Canavan Task 9 - Normal Mode Analysis

From Bioinformatikpedia
Revision as of 18:57, 8 July 2012 by Vorbergs (talk | contribs)

Protocol

Further information can be found in the protocol.

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. Interestingly the modes are not the same for both monomers.

Deformation Energies

Mode IndexDeformation Energy Mode IndexDeformation Energy
7870.03 143740.78
8976.54 154168.69
91562.41 165263.58
102800.99 175461.10
112798.65 185906.92
122954.75 196126.73
133448.49 206356.04

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. The peaks in this plot are mapped to the dimer in figure .... As one can see, these highly motile regions correlate with exposed loop regions.

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">
<xr nolink id="2o53_eigenvaluesplot"/>
</figure>
<figure id="2o53_fluctuationsplot">
<xr nolink id="2o53_fluctuationsplot"/>
</figure>
<figure id="2o53_correlation_matrix">
<xr nolink id="2o53_correlation_matrix"/>
</figure>

</figtable>

2O4H

We uploaded a modified pdb file, where we changed the HETATM entry into ATOM, so that the ligand will be conssidered during normal mode analysis.

Deformation Energies

Mode IndexDeformation Energy Mode IndexDeformation Energy
7890.47 143813.56
81001.20 154209.21
91576.14 165299.13
102832.63 175374.76
112837.90 185750.94
122995.56 196278.71
133417.11 206396.79

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">
<xr nolink id="2o4h_eigenvaluesplot"/>
</figure>
<figure id="2o4h_fluctuationsplot">
<xr nolink id="2o4h_fluctuationsplot"/>
</figure>
<figure id="2o4h_correlation_matrix">
<xr nolink id="2o4h_correlation_matrix"/>
</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, then ElNemo accepted the .pdf files.

2O53

2O4H