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

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

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

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

Citovat

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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