Literature DB >> 26227870

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

Tatiana Didenko1,2,3, Andrew Proudfoot1,2, Samit Kumar Dutta1,2, Pedro Serrano1,2, Kurt Wüthrich4,5,6,7.   

Abstract

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data.
© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  J-UNIO structure determination protocol; NMR spectroscopy; automated data analysis; compressed sensing; proteins

Mesh:

Substances:

Year:  2015        PMID: 26227870      PMCID: PMC4576834          DOI: 10.1002/chem.201502544

Source DB:  PubMed          Journal:  Chemistry        ISSN: 0947-6539            Impact factor:   5.236


  70 in total

1.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

2.  Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).

Authors:  Wolfram Gronwald; Sherif Moussa; Ralph Elsner; Astrid Jung; Bernhard Ganslmeier; Jochen Trenner; Werner Kremer; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2002-08       Impact factor: 2.835

3.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

4.  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

5.  SAGA: rapid automatic mainchain NMR assignment for large proteins.

Authors:  Gordon M Crippen; Aikaterini Rousaki; Matthew Revington; Yongbo Zhang; Erik R P Zuiderweg
Journal:  J Biomol NMR       Date:  2010-03-16       Impact factor: 2.835

6.  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

7.  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

8.  Torsion angle dynamics for NMR structure calculation with the new program DYANA.

Authors:  P Güntert; C Mumenthaler; K Wüthrich
Journal:  J Mol Biol       Date:  1997-10-17       Impact factor: 5.469

9.  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

10.  Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains.

Authors:  Linnéa Isaksson; Maxim Mayzel; Maria Saline; Anders Pedersen; Joakim Rosenlöw; Bernhard Brutscher; B Göran Karlsson; Vladislav Y Orekhov
Journal:  PLoS One       Date:  2013-05-07       Impact factor: 3.240

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