Literature DB >> 26847574

Non-uniform sampling of NMR relaxation data.

Troels E Linnet1, Kaare Teilum2.   

Abstract

The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full data analysis of the resulting non-uniform sampled datasets, we have compared the performance of the multi-dimensional decomposition and iterative re-weighted least-squares algorithms in reconstructing spectra with accurate peak intensities. As long as a single fully sampled spectrum is included in a series of otherwise non-uniform sampled two-dimensional spectra, multi-dimensional decomposition reconstructs the non-uniform sampled spectra with high accuracy. For two of the four analyzed datasets, a coverage of only 20% results in essentially the same results as the fully sampled data. As exemplified by other data, such a low coverage is in general not enough to produce reliable results. We find that a coverage level not compromising the final results can be estimated by recording a single full two-dimensional spectrum and reducing the spectrum quality in silico.

Keywords:  Multi-dimensional decomposition; Non-uniform sampling; Protein NMR; Relaxation dispersion

Mesh:

Year:  2016        PMID: 26847574     DOI: 10.1007/s10858-016-0020-6

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  33 in total

1.  MUNIN: application of three-way decomposition to the analysis of heteronuclear NMR relaxation data.

Authors:  D M Korzhneva; I V Ibraghimov; M Billeter; V Y Orekhov
Journal:  J Biomol NMR       Date:  2001-11       Impact factor: 2.835

2.  Sensitivity enhancement for maximally resolved two-dimensional NMR by nonuniform sampling.

Authors:  David Rovnyak; Mark Sarcone; Ze Jiang
Journal:  Magn Reson Chem       Date:  2011-07-12       Impact factor: 2.447

3.  Analysis of non-uniformly sampled spectra with multi-dimensional decomposition.

Authors:  Vladislav Yu Orekhov; Victor A Jaravine
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2011-02-24       Impact factor: 9.795

4.  Quantification of maximum-entropy spectrum reconstructions.

Authors:  P Schmieder; A S Stern; G Wagner; J C Hoch
Journal:  J Magn Reson       Date:  1997-04       Impact factor: 2.229

5.  Maximum Entropy Spectral Reconstruction of Non-Uniformly Sampled Data.

Authors:  Mehdi Mobli; Jeffrey C Hoch
Journal:  Concepts Magn Reson Part A Bridg Educ Res       Date:  2008-11-01       Impact factor: 0.481

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  Exploring signal-to-noise ratio and sensitivity in non-uniformly sampled multi-dimensional NMR spectra.

Authors:  Sven G Hyberts; Scott A Robson; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2012-12-29       Impact factor: 2.835

8.  Boosting protein dynamics studies using quantitative nonuniform sampling NMR spectroscopy.

Authors:  Yoh Matsuki; Tsuyoshi Konuma; Toshimichi Fujiwara; Kenji Sugase
Journal:  J Phys Chem B       Date:  2011-11-01       Impact factor: 2.991

9.  Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization.

Authors:  Kaare Teilum; Melanie H Smith; Eike Schulz; Lea C Christensen; Gleb Solomentsev; Mikael Oliveberg; Mikael Akke
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-14       Impact factor: 11.205

10.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

View more
  13 in total

1.  Accurate determination of rates from non-uniformly sampled relaxation data.

Authors:  Matthew A Stetz; A Joshua Wand
Journal:  J Biomol NMR       Date:  2016-07-08       Impact factor: 2.835

2.  Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps.

Authors:  Robert L Blum; Jared Rovny; J Patrick Loria; Sean E Barrett
Journal:  J Biomol NMR       Date:  2019-07-10       Impact factor: 2.835

3.  Boosting the resolution of low-field [Formula: see text] relaxation experiments on intrinsically disordered proteins with triple-resonance NMR.

Authors:  Zuzana Jaseňáková; Vojtěch Zapletal; Petr Padrta; Milan Zachrdla; Nicolas Bolik-Coulon; Thorsten Marquardsen; Jean-Max Tyburn; Lukáš Žídek; Fabien Ferrage; Pavel Kadeřávek
Journal:  J Biomol NMR       Date:  2020-01-20       Impact factor: 2.835

4.  Accelerating 2D NMR relaxation dispersion experiments using iterated maps.

Authors:  Jared Rovny; Robert L Blum; J Patrick Loria; Sean E Barrett
Journal:  J Biomol NMR       Date:  2019-07-06       Impact factor: 2.835

5.  Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation.

Authors:  Matthew A Stetz; José A Caro; Sravya Kotaru; Xuejun Yao; Bryan S Marques; Kathleen G Valentine; A Joshua Wand
Journal:  Methods Enzymol       Date:  2018-12-08       Impact factor: 1.600

6.  Pitfalls in compressed sensing reconstruction and how to avoid them.

Authors:  Alexandra Shchukina; Paweł Kasprzak; Rupashree Dass; Michał Nowakowski; Krzysztof Kazimierczuk
Journal:  J Biomol NMR       Date:  2016-11-11       Impact factor: 2.835

7.  Enhanced Nuclear Magnetic Resonance Spectroscopy with Isotropic Mixing as a Pseudodimension.

Authors:  Dariusz Gołowicz; Alexandra Shchukina; Krzysztof Kazimierczuk
Journal:  Anal Chem       Date:  2022-06-13       Impact factor: 8.008

8.  The influence of the probability density function on spectral quality in nonuniformly sampled multidimensional NMR.

Authors:  Matthew A Zambrello; D Levi Craft; Jeffrey C Hoch; David Rovnyak; Adam D Schuyler
Journal:  J Magn Reson       Date:  2019-12-20       Impact factor: 2.229

9.  A simple approach for reconstruction of non-uniformly sampled pseudo-3D NMR data for accurate measurement of spin relaxation parameters.

Authors:  Kyle W East; Frank Delaglio; George P Lisi
Journal:  J Biomol NMR       Date:  2021-05-07       Impact factor: 2.582

10.  Joint non-uniform sampling of all incremented time delays for quicker acquisition in protein relaxation studies.

Authors:  Mateusz Urbańczyk; Michał Nowakowski; Wiktor Koźmiński; Krzysztof Kazimierczuk
Journal:  J Biomol NMR       Date:  2017-05-15       Impact factor: 2.835

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.