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A novel strategy for NMR resonance assignment and protein structure determination

Lemak, Alexander (author)
University of Toronto
Gutmanas, Aleksandras (author)
University of Toronto
Chitayat, Seth (author)
University of Toronto
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Karra, Murthy (author)
University of Toronto
Fares, Christophe (author)
University of Toronto
Sunnerhagen, Maria (author)
Linköpings universitet,Molekylär Bioteknik,Tekniska högskolan
Arrowsmith, Cheryl H (author)
University of Toronto
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 (creator_code:org_t)
2010-12-14
2011
English.
In: JOURNAL OF BIOMOLECULAR NMR. - : Springer Science Business Media. - 0925-2738 .- 1573-5001. ; 49:1, s. 27-38
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Keyword

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

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art (subject category)

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