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 (203 Česká republika, domácí), Jiří NOVÁČEK (203 Česká republika, domácí), Pavel KADEŘÁVEK (203 Česká republika, domácí), A. RABATINOVA (203 Česká republika), L. KRÁSNÝ (203 Česká republika), J. ŽÍDKOVÁ (203 Česká republika), J. BOBÁĽOVÁ (203 Česká republika), Vladimír SKLENÁŘ (203 Česká republika, domácí) a Lukáš ŽÍDEK (203 Česká republika, garant, domácí)

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

Kód RIV

RIV/00216224:14740/17:00095497

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1007/s10858-017-0138-1

UT WoS

000416856600003

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://dx.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 = {http://dx.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://dx.doi.org/10.1007/s10858-017-0138-1.

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