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Automated robust and accurate assignment of protein resonances for solid state NMR

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Abstract

The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not directly applicable for ssNMR due to the inherently lower data quality caused by lower sensitivity and broader lines, leading to overlap between peaks. Recently, the first efforts towards procedures specifically aimed for ssNMR have been realized (Schmidt et al. in J Biomol NMR 56(3):243–254, 2013). Here we present a robust automatic method, which can accurately assign protein resonances using peak lists from a small set of simple 2D and 3D ssNMR experiments, applicable in cases with low sensitivity. The method is demonstrated on three uniformly 13C, 15N labeled biomolecules with different challenges on the assignments. In particular, for the immunoglobulin binding domain B1 of streptococcal protein G automatic assignment shows 100 % accuracy for the backbone resonances and 91.8 % when including all side chain carbons. It is demonstrated, by using a procedure for generating artificial spectra with increasing line widths, that our method, GAMES_ASSIGN can handle a significant amount of overlapping peaks in the assignment. The impact of including different ssNMR experiments is evaluated as well.

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Acknowledgments

We acknowledge Prof. Dr. Chad Rienstra for kindly providing a microcrystalline sample of uniformly 13C, 15N labeled GB1.

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Authors and Affiliations

  1. Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark

    Jakob Toudahl Nielsen, Natalia Kulminskaya, Morten Bjerring & Niels Chr. Nielsen

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  1. Jakob Toudahl Nielsen
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  2. Natalia Kulminskaya
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  4. Niels Chr. Nielsen
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Correspondence to Jakob Toudahl Nielsen.

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Nielsen, J.T., Kulminskaya, N., Bjerring, M. et al. Automated robust and accurate assignment of protein resonances for solid state NMR. J Biomol NMR 59, 119–134 (2014). https://doi.org/10.1007/s10858-014-9835-1

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  • DOI: https://doi.org/10.1007/s10858-014-9835-1

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