Literature DB >> 16043707

Automated projection spectroscopy (APSY).

Sebastian Hiller1, Francesco Fiorito, Kurt Wüthrich, Gerhard Wider.   

Abstract

This work presents the automated projection spectroscopy (APSY) method for the recording of discrete sets of j projections from N-dimensional (N > or = 3) NMR experiments at operator-selected projection angles and automatic identification of the correlation cross peaks. The result from APSY is the fully automated generation of the complete or nearly complete peak list for the N-dimensional NMR spectrum from a geometric analysis of the j experimentally recorded, low-dimensional projections. In the present implementation of APSY, two-dimensional projections of the N-dimensional spectrum are recorded by using techniques developed for projection-reconstruction spectroscopy [Kupce,E.& Freeman, R. (2004) J. Am. Chem. Soc. 126, 6429-6440]. All projections are peak-picked with the available automated routine atnos. The previously undescribed algorithm GAPRO (geometric analysis of projections) uses vector algebra to identify subgroups of peaks in different projections that arise from the same resonance in the N-dimensional spectrum, and from these subgroups it calculates the peak positions in the N-dimensional frequency space. Unambiguous identification thus can be achieved for all cross peaks that are not overlapped with other peaks in at least one of the N dimensions. Because of the correlation between the positions of corresponding peaks in multiple projections, uncorrelated noise is efficiently suppressed, so that APSY should be quite widely applicable for correlation spectra of biological macromolecules, which have intrinsically low peak density in the N-dimensional spectral space.

Year:  2005        PMID: 16043707      PMCID: PMC1182451          DOI: 10.1073/pnas.0504818102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  20 in total

1.  Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2002-11       Impact factor: 2.835

2.  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

3.  Optimizing resolution in multidimensional NMR by three-way decomposition.

Authors:  Vladislav Yu Orekhov; Ilghiz Ibraghimov; Martin Billeter
Journal:  J Biomol NMR       Date:  2003-10       Impact factor: 2.835

4.  NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis.

Authors:  Touraj Etezady-Esfarjani; Torsten Herrmann; Wolfgang Peti; Heath E Klock; Scott A Lesley; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835

5.  (3,2)D GFT-NMR experiments for fast data collection from proteins.

Authors:  Youlin Xia; Guang Zhu; Sudha Veeraraghavan; Xiaolian Gao
Journal:  J Biomol NMR       Date:  2004-08       Impact factor: 2.835

6.  Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction.

Authors:  David Rovnyak; Dominique P Frueh; Mallika Sastry; Zhen-Yu J Sun; Alan S Stern; Jeffrey C Hoch; Gerhard Wagner
Journal:  J Magn Reson       Date:  2004-09       Impact factor: 2.229

7.  Projection-reconstruction of three-dimensional NMR spectra.

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Am Chem Soc       Date:  2003-11-19       Impact factor: 15.419

8.  A relational database for sequence-specific protein NMR data.

Authors:  B R Seavey; E A Farr; W M Westler; J L Markley
Journal:  J Biomol NMR       Date:  1991-09       Impact factor: 2.835

9.  Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling.

Authors:  D Neri; T Szyperski; G Otting; H Senn; K Wüthrich
Journal:  Biochemistry       Date:  1989-09-19       Impact factor: 3.162

10.  Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure.

Authors:  D Neri; M Billeter; K Wüthrich
Journal:  J Mol Biol       Date:  1992-02-05       Impact factor: 5.469

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  104 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.  Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins.

Authors:  Jie Wen; Jihui Wu; Pei Zhou
Journal:  J Magn Reson       Date:  2011-01-04       Impact factor: 2.229

3.  Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments.

Authors:  Barbara Krähenbühl; Daniela Hofmann; Christophe Maris; Gerhard Wider
Journal:  J Biomol NMR       Date:  2011-12-04       Impact factor: 2.835

4.  4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins.

Authors:  Barbara Krähenbühl; Sebastian Hiller; Gerhard Wider
Journal:  J Biomol NMR       Date:  2011-09-27       Impact factor: 2.835

5.  Speeding up sequence specific assignment of IDPs.

Authors:  Wolfgang Bermel; Ivano Bertini; Isabella C Felli; Leonardo Gonnelli; Wiktor Koźmiński; Alessandro Piai; Roberta Pierattelli; Jan Stanek
Journal:  J Biomol NMR       Date:  2012-06-10       Impact factor: 2.835

6.  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

7.  Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding.

Authors:  Andrew Proudfoot; Michael Geralt; Marc-Andre Elsliger; Ian A Wilson; Kurt Wüthrich; Pedro Serrano
Journal:  Structure       Date:  2016-07-07       Impact factor: 5.006

8.  A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection.

Authors:  Shangjin Sun; Si Yan; Changmiao Guo; Mingyue Li; Jeffrey C Hoch; John C Williams; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2012-11-12       Impact factor: 2.991

9.  SEnD NMR: sensitivity enhanced n-dimensional NMR.

Authors:  John M Gledhill; A Joshua Wand
Journal:  J Magn Reson       Date:  2009-11-18       Impact factor: 2.229

10.  Clean absorption-mode NMR data acquisition.

Authors:  Yibing Wu; Arindam Ghosh; Thomas Szyperski
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

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