Publication details

Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis



Year of publication 2010
Type Conference abstract
MU Faculty or unit

Faculty of Science

Description RNA polymerase is responsible for the DNA transcription in a cell. The RNA polymerase of Gram positive bacteria consists of seven subunits. Current project focuses on the delta subunit which increases the transcriptional specificity and efficiency of the RNA synthesis [1][2]. A delta subunit of RNA polymerase is a two domain protein. Only the N-terminal part has a well defined structure, which has been recently solved in our laboratory using multi-dimensional NMR spcectroscopy [3]. The motions of the protein backbone within the structured part were investigated using 1H-15N spectroscopy in order to reveal the functionally relevant parts of the molecule. The study of protein dynamics was based on the analysis of relaxation rates of the backbone 1H-15N spin pairs. To investigate motions on the nano-to-picosecond timescale the standard set of relaxation rates (R1, R2, NOE) was measured. The experiments were performed at two magnetic fields (500 MHz, 600 MHz) and the acquired data were interpreted using the Model-Free approach [4][5]. In addition, motions on the micro-to-milisecond timescale were studied using relaxation dispersion experiments [6][7]. The results show a correlation between the residues undergoing slow exchange and the conserved residues predicted to form an interaction surface with other subunits of the molecular complex. On the contrary, the most flexible residues on the pico-to-nanosecond timescale were located in a non-interacting part of the protein. [1] Dobinson K.F., Spiegelman G.B., Biochemistry, 26, 8206-8213, 1987 [2] Juang Y.L., Helmann J.D., Journal of Molecular Biology, 239, 1-14, 1994 [3] Motáčková V., Šanderová H., Žídek L., Nováček J., Padrta P., Švenková A., Korelusová J., Jonák J., Krásný L., Sklenář V., Proteins, 78, 1807-1810, 2010 [4] Lipari G., Szabo A., Journal of American Chemical Society, 104, 4546-4559, 1982 [5] Lipari G., Szabo A., Journal of American Chemical Society, 104, 4559-4570, 1982 [6] Palmer A.G., Kroenke C.D., Loria J.P., Methods in Enzymology, 339, 204-238, 2001 [7] Long D., Liu M.L., Yang D.W., Journal of American Chemical Society, 130, 2432-2433,2008

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