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A novel strategy for NMR resonance assignment and protein structure determination

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Abstract

The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

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Acknowledgments

The authors would like to thank Doung-uen (Kevin) Lee for help in the initial design of FMCGUI, members of the Arrowsmith Lab for their input, and Dr. Binchen Mao for assistance in running PSVS analysis. This work was supported by the US National Institute of Health Protein Structure Initiative (P50-GM62413-01 and GM67965) through the Northeast Structural Genomics Consortium; the Natural Sciences and Engineering Research Council of Canada; the Canadian Institutes of Health Research (CIHR), and the Ontario Ministry of Health and Long Term Care (OMOHLTC). The views expressed do not necessarily reflect those of the OMOHLTC. SC is the recipient of a CIHR post-doctoral fellowship and CHA holds a Canada Research Chair in Structural Proteomics. MS holds a Vinnmer fellowship from VINNOVA (The Swedish Governmental Agency for Innovation Systems).

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Author notes

  1. Christophe Farès

    Present address: Max-Planck-Institut f. Kohlenforschung, 45470, Mülheim an der Ruhr, Germany

  2. Aleksandras Gutmanas

    Present address: Protein Data Bank Europe, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Authors and Affiliations

  1. Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada

    Alexander Lemak, Aleksandras Gutmanas, Seth Chitayat, Murthy Karra, Christophe Farès & Cheryl H. Arrowsmith

  2. Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden

    Maria Sunnerhagen

  3. The Northeast Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada

    Alexander Lemak, Aleksandras Gutmanas, Christophe Farès & Cheryl H. Arrowsmith

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  1. Alexander Lemak
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  2. Aleksandras Gutmanas
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Correspondence to Cheryl H. Arrowsmith.

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Lemak, A., Gutmanas, A., Chitayat, S. et al. A novel strategy for NMR resonance assignment and protein structure determination. J Biomol NMR 49, 27–38 (2011). https://doi.org/10.1007/s10858-010-9458-0

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