Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins

Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established $$^{15}\hbox {N}$$ 15 N NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of $$^{1}\hbox {H}$$ 1 H 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 $$^{15}\hbox {N}$$ 15 N relaxation parameters ( $$R_1$$ R 1 , $$R_2$$ R 2 , NOE, cross-correlated relaxation rates $$\Gamma _x$$ Γ x and $$\Gamma _z$$ Γ z ) in doubly $$^{13}\hbox {C}$$ 13 C , $$^{15}\hbox {N}$$ 15 N -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 $$\delta$$ δ -subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by $$^{15}\hbox {N}$$ 15 N only showed that the presence of $$^{13}\hbox {C}$$ 13 C has a negligible effect on $$\Gamma _x$$ Γ x , $$\Gamma _z$$ Γ z , and on the cross-relaxation rate (calculated from NOE and $$R_1$$ R 1 ), and that these relaxation rates can be used to calculate accurate spectral density values. Partially $$^{13}\hbox {C}$$ 13 C -labeled sample was used to test if the observed increase of $$^{15}\hbox {N}$$ 15 N $$R_1$$ R 1 in the presence of $$^{13}\hbox {C}$$ 13 C corresponds to the $$^{15}\hbox {N}-^{13}\hbox {C}$$ 15 N - 13 C dipole–dipole interactions in the $$^{13}\hbox {C}$$ 13 C , $$^{15}\hbox {N}$$ 15 N -labeled sample. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Biomolecular NMR Springer Journals

Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins

14 pages

/lp/springer_journal/triple-resonance-15-hbox-n-15-n-nmr-relaxation-experiments-for-studies-oKkDJTKwdQ
Publisher
Springer Netherlands
Subject
Physics; Biological and Medical Physics, Biophysics; Biochemistry, general; Spectroscopy/Spectrometry
ISSN
0925-2738
eISSN
1573-5001
D.O.I.
10.1007/s10858-017-0138-1
Publisher site
See Article on Publisher Site

Abstract

Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established $$^{15}\hbox {N}$$ 15 N NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of $$^{1}\hbox {H}$$ 1 H 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 $$^{15}\hbox {N}$$ 15 N relaxation parameters ( $$R_1$$ R 1 , $$R_2$$ R 2 , NOE, cross-correlated relaxation rates $$\Gamma _x$$ Γ x and $$\Gamma _z$$ Γ z ) in doubly $$^{13}\hbox {C}$$ 13 C , $$^{15}\hbox {N}$$ 15 N -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 $$\delta$$ δ -subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by $$^{15}\hbox {N}$$ 15 N only showed that the presence of $$^{13}\hbox {C}$$ 13 C has a negligible effect on $$\Gamma _x$$ Γ x , $$\Gamma _z$$ Γ z , and on the cross-relaxation rate (calculated from NOE and $$R_1$$ R 1 ), and that these relaxation rates can be used to calculate accurate spectral density values. Partially $$^{13}\hbox {C}$$ 13 C -labeled sample was used to test if the observed increase of $$^{15}\hbox {N}$$ 15 N $$R_1$$ R 1 in the presence of $$^{13}\hbox {C}$$ 13 C corresponds to the $$^{15}\hbox {N}-^{13}\hbox {C}$$ 15 N - 13 C dipole–dipole interactions in the $$^{13}\hbox {C}$$ 13 C , $$^{15}\hbox {N}$$ 15 N -labeled sample.

Journal

Journal of Biomolecular NMRSpringer Journals

Published: Oct 25, 2017

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