Abstract We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such ā??in silicoā?? data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAS).
Content Type Journal Article
Category Article
Pages 1-11
DOI 10.1007/s10858-012-9681-y
Authors
Sabine Gradmann, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Christian Ader, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Ines Heinrich, Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
Deepak Nand, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Marc Dittmann, Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
Abhishek Cukkemane, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Marc van Dijk, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Alexandre M. J. J. Bonvin, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Martin Engelhard, Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
Marc Baldus, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Parallel acquisition of multi-dimensional spectra in protein NMR
Parallel acquisition of multi-dimensional spectra in protein NMR
Abstract We introduce the use of multiple receivers applied in parallel for simultaneously recording multi-dimensional data sets of proteins in a single experiment. The utility of the approach is established through the introduction of the 2D 15N,1HN||13CO HSQC experiment in which a pair of two-dimensional 15N,1HN and 15N,13CO spectra are recorded. The methodology is further extended to higher dimensionality via the 3D 1HN||13CO HNCA in which a pair of data sets recording 13CĪ±,15N,1HN and 13CĪ±,15N,13CO chemical shifts...
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07-20-2012 11:13 PM
Analysis of non-uniformly sampled spectra with multi-dimensional decomposition
Analysis of non-uniformly sampled spectra with multi-dimensional decomposition
Publication year: 2011
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 3</br>
Vladislav Yu. Orekhov, Victor A. Jaravine</br>
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nmrlearner
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03-09-2012 09:16 AM
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
J Magn Reson. 2011 Jul 21;
Authors: Liu Y, Prestegard JH
Most multi-dimensional solution NMR experiments connect one dimension to another using coherence transfer steps that involve evolution under scalar couplings. While experiments of this type have been a boon to biomolecular NMR the need to work on ever larger systems pushes the limits of these procedures. Spin relaxation...
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08-13-2011 12:57 PM
[Question from NMRWiki Q&A forum] transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
How do I transfer data sets ( with pulse sequences for measurements of various cross- -relaxtion rates) collected under Xwinnmr DRX console to an Avance III console with topspin 3. (on the same instrument/probe). Is it a straigtforward copying of the data folders, or are there any caveats involved? thank you for any input
Check if somebody has answered this question on NMRWiki QA forum
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03-06-2011 03:29 AM
Analysis of non-uniformly sampled spectra with Multi-Dimensional Decomposition
Analysis of non-uniformly sampled spectra with Multi-Dimensional Decomposition
Publication year: 2011
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 24 February 2011</br>
Vladislav Yu., Orekhov , Victor A., Jaravine</br>
More...
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02-26-2011 01:07 PM
[NMR paper] Fast multi-dimensional NMR of proteins.
Fast multi-dimensional NMR of proteins.
Related Articles Fast multi-dimensional NMR of proteins.
J Biomol NMR. 2003 Apr;25(4):349-54
Authors: Kupce E, Freeman R
Three-dimensional HNCO and HNCA subspectra from a small protein (agitoxin, 4 kDa, enriched in carbon-13 and nitrogen-15), have been obtained by direct frequency-domain excitation of selected carbon and nitrogen sites. This new technique applies an array of several simultaneous soft radiofrequency spin-inversion pulses, encoded (on or off) according to nested Hadamard matrices, and the...
Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and
Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins
Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 12 June 2010</br>
Dominique, Marion</br>
Resonance assignment of intrinsically disordered proteins is made difficult by the extensive spectral overlaps. High-resolution 3D and 4D spectra are thus essential for this purpose. We have adapted the series of 3D BEST experiments proposed by Lescop et al to the case of unfolded proteins. Longer acquisitions...
Rapid prediction of multi-dimensional NMR data sets
Linear Mode
