Abstract While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space, combined with sparse multidimensional Fourier transform (SMFT), allows for efficient recording of very high dimensional spectra (�4 dimensions) while maintaining high resolution. However, the nature of this data demands for automation of the assignment process. Here we present the program TSAR (Tool for SMFT-based Assignment of Resonances), which exploits all advantages of SMFT input. Moreover, its flexibility allows to process data from any type of experiments that provide sequential connectivities. The algorithm was tested on several protein samples, including a disordered 81-residue fragment of the δ subunit of RNA polymerase from Bacillus subtilis containing various repetitive sequences. For our test examples, TSAR achieves a high percentage of assigned residues without any erroneous assignments.
Content Type Journal Article
Category Article
Pages 1-15
DOI 10.1007/s10858-012-9652-3
Authors
Anna Zawadzka-Kazimierczuk, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Wiktor KoźmiÅ?ski, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Martin Billeter, Biophysics Group, Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
high resolution nuclear magnetic resonance (nmr) spectra
high resolution nuclear magnetic resonance (nmr) spectra
http://anniehalliday.com/biopics/large/missing.jpg
http://anniehalliday.com/proteinnmr.html
21/06/2012 3:50:47 AM GMT
More...
nmrlearner
NMR pictures
0
06-24-2012 03:21 PM
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
nmrlearner
Journal club
0
02-21-2012 03:40 AM
Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra
Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra
Abstract Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next....
nmrlearner
Journal club
0
03-03-2011 02:06 AM
High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field
High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field
Abstract Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly-13C,15N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla (1H frequencies of...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Jie, Wen , Jihui, Wu , Pei, Zhou</br>
Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
nmrlearner
Journal club
0
01-05-2011 11:03 AM
[NMR paper] Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignm
Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment.
Related Articles Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment.
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8009-14
Authors: Szyperski T, Yeh DC, Sukumaran DK, Moseley HN, Montelione GT
A suite of reduced-dimensionality (13)C,(15)N,(1)H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] Tools for the automated assignment of high-resolution three-dimensional protein NMR s
Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques.
Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques.
J Biomol NMR. 1997 Oct;10(3):207-19
Authors: Croft D, Kemmink J, Neidig KP, Oschkinat H
One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where...
TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra
Linear Mode
