Journal of Biomolecular NMR

, Volume 53, Issue 3, pp 223–246 | Cite as

On the calculation of 3Jαβ-coupling constants for side chains in proteins

  • Denise Steiner
  • Jane R. Allison
  • Andreas P. Eichenberger
  • Wilfred F. van Gunsteren
Article

Abstract

Structural knowledge about proteins is mainly derived from values of observables, measurable in NMR spectroscopic or X-ray diffraction experiments, i.e. absorbed or scattered intensities, through theoretically derived relationships between structural quantities such as atom positions or torsional angles on the one hand and observable quantities such as squared structure factor amplitudes, NOE intensities or 3J-coupling constants on the other. The standardly used relation connecting 3J-couplings to torsional angles is the Karplus relation, which is used in protein structure refinement as well as in the evaluation of simulated properties of proteins. The accuracy of the simple and generalised Karplus relations is investigated using side-chain structural and 3Jαβ-coupling data for three different proteins, Plastocyanin, Lysozyme, and FKBP, for which such data are available. The results show that the widely used Karplus relations are only a rough estimate for the relation between 3Jαβ-couplings and the corresponding χ1-angle in proteins.

Keywords

Structure refinement Protein Molecular dynamics simulation NMR 3J-coupling constants 

Supplementary material

10858_2012_9634_MOESM1_ESM.pdf (52 kb)
PDF (52 KB)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Denise Steiner
    • 1
  • Jane R. Allison
    • 1
    • 2
  • Andreas P. Eichenberger
    • 1
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical Chemistry, ETHSwiss Federal Institute of TechnologyZurichSwitzerland
  2. 2.Centre for Theoretical Chemistry and Physics, Institute for Natural SciencesMassey University AlbanyAucklandNew Zealand

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