Normal mode analysis Gaucher Disease

Introduction

Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies.

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">

The Eigenvalues Plot for for protein structure 2NT0 chain A from Webnma@.

</figure>

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">

The Atomic displacements plots for modes 7 to 12 for protein structure 2NT0 chain A from Webnma@.

</figure>

<figure id="fig:fluc_plot">

The normalized squared fluctuations for all modes for protein structure 2NT0 chain A from Webnma@.

</figure>

Correlation Matrix

"The correlation matrix shows the correlated movement of the Calphas in the protein. Both axis denote the Calphas of the protein in sequential order, so that each cell in the plot shows the isotropic correlation of two residues in the protein on a range from -1 (anti-correlated) via 0 (uncorrelated) to 1 (correlated). " - from Webnma@

<figure id="fig:corr_matr">

The correlation matrix for protein structure 2NT0 chain A from Webnma@.

</figure>

ElNemo

<figure id="fig:elne_model7">

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  1: 2nt0.7.x.0.gif

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  2: X

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  3: Y

The model 7 </figure>

References

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