Difference between revisions of "Canavan Task 10 - Molecular Dynamics Simulations"
(→RMSF) |
(→RMSF) |
||
Line 336: | Line 336: | ||
==RMSF== |
==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. |
||
Line 353: | Line 360: | ||
<td style="border-right:solid;" align="center">RMSF Plot</td> |
<td style="border-right:solid;" align="center">RMSF Plot</td> |
||
<td style="border-right:solid;" align="center"><figure id="wt_rmsf_plot">[[File:CD_wt_rms_per_residue.png|thumb|250px|<b><xr nolink id="wt_rmsf_plot"/></b><br>]]</figure></td> |
<td style="border-right:solid;" align="center"><figure id="wt_rmsf_plot">[[File:CD_wt_rms_per_residue.png|thumb|250px|<b><xr nolink id="wt_rmsf_plot"/></b><br>]]</figure></td> |
||
+ | <td style="border-right:solid;" align="center" ><figure id="k213e_rmsf_plot">[[File:CD_k213_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="k213e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for K213E.]]</figure></td> |
||
+ | <td style="border-right:solid;" align="center" ><figure id="a3o5e_rmsf_plot">[[File:CD_a305e_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="a3o5e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for A305E.]]</figure></td> |
||
+ | </tr> |
||
+ | |||
+ | |||
+ | <tr> |
||
+ | <td style="border-right:solid;" align="center">B-Factors </td> |
||
+ | <td style="border-right:solid;" align="center"><figure id="wt_bfactors">[[File:CD_wt__bfactor.png|thumb|250px|<b><xr nolink id="wt_bfactors"/></b><br>]]</figure></td> |
||
<td style="border-right:solid;" align="center" ><figure id="k213e_rmsf_plot">[[File:CD_k213_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="k213e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for K213E.]]</figure></td> |
<td style="border-right:solid;" align="center" ><figure id="k213e_rmsf_plot">[[File:CD_k213_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="k213e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for K213E.]]</figure></td> |
||
<td style="border-right:solid;" align="center" ><figure id="a3o5e_rmsf_plot">[[File:CD_a305e_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="a3o5e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for A305E.]]</figure></td> |
<td style="border-right:solid;" align="center" ><figure id="a3o5e_rmsf_plot">[[File:CD_a305e_scwrl_rmsf.png|thumb|200px|<b><xr nolink id="a3o5e_rmsf_plot"/></b><br>Per residue root-mean-square-fluctution plot for A305E.]]</figure></td> |
||
Line 364: | Line 379: | ||
− | |||
− | |||
− | 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. |
||
For exposed residues the averaged structure shows several possible residue conformers. |
For exposed residues the averaged structure shows several possible residue conformers. |
Revision as of 13:33, 29 July 2012
Contents
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">
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">
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"></figure> | <figure id="k213_scwrl_temp"></figure> | <figure id="a305_scwrl_temp.png"></figure> |
</figtable>
Pressure
<figtable id="energies_temp">
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"></figure> | <figure id="k213_scwrl_pressure"></figure> | <figure id="a305_scwrl_pressure"></figure> |
</figtable>
Potential Energy
<figtable id="energies_potential">
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"></figure> | <figure id="k213_scwrl_poten"></figure> | <figure id="a305_scwrl_potenergy"></figure> |
</figtable>
Total energy
<figtable id="energies_total">
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"></figure> | <figure id="k213_scwrl_toten"></figure> | <figure id="a305e_scwrl_totenergy"></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">
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"></figure> | <figure id="k213e_pi"></figure> | <figure id="a305e_pi"></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">
WT | K213E | A305E | |
RMSF Plot | <figure id="wt_rmsf_plot"></figure> | <figure id="k213e_rmsf_plot"></figure> | <figure id="a3o5e_rmsf_plot"></figure> |
B-Factors | <figure id="wt_bfactors"></figure> | <figure id="k213e_rmsf_plot"></figure> | <figure id="a3o5e_rmsf_plot"></figure> |
</figtable>
For exposed residues the averaged structure shows several possible residue conformers.
<figtable id="wt_rmsf">
<figure id="wt_rmsf_plot"></figure> | <figure id="wt_bfactors"></figure> | <figure 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"></figure> | <figure id="wt_rmsd_all_vs_average"></figure> | <figure id="wt_rmsd_calpha_vs_first"></figure> | <figure 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">
</figure>