Journal of Biomolecular NMR

, Volume 64, Issue 1, pp 27–37 | Cite as

Nuclear overhauser spectroscopy of chiral CHD methylene groups

  • Rafal Augustyniak
  • Jan Stanek
  • Henri Colaux
  • Geoffrey Bodenhausen
  • Wiktor Koźmiński
  • Torsten Herrmann
  • Fabien Ferrage
Article

Abstract

Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.

Keywords

NMR spectroscopy Protein structures Nuclear Overhauser spectroscopy Automatic structure calculation 

Supplementary material

10858_2015_2_MOESM1_ESM.pdf (2.5 mb)
Supplementary material 1 (PDF 2555 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Rafal Augustyniak
    • 1
    • 2
    • 3
  • Jan Stanek
    • 4
  • Henri Colaux
    • 1
    • 2
    • 3
  • Geoffrey Bodenhausen
    • 1
    • 2
    • 3
    • 5
  • Wiktor Koźmiński
    • 4
  • Torsten Herrmann
    • 6
  • Fabien Ferrage
    • 1
    • 2
    • 3
  1. 1.Département de chimieEcole Normale Supérieure – PSL Research UniversityParisFrance
  2. 2.Sorbonne Universités, UPMC Université Paris 6ParisFrance
  3. 3.UMR 7203 LBMCNRSParisFrance
  4. 4.Faculty of ChemistryUniversity of WarsawWarsawPoland
  5. 5.Ecole Polytechnique Fédérale de Lausanne, Institut des Sciences et Ingénierie Chimiques, BCHLausanneSwitzerland
  6. 6.Institut des Sciences Analytiques, Centre de RMN à Très Hauts ChampsUniversité de Lyon/UMR 5280 CNRS/ENS Lyon/UCB Lyon 1VilleurbanneFrance

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