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

J Biomol NMR. 2017 Nov;69(3):133-146. doi: 10.1007/s10858-017-0138-1. Epub 2017 Oct 25.

Abstract

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.

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

MeSH terms

  • Bacillus subtilis / enzymology
  • Carbon Isotopes
  • DNA-Directed RNA Polymerases / chemistry
  • Hydrogen
  • Intrinsically Disordered Proteins / chemistry*
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular / methods*

Substances

  • Carbon Isotopes
  • Intrinsically Disordered Proteins
  • Nitrogen Isotopes
  • Nitrogen-15
  • Hydrogen
  • DNA-Directed RNA Polymerases
  • Carbon-13