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Direct detection of CH/π interactions in proteins

Nature Chemistry volume 2, pages 466–471 (2010)Cite this article

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Abstract

XH/π interactions make important contributions to biomolecular structure and function. These weakly polar interactions, involving π-system acceptor groups, are usually identified from the three-dimensional structures of proteins. Here, nuclear magnetic resonance spectroscopy has been used to directly detect methyl/π (Me/π) interactions in proteins at atomic resolution. Density functional theory calculations predict the existence of weak scalar (J) couplings between nuclei involved in Me/π interactions. Using an optimized isotope-labelling strategy, these J couplings have been detected in proteins using nuclear magnetic resonance spectroscopy. The resulting spectra provide direct experimental evidence of Me/π interactions in proteins and allow a simple and unambiguous assignment of donor and acceptor groups. The use of nuclear magnetic resonance spectroscopy is an elegant way to identify and experimentally characterize Me/π interactions in proteins without the need for arbitrary geometric descriptions or pre-existing three-dimensional structures.

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Figure 1: Analysis of Me/π interactions in a database of 183 three-dimensional protein structures (resolution, < 2.0 Å).
Figure 2: DFT analysis of hπJCMeCaro couplings in Me/π interactions in a model system consisting of toluene and ethane.
Figure 3: Exploitation of weak hπJCMeCaro couplings in proteins by NMR spectroscopy.
Figure 4: Exploitation of weak hπJHMeCaro couplings in proteins by NMR spectroscopy.
Figure 5: Plot comparing calculated and observed hπJCMeCaro and hπJHMeCaro couplings.

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Acknowledgements

The authors wish to thank O. Hamlin and P. Gans for providing labelled acetolactate, B. Brutscher, J.-P. Simorre and D. Marion for a critical reading of the manuscript, I. Ayala for help in preparing protein samples, and the Partnership for Structural Biology for access to integrated structural biology platforms. The clone of GB3 was kindly provided by A. Bax and that of ubiquitin by S. Grzesiek. M.J.P. acknowledges funding from L'Association pour la Recherche sur le Cancer and the EU (FP7-PEOPLE-IRG-2008), J.B. acknowledges funding from Agence Nationale de la Recherche, Human Frontiers Science Programme and Centre National de la Recherche Scientifique, and D.L.B. acknowledges the Natural Sciences and Engineering Research Council of Canada and the High-Performance Virtual Computing Laboratory.

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Authors and Affiliations

  1. CEA, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France

    Michael J. Plevin & Jérôme Boisbouvier

  2. CNRS, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France

    Michael J. Plevin & Jérôme Boisbouvier

  3. Université Joseph Fourier, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France

    Michael J. Plevin & Jérôme Boisbouvier

  4. Department of Chemistry and Centre for Catalysis Research and Innovation, University of Ottawa, K1N 6N5, Ottawa, Canada

    David L. Bryce

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Contributions

All authors conceived and devised the experiments, and co-wrote the manuscript. M.J.P. prepared samples. M.J.P. and J.B. recorded and analysed the NMR data. D.L.B. performed and analysed the DFT calculations.

Corresponding authors

Correspondence to Michael J. Plevin, David L. Bryce or Jérôme Boisbouvier.

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The authors declare no competing financial interests.

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Plevin, M., Bryce, D. & Boisbouvier, J. Direct detection of CH/π interactions in proteins. Nature Chem 2, 466–471 (2010). https://doi.org/10.1038/nchem.650

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