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 thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assignment tool based onpattern recognition techniques. This tool employs user-specified 'templates'to search for patterns of peaks in the original spectra; these patterns maycorrespond to side-chain or backbone fragments. Multiple spectra willnormally be searched simultaneously to reduce the impact of noise. Thesearch generates a preliminary list of putative assignments, which arefiltered by a set of heuristic algorithms to produce the final results list.Each result contains a set of chemical shift values plus information aboutthe peaks found. The results may be used as input for combinatorialroutines, such as sequential assignment procedures, in place of peak lists.Two examples are presented, in which (i) HCCH-COSY and -TOCSY spectra arescanned for side-chain spin systems; and (ii) backbone spin systems aredetected in a set of spectra comprising HNCA, HN(CO)CA, HNCO, HN(CA)CO,CBCANH and CBCA(CO)NH.
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...
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02-21-2012 03:40 AM
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins
Abstract Well-resolved 2Hâ??13C correlation spectra, reminiscent of 1Hâ??13C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of 2H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T 1, allowing for high repetition rates and enabling 3D experiments with a 2Hâ??13C transfer step in a reasonable time....
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11-01-2011 01:52 AM
Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using Signal Separation Algorithm
Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using Signal Separation Algorithm
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 20 October 2011</br>
Jan*Stanek, Rafal*Augustyniak, Wiktor*Ko?mi?ski</br>
The development of non-uniform sampling (NUS) strategies permits to obtain high-dimensional spectra with increased resolution in significantly reduced experimental time. We extended a previously proposed signal separation algorithm (SSA) to process sparse four-dimensional NMR data. It is employed for two experiments...
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10-22-2011 10:16 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....
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03-03-2011 02:06 AM
[NMR paper] The three-dimensional high resolution structure of human interferon alpha-2a determin
The three-dimensional high resolution structure of human interferon alpha-2a determined by heteronuclear NMR spectroscopy in solution.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The three-dimensional high resolution structure of human interferon alpha-2a determined by heteronuclear NMR spectroscopy in solution.
J Mol Biol. 1997 Dec 12;274(4):661-75
Authors: Klaus W, Gsell B, Labhardt AM, Wipf B, Senn H
The solution structure of recombinant human interferon...
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08-22-2010 05:08 PM
[NMR paper] High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspa
High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations.
Related Articles High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations.
Eur Biophys J. 1990;18(1):17-24
Authors: Engelhard M, Hess B, Metz G, Kreutz W, Siebert F, Soppa J, Oesterhelt D
Three mutant strains of Halobacterium sp. GRB with the site of mutation in the bacterioopsin gene (PM 326:...
Tools for the automated assignment of high-resolution three-dimensional protein NMR s
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