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Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data

Wong, L. E. (author)
Masse, J. E. (author)
Jaravine, Victor, 1966 (author)
Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University
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Orekhov, Vladislav, 1966 (author)
Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University
Pervushin, K. (author)
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 (creator_code:org_t)
2008-09-11
2008
English.
In: Journal of Biomolecular Nmr. - : Springer Science and Business Media LLC. - 0925-2738 .- 1573-5001. ; 42:2, s. 77-86
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa C-13,(15) N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.

Subject headings

NATURVETENSKAP  -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
NATURVETENSKAP  -- Biologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

Keyword

MDD
automatic resonance assignment
nonlinear data sampling
targeted
NMR data acquisition
FILTER DIAGONALIZATION METHOD
MULTIDIMENSIONAL NMR
FOURIER-TRANSFORM
COVARIANCE NMR
NOESY SPECTRA
SPIN SYSTEMS
APSY-NMR
GFT NMR
SPECTROSCOPY
RESOLUTION

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ref (subject category)
art (subject category)

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