Literature DB >> 17701276

Automatic maximum entropy spectral reconstruction in NMR.

Mehdi Mobli1, Mark W Maciejewski, Michael R Gryk, Jeffrey C Hoch.   

Abstract

Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system.

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Year:  2007        PMID: 17701276     DOI: 10.1007/s10858-007-9180-8

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.582


  17 in total

1.  New methods for fast multidimensional NMR.

Authors:  Ray Freeman; Eriks Kupce
Journal:  J Biomol NMR       Date:  2003-10       Impact factor: 2.835

2.  Optimization of 13C direct detection NMR methods.

Authors:  Nobuhisa Shimba; Helena Kovacs; Alan S Stern; Anson M Nomura; Ichio Shimada; Jeffrey C Hoch; Charles S Craik; Volker Dötsch
Journal:  J Biomol NMR       Date:  2004-10       Impact factor: 2.835

3.  Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy.

Authors:  Mehdi Mobli; Alan S Stern; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2006-07-11       Impact factor: 2.229

4.  Removal of a time barrier for high-resolution multidimensional NMR spectroscopy.

Authors:  Victor Jaravine; Ilgis Ibraghimov; Vladislav Yu Orekhov
Journal:  Nat Methods       Date:  2006-08       Impact factor: 28.547

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.  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

7.  High-resolution aliphatic side-chain assignments in 3D HCcoNH experiments with joint H-C evolution and non-uniform sampling.

Authors:  Zhen-Yu J Sun; Sven G Hyberts; David Rovnyak; Sunghyouk Park; Alan S Stern; Jeffrey C Hoch; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2005-05       Impact factor: 2.835

8.  Three-dimensional 13C-detected CH3-TOCSY using selectively protonated proteins: facile methyl resonance assignment and protein structure determination.

Authors:  John B Jordan; Helena Kovacs; Yuefeng Wang; Mehdi Mobli; Rensheng Luo; Clemens Anklin; Jeffrey C Hoch; Richard W Kriwacki
Journal:  J Am Chem Soc       Date:  2006-07-19       Impact factor: 15.419

9.  Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data.

Authors:  R A Chylla; J L Markley
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

10.  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

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  26 in total

1.  Solid-state NMR spectroscopy of protein complexes.

Authors:  Shangjin Sun; Yun Han; Sivakumar Paramasivam; Si Yan; Amanda E Siglin; John C Williams; In-Ja L Byeon; Jinwoo Ahn; Angela M Gronenborn; Tatyana Polenova
Journal:  Methods Mol Biol       Date:  2012

2.  Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases.

Authors:  Rajesh Ghai; Mehdi Mobli; Suzanne J Norwood; Andrea Bugarcic; Rohan D Teasdale; Glenn F King; Brett M Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-21       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.  Z-matrix formalism for quantitative noise assessment of covariance nuclear magnetic resonance spectra.

Authors:  David A Snyder; Arindam Ghosh; Fengli Zhang; Thomas Szyperski; Rafael Brüschweiler
Journal:  J Chem Phys       Date:  2008-09-14       Impact factor: 3.488

5.  Randomization improves sparse sampling in multidimensional NMR.

Authors:  Jeffrey C Hoch; Mark W Maciejewski; Blagoje Filipovic
Journal:  J Magn Reson       Date:  2008-05-21       Impact factor: 2.229

6.  Parallel screening and optimization of protein constructs for structural studies.

Authors:  Rodolfo M Rasia; Marjolaine Noirclerc-Savoye; Nicolás G Bologna; Benoit Gallet; Michael J Plevin; Laurence Blanchard; Javier F Palatnik; Bernhard Brutscher; Thierry Vernet; Jérôme Boisbouvier
Journal:  Protein Sci       Date:  2009-02       Impact factor: 6.725

7.  A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment.

Authors:  Mehdi Mobli; Alan S Stern; Wolfgang Bermel; Glenn F King; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2010-03-01       Impact factor: 2.229

8.  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

9.  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

10.  Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic Angle Spinning NMR Spectroscopy.

Authors:  Shangjin Sun; Andrew H Butterworth; Sivakumar Paramasivam; Si Yan; Christine M Lightcap; John C Williams; Tatyana Polenova
Journal:  Can J Chem       Date:  2011-08-04       Impact factor: 1.118

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