Canavan Task 9 - Normal Mode Analysis
Contents
Protocol
Further information can be found in the protocol.
Choosing structures
For human Aspartoacylase, there are four structures available in the PDB. For a closer description of the structures have a look at task 4.
One important difference between the structures is the conformation of a loop formed by residues 158 - 164. This loop represents the gate for the binding site, which can either be closed or open. 2O53 and 2O4H both represent the closed conformation, whereas 2I3C and 2Q51 represent the open conformation.
Therefore we thought it would be interesting to investigate the normal modes of a structure with the closed and the open conformation.
We also looked at 2O53 and 2O4H in order to examine if there are differences between the ligand bound and apo-structure.
Webnm@
- Deformation Energies and Eigenvalue Plot:
Deformation energies and eigenvalues reflect the energy associated with each mode and are inversely related to the amplitude of the motion described by a the corresponding modes.
- Atomic Displacement Analysis:
Plots the displacement of each Calpha atom, i.e. highlights which parts of the protein are the most displaced for each mode.
- Correlation Matrix Analysis:
Plots the correlation of motions between all the Calphas in the protein structure.
- Mode Visualisation:
Webnm@ provides the possibility to visualize the modes as well as the download option of dcd and vmd files.
2O53
We used the PDB identifier 2O53. Therefore Webnm@ used the dimer from the PDB. 2O53 is a Holodimer without bound substrate and is in the closed conformation.
Deformation Energies
<figtable id="2o53_def_energy">
Mode Index | Deformation Energy | Mode Index | Deformation Energy |
7 | 870.03 | 14 | 3740.78 |
8 | 976.54 | 15 | 4168.69 |
9 | 1562.41 | 16 | 5263.58 |
10 | 2800.99 | 17 | 5461.10 |
11 | 2798.65 | 18 | 5906.92 |
12 | 2954.75 | 19 | 6126.73 |
13 | 3448.49 | 20 | 6356.04 |
</figtable>
Eigenvalues Plot
The eigenvalues are inversely related to the motion of the modes. Therefore mode 7 describes the highest amplitude of motion in the protein and the other modes describe a decreasing amplitude of motion.
The eigenvalue plot can be seen in <xr id="2o53_eigenvaluesplot"/>
Atomic Displacements
In the lowest mode (7) there are quite random displacements. They are scattered all over the protein. The same can be said for mode 9. For mode 8, 10 and 12 there are peaks around residue 400, which is a long solvent exposed loop. For modes 8,10,11 there is a peak around residue 100 in chain A which corresponds to the peak for the residues around position 400 in chain B. For mode 11 and 12 there are two sharp peaks around residues 250 and 265. This regions are composed of many solvent exposed flexible loops of the C-terminal domain. [AD for modes 7 to 12]
In the fluctuations plot averaged over all modes, it can be seen that the atomic movements are different for the two monomers.
Correlation Matrix Analysis
From the correlation matrix it can be found, that the C-terminal domain (residue 211-311) shows correlated movements. In chain B this domain can be found starting at residue 520.
There are some other smaller correalted motions, that are not very emphasized.
Plot
<figtable id="2o53_plots">
<figure id="2o53_eigenvaluesplot"></figure> | <figure id="2o53_fluctuationsplot"></figure> | <figure id="2o53_correlation_matrix"></figure> |
</figtable>
2O4H
In 2O4H an intermediate substrate has been cocrystallized and the enzyme is in the closed conformation. We uploaded a modified pdb file, where we changed the HETATM entry into ATOM, so that the ligand will be considered during normal mode analysis.
Deformation Energies
<figtable id="2o4h_def_energy">
Mode Index | Deformation Energy | Mode Index | Deformation Energy |
7 | 890.47 | 14 | 3813.56 |
8 | 1001.20 | 15 | 4209.21 |
9 | 1576.14 | 16 | 5299.13 |
10 | 2832.63 | 17 | 5374.76 |
11 | 2837.90 | 18 | 5750.94 |
12 | 2995.56 | 19 | 6278.71 |
13 | 3417.11 | 20 | 6396.79 |
</figtable>
Eigenvalues Plot
The eigenvalues are inversely related to the motion of the modes. Therefore mode 7 describes the highest amplitude of motion in the protein and the other modes describe a decreasing amplitude of motion.
The eigenvalue plot can be seen in <xr id="2o4h_eigenvaluesplot"/>
Atomic Displacements
The plots for mode 7 to 12 are identical with the plots for 2O53. Therefore the ligand in the structure does not influence the movement of the protein at all. The atomic displacements for all modes can be seen her: [AD for modes 7 to 12]
The fluctuations plot averaged over all modes is also identical with the plot for 2o53. Even very small fluctuations are exactly the same.
Correlation Matrix Analysis
And again, the correlation matrix is also totally identical with the correlation matrix for 2O53.
Plot
<figtable id="2o4h_plots">
<figure id="2o4h_eigenvaluesplot"></figure> | <figure id="2o4h_fluctuationsplot"></figure> | <figure id="2o4h_correlation_matrix"></figure> |
</figtable>
2I3C
This structure shows the binding site in an open conformation.
Some amino acids have been replaced by artificial amino acids and are not considered by webnm@ in the normal mode analysis.
Deformation Energies
<figtable id="2i3c_def_energy">
Mode Index | Deformation Energy | Mode Index | Deformation Energy |
7 | 819.58 | 14 | 3831.12 |
8 | 897.71 | 15 | 4275.48 |
9 | 1423.78 | 16 | 5370.37 |
10 | 2661.79 | 17 | 5549.08 |
11 | 2485.43 | 18 | 5226.29 |
12 | 2576.98 | 19 | 6459.76 |
13 | 3362.10 | 20 | 5641.86 |
</figtable>
Eigenvalues Plot
The eigenvalue plot looks as for the proteins analysed before: almost linear increase in eigenvalue for the modes.
The eigenvalue plot can be seen in <xr id="2i3c_eigenvalues"/>
Atomic Displacements
The plots are very similar to the plots for 2O53 and 2O4H. The plots for atomic displacement for modes 7 to 12 can be seen here: [AD for modes 7 to 12]
=Correlation Matrix analysis
As for the other proteins, the C-terminal domain shows correlated movements.
Plot
<figtable id="2i3c_plots">
<figure id="2i3c_eigenvalues"></figure> | <figure id="2i3c_fluctuationsplot"></figure> | <figure id="2i3c_correlation_matrix"></figure> |
</figtable>
Comparison 2I3C and 2O53
Deformation Energy
For mode 7 - 13, 2I3C has the lower deformation energies. Then it is almost vice.versa and 2O53 has lower deformation energies.
Fluctuation
As you can see in <xr id="comparison_2o53_2i3c_fluctuations"/>, the fluctuations for all modes for both proteins are identical.
Atomic Displacements
The atomic displacements for 2O53 and 2I3C are very similar. Yet, especially for the higher modes, there are some differences. First, the amplitude of some peaks is different for 2O53 and 2I3C. And second, there are some additional peaks in some modes for 2I3C, which represent different local felxibility.
Modes 11 and 12 deviate the most. 2O53 shows more and stronger peaks for these both modes, which indicates stronger low level movements. In <xr id="omparison 2o53_2i3c_mode11_12"/>these differences are illustrated.
Plots
<figtable id="comp_plots">
<figure id="comp_def_ener"></figure> | <figure id="comparison_2o53_2i3c_fluctuations"></figure> | <figure id="comparison 2o53_2i3c_mode11_12"></figure> |
</figtable>
ElNemo
In order for ElNemo to accept our proteins, we had to modify the pdf files. We eliminated all records except for the ATOM records.
2O53
Normal Mode Analysis for ID 12070820013211761
Correlation= 0.322 for 604 C-alpha atoms.
<R2> frequency collectivity mode 7 1.00 0.6719 mode 8 1.26 0.6285 mode 9 1.76 0.7056 mode 10 2.16 0.7016 mode 11 2.31 0.5394 mode 12 2.39 0.6059 mode 13 2.46 0.4075 mode 14 2.66 0.6475 mode 15 2.75 0.4065 mode 16 3.06 0.3493 mode 17 3.08 0.4132 mode 18 3.19 0.4097 mode 19 3.26 0.3425 mode 20 3.37 0.2945