Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.
J Biomol NMR. 2016 Sep 28;
Authors: Seginer A, Olsen GL, Frydman L
Abstract
Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the [Formula: see text]-[Formula: see text] plane, that will deliver the spectrum being sought after a 1D Fourier transformation versus [Formula: see text]. This need to simultaneously digitize two domains, tends to impose bandwidth limitations along all spectral axes. Along the [Formula: see text]/[Formula: see text] dimension this problem is exacerbated by the fact that odd and even time points are not equispaced, and by additional artifacts such as time shifts between time points sampled while under the action of positive and negative decoding gradients. As a result, odd and even [Formula: see text] points are typically Fourier transformed separately, halving the potential spectral width along this dimension. While this halving of the [Formula: see text] span can be overcome by an interlaced Fourier transform, this post-processing is seldom used because of its sensitivity to hardware inaccuracies requiring even finer corrections of the even/odd [Formula: see text] data points. These corrections have so far been done manually, but are challenging to implement when dealing with low signal-to-noise ratio signals like those associated with biomolecular NMR experiments. This study introduces an algorithm for an automatic correction of all even/odd ultrafast NMR inconsistencies, based on the acquisition of a reference scan on the solvent. This algorithm was verified experimentally using an [Formula: see text]-[Formula: see text] UF-HSQC variant on ubiquitin at 600*MHz. Features of this method as well as of the interlaced Fourier transformation in general, are discussed.
PMID: 27683189 [PubMed - as supplied by publisher]
Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction
Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction
Abstract
Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the \({\hbox {F}_{1}}\) â?? \(t_{2}\) ...
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09-29-2016 06:58 AM
[NMR paper] Applications of high dimensionality experiments to biomolecular NMR.
Applications of high dimensionality experiments to biomolecular NMR.
Applications of high dimensionality experiments to biomolecular NMR.
Prog Nucl Magn Reson Spectrosc. 2015 Nov;90-91:49-73
Authors: Nowakowski M, Saxena S, Stanek J, ?erko S, Ko?mi?ski W
Abstract
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable...
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11-26-2015 12:13 AM
Applications of high dimensionality experiments to biomolecular NMR
Applications of high dimensionality experiments to biomolecular NMR
Publication date: Available online 11 July 2015
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Micha? Nowakowski , Saurabh Saxena , Jan Stanek , Szymon ?erko , Wiktor Ko?mi?ski</br>
High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review...
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07-12-2015 07:12 AM
[NMR paper] A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions.
A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions.
A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions.
J Magn Reson. 2014 Nov 15;250C:37-44
Authors: Zhang R, Damron J, Vosegaard T, Ramamoorthy A
Abstract
Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies...
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12-09-2014 01:13 PM
[NMR paper] Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Phys Chem Chem Phys. 2014 Jul 23;
Authors: Zhu T, Zhang JZ, He X
Abstract
In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated...
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07-24-2014 11:56 AM
Correction for Li et al., Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion [Correction]
Correction for Li et al., Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion
...
Date: 2013-11-26
BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for “Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion,” by Ying Li, Nicole L. Altorelli, Fabiana Bahna, Barry Honig, Lawrence Shapiro, and Arthur G. Palmer III, which appeared in issue 41, October 8, 2013, of Proc Natl Acad Sci USA (110:16462–16467; first published September... Read More
PNAS:
Number: 48
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11-27-2013 01:50 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
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.
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