A novel strategy for NMR resonance assignment and protein structure determination

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A novel strategy for NMR resonance assignment and protein structure determination


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 â?? 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.

• Content Type Journal Article
• DOI 10.1007/s10858-010-9458-0
• Authors
  • Alexander Lemak, 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
  • Aleksandras Gutmanas, 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
  • Seth Chitayat, 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
  • Murthy Karra, 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
  • Christophe Farès, 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
  • Maria Sunnerhagen, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
  • Cheryl H. Arrowsmith, 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

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR