Difference between revisions of "Canavan Task 7 - Structure-based mutation analysis"

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(Mapping of mutations)
(Mapping of mutations)
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<td style="border-bottom:solid;border-right:solid">E285A</td>
 
<td style="border-bottom:solid;border-right:solid">E285A</td>
 
<td style="border-bottom:solid;border-right:solid">E285 is located in the binding pocket with a distance of 3.6 A to the substrate analog of 2O4H. It does not interact with the substrate, but has hydrogen bonds interactions to T118 and the backbone of Y288. These hydrogen bonds can not be established by the mutant residue alanine </td>
 
<td style="border-bottom:solid;border-right:solid">E285 is located in the binding pocket with a distance of 3.6 A to the substrate analog of 2O4H. It does not interact with the substrate, but has hydrogen bonds interactions to T118 and the backbone of Y288. These hydrogen bonds can not be established by the mutant residue alanine </td>
<td style="border-bottom:solid;border-right:solid"><figure id="e285a_hb" >[[File:e285a_interactions.png|thumb|right|300px|<b> <xr nolink id="e285a_hb"/></b><br>.]]</figure></td>
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<td style="border-bottom:solid;border-right:solid"><figure id="e285a_hb" >[[File:e285a_interactions.png|thumb|right|300px|<b> <xr nolink id="e285a_hb"/></b>]]</figure></td>
 
</tr>
 
</tr>
   
 
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<td style="border-bottom:solid;border-right:solid">A305E</td>
 
<td style="border-bottom:solid;border-right:solid">A305E</td>
  +
<td style="border-bottom:solid;border-right:solid">A305 is located at the end of the 13th beta sheet at the C-terminus of the protein. In figure <xr nolink id="a305e_crowded"/> the mutated residue glutamic acid is shown in red. The space at this position is rather crowded, so that alanine as a small residue fits very well in this position. Glutamic acid instead, hardly finds space and overlaps with neighboring residues.</td>
<td style="border-bottom:solid;border-right:solid">E285 is </td>
 
<td style="border-bottom:solid;border-right:solid"><figure id="a305e_crowded">[[File:a305e_crowded.png|thumb|right|250px|<b><xr nolink id="a305e_crowded"/></b><br>Presented is a possible orientation for the mutated residue E305. As can be seen from the overlap of the spheres of E305 with neighboring residues there is not enough space for glutamic acid at this position.]]</figure></td>
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<td style="border-bottom:solid;border-right:solid"><figure id="a305e_crowded">[[File:a305e_crowded.png|thumb|right|250px|<b><xr nolink id="a305e_crowded"/></b>]]</figure></td>
 
</tr>
 
</tr>
   
 
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<td style="border-bottom:solid;border-right:solid">G123E</td>
 
<td style="border-bottom:solid;border-right:solid">G123E</td>
<td style="border-bottom:solid;border-right:solid">The mutated residue E123 is presented in red. There is no steric hindrance for this mutated residue. </td>
+
<td style="border-bottom:solid;border-right:solid">G123 is located at the beginning of the fourth beta strand in Aspartoacylase. This strand is not buried but is solvent accessible. In figure <xr nolink id="g123e_space"/>, the mutated residue E123 is presented in red. Eventhough glutamic acid is much larger than glycin, there is enough space and no clashes occur. Furthermore, Glycin is not involved in any interactions. </td>
 
<td style="border-bottom:solid;border-right:solid"><figure id="g123e_space">[[File:g123e_space.png|thumb|right|250px|<b><xr nolink id="g123e_space"/></b><br>.]]</figure></td>
 
<td style="border-bottom:solid;border-right:solid"><figure id="g123e_space">[[File:g123e_space.png|thumb|right|250px|<b><xr nolink id="g123e_space"/></b><br>.]]</figure></td>
 
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Revision as of 14:13, 20 June 2012

Protocol

Further information can be found in the protocol.

Mapping of mutations

<figure id="aspa_mut_overview">

<xr nolink id="aspa_mut_overview"/>
ChainA of the aspa structure is shown in cartoon representation. Chain B is shown in surface representation to emphasize the dimer interface. The intermediate substrate analog is shown in blue. Disease causing mutations are shown in red and non-disease causing SNPs are colored in orange.

</figure>

We use the same mutations for this analysis as for the sequence based mutation analysis.

As a struture we used 2O4H which was crystallized as a dimer (see protocol for further info). For our analysis we will only consider chainA.

In <xr id="aspa_mut_overview"/> you can see an overview of the Aspa structure with the mutations mapped onto the structure.

<figtable id="mutation_vis_table">

<xr nolink id="mutation_vis_table"/> Visualization of each mutations and analysis
Mutation Comment Visualization
E285A E285 is located in the binding pocket with a distance of 3.6 A to the substrate analog of 2O4H. It does not interact with the substrate, but has hydrogen bonds interactions to T118 and the backbone of Y288. These hydrogen bonds can not be established by the mutant residue alanine <figure id="e285a_hb" >
<xr nolink id="e285a_hb"/>
</figure>
A305E A305 is located at the end of the 13th beta sheet at the C-terminus of the protein. In figure <xr nolink id="a305e_crowded"/> the mutated residue glutamic acid is shown in red. The space at this position is rather crowded, so that alanine as a small residue fits very well in this position. Glutamic acid instead, hardly finds space and overlaps with neighboring residues. <figure id="a305e_crowded">
<xr nolink id="a305e_crowded"/>
</figure>
G123E G123 is located at the beginning of the fourth beta strand in Aspartoacylase. This strand is not buried but is solvent accessible. In figure <xr nolink id="g123e_space"/>, the mutated residue E123 is presented in red. Eventhough glutamic acid is much larger than glycin, there is enough space and no clashes occur. Furthermore, Glycin is not involved in any interactions. <figure id="g123e_space">
<xr nolink id="g123e_space"/>
.
</figure>
R71H E285 is <figure id="r71h_hbonds">
<xr nolink id="r71h_hbonds"/>
The mutated residue H71 is presented in red. H71 is not able to build the Hbonds with the substrate or neighboring residues as does R71.
</figure>
R71K E285 is <figure id="r71k_hbonds">
<xr nolink id="r71k_hbonds"/>
The mutated residue K71 is presented in red. K71 almost has the same shape as R71 and might also be able to form an Hbond to the substrate or D68.
</figure>

</figtable>