Enhanced spectral density mapping through combined multiple-field deuterium 13 CH 2 D methyl spin relaxation NMR spectroscopy

Methods. 2018 Apr 1;138-139:76-84. doi: 10.1016/j.ymeth.2017.12.020. Epub 2017 Dec 27.

Abstract

Quadrupolar relaxation of 2H (D) nuclear spins is a powerful probe of conformational dynamics in biological macromolecules. Deuterium relaxation rate constants are determined by the spectral density function for reorientation of the C-D bond vector at zero, single-quantum, and double-quantum 2H frequencies. In the present work, 2H relaxation rate constants were measured for an E. coli ribonuclease H [U-2H, 15N] ILV-[13CH2D] sample using 400, 500, 800, and 900 MHz NMR spectrometers and analyzed by three approaches to determine spectral density values. First, data recorded at each static magnetic field were analyzed independently. Second, data recorded at 400 and 800 MHz were analyzed jointly and data recorded at other fields were analyzed independently. Third, data recorded at 400 and 500 MHz were interpolated to 450 MHz, and the resulting two pairs of data, corresponding to 400 MHz/800 MHz and 450 MHz/900 MHz, were analyzed jointly. The second and third approaches rely on the identity between the double quantum frequency at the lower field and the single quantum frequency at the higher field. Spectral density values for 32 of the 48 resolvable ILV methyl resonances were fit by the Lipari-Szabo model-free formalism and used to validate the three methods. The three spectral density mapping methods performed equally well in cross validation with data recorded at 700 MHz. However, the third method yielded approximately 10-15% more precise estimates of model-free parameters and consequently provides a general strategy for analysis of 2H spin relaxation data in biological macromolecules.

Keywords: Deuterium relaxation; Protein dynamics; Ribonuclease H; Spectral density mapping.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Deuterium
  • Escherichia coli / enzymology*
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation
  • Ribonucleases / analysis
  • Ribonucleases / chemistry
  • Ribonucleases / metabolism*

Substances

  • Deuterium
  • Ribonucleases