by Benjamin Drexler and Fabian Grandke
Introduction
In this task we analysed the simulated data that have been created within task 8. We used several tools of GROMACS to analyse the data and Pymol to visualize them. The single steps were done according to the tutorial from the task 10 page.
Methods/Materials
Results
Brief check of the results
How many frames are in the trajectory file and what is the time resolution?
| Wildtype
|
Mutation 3
|
Mutation 8
|
| 2001 frames
|
2001 frames
|
2001 frames
|
| time resolution of 5ps |
time resolution of 5ps |
time resolution of 5ps
|
How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second?
| Wildtype
|
Mutation 3
|
Mutation 8
|
| 18h06:37 |
18h29:13 |
18h19:11
|
| 13.252 ns/day |
12.982 ns/day |
13.101 ns/day
|
| ~206740 years |
~211040 years |
~209123 years
|
Which contribution to the potential energy accounts for most of the calculations?
| Wildtype
|
Mutation 3
|
Mutation 8
|
| -8.52573e+05 kJ/mol |
-8.53327e+05 kJ/mol |
-8.52539e+05 kJ/mol
|
Visualization of the results
| Wildtype
|
Mutation 3
|
Mutation 8
|
 Figure 1: Molecular Dynamics simulation of the wildtype protein. |
 Figure 2: Molecular Dynamics simulation of the mutation 3 protein. |
 Figure 3: Molecular Dynamics simulation of the mutation 8 protein. |
Figures 1,2 ,and 3 show every ~30 frame of the molecular dynamics simulation. An animated figure of all 1000 simulated frames would be to large for this wiki. All animations show similar but not identical movement of the protein.
Quality assurance
Convergence of energy terms
Temperature
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Max(kJ/mol) |
301.3734 |
302.0039 |
301.7407
|
| Min(kJ/mol) |
293.9565 |
294.0463 |
293.9268
|
| Average(kJ/mol) |
297.9275 |
297.9489 |
297.9303
|
| Plot
|
 Figure 4: Temperature over time for wildtype. |
 Figure 5: Temperature over time for mutation 3. |
 Figure 6: Temperature over time for mutation 8. |
The mutated proteins (Figures 5 and 6) temperatures averages are slightly higher than the wildtype proteins (Figure 4) one, but there is no significant increase. The lowest temperature of the mutation 8 protein is even lower than the minimum of the wildtype. The general appearance of the temperature diagram differs between the proteins, but there is no change into a certain direction.
Pressure
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Max(kJ/mol) |
346.2387 |
385.5467 |
326.9994
|
| Min(kJ/mol) |
-308.7182 |
-357.4386 |
-291.1198
|
| Average(kJ/mol) |
0.4503482 |
-1.521002 |
-0.7279793
|
| Plot
|
 Figure 7: Pressure over time for wildtype. |
 Figure 8: Pressure over time for mutation 3. |
 Figure 9: Pressure over time for mutation 8. |
Figures 7, 8 and 9 show the pressure values during the simulation. All proteins have high levels of variation (>600 kJ/mol) and have averages around zero. The mutated proteins averages both are slightly negative, but in the circumstances of the high overall variation this seems not significant.
Potential
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Max(kJ/mol) |
-849914.5 |
-850058.5 |
-849804.2
|
| Min(kJ/mol) |
-855729.5 |
-856170.2 |
-855717.7
|
| Average(kJ/mol) |
-852568.2 |
-853314.1 |
-852547.7
|
| Plot
|
 Figure 10: Potential over time for wildtype. |
 Figure 11: Potential over time for mutation 3. |
 Figure 12: Potential over time for mutation 8. |
Figures 10, 11 and 12 show the potential values during the simulation. Similar to the pressure values, there are high variations around a value of -853,000 and the simulations seem to have not reached the certain equilibria and there is no obvious difference between the wildtype protein and the mutated ones.
Total Energy
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Max(kJ/mol) |
-695814.5 |
-696662.8 |
-695560
|
| Min(kJ/mol) |
-703550.4 |
-703769 |
-702829.8
|
| Average(kJ/mol) |
-699602.2 |
-700202.2 |
-699497.3
|
| Plot
|
 Figure 13: Total energy over time for wildtype. |
 Figure 14: Total energy over time for mutation 3. |
 Figure 15: Total energy over time for mutation 8. |
Figures 13,14 and 15 show the values of the total energy during the simulation. All diagrams show variation around a value of ~700,000 and there are no results that show a reasonable difference between the proteins.
Minimum distances between periodic images
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Minimum distance(nm) |
1.932 |
1.992 |
2.007
|
| Time of occurance |
370 |
7910 |
5940
|
| Plot
|
 Figure 16: Minimum distance between periodic boundary cells for wildtype. |
 Figure 17: Minimum distance between periodic boundary cells for mutation 3. |
 Figure 18: Minimum distance between periodic boundary cells for mutation 8. |
Figures 16,17 and 18 show the minimum distance between periodic boundary cells for the certain proteins. The minimum distances of the mutated proteins are slightly higher than the wildtype protein ones. If the minimum distance would be smaller and be under a cutoff value, that would mean that there would be interactions of different parts of the molecule what would cause huge changes in molecular dynamics movement, and the results would be completely different.
Root mean square fluctuations
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 19: Root mean square fluctuations for wildtype protein. |
 Figure 20: Root mean square fluctuations for mutation 3 protein. |
 Figure 21: Root mean square fluctuations for mutation 8 protein. |
| Plot
|
 Figure 22: Root mean square fluctuations for wildtype C-alpha. |
 Figure 23: Root mean square fluctuations for mutation 3 C-alpha. |
 Figure 24: Root mean square fluctuations for mutation 8 C-alpha. |
| Plot
|
 Figure 25: Image of aligned average and b-factor protein for wildtype protein. |
 Figure 26: Image of aligned average and b-factor protein for mutation 3 protein. |
 Figure 27: Image of aligned average and b-factor protein for mutation 8 protein. |
| Plot
|
 Figure 28: Image of aligned average and b-factor protein for wildtype C-alpha. |
 Figure 29: Image of aligned average and b-factor protein for mutation 3 C-alpha. |
 Figure 30: Image of aligned average and b-factor protein for mutation 8 C-alpha. |
Convergence of radius of gyration
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 31: Radius of gyration over time for wildtype protein. |
 Figure 32: Radius of gyration over time for mutation 3 protein. |
 Figure 33: Radius of gyration over time for mutation 8 protein. |
Solvent accessible surface area
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 34: Solvent accessible surface area over time for wildtype protein. |
 Figure 35: Solvent accessible surface area over time for mutation 3 protein. |
 Figure 36: Solvent accessible surface area over time for mutation 8 protein. |
| Plot
|
 Figure 37: Solvent accessible surface area per atom for wildtype protein. |
 Figure 38: Solvent accessible surface area per atom for mutation 3 protein. |
 Figure 39: Solvent accessible surface area per atom for mutation 8 protein. |
| Plot
|
 Figure 40: Solvent accessible surface area per residue for wildtype protein. |
 Figure 41: Solvent accessible surface area per residue for mutation 3 protein. |
 Figure 42: Solvent accessible surface area per residue for mutation 8 protein. |
Hydrogen bonds
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 43: Internal hydrogen bonds over time for wildtype protein. |
 Figure 44: Internal hydrogen bonds over time for mutation 3 protein. |
 Figure 45: Internal hydrogen bonds over time for mutation 8 protein. |
| Plot
|
 Figure 46: Hydrogen bonds between protein and surrounding solvents for wildtype protein. |
 Figure 47: Hydrogen bonds between protein and surrounding solvents for mutation 3 protein. |
 Figure 48: Hydrogen bonds between protein and surrounding solvents for mutation 8 protein. |
Ramachandran (phi/psi) plots
| General Ramachandran
|
Wildtype
|
Mutation 3
|
Mutation 8
|
|
|
 Figure 50: Internal hydrogen bonds over time for wildtype protein. |
 Figure 51: Internal hydrogen bonds over time for mutation 3 protein. |
 Figure 52: Internal hydrogen bonds over time for mutation 8 protein. |
Analysis of dynamics and time-averaged properties
Root mean square deviations again
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 53: RMSD matrix for wildtype protein. |
 Figure 54: RMSD matrix for mutation 3 protein. |
 Figure 55: RMSD matrix for mutation 8 protein. |
Cluster analysis
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 56: RMS distribution for wildtype protein. |
 Figure 57: RMS distribution for mutation 3 protein. |
 Figure 58: RMS distribution for mutation 8 protein. |
| Plot
|
 Figure 59: Image of the largest two clusters of wildtype protein. |
 Figure 60: Image of the largest two clusters of mutation 3 protein. |
 Figure 61: Image of the largest two clusters of mutation 8 protein. |
Distance RMSD
| Description
|
Wildtype
|
Mutation 3
|
Mutation 8
|
| Plot
|
 Figure 62: RMS deviation for wildtype protein. |
 Figure 63: RMS deviation for mutation 3 protein. |
 Figure 64: RMS deviation for mutation 8 protein. |
References
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