Task 10 (MSUD)

Results

Lab journal

WEBnm@

The informations that are provided on the results page include:

• deformation energies and eigenvalues for the lowest-frequency non-trivial modes
• atomic displacement and fluctuation plots
• mode visualization with Jmol and vector field represention of modes
• correlation matrix for motions between Calphas
• overlap analysis for different conformations of the same protein

For the calculation of normal modes, WEBnm@ takes only Calpha atoms. The mass of the whole residue is assigned to its Calpha atom for the analysis.

The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12.

In all modes that are visualized by the server, a movement of alpha and beta chain against each other can be observed, sometimes there is a hinge-movement (mode 7) and in other modes there is a torsion between the subunits. In most modes, a part at the end of alpha subunit (BCKDHA), consisting of 3 small helices that reach into the beta subunit, moves independently from the rest of the alpha subunit but together with beta subunit. An exception is mode 9, where this part moves a lot compared to the rest of the protein. Vector representations of modes 7 and 9:

• 

  Normal mode 7 of 2BFF, alpha and beta chain move against each other.

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  Normal mode 9 of 2BFF, end of alpha chain moves strongly.

The analysis was also performed for the alpha subunit (chain A) alone, but the results are similar to those presented for the whole structure (see above), only the frequency of motion was higher compared to the whole structure.

The part at the beginning and end of the alpha chain are most flexible, as can be seen in the atomic dicplacement plots for modes 7-12 (at approximately position 400 in the plot beta chain begins):

In the correlation matrix, that shows the correlation of motions between different Calpha atoms, the two chains can clearly be identified as differently moving domains:

For BCKDHA (alpha chain in the structure) we can identify only one domain, which is consistent with the domain listed in the databases:

• CATH: 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial, Homo sapiens
• SCOP: Branched-chain alpha-keto acid dehydrogenase PP module (pyrophosphate-binding)
• Pfam: Dehydrogenase E1 component (E1_dh) at residues 106-405

In the comparative analysis no difference in the normal modes between the structure with and without ligand could be observed.

ElNémo

The web tool ElNémo provides following information:

• Predicted B-factors for all residues
• Mode frequencies and collectivities. Collectivity is defined by the fraction of residues which are significantly affected in the given mode. Modes are sorted by frequency in ascending order.
• Fluctuation maps for selected top-10 normal modes. The maps are derived from Cα-Cα distances.
• Cα atom strains for each residue
• R²(normalized mean square displacement) of all Cα-atoms in the protein.
• PDB structures for the corresponding modes.
• Animation for each of the top-10 modes.

Totally 100 modes were generated by ElNémo. They are sorted by frequency in ascending order. Analysis over the first 10 modes with highest frequencies were automatically done by ElNémo. Among the top-10 modes, 6 modes have low collectivity. Following table shows 5 of the top-10 modes which we found they are interesting for interpretation:

Mode properties	Mode 8	Mode 12	Mode 13	Mode 14	Mode 16
Frequency	1.82	8.91	10.51	10.94	14.59
Collectivity	0.0365	0.3276	0.5536	0.2636	0.5809
Movements	Long flexible loop at N-terminal has large movement. Rest part of protein does not show obvious movements.	Two subunits of the protein have small change in conformation. Slight structural changes take place within subunit.	Large conformational change between two subunits. Structural changes within subunits are larger.	Large conformational change between two subunits. No obvious intra-subunit structural change.	Large conformational change between two subunits. Large part of subunits are moving apart to each other.
Animation
Fluctuation map

• R2 of mode 8, 12 13 14 and 16. It seems only R2 values for chain A were calculated.
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  R² of mode 8.

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  R² of mode 12.

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  R² of mode 13.

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  R² of mode 14.

• 

  R² of mode 16.

Discussion

• Both servers find that beginning and end of the alpha subunit are most flexible and that there is a motion between the two subunits.
• An advantage of NMA compared to MD is that it is less computationally expensive. A disadvantage is that it only looks at motions in a big scale, e. g. domain movements, and not at single atoms. To understand the mechanism of an enzymatical reaction, it is necessary to analyse the dynamics at single side chains.