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Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some ‘with a little help from a friend’

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Abstract

We present a systematic investigation into the attainable accuracy and precision of protein structures determined by heteronuclear magic angle spinning solid-state NMR for a set of four proteins of varied size and secondary structure content. Structures were calculated using synthetically generated random sets of C-C distances up to 7 Å at different degrees of completeness. For single-domain proteins, 9–15 restraints per residue are sufficient to derive an accurate model structure, while maximum accuracy and precision are reached with over 15 restraints per residue. For multi-domain proteins and protein assemblies, additional information on domain orientations, quaternary structure and/or protein shape is needed. As demonstrated for the HIV-1 capsid protein assembly, this can be accomplished by integrating MAS NMR with cryoEM data. In all cases, inclusion of TALOS-derived backbone torsion angles improves the accuracy for small number of restraints, while no further increases are noted for restraint completeness above 40%. In contrast, inclusion of TALOS-derived torsion angle restraints consistently increases the precision of the structural ensemble at all degrees of distance restraint completeness.

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Acknowledgements

This work was supported by the National Institutes of Health (NIH Grant-P50GM082251, Technology Development Project 2) and is a contribution from the Pittsburgh Center for HIV Protein Interactions. JK is supported by the National Science Foundation Graduate Research Fellowship Program (#1247394). We acknowledge the support of the NSF CHE0959496 grant for acquisition of the 850 MHz NMR spectrometer and of the NIGMS P30GM110758 grant for the support of core instrumentation infrastructure at the University of Delaware. The cryoEM map was kindly provided by Peijun Zhang and Juan Perilla.

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  1. Department of Chemistry and Biochemistry, University of Delaware, 19716, Newark, DE, USA

    Ryan W. Russell, Matthew P. Fritz, Jodi Kraus, Caitlin M. Quinn & Tatyana Polenova

  2. Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA

    Ryan W. Russell, Matthew P. Fritz, Jodi Kraus, Caitlin M. Quinn, Tatyana Polenova & Angela M. Gronenborn

  3. Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave, 15261, Pittsburgh, PA, USA

    Angela M. Gronenborn

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Russell, R.W., Fritz, M.P., Kraus, J. et al. Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some ‘with a little help from a friend’. J Biomol NMR 73, 333–346 (2019). https://doi.org/10.1007/s10858-019-00233-9

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