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Triple resonance 15Ν NMR relaxation experiments for studies of intrinsically disordered proteins
P. Srb, J. Nováček, P. Kadeřávek, A. Rabatinová, L. Krásný, J. Žídková, J. Bobálová, V. Sklenář, L. Žídek,
Language English Country Netherlands
Document type Journal Article
NLK
ProQuest Central
from 1997-01-01 to 1 year ago
Medline Complete (EBSCOhost)
from 2000-01-01 to 1 year ago
Health & Medicine (ProQuest)
from 1997-01-01 to 1 year ago
- MeSH
- Bacillus subtilis enzymology MeSH
- DNA-Directed RNA Polymerases chemistry MeSH
- Nitrogen Isotopes MeSH
- Carbon Isotopes MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Intrinsically Disordered Proteins chemistry MeSH
- Hydrogen MeSH
- Publication type
- Journal Article MeSH
Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] 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 [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-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 [Formula: see text]-subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by [Formula: see text] only showed that the presence of [Formula: see text] has a negligible effect on [Formula: see text], [Formula: see text], and on the cross-relaxation rate (calculated from NOE and [Formula: see text]), and that these relaxation rates can be used to calculate accurate spectral density values. Partially [Formula: see text]-labeled sample was used to test if the observed increase of [Formula: see text] [Formula: see text] in the presence of [Formula: see text] corresponds to the [Formula: see text] dipole-dipole interactions in the [Formula: see text],[Formula: see text]-labeled sample.
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- $a Srb, Pavel $u Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí, 542/2, 166 10, Praha 6, Czech Republic.
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- $a Triple resonance 15Ν NMR relaxation experiments for studies of intrinsically disordered proteins / $c P. Srb, J. Nováček, P. Kadeřávek, A. Rabatinová, L. Krásný, J. Žídková, J. Bobálová, V. Sklenář, L. Žídek,
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- $a Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] 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 [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-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 [Formula: see text]-subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by [Formula: see text] only showed that the presence of [Formula: see text] has a negligible effect on [Formula: see text], [Formula: see text], and on the cross-relaxation rate (calculated from NOE and [Formula: see text]), and that these relaxation rates can be used to calculate accurate spectral density values. Partially [Formula: see text]-labeled sample was used to test if the observed increase of [Formula: see text] [Formula: see text] in the presence of [Formula: see text] corresponds to the [Formula: see text] dipole-dipole interactions in the [Formula: see text],[Formula: see text]-labeled sample.
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- $a Sklenář, Vladimír $u Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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- $a Žídek, Lukáš $u Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. lzidek@chemi.muni.cz. National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. lzidek@chemi.muni.cz.
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