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

a 2010

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

KADEŘÁVEK, Pavel, Veronika MOTÁČKOVÁ, Petr PADRTA, Carl DIEHL, Hana ŠANDEROVÁ et. al.

Basic information

Original name

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

Authors

KADEŘÁVEK, Pavel, Veronika MOTÁČKOVÁ, Petr PADRTA, Carl DIEHL, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ and Mikael AKKE

Edition

International school of biological magnetic resonance, 10th Course, Biophysics and Structure to Counter Threats and Challenges, Erice 2010, 2010

Other information

Type of outcome

Konferenční abstrakt

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Organization unit

Faculty of Science

Změněno: 3/7/2010 19:38, Mgr. Pavel Kadeřávek, Ph.D.

Abstract

V originále

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

Citovat

KADEŘÁVEK, Pavel, Veronika MOTÁČKOVÁ, Petr PADRTA, Carl DIEHL, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ and Mikael AKKE. Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis. In International school of biological magnetic resonance, 10th Course, Biophysics and Structure to Counter Threats and Challenges, Erice 2010. 2010.

@proceedings{890215,
   author = {Kadeřávek, Pavel and Motáčková, Veronika and Padrta, Petr and Diehl, Carl and Šanderová, Hana and Žídek, Lukáš and Krásný, Libor and Sklenář, Vladimír and Akke, Mikael},
   booktitle = {International school of biological magnetic resonance, 10th Course, Biophysics and Structure to Counter Threats and Challenges, Erice 2010},
   title = {Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis},
   url = {http://smrl.stanford.edu/erice2010/},
   year = {2010}
}

TY  - CONF
ID  - 890215
AU  - Kadeřávek, Pavel - Motáčková, Veronika - Padrta, Petr - Diehl, Carl - Šanderová, Hana - Žídek, Lukáš - Krásný, Libor - Sklenář, Vladimír - Akke, Mikael
PY  - 2010
TI  - Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis
UR  - http://smrl.stanford.edu/erice2010/
N2  - 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
ER  -

KADEŘÁVEK, Pavel, Veronika MOTÁČKOVÁ, Petr PADRTA, Carl DIEHL, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ and Mikael AKKE. Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis. In \textit{International school of biological magnetic resonance, 10th Course, Biophysics and Structure to Counter Threats and Challenges, Erice 2010}. 2010.

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