| 1. |
- Jaravine, Victor, 1966, et al.
(författare)
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Hyper-dimensional NMR spectroscopy with nonlinear sampling
- 2008
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Ingår i: Journal of the American Chemical Society. ; 130:12, s. 3927-3936
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Tidskriftsartikel (refereegranskat)abstract
- An approach is described for joint interleaved recording, real-time processing, and analysis of NMR data sets. The method employs multidimensional decomposition to find common information in a set of conventional triple-resonance spectra recorded in the nonlinear sampling mode, and builds a model of hyperdimensional (HD) spectrum. While preserving sensitivity per unit of measurement time and allowing for maximal spectral resolution, the approach reduces data collection time on average by 2 orders of magnitude compared to the conventional method. The 7-10 dimensional HD spectrum, which is represented as a set of deconvoluted 1D vectors, is easy to handle and amenable for automated analysis. The method is exemplified by automated assignment for two protein systems of low and high spectral complexity: ubiquitin (globular, 8 kDa) and cyt (naturally disordered, 13 kDa). The collection and backbone assignment of the data sets are achieved in real time after approximately 1 and 10 h, respectively. The approach removes the most critical time bottlenecks in data acquisition and analysis. Thus, it can significantly increase the value of NMR spectroscopy in structural biology, for example, in high-throughput structural genomics applications.
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| 2. |
- Jaravine, Victor, 1966, et al.
(författare)
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Removal of a time barrier for high-resolution multidimensional NMR spectroscopy
- 2006
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Ingår i: Nature Methods. - 1548-7091. ; 3:8, s. 605-607
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a recursive multi-dimensional decomposition (R-MDD) method to speed-up recording of high-resolution NMR spectra. This method has a logarithmic dependence of measurement time on the size of indirect spectral dimensions, enjoys sensitivity and resolution advantages of optimized non-uniform acquisition schemes, and is applicable to all types of spectra of biomolecules. We demonstrate performance for several triple resonance experiments recorded on three globular proteins with molecular weights 8-22 kDa.
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| 3. |
- Jaravine, Victor, 1966, et al.
(författare)
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Targeted acquisition for real-time NMR spectroscopy
- 2006
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 128:41, s. 13421-13426
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Tidskriftsartikel (refereegranskat)
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| 4. |
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| 5. |
- Tikole, S., et al.
(författare)
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Effects of NMR Spectral Resolution on Protein Structure Calculation
- 2013
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7
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Tidskriftsartikel (refereegranskat)abstract
- Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.
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| 6. |
- Wong, L. E., et al.
(författare)
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Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data
- 2008
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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
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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