011</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>==Discussion ==</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>In all cases, the simulation parameter, like temperature, pressure and so on behave the same. So, we assume that all simulation reached the same state and are comparable. </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>In all cases, the simulation parameter, like temperature, pressure and so on behave the same. So, we assume that all simulation reached the same state and are comparable. </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>'''The Solvent''' accessible surface remains the same in all simulations, just in the case of 282a, we see a slightly change towards the hydrophobix residues on the surface. For the wild-type and the 282b structure, an equal amount of hydrophilic and hydrophobic residues are accessible. The high hydrophilic fraction of the surface is probably due to the fact that the HFE protein is located in the plasmamembrane, whereat the membrane region is not part of the simulated structure. '''The Ramachandran''' plots of the simulations show, that the wild-type is more diverse than the two mutated structures. A larger difference is specialy in the positive phi range observable (Figures 1.25 2.25 3.25). Here, many angle compinations present in the wild-type are missing in the mutated structures. The two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimansional counterpart. For the wild-type and the 282b structure, we see a slowe divergence than in the case of 282a. </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 Solvent''' accessible surface remains the same in all simulations, just in the case of 282a, we see a slightly change towards the hydrophobix residues on the surface. For the wild-type and the 282b structure, an equal amount of hydrophilic and hydrophobic residues are accessible. The high hydrophilic fraction of the surface is probably due to the fact that the HFE protein is located in the plasmamembrane, whereat the membrane region is not part of the simulated structure. '''The Ramachandran''' plots of the simulations show, that the wild-type is more diverse than the two mutated structures. A larger difference is specialy in the positive phi range observable (Figures 1.25 2.25 3.25). Here, many angle compinations present in the wild-type are missing in the mutated structures. The two dimensional '''Root mean square deviation''' over time shows in all three cases the same picture as the one dimansional counterpart. For the wild-type and the 282b structure, we see a slowe divergence than in the case of 282a. <ins class="diffchange diffchange-inline">WT and 282b show a larger divergence in the early states of the simulation while 282a is changing just slightly. This indicates a less flexibility in this structure and a larger one in the other two. This is exactliy what one can observe in the flexibility analysis. '''The flexibility''' is the most interessting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsf) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connectiing two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whitin a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole princible can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows thze wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a differents at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connnected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the tyronine is replaced by an cystein, which also could form a hydrogen bondy<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfid bond can be formed. This disulfid bond is more stabile as the hydrogen bonds since no water nach attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibilty is decreased by the serin in structure 282a. To get a better idea what happend here exactly, the flexibility for all other possible mutations should be calculated.</ins></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;"></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 flexibility''' is the most interessting part. While the structure 282a is less flexible, the mutated structure 282b is more flexible than the wild-type. The structure 282a has a flexibility index (sum over the rmsf) of 49.57 and the structure has a flexibility index of 53.457, while the wild-type has one of 51.4624 which is very close to the mean of 51.4966. So, the wild-type can be called a mean structure in this case. We can observe four interesting points in the flexibility distribution shown in Figure 4.1. These regions are also marked in the structures shown in Figure 4.2. The first one is within a loop connectiing two beta-strands. Here the structure 282a is more flexible than the other structures, so this could causes issues by forming a beta-sheet by the two beta-strands. Therefore the stability of the whole protein could be affected. In the second case, both mutated structures are less flexible than the wild type. The position is also whitin a loop, this time connecting a beta-sheet with an alpha helix. As this helix is assumed to be part of an active site, a loss in flexibility could cause issues at binding at the transferrin protein. So, a key-hole princible can no longer act. The third case is also a transfer from a beta-sheet into an alpha-helix. Here we have an interesting change in flexibility as first, the flexibility is increased at the structure 282b and 282a follows thze wild-type, while just a few residues later the flexibility changes and the structure follows the wild-type. The other mutated structure (282a) behaves the opposite. The fourth case shows a differents at a very flexible region. The mutation 282a causes a high loss in flexibility at this point, while the flexibility is not affected by the other mutation. All cases have in common that they are not connnected to the mutated side in sequence and in structure. Just in case 4, the mutated residue is interacting with the beta-sheet which is connected by the flexible region marked as 4. The mutated residue interacts with a cysteine (Figure 4.3). In the wild-type structure a tyrosine is placed. In case of 282a, the tyrosine is replaced by an serin, which are both polar and neutral, and both have an OH-group to form a hydrogen bond. In the case of 282b, the tyronine is replaced by an cystein, which also could form a hydrogen bondy<ref>Gregoret LM, Rader SD, Fletterick RJ, Cohen FE.: Hydrogen bonds involving sulfur atoms in proteins.</ref> but as on the other site also a cystein is placed, so a disulfid bond can be formed. This disulfid bond is more stabile as the hydrogen bonds since no water nach attack to break up the secondary structure. Therefor it is surprisingly, that the 282b structure is flexible as the wild-type while the flexibilty is decreased by the serin in structure 282a. To get a better idea what happend here exactly, the flexibility for all other possible mutations should be calculated.</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;"></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>Most interestingly is, that both mutations are at the same position and change the properties of the protein different, so the loss in function is more due to the spesific residue than due to the spesific position as this position is not directly interacting with the known interaction partners.</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>All in all, we see two different mutation which changes the flexibility all over the protein, not just in the mutated region. As the region is not interaction directly with a binding partner, and also the biochemical properties if the amino acid is not changed, the loss of function is most likely due to the change in flexibility. A major question which remains unanswered is, why are so many regions affected which are placed not even in the same domain. As the HFE forms a complex with Beta-2-Microglobulin (B2M) to stabilize itself and avoid scissors movment like it is observable in the normal mode analysis, the beta-sheet close to the mutated residue could be affected (Figure 4.3) and the stabilizing effect can not take place. It also would be very intersting to see which of the other possible amino acids lead to a gain or loss in flexibility to compare this an analyze the effect.</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;"></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>As both mutations are at the same position and change the properties of the protein different, the loss in function is probaly more due to the specific residue than due to the spesific position at this position is not interacting directly with the known interaction partners. Also we are sure that the reason for the loss in function is in both cases a diffrent one. In the case of 282a, the loss in function is most likely due to a loss in flexibility and a change in the properties of the surface while the functional loss for the other mutation (282b) is more due to</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>== References ==</div></td>
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</table>Landerer