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Graphical interpretation of Boolean operators for protein NMR assignments

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Abstract

We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies “AND”-, “OR”- and “NOT”-like operations on planes pulled out of the classical three-dimensional spectra to obtain its functionality. The method’s strength lies in the continuous graphical presentation of the spectra, allowing both a semi-automatic peaklist construction and sequential assignment. We demonstrate here its general use for the case of a folded protein with a well-dispersed spectrum, but equally for a natively unfolded protein where spectral resolution is minimal.

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Acknowledgments

We thank Dr. I. Landrieu for sample preparation, Dr. J.-M. Wieruszeski for collecting the NMR spectra and Dr. T. Stevens and W. Boucher of the University of Cambridge, Department of Biochemistry for implementing our protein NMR assignment tools in the CcpNmr software suite. The 600 MHz facility used in this study was funded by the Région Nord—Pas de Calais (France), the CNRS and the Institut Pasteur de Lille. Part of this work was funded by a grant of the Agence National de la Recherche (ANR 05 BLAN 0320-0; Tau:Tubulin). D.V. received a predoctoral grant of the French Ministère de la Recherche.

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  1. Unité de Glycobiologie Structurale et Fonctionelle, UMR 8576 CNRS, IFR 147, Université des Sciences et Technologies de Lille, 59655, Villeneuve d’Ascq, France

    Dries Verdegem, Xavier Hanoulle & Guy Lippens

  2. Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands

    Klaas Dijkstra

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  1. Dries Verdegem
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Verdegem, D., Dijkstra, K., Hanoulle, X. et al. Graphical interpretation of Boolean operators for protein NMR assignments. J Biomol NMR 42, 11–21 (2008). https://doi.org/10.1007/s10858-008-9262-2

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