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.

Basic information

Original name

Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins

Authors

SRB, Pavel (203 Czech Republic, belonging to the institution); Jiří NOVÁČEK (203 Czech Republic, belonging to the institution); Pavel KADEŘÁVEK (203 Czech Republic, belonging to the institution); A. RABATINOVA (203 Czech Republic); L. KRÁSNÝ (203 Czech Republic); J. ŽÍDKOVÁ (203 Czech Republic); J. BOBÁĽOVÁ (203 Czech Republic); Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution) and Lukáš ŽÍDEK (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 2.534

RIV identification code

RIV/00216224:14740/17:00095497

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000416856600003

EID Scopus

2-s2.0-85032189568

Keywords in English

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

Abstract

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.

Links

EE2.3.30.0009, research and development project

Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GA13-16842S, research and development project

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

Investor: Czech Science Foundation

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Cite

SRB, Pavel; Jiří NOVÁČEK; Pavel KADEŘÁVEK; A. RABATINOVA; L. KRÁSNÝ; J. ŽÍDKOVÁ; J. BOBÁĽOVÁ; Vladimír SKLENÁŘ and Lukáš ŽÍDEK. Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. Journal of Biomolecular NMR. Dordrecht: Springer, 2017, vol. 69, No 3, p. 133-146. ISSN 0925-2738. Available from: 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 and Lukáš ŽÍDEK. Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. \textit{Journal of Biomolecular NMR}. Dordrecht: Springer, 2017, vol.~69, No~3, p.~133-146. ISSN~0925-2738. Available from: https://dx.doi.org/10.1007/s10858-017-0138-1.

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