Normal mode analysis Gaucher Disease
Contents
Introduction
Technical details are reported in our 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. The protein structure moves along all the normal modes at once. A mode should only be interpreted in isolation if it is energetically well separated from other modes. " - from Webnma@
Below are the values of the deformation energy for modes 7 to 20.
<figtable id="tab:defor_enery">
| Mode Index | Deformation Energy | Mode Index | Deformation Energy | ||
|---|---|---|---|---|---|
| 7 | 1663.91 | 14 | 6698.31 | ||
| 8 | 2377.48 | 15 | 9791.69 | ||
| 9 | 2720.71 | 16 | 9534.10 | ||
| 10 | 5191.86 | 17 | 10022.74 | ||
| 11 | 5033.67 | 18 | 11137.44 | ||
| 12 | 6174.70 | 19 | 11592.80 | ||
| 13 | 6360.72 | 20 | 12045.03 | ||
The deformation energy for modes 7 to 20 for protein structure 2NT0 chain A from Webnma@. </figtable>
<figure id="fig:Eingenvalues_plot">
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Atomic Displacement
" Atomic displacements:
The square of the displacement of each Calpha atom (for modes 7 to 12), normalized so that the sum over all residues is equal to 100.
Highest values correspond to the most displaced regions. On the plots, one should look for cluster of peaks, those identify significantly big regions. Isolated peaks reflect local flexibility and are not relevant. Fluctuations
The square of the fluctuation of each Calpha atom (for all non-trivial modes), normalized so that the sum over all residues is equal to 100.
The fluctuations are the sum of the atomic displacements in each mode weighted by the inverse of their corresponding eigenvalues. These are equivalent to the normalized temperature factors.
Results can be retrieved as plots at the PNG format or raw data (first column: resid, second column: normalized squared atomic displacement/fluctuation) " - from Webnma@
<figure id="fig:atom_disp_7to12">
</figure>
