Journal of Biomolecular NMR

, Volume 49, Issue 1, pp 27–38 | Cite as

A novel strategy for NMR resonance assignment and protein structure determination

  • Alexander Lemak
  • Aleksandras Gutmanas
  • Seth Chitayat
  • Murthy Karra
  • Christophe Farès
  • Maria Sunnerhagen
  • Cheryl H. Arrowsmith
Article

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.

Keywords

NMR data collection and processing Chemical shift assignment Protein structure determination and refinement Structure validation 

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Alexander Lemak
    • 1
    • 3
  • Aleksandras Gutmanas
    • 1
    • 3
    • 5
  • Seth Chitayat
    • 1
  • Murthy Karra
    • 1
  • Christophe Farès
    • 1
    • 3
    • 4
  • Maria Sunnerhagen
    • 2
  • Cheryl H. Arrowsmith
    • 1
    • 3
  1. 1.Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical BiophysicsUniversity of TorontoTorontoCanada
  2. 2.Division of Molecular Biotechnology, Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
  3. 3.The Northeast Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
  4. 4.Max-Planck-Institut f. KohlenforschungMülheim an der RuhrGermany
  5. 5.Protein Data Bank EuropeEuropean Bioinformatics InstituteHinxton, CambridgeUK

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