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

From Bioinformatikpedia
(Mapping of mutations)
(Mapping of mutations)
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<td style="border-bottom:solid;border-right:solid;font-weight:bold" >Mutation</td>
 
<td style="border-bottom:solid;border-right:solid;font-weight:bold" >Mutation</td>
 
<td style="border-bottom:solid;border-right:solid;font-weight:bold" >Comment</td>
 
<td style="border-bottom:solid;border-right:solid;font-weight:bold" >Comment</td>
<td style="border-bottom:solid;border-right:solid;font-weight:bold" >Visualization</td>
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<td style="border-bottom:solid;border-right:solid;font-weight:bold" > Pymol</td>
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<td style="border-bottom:solid;border-right:solid;font-weight:bold" > Scwrl</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>
 
<td style="border-bottom:solid;border-right:solid"><figure id="e285a_hb" >[[File:e285a_interactions.png|thumb|right|200px|<b> <xr nolink id="e285a_hb"/></b>]]</figure></td>
 
<td style="border-bottom:solid;border-right:solid"><figure id="e285a_hb" >[[File:e285a_interactions.png|thumb|right|200px|<b> <xr nolink id="e285a_hb"/></b>]]</figure></td>
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<td style="border-bottom:solid;border-right:solid"><figure id="e285a_scwrl" >[[File:e285a_sqwrl.png|thumb|right|200px|<b> <xr nolink id="e285a_scwrl"/></b>]]</figure></td>
 
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Revision as of 17:55, 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 Pymol Scwrl
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>
<figure id="e285a_scwrl" >
<xr nolink id="e285a_scwrl"/>
</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 solvent accessible. In <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 R71 is located at the end of the fourth helix in the active site of the enzyme. It is involved in substrate binding via one Hbond. It also forms other Hbonds with an active water molecule and D68. In <xr nolink id="r71h_hbonds"/> the mutated residue H71 is presented in red and the intermediate substrate analog in blue. H71 is not able to build the Hbonds with the substrate or neighboring residues as does R71 <figure id="r71h_hbonds">
<xr nolink id="r71h_hbonds"/>
</figure>
R71K R71 is located at the end of the fourth helix in the active site of the enzyme. It is involved in substrate binding via one Hbond. It also forms other Hbonds with an active water molecule and D68. In <xr nolink id="r71k_hbonds"/> the mutated residue K71 is presented in red and the intermediate substrate analog in blue. K71 almost has the same shape as R71 and might also be able to form an Hbond to the substrate or D68. <figure id="r71k_hbonds">
<xr nolink id="r71k_hbonds"/>
</figure>
K213E K213 is located on the loop connecting the N-, and C-terminal of the enzyme. It is on the surface of the protein, far away from the binding site or the dimer interaction site. In <xr nolink id="k213e_pymol"/>, the mutated residue K213E as computed by PyMol is presented in red and the reference structure and residue in green. The mutated residue Glutamic Acid is able to form an HBond with the neighbouring helix. <xr nolink id="k213e_scwrl"/> shows the mutated residue as computed by scwrl. <figure id="k213e_pymol">
<xr nolink id="k213e_pymol"/>
</figure>
<figure id="k213e_scwrl">
<xr nolink id="k213e_scwrl"/>
</figure>
V278M V278M is located on a loop in the C-terminal of the enzyme. It is also on the surface of the protein, far away from the binding site or the dimer interaction site. In <xr nolink id="v278m_pymol"/>, the mutated residue V278M as computed by PyMol is presented in red and the reference structure and residue in green. Both the mutated and the original residue are part of a beta-sheet and form two HBonds each. <xr nolink id="v278m_scwrl"/> shows the mutated residue as computed by scwrl. <figure id="v278m_pymol">
<xr nolink id="v278m_pymol"/>
</figure>
<figure id="v278m_scwrl">
<xr nolink id="v278m_scwrl"/>
</figure>
M82T M82T is located on a loop in the N-terminal of the enzyme. It is on the surface of the protein, not close to the interaction site, but in the neighbourhood of the dimer interaction site. In <xr nolink id="m82t_pymol"/>, the mutated residue M82T as computed by PyMol is presented (colours as before). This residue does not form any HBonds. <xr nolink id="m82t_scwrl"/> shows the mutated residue as computed by scwrl. <figure id="m82t_pymol">
<xr nolink id="m82t_pymol"/>
</figure>
<figure id="m82t_scwrl">
<xr nolink id="m82t_scwrl"/>
</figure>
E235K This residue is again located on a loop in the C-terminal region of the enzyme. It also lies on the surface of the protein, in close neighbourhood to the dimer interaction site. In <xr nolink id="e235k_pymol"/>, the mutated residue E235K as computed by PyMol is presented (colours as before). This residue points out into the solvent and does not form any intra-molecular HBonds. <xr nolink id="e235k_scwrl"/> shows the mutated residue as computed by scwrl. <figure id="e235k_pymol">
<xr nolink id="e235k_pymol"/>
</figure>
<figure id="e235k_scwrl">
<xr nolink id="e235k_scwrl"/>
</figure>
I270T This residue is located on a beta-strand in the C-Terminal region of the protein where it forms HBonds to a neighbouring beta-strand. It also lies on the surface of the protein, and also in close neighbourhood to the dimer interaction site. In <xr nolink id="i270t_pymol"/>, the mutated residue I270T as computed by PyMol is presented (colours as before). <xr nolink id="i270t_scwrl"/> shows the mutated residue as computed by scwrl. <figure id="i270t_pymol">
<xr nolink id="i270t_pymol"/>
</figure>
<figure id="i270t_scwrl">
<xr nolink id="i270t_scwrl"/>
</figure>

</figtable>

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