Difference between revisions of "Canavan Task 8 - Molecular Dynamics Simulations"

From Bioinformatikpedia
(Choosing Mutants)
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</table>
 
</table>
 
</figtable>
 
</figtable>
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==Running Jobs ==
  +
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We had no problems to get the jobs started.
  +
squeue -u di34fog --cluster mpp1
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There are currently 5 jobs running:
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* wt MD run with original 2O4H:A
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* K213E mutant based on Scwrl_min structure
  +
* K213E mutant based on Foldx_min structure
  +
* A305E mutant based on Scwrl_min structure
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* A305E mutant based on Foldx_min structure

Revision as of 16:01, 27 June 2012

Protocol

Further information can be found in the protocol.


Choosing Mutants

We decided to use A305E and K213E for the MD analysis. In <xr id="CD_MD_mutants"/>.


<figtable id="CD_MD_mutants">

<xr nolink id="CD_MD_mutants"/> Description of the structural environment of each mutation and visualization of the pymol mutation and the scwrl mutation output.
Mutation Comment Visualisation
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.
We decided to use this mutation, since we expect to see a huge effect in structure with the MD simulation.
<figure id="a305e_crowded">
<xr nolink id="a305e_crowded"/>
</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 blue and the reference structure and residue in green. The mutated residue Glutamic Acid is able to form an HBond with the neighbouring helix. We chose this mutation since we do not expect to see any effect from this mutation. Also, our analysis so far suggests, that this mutation is not disease causing. Yet, it is annotated in the HGMD to cause Canavan Disease. We are curious about the MD outcome to either see the HGMD annotation confirmed or our predictions confirmed. <figure id="k213e_pymol">
<xr nolink id="k213e_pymol"/>
</figure>

</figtable>


Running Jobs

We had no problems to get the jobs started.

squeue -u di34fog --cluster mpp1

There are currently 5 jobs running:

  • wt MD run with original 2O4H:A
  • K213E mutant based on Scwrl_min structure
  • K213E mutant based on Foldx_min structure
  • A305E mutant based on Scwrl_min structure
  • A305E mutant based on Foldx_min structure