Molecular Dynamics Simulations TSD

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Revision as of 22:39, 29 June 2012 by Reeb (talk | contribs) (Intermediate Structures)

The journal for this task can be found here.

Mutations

Based on previous analyses the following two mutations were chosen for the MD analysis.
R178H because it is a disease causing mutation with a strong effect on the active site. R178C was not chosen, since there seems to be no possibility to make it work at all, while for the mutation to histidine it should be possible ot fit the residue in the binding pocket. This will still not allow coordination of the ligand, so the mutation is disease-causing for sure, but it will still be interesting to see where the sidechain is placed and what alternative interactions might arise.
The second mutation is P182L. The residue is found at the protein surface, near the binding site to the beta-subunit. However it does not seem to play a role in the interaction. It will be interesting to see how this changes due to MD simulation. In addition, it should be oberserved how the helix changes, now that the helix breaker proline is not present anymore.

Simulations

Intermediate Structures

In the AGroS pipeline several structures are created in intermediate steps. <xr id="tbl:intermed"/> lists all of these and gives an explanation of their content.

<figtable id="tbl:intermed">

TODO
File Description

</figtable>


The state of the job and whether it really sits in the queue can be checked with the command squeue -u <username> <queue> where the queue can either be --clusters=mpp1 or --partition=mpp1_inter.
Once this all worked you have to wait and write a bit about the different steps of the simulation etc.
We also want you to look at the intermediate PDB files created in the workflow, visualize them and explain what is special, different about them and why we need them.

References

<references/>