Difference between revisions of "Molecular Dynamics Simulations Analysis Hemochromatosis"

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In these part we evaluate the model averages and b-factors of each position. Because it is an average over all timesteps this averaged structure can be impossible in nature.
   
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As one can see there is a big change of b-factors when comparing the wildtype and both mutations we calculated. From both mutations the R224W one shows a bigger difference to the wildtype. As expected the positions "at the edges" <!-- most exposed?--> and those not in a secondary structure tend to have higher fluctuations/higher b-factors. It is worth noting, that even the beta sheets on the right side of the R224W picture (position 180 and higher) have (compared to wildtype and C282S mutation) pretty high b-factors. Also one can see that a little helix is inserted into the average structure of the R224W average model (right part of the picture, high b-factor [red], position ~220-225).
 
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Revision as of 10:46, 31 August 2012

Hemochromatosis>>Task 10: Molecular dynamics simulations analysis


Short task description

Detailed description: Molecular dynamics simulations analysis


Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.


Dummy

Note: All pictures/graphs shown here are from the first run (in case of 1a6zC[wildtype]-pictures) or second run (in case of R224W- or C282S-mutation). The reason for this is depicted under LINKTOMINDISTTODO.


Calculation statistics

<figtable id="tab:simulation_stats"> Statistics of the MD simulations

Input Calc. time Calc. speed time to reach 1 s
Wildtype 13h31:15 17.750 ns/day 154350,8 years
C282S 13h35:05 17.667 ns/day 155075,9 years
R224W 13h35:02 17.668 ns/day 155067,1 years

</figtable>

GMXcheck revealed for all calculations that all 2001 frames were calculated, resulting in a 10ns model.

Energies

Pressure

<figtable id="tab:pressure">

Hemo MD 1a6zC pressure.png
Hemo MD R224W pressure Run2.png
Hemo MD C282S pressure Run2.png
Table 2: different pressures of the three calculated models over time. The red line denotes the average over 100 steps (500ps). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutatuin at position 282 (C282S)

</figtable> The plots in <xr id="tab:pressure"/> show the pressures of the calculated systems over time. These show that, although the pressures differ greatly in some cases, the average is still at about 0 (with minor fluctuations).

Temperature

<figtable id="tab:temperature">

Hemo MD 1a6zC temperature.png
Hemo MD R224W temperature Run2.png
Hemo MD C282S temperature Run2.png
Table 3: different temperature energies of the three calculated models over time. The red line denotes the average over 100 steps (500ps). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable> The next thing we calculated were the temperatures. For all three models they can be seen in <xr id="tab:temperature"/>. The maximal deviation from the average is about 4 degrees for all models.

Potential

<figtable id="tab:potential">

Hemo MD 1a6zC potential.png
Hemo MD R224W potential Run2.png
Hemo MD C282S potential Run2.png
Table 4: different potential energies of the three calculated models over time. The red line denotes the average over 100 steps (500ps). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable> With gromacs we could also extract the potentials, as can be seen in <xr id="tab:potential"/>. As in the plots before the average is all the time around the same value for all three models.

Total energy

<figtable id="tab:total_energy">

Hemo MD 1a6zC totalEnergy.png
Hemo MD R224W totalEnergy Run2.png
Hemo MD C282S totalEnergy Run2.png
Table 5: different total energies of the three calculated models over time. The red line denotes the average over 100 steps (500ps). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable> In <xr id="tab:total_energy"/> the values of the total energies are denoted over the different states in time. Again we get an average with minor fluctuation at around the same value for each model.

All these plots show the same behavior: average around the same value and look different between the three models. This can be expected as minor changes can introduce or eradicate bindings, therefore changing the overall energies which then influence all further steps.



Minimum distance between periodic boundary cells

<figtable id="comparison">

Hemo MD 1a6zC minPeriodicDist.png
Hemo MD R224W minPeriodicDist.png
Hemo MD C282S minPeriodicDist.png
Table 6: different total energies of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

The first calculations for the mutations resulted in the minimum distances of TABLETODO. As there should be at least 2 nm distance in between at all time one can see that the mutations show the opposite. Therefore it might be possible that the protein affects itself which is not desired. To see if this states were calculated just by chance (random fluctuations that built up over time into an undesired direction) we repeated the calculations for all three models.

<figtable id="comparison">

Hemo MD 1a6zC minPeriodicDist Run2.png
Hemo MD R224W minPeriodicDist Run2.png
Hemo MD C282S minPeriodicDist Run2.png
Table 7: different total energies of the three calculated models over time. The calculations are from the second run. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable> The resulting minimal distances were:
We therefore decided to use the model of the first calculation for the wildtype, and the models of the second calculation for the mutation types.

RMSF for protein and C-alpha

Protein based

<figtable id="tab:rmsf_prot">

Hemo MD 1a6zC prot rmsf.png
Hemo MD R224W prot rmsf Run2.png
Hemo MD C282S prot rmsf Run2.png
Table 8: different RMS fluctuations (based on the whole protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

C-Alpha based

<figtable id="tab:rmsf_ca">

Hemo MD 1a6zC ca rmsf.png
Hemo MD R224W ca rmsf Run2.png
Hemo MD C282S ca rmsf Run2.png
Table 9: different RMS fluctuations (based on the the C-alpha atoms of the protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>


Statistical values

With the GIVENSCRIPTTODO we calculated the values for the t-Test:

1a6zC to R224W : 8.079405e-57**

1a6zC to C282S : 2.87453e-56**

R224W to C282S : 5.45069e-25**

Pymol analysis of average and bfactor

<figtable id="tab:avg_bfactor">

Hemo MD 1a6zCProtAvg.png
Hemo MD R224WProtAvg Run2.png
Hemo MD C282SProtAvg Run2.png
Table 11: Pictures of the model averages (average over MD calculated states) colored by the b-factor. The range is from blue (bfactor value beneath threshold [500]) to red (high b-factor values). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable> In these part we evaluate the model averages and b-factors of each position. Because it is an average over all timesteps this averaged structure can be impossible in nature.

As one can see there is a big change of b-factors when comparing the wildtype and both mutations we calculated. From both mutations the R224W one shows a bigger difference to the wildtype. As expected the positions "at the edges" and those not in a secondary structure tend to have higher fluctuations/higher b-factors. It is worth noting, that even the beta sheets on the right side of the R224W picture (position 180 and higher) have (compared to wildtype and C282S mutation) pretty high b-factors. Also one can see that a little helix is inserted into the average structure of the R224W average model (right part of the picture, high b-factor [red], position ~220-225).

Radius of gyration

<figtable id="tab:gyration_ca">

Hemo MD 1a6zC ca gyration.png
Hemo MD R224W ca gyration Run2.png
Hemo MD C282S ca gyration Run2.png
Table 12: different gyrations (based on the the C-alphas of the backbone of the protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>


<figtable id="tab:gyration_prot">

Hemo MD 1a6zC prot gyration.png
Hemo MD R224W prot gyration Run2.png
Hemo MD C282S prot gyration Run2.png
Table 13: different gyrations (based on the the whole protein) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

solvent accessible surface area

<figtable id="tab:sas">

Hemo MD 1a6zC SAS.png
Hemo MD R224W SAS Run2.png
Hemo MD C282S SAS Run2.png
Table 14: display of the different solvent accessible surface sizes of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

<figtable id="tab:sas_res">

Hemo MD 1a6zC resSAS.png
Hemo MD R224W resSAS Run2.png
Hemo MD C282S resSAS Run2.png
Table 15: display of the different solvent accessible surface sizes (normalized to per residue values) of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>


hydrogen-bonds between protein and protein / protein and water

Protein-Protein

<figtable id="tab:hbonds_pp">

Hemo MD 1a6zC hBondsP2P.png
Hemo MD R224W hBondsP2P Run2.png
Hemo MD C282S hBondsP2P Run2.png
Table 16: the number of hydrogen bonds inside the protein of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>

Protein-Water

<figtable id="tab:hbonds_pw">

Hemo MD 1a6zC hBondsP2W.png
Hemo MD R224W hBondsP2W Run2.png
Hemo MD C282S hBondsP2W Run2.png
Table 17: the number of hydrogen bonds of the protein with water of the three calculated models over time. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>


Ramachandran plots

<figtable id="tab:ramachandran">

Hemo MD 1a6zC ramaPlot.png
Hemo MD R224W ramaPlot Run2.png
Hemo MD C282S ramaPlot Run2.png
Table 18: ramachandran Plots of the three calculated models. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>



RMSD matrix

<figtable id="tab:rmsd_matrix_prot">

Hemo MD 1a6zC PP rmsd-matrix.png
Hemo MD R224W PP rmsd-matrix Run2.png
Hemo MD C282S PP rmsd-matrix Run2.png
Table 19: rmsd matrices of the three calculated models over time (based on the whole protein) showing the rmsd between two models. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>


<figtable id="tab:rmsd_matrix_mcb">

Hemo MD 1a6zC MCB rmsd-matrix.png
Hemo MD R224W MCB rmsd-matrix Run2.png
Hemo MD C282S MCB rmsd-matrix Run2.png
Table 20: rmsd matrices of the three calculated models over time (based on the mainchain and C-betas) showing the rmsd between two models. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>



cluster analysis

whole protein based

<figtable id="tab:cluster_size_prot">

Hemo MD 1a6zC PP cluster-sizes.png
Hemo MD R224W PP cluster-sizes Run2.png
Hemo MD C282S PP cluster-sizes Run2.png
Table 21: Graphs showing the cluster sizes of the three models. The clustering was based on the protein. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>



C-alpha based

<figtable id="cluster_size_ca">

Hemo MD 1a6zC MCB cluster-sizes.png
Hemo MD R224W MCB cluster-sizes Run2.png
Hemo MD C282S MCB cluster-sizes Run2.png
Table 22: Graphs showing the cluster sizes of the three models. The clustering was based on the C-alpha atoms of the protein. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>



internal RMSD

against starting structure

<figtable id="tab:rmsd_vs_start">

Hemo MD 1a6zC rmsd-allProt-atom-vs-start.png
Hemo MD R224W rmsd-allProt-atom-vs-start Run2.png
Hemo MD C282S rmsd-allProt-atom-vs-start Run2.png
Table 23: rmsd of the calculated models over time against the beginning structure. From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>




against average structure

<figtable id="tab:rmsd_vs_avg">

Hemo MD 1a6zC rmsd-all-atom-vs-average.png
Hemo MD R224W rmsd-all-atom-vs-average Run2.png
Hemo MD C282S rmsd-all-atom-vs-average Run2.png
Table 24: rmsd of the calculated models over time against the average structure (average based on all models over time). From left to right: 1a6zC (wildtype), mutation at position 224 (R224W) and mutation at position 282 (C282S)

</figtable>




References

<references/>