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 based reconstruction of undersampled spectra that encompass a wide signal dynamic range is strongly impeded by the non-linear behaviour of many methods, which further compromises the detection of weak peaks. Here we show, through an application to a larger α-helical membrane protein under crowded spectral conditions, the potential use of compressed sensing (CS) l 1-norm minimization to reconstruct undersampled 3D NOESY spectra. Substantial signal overlap and low sensitivity make this a demanding application, which strongly benefits from the improvements in signal-to-noise and resolution per unit time achieved through the undersampling approach. The quality of the reconstructions is assessed under varying conditions. We show that the CS approach is robust to noise and, despite significant spectral overlap, is able to reconstruct high quality spectra from data sets recorded in far less than half the amount of time required for regular sampling.
Content Type Journal Article
Category Article
Pages 1-18
DOI 10.1007/s10858-012-9643-4
Authors
Mark J. Bostock, Department of Biochemistry, University of Cambridge, Cambridge, UK
Daniel J. Holland, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
Daniel Nietlispach, Department of Biochemistry, University of Cambridge, Cambridge, UK
Efficient Acquisition of High-Resolution 4-D Diagonal-Suppressed Methyl-Methyl NOESY for Large Proteins
Efficient Acquisition of High-Resolution 4-D Diagonal-Suppressed Methyl-Methyl NOESY for Large Proteins
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Jie Wen, Jihui Wu, Pei Zhou</br>
The methyl-methyl NOESYexperimentplays an important role in determiningthe global folds of large proteins. Despite the high sensitivity of this experiment, the analysisof methyl-methyl NOEs is frequently hindered by the limited chemical shift dispersion of methyl groups, particularly methyl protons. Thismakes it difficult to unambiguously assign all of the methyl-methyl...
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03-10-2012 10:54 AM
Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling
Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling
Abstract The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would...
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02-16-2012 05:24 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
[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.
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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.
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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....
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[NMR paper] 3D NMR experiments for measuring 15N relaxation data of large proteins: application t
3D NMR experiments for measuring 15N relaxation data of large proteins: application to the 44 kDa ectodomain of SIV gp41.
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J Magn Reson. 1998 Dec;135(2):368-72
Authors: Caffrey M, Kaufman J, Stahl SJ, Wingfield PT, Gronenborn AM, Clore GM
A suite of 3D NMR experiments for measuring 15N-¿1H¿ NOE, 15N T1, and 15N T1rho values in large proteins, uniformly labeled with 15N and 13C, is presented. These...
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[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
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J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
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[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins
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