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Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

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Abstract

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks.

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Acknowledgments

We gratefully acknowledge financial support by the Lichtenberg program of the Volkswagen Foundation and a Grant-in-Aid for Scientific Research of the Japan Society for the Promotion of Science (JSPS).

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Authors and Affiliations

  1. Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany

    Lena Buchner & Peter Güntert

  2. Laboratory of Physical Chemistry, ETH Zürich, Zurich, Switzerland

    Peter Güntert

  3. Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan

    Peter Güntert

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  1. Lena Buchner
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Correspondence to Peter Güntert.

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Buchner, L., Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR 62, 81–95 (2015). https://doi.org/10.1007/s10858-015-9921-z

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