Convergent views on disordered protein dynamics from NMR and
computational approaches

J 2022

Convergent views on disordered protein dynamics from NMR and computational approaches

SALVI, Nicola, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA et. al.

Základní údaje

Originální název

Convergent views on disordered protein dynamics from NMR and computational approaches

Autoři

SALVI, Nicola, Vojtěch ZAPLETAL (203 Česká republika, domácí), Zuzana JASEŇÁKOVÁ (703 Slovensko, domácí), Milan ZACHRDLA, Petr PADRTA (203 Česká republika, domácí), Subhash NARASIMHAN (356 Indie, domácí), Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK (203 Česká republika, domácí), Martin BLACKLEDGE, Fabien FERRAGE a Pavel KADEŘÁVEK (203 Česká republika, garant, domácí)

Vydání

BIOPHYSICAL JOURNAL, UNITED STATES, CELL PRESS, 2022, 0006-3495

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.400

Kód RIV

RIV/00216224:14740/22:00126947

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1016/j.bpj.2022.09.016

UT WoS

000928435100005

Klíčová slova anglicky

NMR; protein dynamics

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2024 14:19, Ing. Martina Blahová

Anotace

V originále

Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.

Návaznosti

EF18_070/0009846, projekt VaV

Název: MSCAfellow2@MUNI

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

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

SALVI, Nicola, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE a Pavel KADEŘÁVEK. Convergent views on disordered protein dynamics from NMR and computational approaches. BIOPHYSICAL JOURNAL. UNITED STATES: CELL PRESS, 2022, roč. 121, č. 20, s. 3785-3794. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2022.09.016.

@article{2225678,
   author = {Salvi, Nicola and Zapletal, Vojtěch and Jaseňáková, Zuzana and Zachrdla, Milan and Padrta, Petr and Narasimhan, Subhash and Marquardsen, Thorsten and Tyburn, JeanandMax and Žídek, Lukáš and Blackledge, Martin and Ferrage, Fabien and Kadeřávek, Pavel},
   article_location = {UNITED STATES},
   article_number = {20},
   doi = {http://dx.doi.org/10.1016/j.bpj.2022.09.016},
   keywords = {NMR; protein dynamics},
   language = {eng},
   issn = {0006-3495},
   journal = {BIOPHYSICAL JOURNAL},
   title = {Convergent views on disordered protein dynamics from NMR and computational approaches},
   url = {https://linkinghub.elsevier.com/retrieve/pii/S0006-3495(22)00766-4},
   volume = {121},
   year = {2022}
}

TY  - JOUR
ID  - 2225678
AU  - Salvi, Nicola - Zapletal, Vojtěch - Jaseňáková, Zuzana - Zachrdla, Milan - Padrta, Petr - Narasimhan, Subhash - Marquardsen, Thorsten - Tyburn, Jean-Max - Žídek, Lukáš - Blackledge, Martin - Ferrage, Fabien - Kadeřávek, Pavel
PY  - 2022
TI  - Convergent views on disordered protein dynamics from NMR and computational approaches
JF  - BIOPHYSICAL JOURNAL
VL  - 121
IS  - 20
SP  - 3785-3794
EP  - 3785-3794
PB  - CELL PRESS
SN  - 00063495
KW  - NMR
KW  - protein dynamics
UR  - https://linkinghub.elsevier.com/retrieve/pii/S0006-3495(22)00766-4
N2  - Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.
ER  -

SALVI, Nicola, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE a Pavel KADEŘÁVEK. Convergent views on disordered protein dynamics from NMR and computational approaches. \textit{BIOPHYSICAL JOURNAL}. UNITED STATES: CELL PRESS, 2022, roč.~121, č.~20, s.~3785-3794. ISSN~0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2022.09.016.

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