Difference between revisions of "Molecular Dynamics Simulations TSD"

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(Intermediate Structures)
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== Final structures ==
 
== Final structures ==
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Waiting for jobs to start/finish
 
===Wildtype===
 
===Wildtype===
 
===P182L===
 
===P182L===

Revision as of 18:33, 2 July 2012

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. Three scripts are repeatedly used:

  • findBreaks.pl: Checks for breaks in the structure. Sometimes parts are unresolved e.g. because they would hinder crystallization.
  • clshwtr.pl: Removes water molecules that have a Euclidian distance to the protein below a user defined cutoff.
  • repairPDB.pl: PDB files tend to be highly heterogenous. This script addresses several of the common issues and for example allows to remove water atoms, hydrogens, extract only the protein part or renumber residues.

<figtable id="tbl:intermed">

List of intermediate structures created during an AGroS run. Structures are sorted by time of creation in the pipeline beginning with the oldest ones. After the input file, only the suffixes added to the filename are denoted. The extension for all files is .pdb unless denoted otherwise. Scripts denotes the scripts involved in creation of the file and the important parameters given.
File Description Scripts
2gjx178H Input structure, with waters removed repairdPDB.sh -nohoh, clshwtr.pl with cutoff 2.6
_br Protein part only repairdPDB.sh -jprot
_br_0 Structure until the first break. Since there are none, it is the full structure again findBreaks.pl
.pdb2 2gjx178H.pdb with hydrogens removed repairPDB -noh
_repair Indices changed to begin with 0 and DNA removed repairPDB -nodna -offset
_repair_0 Recalculated indices, if several chains present in input sepPDB, repairPDB -rres
_water Waters with B-value below 15 Å extracted from the structure repairPDB -ssw 15
_dna DNA extracted from the structure repairPDB -dna
_sc Side chain placements by SCWRLv4 scwrl
_nh Protein part only from _sc. In addition structural water and DNA (previously extracted _water and _dna files) repairPDB -jprot
_solv_tmp Addition of ions (Na+ and Cl-) genion -pname NA+ -nname CL-
_solv Remove overlapping solvents from _solv_tmp repairPDB -cleansol
_solv.pdb2 DNA and protein part only from _solv_tmp repairPDB -dna, repairPDB -jprot
solv_0 Input for creation of custom position restraints for several chains, if present ?
_solv_min Minimization run with only solvent flexible. Protein backbone and sidechains are fixed grompp, mdrun
_solv_min.pdb2 Protein only extracted from _solv_min.pdb repairPDB -jprot
_solv_min_0 Input for creation of custom position restraints for several chains, if present ?
_solv_min2 Minimization with only backbone fixed grompp, mdrun
_solv_min3 Another minimization with fixed backbone, this time using conjugate gradient as integrator grompp, mdrun
step *?

</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.

Final structures

Waiting for jobs to start/finish

Wildtype

P182L

R178H

References

<references/>