NMR is a unique methodology for obtaining information about the conformational dynamics of proteins in heterogeneous biomolecular systems. In various NMR methods, such as transferred cross-saturation, relaxation dispersion, and paramagnetic relaxation enhancement experiments, fast determination of the signal intensity ratios in the NMR spectra with high accuracy is required for analyses of targets with low yields and stabilities. However, conventional methods for the reconstruction of spectra from undersampled time-domain data, such as linear prediction, spectroscopy with integration of frequency and time domain, and analysis of Fourier, and compressed sensing were not effective for the accurate determination of the signal intensity ratios of the crowded two-dimensional spectra of proteins. Here, we developed an NMR spectra reconstruction method, â??conservation of experimental data in analysis of Fourierâ?? (Co-ANAFOR), to reconstruct the crowded spectra from the undersampled time-domain data. The number of sampling points required for the transferred cross-saturation experiments between membrane proteins, photosystem I and cytochrome b6f, and their ligand, plastocyanin, with Co-ANAFOR was half of that needed for linear prediction, and the peak height reduction ratios of the spectra reconstructed from truncated time-domain data by Co-ANAFOR were more accurate than those reconstructed from non-uniformly sampled data by compressed sensing.
[NMR paper] Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.
Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.
Related Articles Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.
Phys Med Biol. 2014 May 1;59(11):2639-2658
Authors: Proverbio A, Siow BM, Lythgoe MF, Alexander DC, Gibson AP
Abstract
Combining datasets with a model of the underlying physics prior to mapping of tissue provides a novel approach improving the estimation of parameters. We...
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05-03-2014 10:42 PM
[NMR paper] Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
J Biomol NMR. 2013 May 25;
Authors: Miao Y, Cross TA, Fu R
Abstract
The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially...
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05-28-2013 06:36 PM
Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins
Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins
Abstract Central to structural studies of biomolecules are multidimensional experiments. These are lengthy to record due to the requirement to sample the full Nyquist grid. Time savings can be achieved through undersampling the indirectly-detected dimensions combined with non-Fourier Transform (FT) processing, provided the experimental signal-to-noise ratio is sufficient. Alternatively, resolution and signal-to-noise can be improved within a given experiment time. However, non-FT...
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07-30-2012 07:42 AM
Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.
Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.
Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.
J Magn Reson. 2011 Apr;209(2):352-8
Authors: Shrot Y, Frydman L
A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have...
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07-23-2011 08:54 AM
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR.
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR.
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR.
J Magn Reson. 2011 Mar 17;
Authors: Traaseth NJ, Veglia G
We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR...
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04-13-2011 11:57 PM
FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation
FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation
Abstract Non-uniform sampling (NUS) enables recording of multidimensional NMR data at resolutions matching the resolving power of modern instruments without using excessive measuring time. However, in order to obtain satisfying results, efficient reconstruction methods are needed. Here we describe an optimized version of the Forward Maximum entropy (FM) reconstruction method, which can reconstruct up to three indirect dimensions. For complex datasets, such as NOESY spectra,...
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01-09-2011 12:46 PM
[NMR paper] Generalized reconstruction of n-D NMR spectra from multiple projections: application
Generalized reconstruction of n-D NMR spectra from multiple projections: application to the 5-D HACACONH spectrum of protein G B1 domain.
Related Articles Generalized reconstruction of n-D NMR spectra from multiple projections: application to the 5-D HACACONH spectrum of protein G B1 domain.
J Am Chem Soc. 2004 Feb 4;126(4):1000-1
Authors: Coggins BE, Venters RA, Zhou P
Reconstructing multidimensional NMR spectra from 2-D projections significantly reduces the time needed for data collection over conventional methodology. Here, we provide a...
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11-24-2010 09:25 PM
[NMR paper] Projection-reconstruction of three-dimensional NMR spectra.
Projection-reconstruction of three-dimensional NMR spectra.
Related Articles Projection-reconstruction of three-dimensional NMR spectra.
J Am Chem Soc. 2003 Nov 19;125(46):13958-9
Authors: Kupce E, Freeman R
When three-dimensional NMR spectra are presented as two stereoscopic images, they create a convincing three-dimensional impression for the viewer. In an extension of this principle, we record plane projections of a three-dimensional spectrum at different angles, and use this limited information to reconstruct the entire spectrum....
Development of a method for reconstruction of crowded NMR spectra from undersampled time-domain data
Linear Mode
