Task 10 (MSUD)
Contents
Results
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.
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.
