P. Kadeřávek1, C. Diehl2 , V. Motáčková1, H. Šanderová3, L. Žídek1, L. Krásný3, V. Sklenář1, M. Akke2


1National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic

2Center  for Molecular Protein Science, Biophysical Chemistry, Lund University, 22100 Lund, Sweden

3Institute of Microbiology and Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220 Praha 4-Krč, Czech Republic


RNA polymerase plays a fundamental role in the process of protein synthesis because it is responsible for the DNA transcription. The RNA polymerase of Gram positive bacteria consists of seven subunits. The motions of delta subunit from Bacillus subtilis was investigated within this project. The previous experiments revealed the delta subunit increases the transcriptional specificity [1][2][3][4][5][6]  and efficiency of RNA synthesis [4][5][6]. Delta subunit is a two domain protein. The N-terminal domain has a well defined structure while the C-terminal domain is disordered. The backbone dynamics of the N-terminal domain of delta subunit was studied to revealed the functionally important parts of the molecule.

The dynamics of the system was investigated by NMR techniques. The experiments were based on the measurement of relaxation rates of backbone 15N-1H spin pair. Both the motions at fast (ps-ns) and slow (μs-ms) timescales were studied. In order to explore subnanoseconds motions, the standard set of NMR experiments including R1, R2 and NOE were performed at two magnetic fields (500 MHz, 600 MHz) and the obtained data were interpreted within the Model-Free approach [7][8]. The CPMG [9][10] and T [9] experiments were utilized to inspect the slow motions. The experiments and dynamic analyses were carried out at two temperatures 300 K and 280 K to obtain the temperature dependence of the dynamical parameters.

It was revealed that the parts of the molecule which exhibit extensive motions at the μs-ms timescale correlates with the conserved residues in the sequence, expected to form an interaction surface with other subunits. On the other hand the residues which are the most flexible on the ps-ns timescale are located in another part of the protein.


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[9] Palmer A.G., Kroenke C.D., Loria J.P., Methods in Enzymology, 339, 204-238, 2001

[10]Long D., Liu M.L., Yang D.W.,  Journal of American Chemical Society, 130, 2432-2433, 2008



This work was supported by the Swedish Research Council and by the Grants MSM0021622413 and LC06030 from the Ministry of Education, Youth and Physical Culture of the Czech Republic, by the Grant 204/09/0583 from Czech Science Foundation, FRVŠ 1851/2010, and by the Grant NK/9138-3 from the Ministry of Health.