Study of the Dynamics of Flexible Subunits of RNA Polymerase
from Bacillus subtilis

p 2023

Study of the Dynamics of Flexible Subunits of RNA Polymerase from Bacillus subtilis

TUŽINČIN, Dávid, Nicola SALVI, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA et. al.

Základní údaje

Originální název

Study of the Dynamics of Flexible Subunits of RNA Polymerase from Bacillus subtilis

Autoři

TUŽINČIN, Dávid, Nicola SALVI, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE a Pavel KADEŘÁVEK

Vydání

2023

Další údaje

Jazyk

angličtina

Typ výsledku

Vyžádané přednášky

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Slovensko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

NMR; protein dynamics

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 25. 3. 2024 08:55, Mgr. Eva Dubská

Anotace

V originále

The RNA polymerase found in Gram-positive bacteria is composed of multiple subunits, some of which exhibit interesting dynamic behaviors at various timescales. Nuclear magnetic resonance (NMR) is known as an unique technique capable of delivering insights into protein motions with atomic resolution. While analyzing the internal motion of structured proteins within the picosecond to nanosecond timescale relies on a well-established approach involving relaxation rate measurements and analysis [1], investigating the dynamics of intrinsically disordered proteins (IDPs) proves notably more challenging task for multiple reasons (complexity of motions, signal overlaps in NMR spectra, etc.). This study presents an exploration of the C-terminal domain of the delta subunit of RNA polymerase, which represents a disorder region posing particular investigative challenges. In order to obtain detailed information about significant, slower segmental motions occurring within the nanosecond timescale, a specialized NMR methodology called high-resolution relaxometry [2] was employed. This approach resulted in a collection of unprecedented amounts of data covering the relaxation of backbone amides under a broad range of magnetic fields spanning two orders of magnitude. In order to validate the analysis process, a novel NMR experiment was devised, enabling the measurement of relaxation rates at an exceptionally low magnetic field strength (0.33 T)[3] using a unique two-field NMR spectrometer [4]. This experiment successfully confirmed the applied protocol and analysis methods. Beyond its ability to study rapid picosecond-to-nanosecond motions, NMR enables the exploration of slower structural rearrangements through the analysis of relaxation dispersion experiments [5]. These experiments provide access to motions at the microsecond-to-millisecond timescale. Such motions are typically associated with important biological functions of biomolecules and they were detected also within domain 1.1 of the sigma subunit of the RNA polymerase. Analyzing the results of relaxation dispersion experiments revealed that the studied domain naturally inclines toward adopting a more disordered state, even at room temperature. By extending the study to multiple temperatures, the thermodynamic parameters associated with this transition were determined, and an increasing significance of the observed event with rising temperatures was predicted. Complementing the investigation was a functional characterization of domain 1.1 and results clearly proved the biological importance of the identified phenomena. References 1. Korzhnev, D.M., Billeter, M., Arseniev, A.S., & Orekhov, V.Y. (2001). NMR studies of Brownian tumbling and internal motions in proteins. Progress in Nuclear Magnetic Resonance Spectroscopy, 38 (3), 197-266. 2. Redfield A.G. (2003). Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument. Magnetic Resonance in Chemistry, 41(10), 753-768 3. Jaseňáková Z., Zapletal V., Padrta P., Zachrdla M., Bolik-Coulon N., Marquardsen T., Tyburn J., Žídek L., Ferrage F., Kadeřávek P. (2020). Boosting the resolution of low-field 15N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. Journal of Biomolecular NMR, 74(2-3), 139-145 4. Cousin S.F., Charlier C., Kadeřávek P., Marquardsen T., Tyburn J.M., Bovier P.A., Ulzega S., Speck T., Wilhelm D., Engelke F., Maas W., Sakellariou D., Bodenhausen G., Pelupessy P., Ferrage F. (2016). High-resolution two-field nuclear magnetic resonance spectroscopy. Physical Chemistry Chemical Physics, 18(48), 33187–33194 5. Sekhar A., Kay L.E. (2013). NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. The Proceedings of the National Academy of Sciences, 110(32),12867-12874

Návaznosti

EF18_070/0009846, projekt VaV

Název: MSCAfellow2@MUNI

GA22-12023S, projekt VaV

Název: Neuspořádanost proteinových struktur vnáší řád do bakteriální transkripce

Investor: Grantová agentura ČR, Neuspořádanost proteinových struktur vnáší řád do bakteriální transkripce

GJ18-04197Y, projekt VaV

Název: Charakterizace flexibilních oblastí RNA polymerázy Bacillus subtilis

Investor: Grantová agentura ČR, Characterization of dynamical regions in RNA polymerase from Bacillus subtilis

LX22NPO5103, projekt VaV

Název: Národní institut virologie a bakteriologie (Akronym: NIVB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní institut virologie a bakteriologie, 5.1 EXCELES

Citovat

@misc{2386901,
   author = {Tužinčin, Dávid and Salvi, Nicola and Zapletal, Vojtěch and Jaseňáková, Zuzana and Zachrdla, Milan and Padrta, Petr and Narasimhan, Subhash and Marquardsen, Thorsten and Tyburn, JeanandMax and Šanderová, Hana and Rabatinová, Alžběta and Bendová, Kateřina and Krásný, Libor and Žídek, Lukáš and Blackledge, Martin and Ferrage, Fabien and Kadeřávek, Pavel},
   keywords = {NMR; protein dynamics},
   language = {eng},
   title = {Study of the Dynamics of Flexible Subunits of RNA Polymerase from Bacillus subtilis},
   url = {https://ssb2023.saske.sk/#book%20of%20contributions},
   year = {2023}
}

TY  - SLIDE
ID  - 2386901
AU  - Tužinčin, Dávid - Salvi, Nicola - Zapletal, Vojtěch - Jaseňáková, Zuzana - Zachrdla, Milan - Padrta, Petr - Narasimhan, Subhash - Marquardsen, Thorsten - Tyburn, Jean-Max - Šanderová, Hana - Rabatinová, Alžběta - Bendová, Kateřina - Krásný, Libor - Žídek, Lukáš - Blackledge, Martin - Ferrage, Fabien - Kadeřávek, Pavel
PY  - 2023
TI  - Study of the Dynamics of Flexible Subunits of RNA Polymerase from Bacillus subtilis
KW  - NMR
KW  - protein dynamics
UR  - https://ssb2023.saske.sk/#book%20of%20contributions
N2  - The RNA polymerase found in Gram-positive bacteria is composed of multiple subunits, some of which exhibit interesting dynamic behaviors at various timescales. Nuclear magnetic resonance (NMR) is known as an unique technique capable of delivering insights into protein motions with atomic resolution. While analyzing the internal motion of structured proteins within the picosecond to nanosecond timescale relies on a well-established approach involving relaxation rate measurements and analysis [1], investigating the dynamics of intrinsically disordered proteins (IDPs) proves notably more challenging task for multiple reasons (complexity of motions, signal overlaps in NMR spectra, etc.). This study presents an exploration of the C-terminal domain of the delta subunit of RNA polymerase, which represents a disorder region posing particular investigative challenges. In order to obtain detailed information about significant, slower segmental motions occurring within the nanosecond timescale, a specialized NMR methodology called high-resolution relaxometry [2] was employed. This approach resulted in a collection of unprecedented amounts of data covering the relaxation of backbone amides under a broad range of magnetic fields spanning two orders of magnitude. In order to validate the analysis process, a novel NMR experiment was devised, enabling the measurement of relaxation rates at an exceptionally low magnetic field strength (0.33 T)[3] using a unique two-field NMR spectrometer [4]. This experiment successfully confirmed the applied protocol and analysis methods. Beyond its ability to study rapid picosecond-to-nanosecond motions, NMR enables the exploration of slower structural rearrangements through the analysis of relaxation dispersion experiments [5]. These experiments provide access to motions at the microsecond-to-millisecond timescale. Such motions are typically associated with important biological functions of biomolecules and they were detected also within domain 1.1 of the sigma subunit of the RNA polymerase. Analyzing the results of relaxation dispersion experiments revealed that the studied domain naturally inclines toward adopting a more disordered state, even at room temperature. By extending the study to multiple temperatures, the thermodynamic parameters associated with this transition were determined, and an increasing significance of the observed event with rising temperatures was predicted. Complementing the investigation was a functional characterization of domain 1.1 and results clearly proved the biological importance of the identified phenomena. References 1. Korzhnev, D.M., Billeter, M., Arseniev, A.S., & Orekhov, V.Y. (2001). NMR studies of Brownian tumbling and internal motions in proteins. Progress in Nuclear Magnetic Resonance Spectroscopy, 38 (3), 197-266. 2. Redfield A.G. (2003). Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument. Magnetic Resonance in Chemistry, 41(10), 753-768 3. Jaseňáková Z., Zapletal V., Padrta P., Zachrdla M., Bolik-Coulon N., Marquardsen T., Tyburn J., Žídek L., Ferrage F., Kadeřávek P. (2020). Boosting the resolution of low-field 15N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. Journal of Biomolecular NMR, 74(2-3), 139-145 4. Cousin S.F., Charlier C., Kadeřávek P., Marquardsen T., Tyburn J.M., Bovier P.A., Ulzega S., Speck T., Wilhelm D., Engelke F., Maas W., Sakellariou D., Bodenhausen G., Pelupessy P., Ferrage F. (2016). High-resolution two-field nuclear magnetic resonance spectroscopy. Physical Chemistry Chemical Physics, 18(48), 33187–33194 5. Sekhar A., Kay L.E. (2013). NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. The Proceedings of the National Academy of Sciences, 110(32),12867-12874
ER  -

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