Literature DB >> 12913413

Optimizing resolution in multidimensional NMR by three-way decomposition.

Vladislav Yu Orekhov1, Ilghiz Ibraghimov, Martin Billeter.   

Abstract

Resolution depends on the number of points sampled in a FID; in indirectly detected dimensions it is an important determinant of the total experiment time. Based on the high redundancy present in NMR data, we propose the following timesaving scheme for three-dimensional spectra. An extensive grid of discrete t1- and t2-values is used, which increases resolution while preserving the spectral width. Total experiment time is reduced by avoiding the recording of t3-FIDs for selected pairs of t1 and t2; typically the recording is omitted for about 75% of the (t1,t2) combinations. These data sets are referred to as sparse, and post-experimental processing making optimal use of spectral redundancy provides the missing, non-recorded data. We have previously shown that three-way decomposition (TWD) within the MUNIN approach provides a practical way to process dense NMR data sets. Here, a novel TWD algorithm [Ibraghimov, (2002) Numer. Linear Algebra Appl. 9, 551-565] is used to complement a sparsely recorded time-domain data set by providing the missing FIDs for all (t1,t2) combinations omitted in the experiment. A necessary condition is that for each t1-value at least a few FIDs are recorded, and similar for each t2-value. The method is demonstrated on non-uniformly sampled (15)N-NOESY-HSQC data sets recorded for the 14 kD protein azurin. The spectra obtained by TWD, reconstruction and ordinary transform to frequency-domain are, in spite of the large number of signals and the high dynamic range typical for NOESYs, highly similar to a corresponding reference spectrum, for which all (t1,t2) combinations were recorded.

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Year:  2003        PMID: 12913413     DOI: 10.1023/a:1024944720653

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


  9 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

Review 2.  Maximum entropy reconstruction, spectrum analysis and deconvolution in multidimensional nuclear magnetic resonance.

Authors:  J C Hoch; A S Stern
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

3.  Modern spectrum analysis in multidimensional NMR spectroscopy: comparison of linear-prediction extrapolation and maximum-entropy reconstruction.

Authors:  Alan S Stern; Kuo-Bin Li; Jeffrey C Hoch
Journal:  J Am Chem Soc       Date:  2002-03-06       Impact factor: 15.419

4.  Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.

Authors:  Charlotta S Damberg; Vladislav Yu Orekhov; Martin Billeter
Journal:  J Med Chem       Date:  2002-12-19       Impact factor: 7.446

5.  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

6.  Application of nonlinear sampling schemes to COSY-type spectra.

Authors:  P Schmieder; A S Stern; G Wagner; J C Hoch
Journal:  J Biomol NMR       Date:  1993-09       Impact factor: 2.835

7.  Matrix decompositions of two-dimensional nuclear magnetic resonance spectra.

Authors:  T F Havel; I Najfeld; J X Yang
Journal:  Proc Natl Acad Sci U S A       Date:  1994-08-16       Impact factor: 11.205

8.  Expression of the blue copper protein azurin from Pseudomonas aeruginosa in Escherichia coli.

Authors:  B G Karlsson; T Pascher; M Nordling; R H Arvidsson; L G Lundberg
Journal:  FEBS Lett       Date:  1989-03-27       Impact factor: 4.124

9.  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

  9 in total
  67 in total

Review 1.  Radial sampling for fast NMR: Concepts and practices over three decades.

Authors:  Brian E Coggins; Ronald A Venters; Pei Zhou
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-07-30       Impact factor: 9.795

2.  Random phase detection in multidimensional NMR.

Authors:  Mark W Maciejewski; Matthew Fenwick; Adam D Schuyler; Alan S Stern; Vitaliy Gorbatyuk; Jeffrey C Hoch
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-26       Impact factor: 11.205

3.  Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets.

Authors:  Jan Stanek; Wiktor Koźmiński
Journal:  J Biomol NMR       Date:  2010-04-07       Impact factor: 2.835

4.  HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins.

Authors:  Christoph Wiedemann; Nishit Goradia; Sabine Häfner; Christian Herbst; Matthias Görlach; Oliver Ohlenschläger; Ramadurai Ramachandran
Journal:  J Biomol NMR       Date:  2015-08-18       Impact factor: 2.835

5.  Advances in Nuclear Magnetic Resonance for Drug Discovery.

Authors:  Robert Powers
Journal:  Expert Opin Drug Discov       Date:  2009-10-01       Impact factor: 6.098

6.  Automated projection spectroscopy (APSY).

Authors:  Sebastian Hiller; Francesco Fiorito; Kurt Wüthrich; Gerhard Wider
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-25       Impact factor: 11.205

7.  Random sampling of evolution time space and Fourier transform processing.

Authors:  Krzysztof Kazimierczuk; Anna Zawadzka; Wiktor Koźmiński; Igor Zhukov
Journal:  J Biomol NMR       Date:  2006-09-21       Impact factor: 2.835

8.  Sampling of the NMR time domain along concentric rings.

Authors:  Brian E Coggins; Pei Zhou
Journal:  J Magn Reson       Date:  2006-10-27       Impact factor: 2.229

9.  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

10.  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

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