Difference between revisions of "Molecular Dynamics Analysis GLA"
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| [[Image:GLA_Wt_radius.png|thumb|400px|Figure 31: Radius of gyration over time for wildtype protein.]] |
| [[Image:GLA_Wt_radius.png|thumb|400px|Figure 31: Radius of gyration over time for wildtype protein.]] |
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| [[Image:GLA_3_radius.png|thumb|400px|Figure 32: Radius of gyration over time for mutation 3 protein.]] |
| [[Image:GLA_3_radius.png|thumb|400px|Figure 32: Radius of gyration over time for mutation 3 protein.]] |
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+ | Figures 31, 32 and 33 show the radius of gyration of the proteins. The black line shows the general change of the proteins structure during the simulation. The green, red and blue lines show the certain values for the X-, Y- and Z-axis, respectively. The general structure seems not to change at all, despite by very little variation. The blue and red line seem to be anti proportional, every time one has an upswing, the other one has a downswing. They are not exactly mirrored, but the general tendency is very obvious. The green line is more independent. It behaves different in every protein and does not seem to influence the general change of the proteins structures. |
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=== Solvent accessible surface area === |
=== Solvent accessible surface area === |
Revision as of 16:14, 19 October 2011
by Benjamin Drexler and Fabian Grandke
Contents
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 |
---|---|---|
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 |
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 |
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 |
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 |
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 |
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
Wildtype | Mutation 3 | Mutation 8 |
---|---|---|
Figures 19, 20 and 21 show the RMS fluctuation of the proteins. The diagrams are scaled differently so, but the pattern of peaks are very similar. The only difference and the reason for the different scaling is the last upswing. It is most extreme in mutation 3 protein(>5) and smallest in mutation 8 protein (~2.5). The other values are almost the same. So again there is no obvious difference between the wildtype and the mutated proteins.
Figures 22, 23 and 24 show the RMS fluctuations of the proteins C-alphas. The results have the same character as the previous ones. Again there is only a difference in the last upswing.
Figures 25, 26 and 27 show alignments of the average proteins and the b-factor ones from pymol. They look very similar, as well. On the left side of the picture is a helix that "points" towards the viewer. It is the only part of the protein that is red colored in red. It is the same end of the protein that showed significant behavior in the two steps before. The other parts of the proteins are mostly color dark blue or light blue. The segments that are highlighted light blue are mostly similar for all proteins. Only the mutation 8 protein has some of those colored in green. That means that the b-factor values of those are a little bit higher. All three proteins align very well.
Figures 28, 29 and 30 show alignments of the average proteins C-alpha and the b-factor ones from pymol. Despite some small differences the alignments look very similar. Again only the end of the chain is colored significantly. The dark blue averages and light blue b-factor atoms align very well, again.
Convergence of radius of gyration
Wildtype | Mutation 3 | Mutation 8 |
---|---|---|
Figures 31, 32 and 33 show the radius of gyration of the proteins. The black line shows the general change of the proteins structure during the simulation. The green, red and blue lines show the certain values for the X-, Y- and Z-axis, respectively. The general structure seems not to change at all, despite by very little variation. The blue and red line seem to be anti proportional, every time one has an upswing, the other one has a downswing. They are not exactly mirrored, but the general tendency is very obvious. The green line is more independent. It behaves different in every protein and does not seem to influence the general change of the proteins structures.
Solvent accessible surface area
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot | |||
Plot |
Hydrogen bonds
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot |
Ramachandran (phi/psi) plots
General Ramachandran | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
![]() Figure 49: General ramachandran plot.<ref name=rama_wiki>http://en.wikipedia.org/wiki/Ramachandran_plot</ref> |
Analysis of dynamics and time-averaged properties
Root mean square deviations again
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
Cluster analysis
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot | |||
Plot |
Distance RMSD
Description | Wildtype | Mutation 3 | Mutation 8 |
---|---|---|---|
Plot |
References
<references />