Difference between revisions of "Canavan Task 9 - Normal Mode Analysis"

From Bioinformatikpedia
(Webnm@)
(=Deformation Energies)
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We used the PDB identifier 2O53. Therefore Webnm@ used the dimer from the PDB. Interestingly the modes are not the same for both monomers.
 
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===
+
====Deformation Energies====
   
  +
<table>
<table><tr><td>Mode Index</td><td>Deformation Energy </td> <td>Mode Index</td><td>Deformation Energy </td></tr></table>
 
  +
<tr><td>Mode Index</td><td>Deformation Energy </td> <td>Mode Index</td><td>Deformation Energy </td></tr>
   
 
<tr><td>7</td><td>870.03 </td> <td>14</td><td>3740.78 </td></tr>
 
<tr><td>7</td><td>870.03 </td> <td>14</td><td>3740.78 </td></tr>

Revision as of 17:45, 8 July 2012

Protocol

Further information can be found in the protocol.

Webnm@

  • Deformation Energies:

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

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]


<figure id="2o53_fluctuationsplot">

<xr nolink id="2o53_fluctuationsplot"/>

</figure>

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.

<figure id="2o53_correlation_matrix">

<xr nolink id="2o53_correlation_matrix"/>

</figure>