Literature DB >> 21796515

Applications of non-uniform sampling and processing.

Sven G Hyberts1, Haribabu Arthanari, Gerhard Wagner.   

Abstract

Modern high-field NMR instruments provide unprecedented resolution. To make use of the resolving power in multidimensional NMR experiment standard linear sampling through the indirect dimensions to the maximum optimal evolution times (~1.2T (2)) is not practical because it would require extremely long measurement times. Thus, alternative sampling methods have been proposed during the past 20 years. Originally, random nonlinear sampling with an exponentially decreasing sampling density was suggested, and data were transformed with a maximum entropy algorithm (Barna et al., J Magn Reson 73:69-77, 1987). Numerous other procedures have been proposed in the meantime. It has become obvious that the quality of spectra depends crucially on the sampling schedules and the algorithms of data reconstruction. Here we use the forward maximum entropy (FM) reconstruction method to evaluate several alternate sampling schedules. At the current stage, multidimensional NMR spectra that do not have a serious dynamic range problem, such as triple resonance experiments used for sequential assignments, are readily recorded and faithfully reconstructed using non-uniform sampling. Thus, these experiments can all be recorded non-uniformly to utilize the power of modern instruments. On the other hand, for spectra with a large dynamic range, such as 3D and 4D NOESYs, choosing optimal sampling schedules and the best reconstruction method is crucial if one wants to recover very weak peaks. Thus, this chapter is focused on selecting the best sampling schedules and processing methods for high-dynamic range spectra.

Entities:  

Mesh:

Year:  2012        PMID: 21796515      PMCID: PMC3292636          DOI: 10.1007/128_2011_187

Source DB:  PubMed          Journal:  Top Curr Chem        ISSN: 0340-1022


  31 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.  Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction.

Authors:  Nobuhisa Shimba; Alan S Stern; Charles S Craik; Jeffrey C Hoch; Volker Dötsch
Journal:  J Am Chem Soc       Date:  2003-03-05       Impact factor: 15.419

3.  GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information.

Authors:  Seho Kim; Thomas Szyperski
Journal:  J Am Chem Soc       Date:  2003-02-05       Impact factor: 15.419

4.  MUNIN: a new approach to multi-dimensional NMR spectra interpretation.

Authors:  V Y Orekhov; I V Ibraghimov; M Billeter
Journal:  J Biomol NMR       Date:  2001-05       Impact factor: 2.835

5.  Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction.

Authors:  Sven G Hyberts; Gregory J Heffron; Nestor G Tarragona; Kirty Solanky; Katherine A Edmonds; Harry Luithardt; Jasna Fejzo; Michael Chorev; Huseyin Aktas; Kimberly Colson; Kenneth H Falchuk; Jose A Halperin; Gerhard Wagner
Journal:  J Am Chem Soc       Date:  2007-03-28       Impact factor: 15.419

6.  Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data.

Authors:  Sven G Hyberts; Koh Takeuchi; Gerhard Wagner
Journal:  J Am Chem Soc       Date:  2010-02-24       Impact factor: 15.419

7.  High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN.

Authors:  Brian E Coggins; Pei Zhou
Journal:  J Biomol NMR       Date:  2008-10-14       Impact factor: 2.835

8.  FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation.

Authors:  Sven G Hyberts; Dominique P Frueh; Haribabu Arthanari; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2009-08-25       Impact factor: 2.835

9.  Coupled decomposition of four-dimensional NOESY spectra.

Authors:  Sebastian Hiller; Ilghis Ibraghimov; Gerhard Wagner; Vladislav Y Orekhov
Journal:  J Am Chem Soc       Date:  2009-09-16       Impact factor: 15.419

10.  Three-way decomposition of a complete 3D 15N-NOESY-HSQC.

Authors:  Aleksandras Gutmanas; Patrik Jarvoll; Vladislav Yu Orekhov; Martin Billeter
Journal:  J Biomol NMR       Date:  2002-11       Impact factor: 2.835

View more
  50 in total

1.  Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR.

Authors:  Melissa R Palmer; Broc R Wenrich; Phillip Stahlfeld; David Rovnyak
Journal:  J Biomol NMR       Date:  2014-03-29       Impact factor: 2.835

2.  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

3.  (1)H(N), (13)C, and (15)N resonance assignments of the CDTb-interacting domain (CDTaBID) from the Clostridium difficile binary toxin catalytic component (CDTa, residues 1-221).

Authors:  Braden M Roth; Kristen M Varney; Richard R Rustandi; David J Weber
Journal:  Biomol NMR Assign       Date:  2016-06-28       Impact factor: 0.746

4.  Accurate scoring of non-uniform sampling schemes for quantitative NMR.

Authors:  Phillip C Aoto; R Bryn Fenwick; Gerard J A Kroon; Peter E Wright
Journal:  J Magn Reson       Date:  2014-07-02       Impact factor: 2.229

5.  Nonuniform sampling and maximum entropy reconstruction in multidimensional NMR.

Authors:  Jeffrey C Hoch; Mark W Maciejewski; Mehdi Mobli; Adam D Schuyler; Alan S Stern
Journal:  Acc Chem Res       Date:  2014-01-09       Impact factor: 22.384

Review 6.  Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer.

Authors:  Pramodh Vallurupalli; Ashok Sekhar; Tairan Yuwen; Lewis E Kay
Journal:  J Biomol NMR       Date:  2017-03-19       Impact factor: 2.835

7.  Assembly of phospholipid nanodiscs of controlled size for structural studies of membrane proteins by NMR.

Authors:  Franz Hagn; Mahmoud L Nasr; Gerhard Wagner
Journal:  Nat Protoc       Date:  2017-12-07       Impact factor: 13.491

8.  Analysis of DNA binding by human factor xeroderma pigmentosum complementation group A (XPA) provides insight into its interactions with nucleotide excision repair substrates.

Authors:  Norie Sugitani; Markus W Voehler; Michelle S Roh; Agnieszka M Topolska-Woś; Walter J Chazin
Journal:  J Biol Chem       Date:  2017-08-31       Impact factor: 5.157

Review 9.  Magic angle spinning NMR of viruses.

Authors:  Caitlin M Quinn; Manman Lu; Christopher L Suiter; Guangjin Hou; Huilan Zhang; Tatyana Polenova
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2015-02-16       Impact factor: 9.795

Review 10.  Perspectives in magnetic resonance: NMR in the post-FFT era.

Authors:  Sven G Hyberts; Haribabu Arthanari; Scott A Robson; Gerhard Wagner
Journal:  J Magn Reson       Date:  2014-04       Impact factor: 2.229

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.