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Automatic assignmen...
Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data
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Wong, L. E. (författare)
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Masse, J. E. (författare)
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- Jaravine, Victor, 1966 (författare)
- Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University
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- Orekhov, Vladislav, 1966 (författare)
- Gothenburg University,Göteborgs universitet,Svenskt NMR-centrum vid Göteborgs universitet,Swedish NMR Centre at Göteborg University
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Pervushin, K. (författare)
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(creator_code:org_t)
- 2008-09-11
- 2008
- Engelska.
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Ingår i: Journal of Biomolecular Nmr. - : Springer Science and Business Media LLC. - 0925-2738 .- 1573-5001. ; 42:2, s. 77-86
- Relaterad länk:
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https://www.research...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- 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)
Nyckelord
- 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
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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