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Journal of Biomolecular NMR

, Volume 73, Issue 6–7, pp 333–346 | Cite as

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

  • Ryan W. Russell
  • Matthew P. Fritz
  • Jodi Kraus
  • Caitlin M. Quinn
  • Tatyana PolenovaEmail author
  • Angela M. GronenbornEmail author
Article

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.

Keywords

Protein structure calculation Magic angle spinning Integrated structural biology 

Notes

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.

Supplementary material

10858_2019_233_MOESM1_ESM.pdf (977 kb)
Supplementary material 1 (PDF 976 KB)

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of DelawareNewarkUSA
  2. 2.Pittsburgh Center for HIV Protein InteractionsUniversity of Pittsburgh School of MedicinePittsburghUSA
  3. 3.Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghUSA

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