Triple resonance NMR relaxation experiments for studies of
intrinsically disordered proteins

J 2017

Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins

SRB, Pavel; Jiří NOVÁČEK; Pavel KADEŘÁVEK; A. RABATINOVA; L. KRÁSNÝ et al.

Základní údaje

Originální název

Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins

Autoři

SRB, Pavel; Jiří NOVÁČEK; Pavel KADEŘÁVEK; A. RABATINOVA; L. KRÁSNÝ; J. ŽÍDKOVÁ; J. BOBÁĽOVÁ; Vladimír SKLENÁŘ a Lukáš ŽÍDEK

Vydání

Journal of Biomolecular NMR, Dordrecht, Springer, 2017, 0925-2738

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.534

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/17:00095497

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1007/s10858-017-0138-1

UT WoS

000416856600003

EID Scopus

2-s2.0-85032189568

Klíčová slova anglicky

Nuclear magnetic resonance; Relaxation; Non-uniform sampling; Intrinsically disordered proteins

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 3. 2018 14:35, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five relaxation parameters (, , NOE, cross-correlated relaxation rates and ) in doubly ,-labeled proteins. We show that the third spectral dimension combined with non-uniform sampling provides relaxation rates for almost all residues of a protein with extremely poor chemical shift dispersion, the C terminal domain of -subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by only showed that the presence of has a negligible effect on , , and on the cross-relaxation rate (calculated from NOE and ), and that these relaxation rates can be used to calculate accurate spectral density values. Partially -labeled sample was used to test if the observed increase of in the presence of corresponds to the dipole-dipole interactions in the ,-labeled sample.

Návaznosti

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-16842S, projekt VaV

Název: PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA

Investor: Grantová agentura ČR, Podjednotky urcující DNA specificitu bakteriální RNA polymerázy s flexibilními doménami: funkce a dynamika

LM2015043, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

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

Citovat

SRB, Pavel; Jiří NOVÁČEK; Pavel KADEŘÁVEK; A. RABATINOVA; L. KRÁSNÝ; J. ŽÍDKOVÁ; J. BOBÁĽOVÁ; Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. Journal of Biomolecular NMR. Dordrecht: Springer, 2017, roč. 69, č. 3, s. 133-146. ISSN 0925-2738. Dostupné z: https://doi.org/10.1007/s10858-017-0138-1.

@article{1408290,
   author = {Srb, Pavel and Nováček, Jiří and Kadeřávek, Pavel and Rabatinova, A. and Krásný, L. and Žídková, J. and Bobáľová, J. and Sklenář, Vladimír and Žídek, Lukáš},
   article_location = {Dordrecht},
   article_number = {3},
   doi = {https://doi.org/10.1007/s10858-017-0138-1},
   keywords = {Nuclear magnetic resonance; Relaxation; Non-uniform sampling; Intrinsically disordered proteins},
   language = {eng},
   issn = {0925-2738},
   journal = {Journal of Biomolecular NMR},
   title = {Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins},
   url = {https://link.springer.com/article/10.1007%2Fs10858-017-0138-1},
   volume = {69},
   year = {2017}
}

TY  - JOUR
ID  - 1408290
AU  - Srb, Pavel - Nováček, Jiří - Kadeřávek, Pavel - Rabatinova, A. - Krásný, L. - Žídková, J. - Bobáľová, J. - Sklenář, Vladimír - Žídek, Lukáš
PY  - 2017
TI  - Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins
JF  - Journal of Biomolecular NMR
VL  - 69
IS  - 3
SP  - 133-146
EP  - 133-146
PB  - Springer
SN  - 09252738
KW  - Nuclear magnetic resonance
KW  - Relaxation
KW  - Non-uniform sampling
KW  - Intrinsically disordered proteins
UR  - https://link.springer.com/article/10.1007%2Fs10858-017-0138-1
N2  - Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five relaxation parameters (, , NOE, cross-correlated relaxation rates and ) in doubly ,-labeled proteins. We show that the third spectral dimension combined with non-uniform sampling provides relaxation rates for almost all residues of a protein with extremely poor chemical shift dispersion, the C terminal domain of -subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by only showed that the presence of has a negligible effect on , , and on the cross-relaxation rate (calculated from NOE and ), and that these relaxation rates can be used to calculate accurate spectral density values. Partially -labeled sample was used to test if the observed increase of in the presence of corresponds to the dipole-dipole interactions in the ,-labeled sample.
ER  -

SRB, Pavel; Jiří NOVÁČEK; Pavel KADEŘÁVEK; A. RABATINOVA; L. KRÁSNÝ; J. ŽÍDKOVÁ; J. BOBÁĽOVÁ; Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. \textit{Journal of Biomolecular NMR}. Dordrecht: Springer, 2017, roč.~69, č.~3, s.~133-146. ISSN~0925-2738. Dostupné z: https://doi.org/10.1007/s10858-017-0138-1.

Přehled o publikaci