Quantitative Conformational Analysis of Functionally Important
Electrostatic Interactions in the Intrinsically Disordered
Region of Delta Subunit of Bacterial RNA Polymerase

J 2019

Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase

KUBÁŇ, Vojtěch, Pavel SRB, Hana ŠTÉGNEROVÁ, Petr PADRTA, Milan ZACHRDLA et. al.

Základní údaje

Originální název

Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase

Autoři

KUBÁŇ, Vojtěch (203 Česká republika, domácí), Pavel SRB (203 Česká republika, domácí), Hana ŠTÉGNEROVÁ (203 Česká republika, domácí), Petr PADRTA (203 Česká republika, domácí), Milan ZACHRDLA (203 Česká republika, domácí), Zuzana JASEŇÁKOVÁ (703 Slovensko, domácí), H. SANDEROVA (203 Česká republika), D. VITOVSKA (203 Česká republika), L. KRASNY (203 Česká republika), T. KOVAL (203 Česká republika), J. DOHNALEK (203 Česká republika), J. ZIEMSKA-LEGIECKA (616 Polsko), M. GRYNBERG (616 Polsko), P. JARNOT (616 Polsko), A. GRUCA (616 Polsko), M.R. JENSEN (250 Francie), M. BLACKLEDGE (250 Francie) a Lukáš ŽÍDEK (203 Česká republika, garant, domácí)

Vydání

Journal of the American Chemical Society, Washington, American Chemical Society, 2019, 0002-7863

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10400 1.4 Chemical sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 14.612

Kód RIV

RIV/00216224:14740/19:00108078

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/jacs.9b07837

UT WoS

000492800500036

Klíčová slova anglicky

RESIDUAL DIPOLAR COUPLINGS; BACILLUS-SUBTILIS; GENE-EXPRESSION; RAPID CHANGES; PROTEINS; NMR; TRANSCRIPTION; DETERMINANTS; PREDICTION; SCATTERING

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2024 14:10, Ing. Martina Blahová

Anotace

V originále

Electrostatic interactions play important roles in the functional mechanisms exploited by intrinsically disordered proteins (IDPs). The atomic resolution description of long-range and local structural propensities that can both be crucial for the function of highly charged IDPs presents significant experimental challenges. Here, we investigate the conformational behavior of the delta subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering. This strategy allows the resolution of long-range and local ensemble averaged structural contributions to the experimental RDCs, and reveals that the negatively charged segment folds back onto the positively charged strand, compacting the conformational sampling of the protein while remaining highly flexible in solution. Mutation of the positively charged region abrogates the long-range contact, leaving the disordered domain in an extended conformation, possibly due to local repulsion of like-charges along the chain. Remarkably, in vitro studies show that this mutation also has a significant effect on transcription activity, and results in diminished cell fitness of the mutated bacteria in vivo. This study highlights the importance of accurately describing electrostatic interactions for understanding the functional mechanisms of IDPs.

Návaznosti

GA19-12956S, projekt VaV

Název: Klíčové aspekty mykobakteriální transkriprce: SigA, podjednotka RNAP rozpoznávající promotor a její nově identifikovaný vazebný partner.

Investor: Grantová agentura ČR, Klíčové aspekty mykobakteriální transkriprce: SigA, podjednotka RNAP rozpoznávající promotor a její nově identifikovaný vazebný partner.

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

90043, velká výzkumná infrastruktura

Název: CIISB

Citovat

KUBÁŇ, Vojtěch, Pavel SRB, Hana ŠTÉGNEROVÁ, Petr PADRTA, Milan ZACHRDLA, Zuzana JASEŇÁKOVÁ, H. SANDEROVA, D. VITOVSKA, L. KRASNY, T. KOVAL, J. DOHNALEK, J. ZIEMSKA-LEGIECKA, M. GRYNBERG, P. JARNOT, A. GRUCA, M.R. JENSEN, M. BLACKLEDGE a Lukáš ŽÍDEK. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. Journal of the American Chemical Society. Washington: American Chemical Society, 2019, roč. 141, č. 42, s. 16817-16828. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.9b07837.

@article{1607006,
   author = {Kubáň, Vojtěch and Srb, Pavel and Štégnerová, Hana and Padrta, Petr and Zachrdla, Milan and Jaseňáková, Zuzana and Sanderova, H. and Vitovska, D. and Krasny, L. and Koval, T. and Dohnalek, J. and ZiemskaandLegiecka, J. and Grynberg, M. and Jarnot, P. and Gruca, A. and Jensen, M.R. and Blackledge, M. and Žídek, Lukáš},
   article_location = {Washington},
   article_number = {42},
   doi = {http://dx.doi.org/10.1021/jacs.9b07837},
   keywords = {RESIDUAL DIPOLAR COUPLINGS; BACILLUS-SUBTILIS; GENE-EXPRESSION; RAPID CHANGES; PROTEINS; NMR; TRANSCRIPTION; DETERMINANTS; PREDICTION; SCATTERING},
   language = {eng},
   issn = {0002-7863},
   journal = {Journal of the American Chemical Society},
   title = {Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase},
   url = {https://pubs.acs.org/doi/10.1021/jacs.9b07837},
   volume = {141},
   year = {2019}
}

TY  - JOUR
ID  - 1607006
AU  - Kubáň, Vojtěch - Srb, Pavel - Štégnerová, Hana - Padrta, Petr - Zachrdla, Milan - Jaseňáková, Zuzana - Sanderova, H. - Vitovska, D. - Krasny, L. - Koval, T. - Dohnalek, J. - Ziemska-Legiecka, J. - Grynberg, M. - Jarnot, P. - Gruca, A. - Jensen, M.R. - Blackledge, M. - Žídek, Lukáš
PY  - 2019
TI  - Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase
JF  - Journal of the American Chemical Society
VL  - 141
IS  - 42
SP  - 16817-16828
EP  - 16817-16828
PB  - American Chemical Society
SN  - 00027863
KW  - RESIDUAL DIPOLAR COUPLINGS
KW  - BACILLUS-SUBTILIS
KW  - GENE-EXPRESSION
KW  - RAPID CHANGES
KW  - PROTEINS
KW  - NMR
KW  - TRANSCRIPTION
KW  - DETERMINANTS
KW  - PREDICTION
KW  - SCATTERING
UR  - https://pubs.acs.org/doi/10.1021/jacs.9b07837
L2  - https://pubs.acs.org/doi/10.1021/jacs.9b07837
N2  - Electrostatic interactions play important roles in the functional mechanisms exploited by intrinsically disordered proteins (IDPs). The atomic resolution description of long-range and local structural propensities that can both be crucial for the function of highly charged IDPs presents significant experimental challenges. Here, we investigate the conformational behavior of the delta subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering. This strategy allows the resolution of long-range and local ensemble averaged structural contributions to the experimental RDCs, and reveals that the negatively charged segment folds back onto the positively charged strand, compacting the conformational sampling of the protein while remaining highly flexible in solution. Mutation of the positively charged region abrogates the long-range contact, leaving the disordered domain in an extended conformation, possibly due to local repulsion of like-charges along the chain. Remarkably, in vitro studies show that this mutation also has a significant effect on transcription activity, and results in diminished cell fitness of the mutated bacteria in vivo. This study highlights the importance of accurately describing electrostatic interactions for understanding the functional mechanisms of IDPs.
ER  -

KUBÁŇ, Vojtěch, Pavel SRB, Hana ŠTÉGNEROVÁ, Petr PADRTA, Milan ZACHRDLA, Zuzana JASEŇÁKOVÁ, H. SANDEROVA, D. VITOVSKA, L. KRASNY, T. KOVAL, J. DOHNALEK, J. ZIEMSKA-LEGIECKA, M. GRYNBERG, P. JARNOT, A. GRUCA, M.R. JENSEN, M. BLACKLEDGE a Lukáš ŽÍDEK. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. \textit{Journal of the American Chemical Society}. Washington: American Chemical Society, 2019, roč.~141, č.~42, s.~16817-16828. ISSN~0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.9b07837.

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