Difference between revisions of "Canavan Task 7 - Structure-based mutation analysis"
From Bioinformatikpedia
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<td style="border-bottom:solid;border-right:solid">E285A</td> |
<td style="border-bottom:solid;border-right:solid">E285A</td> |
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<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> |
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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> |
+ | <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> |
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<td style="border-bottom:solid;border-right:solid">A305E</td> |
<td style="border-bottom:solid;border-right:solid">A305E</td> |
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+ | <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> |
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− | <td style="border-bottom:solid;border-right:solid">E285 is </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> |
+ | <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> |
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<td style="border-bottom:solid;border-right:solid">G123E</td> |
<td style="border-bottom:solid;border-right:solid">G123E</td> |
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− | <td style="border-bottom:solid;border-right:solid"> |
+ | <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">
</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">
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" ></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"></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"></figure> |
R71H | E285 is | <figure id="r71h_hbonds"></figure> |
R71K | E285 is | <figure id="r71k_hbonds"></figure> |
</figtable>