Canavan Task 10 - Molecular Dynamics Simulations

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Revision as of 14:33, 29 July 2012 by Vorbergs (talk | contribs) (RMSF)

Protocol

Further information and commands can be found in the protocol.

Initial Checks

For all three runs, there are 2000 time frames, with a resolution of 5 psec. Therefore the whole simulation ran for 10000 psec = 10 nsec. No errors occured during the run and the simulation finished properly.

<figtable id="gmxcheck">

<xr nolink id="gmxcheck"/> Results from gmxcheck and the logfile
WT K213E A305E
run time 5h 22:37 5h 08:54 5h 08:35
atoms outside of box 406, 408, 480, 482, 483, 484, 485, 486, 500, 501,.. 406, 480, 482, 483, 484, 485, 486, 500, 502, 503,.. 406, 408, 480, 482, 483, 484, 485, 486, 500, 501,..
Last frame 2000 time 10000.000 2000 time 10000.000 2000 time 10000.000

</figtable>

Energies

For all analysed thermodynamical parameters convergence could be observed. Though, for pressure the values vary enormously, but the average pressure is close to the specified value of 1 bar.

Temperature

<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: temperature.
WT K213E A305E
Reference Value 298 K 298 K 298 K
Average 297.914 K 297.908 297.917
Err.Est. 0.0072 0.0059 0.0047
RMSD 1.38693 1.38991 1.3981
Total Drift -0.00042403 (K) 0.00867898 (K) 0.0154339 (K)
Plot <figure id="wt_temp">
<xr nolink id="wt_temp"/>
Temperature of the system for the wildtype smoothed over a window of 20.
</figure>
<figure id="k213_scwrl_temp">
<xr nolink id="k213_scwrl_temp"/>
Temperature of the system for K213E smoothed over a window of 20.
</figure>
<figure id="a305_scwrl_temp.png">
<xr nolink id="a305_scwrl_temp.png"/>
Temperature of the system for A305E smoothed over a window of 20.
</figure>

</figtable>

Pressure

<figtable id="energies_temp">

<xr nolink id="energies_temp"/> Quality check for convergence of energy values: pressure.
WT K213E A305E
Reference Value 1.0 (Berendsen barostat) 1.0 (Berendsen barostat) 1.0 (Berendsen barostat)
Average 1.00763 1.00683 1.00797
Err.Est. 0.018 0.015 0.022
RMSD 111.943 112.761 112.987
Total Drift -0.0713928 (bar) -0.0585283 (bar) -0.100316 (bar)
Plot <figure id="wt_pressure">
<xr nolink id="wt_pressure"/>
Pressure of the system for the wildtype smoothed over a window of 20.
</figure>
<figure id="k213_scwrl_pressure">
<xr nolink id="k213_scwrl_pressure"/>
Pressure of the system for K213E smoothed over a window of 20.
</figure>
<figure id="a305_scwrl_pressure">
<xr nolink id="a305_scwrl_pressure"/>
Pressure of the system for A305E smoothed over a window of 20.
</figure>

</figtable>

Potential Energy

<figtable id="energies_potential">

<xr nolink id="energies_potential"/> Quality check for convergence of energy values: potential energy.
WT K213E A305E
Average -592161 -585993 -583187
Err.Est. 55 65 46
RMSD 721.947 726.81 722.076
Total Drift -252.112 (kJ/mol) -425.823 (kJ/mol) -290.165 (kJ/mol)
Plot <figure id="CD_wt_potenergy">
<xr nolink id="CD_wt_potenergy"/>
Potential energy of the system for the wildtype smoothed over a window of 20
</figure>
<figure id="k213_scwrl_poten">
<xr nolink id="k213_scwrl_poten"/>
Potential energy of the system for K213E smoothed over a window of 20
</figure>
<figure id="a305_scwrl_potenergy">
<xr nolink id="a305_scwrl_potenergy"/>
Potential energy of the system for A305E smoothed over a window of 20
</figure>

</figtable>

Total energy

<figtable id="energies_total">

<xr nolink id="energies_total"/> Quality check for convergence of energy values: total energy.
WT K213E A305E
Average -485680 -480905 -478506
Err.Est. 54 64 45
RMSD 886.726 888.522 887.724
Total Drift -252.262 (kJ/mol) -422.763 (kJ/mol) -284.743 (kJ/mol)
Plot <figure id="wt_tot_energy">
<xr nolink id="wt_tot_energy"/>
Total energy of the system for the wildtype, smoothed over a window of 20 timesteps.
</figure>
<figure id="k213_scwrl_toten">
<xr nolink id="k213_scwrl_toten"/>
Total energy of the system for K213E, smoothed over a window of 20 timesteps.
</figure>
<figure id="a305e_scwrl_totenergy">
<xr nolink id="a305e_scwrl_totenergy"/>
Total energy of the system for A305E smoothed over a window of 20
</figure>

</figtable>

distances between periodic boundaries

We calculated the minimum distance between periodic images for the whole protein (not only C-alpha atoms). The suggested distance limit of 2nm is undercut at some timesteps during the simulation. Especially for the mutant K213E the distance often is below 2nm. This might have caused undesired unphysical interactions.

<figtable id="periodic_boundary">

<xr nolink id="periodic_boundary"/> Minimum distances between periodic images for the simulation run calculated with g_mindist.
WT K213E A305E
shortest dist 1.6456 (nm) 1.47431 (nm) 1.59859 (nm)
at time step 7675 (ps) 7515 (ps) 2460 (ps)
between atoms 15 and 4507 598 and 4497 597 and 4507
Plot <figure id="wt_pi">
<xr nolink id="wt_pi"/>
</figure>
<figure id="k213e_pi">
<xr nolink id="k213e_pi"/>
Minimum distance of periodic images for K213E. Almost during the whole simulation the minimal distance is less than 2 nm.
</figure>
<figure id="a305e_pi">
<xr nolink id="a305e_pi"/>
Minimum distance of periodic images for A305E. The minimum distance between periodic images is larger than 2nm for most of the simulation.
</figure>

</figtable>



RMSF

Only small fluctuations can be observed for the residues of the three proteins.

For all three proteins there is a peak around residues 60-75, which defines this region as rather felxible. Especially for K213E, this region is very flexible with deviations of more than 0.35 nm.

For the wildtype, there is a region between residues 120 and 180 that is especially rigid. When looking at the bfactors one finds the same results. The whole protein is rather rigid and only some exposed loops have higher bfactors.


<figtable id="rmsf">

<xr nolink id="rmsf"/> Root Mean Square Fluctuations for the MD simulation run calculated per residue with g_rmsf.
WT K213E A305E
RMSF Plot <figure id="wt_rmsf_plot">
<xr nolink id="wt_rmsf_plot"/>
</figure>
<figure id="k213e_rmsf_plot">
<xr nolink id="k213e_rmsf_plot"/>
Per residue root-mean-square-fluctution plot for K213E.
</figure>
<figure id="a3o5e_rmsf_plot">
<xr nolink id="a3o5e_rmsf_plot"/>
Per residue root-mean-square-fluctution plot for A305E.
</figure>
B-Factors <figure id="wt_bfactors">
<xr nolink id="wt_bfactors"/>
</figure>
<figure id="k213e_rmsf_plot">
<xr nolink id="k213e_rmsf_plot"/>
Per residue root-mean-square-fluctution plot for K213E.
</figure>
<figure id="a3o5e_rmsf_plot">
<xr nolink id="a3o5e_rmsf_plot"/>
Per residue root-mean-square-fluctution plot for A305E.
</figure>

</figtable>




For exposed residues the averaged structure shows several possible residue conformers.

<figtable id="wt_rmsf">

<figure id="wt_rmsf_plot">
<xr nolink id="wt_rmsf_plot"/>
</figure>
<figure id="wt_bfactors">
<xr nolink id="wt_bfactors"/>
</figure>
<figure id="wt_average">
<xr nolink id="wt_average"/>
</figure>

</figtable>

Convergence of RMSD

As expected, the RMSD increases when using the starting structure as a reference. Over the simulation the structure changes and deviates more and more from the starting structure. Yet these changes are not tremendous, as the starting structure is the crystal structure and therefore should already have adopted a optimal conformation.

When taking the average structure as reference, the RMSD is higher at the beginning of the simulation and finally converges as the structure reaches an equilibrium.

When only taking the Calpha atoms into accounts, the deviations are even smaller, than when also calculating RMSD values for the flexible side chains.


<figtable id="CD_wt_rmsf">

<figure id="wt_rmsd_all_vs_first">
<xr nolink id="wt_rmsd_all_vs_first"/>
</figure>
<figure id="wt_rmsd_all_vs_average">
<xr nolink id="wt_rmsd_all_vs_average"/>
</figure>
<figure id="wt_rmsd_calpha_vs_first">
<xr nolink id="wt_rmsd_calpha_vs_first"/>
</figure>
<figure id="wt_rmsd_calpha_vs_average">
<xr nolink id="wt_rmsd_calpha_vs_average"/>
</figure>

</figtable>


Radius of gyration

Against our expectations, the radius of gyration increases for the wildtype protein. As the energy of the system decreases during hte rund, we would expect that the protein becomes more compact. One idea is, that we used the monomeric form of the protein for the simulation, whereas in the crystal structure it is a dimer.


<figure id="wt_rg">

<xr nolink id="wt_rg"/>

</figure>