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A novel strategy for NMR resonance assignment and protein structure determination
University of Toronto.
University of Toronto.
University of Toronto.
University of Toronto.
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2011 (English)In: JOURNAL OF BIOMOLECULAR NMR, ISSN 0925-2738, Vol. 49, no 1, 27-38 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Springer Science Business Media , 2011. Vol. 49, no 1, 27-38 p.
Keyword [en]
NMR data collection and processing, Chemical shift assignment, Protein structure determination and refinement, Structure validation
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-66290DOI: 10.1007/s10858-010-9458-0ISI: 000286196000005OAI: oai:DiVA.org:liu-66290DiVA: diva2:403138
Available from: 2011-03-11 Created: 2011-03-11 Last updated: 2011-03-11

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Sunnerhagen, Maria

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Molecular Biotechnology The Institute of Technology
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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf