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

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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 3 J-coupling constants on the other. The standardly used relation connecting 3 J-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 3 J αβ-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 3 J αβ-couplings and the corresponding χ1-angle in proteins.

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Acknowledgments

This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology and by grant number 200020-137827 of the Swiss National Science Foundation, and by grant number 228076 of the European Research Council, which is gratefully acknowledged.

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  1. Jane R. Allison

    Present address: Centre for Theoretical Chemistry and Physics, Institute for Natural Sciences, Massey University Albany, Albany Highway, Auckland, 0632, New Zealand

Authors and Affiliations

  1. Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland

    Denise Steiner, Jane R. Allison, Andreas P. Eichenberger & Wilfred F. van Gunsteren

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  1. Denise Steiner
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  2. Jane R. Allison
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  3. Andreas P. Eichenberger
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  4. Wilfred F. van Gunsteren
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Correspondence to Wilfred F. van Gunsteren.

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Steiner, D., Allison, J.R., Eichenberger, A.P. et al. On the calculation of 3 J αβ-coupling constants for side chains in proteins. J Biomol NMR 53, 223–246 (2012). https://doi.org/10.1007/s10858-012-9634-5

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