Gaucher Disease: Task 10 - Normal mode analysis

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lab journal

With normal mode analysis (NMA), you are able to simulate or analyse the natural resonant movements of proteins. There are two different webserver available to do a NMA, WEBnm@ and ElNemo. They provide the following information.

WEBnm@

• Deformation energy
• atomic fluctuations

ElNemo

• amplitudes that were applied in the normal mode perturbation as DQMIN(DQSTEP)DQMAX (perturbation)
• animations of the top five modes in GIF format (small/large)
• distance fluctuations between all C-alpha atoms (CA-vari)
• RMSD with respect to the reference structure
• visualization of the mean square displacement of all C-alpha atoms associated with a given mode (<R2>)
• frequency of a mode
• collectivity of a mode

WEBnm@

WEBnm@ uses only alpha-carbon atoms in the models for the normal mode analysis.

<figtable id="energy">

Mode	Deformation Energy
7	1633.42
8	2358.92
9	2686.12
10	4886.37
11	5221.34

Five best values of the deformation energy for the lowest-frequency non-trivial modes.

</figtable>

ElNemo

ElNemo uses also only the C_α atoms of the structure for normal mode analysis, therefore it takes only the ATOM record from the PDB file, ignoring the HETATM record of a ligand. As we do not have a structure completely without a ligand, but only structures with different not native ligands (hier kommt der Name von unserem Liganden), we do not have structures with different conformations. Therefore, we could not do the option of calculation of normal modes with two different structures. We ran ElNemo with our reference structure 1OGS.

100 modes were calculated. We analyze the best five best modes, i.e. with lowest frequency and the highest collectivity of the motions. B-factor analysis yielded correlation of 0.662 for 1006 C-alpha atoms.

<figtable id="elnemo_modes">

Mode	Animations			Description
	a	b	c
7				TODO
8				TODO
9				TODO
10				TODO
11				TODO

Five lowest-frequency modes for the structure 1OGS created by ElNemo (cutoff used to identify elastic interactions=10).

</figtable>

Sources

WEBnm@:
WEBnm@ server
ElNemo:

1. ElNemo server
   
2. K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004.
   
3. K. Suhre & Y.H. Sanejouand, On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004 © International Union of Crystallography.