A flexible and scalable approach for protein NMR is introduced that builds on rapid data collection via projection spectroscopy and analysis of the spectral input data via joint decomposition. Input data may originate from various types of spectra, depending on the ultimate goal: these may result from experiments based on triple-resonance pulse sequences, or on TOCSY or NOESY sequences, or mixtures thereof. Flexible refers to the free choice of spectra for the joint decompositions depending on the purpose: assignments, structure, dynamics, interactions. Scalable means that the approach is open to the addition of similar or different experiments, e.g. larger proteins may require a wider selection of triple-resonance based experiments. Central to the proposed approach is the mutual support among the different spectra during the spectral analysis: for example, sparser triple-resonance spectra may help decomposing (separating) spin systems in a TOCSY or identifying unique NOEs. In the example presented, backbone plus side chain assignments of ubiquitin were obtained from the combination of either two or three of the following projection experiments: a 4D HCCCONH, a 4D HNCACO and a 3D HNCACB. In all cases, TOCSY data (4D HCCCONH) proved crucial not only for the side chain assignments, but also for the sequential assignment. Even when total recording time was reduced to about 10 h, nearly complete assignments were obtained, with very few missing assignments and even fewer differences to a reference.
[NMR paper] Complete NMR assignment of cyclic octapeptide CTAP.
Complete NMR assignment of cyclic octapeptide CTAP.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary_FullTextOnline_120x27.gif Related Articles Complete NMR assignment of cyclic octapeptide CTAP.
Magn Reson Chem. 2014 Aug;52(8):467-9
Authors: Gao Y, Huo Y, Wang Z, Liu Y, Zhang H
PMID: 24911419
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[NMR paper] Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
J Biomol NMR. 2013 Aug 14;
Authors: Bellstedt P, Seiboth T, Häfner S, Kutscha H, Ramachandran R, Görlach M
Abstract
NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though...
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[NMR paper] Reconsidering complete search algorithms for protein backbone NMR assignment.
Reconsidering complete search algorithms for protein backbone NMR assignment.
Related Articles Reconsidering complete search algorithms for protein backbone NMR assignment.
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii230-6
Authors: Vitek O, Bailey-Kellogg C, Craig B, Kuliniewicz P, Vitek J
MOTIVATION: Nuclear magnetic resonance (NMR) spectroscopy is widely used to determine and analyze protein structures. An essential step in NMR studies is determining the backbone resonance assignment, which maps individual atoms to experimentally measured...
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[NMR paper] Complete assignment of heteronuclear protein resonances by protonless NMR spectroscop
Complete assignment of heteronuclear protein resonances by protonless NMR spectroscopy.
Related Articles Complete assignment of heteronuclear protein resonances by protonless NMR spectroscopy.
Angew Chem Int Ed Engl. 2005 May 13;44(20):3089-92
Authors: Bermel W, Bertini I, Duma L, Felli IC, Emsley L, Pierattelli R, Vasos PR
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[NMR paper] G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment
G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment.
Related Articles G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment.
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9642-7
Authors: Atreya HS, Szyperski T
A G-matrix Fourier transform (GFT) NMR spectroscopy-based strategy for resonance assignment of proteins is described. Each of the GFT NMR experiments presented here rapidly affords four-, five-, or six-dimensional spectral information in combination with precise...
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[NMR paper] Automated analysis of large sets of heteronuclear correlation spectra in NMR-based dr
Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
Related Articles Automated analysis of large sets of heteronuclear correlation spectra in NMR-based drug discovery.
J Med Chem. 2002 Dec 19;45(26):5649-54
Authors: Damberg CS, Orekhov VY, Billeter M
Drug discovery procedures based on NMR typically require the analysis of thousands of NMR spectra. For example, in "SAR by NMR", two-dimensional NMR spectra are recorded for a target protein mixed with ligand candidates from a comprehensive library of...
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[NMR paper] Complete 1H and 13C assignment of Lys and Leu sidechains of staphylococcal nuclease u
Complete 1H and 13C assignment of Lys and Leu sidechains of staphylococcal nuclease using HCCH-COSY and HCCH-TOCSY 3D NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Complete 1H and 13C assignment of Lys and Leu sidechains of staphylococcal nuclease using HCCH-COSY and HCCH-TOCSY 3D NMR spectroscopy.
FEBS Lett. 1991 Apr 9;281(1-2):33-8
Authors: Baldisseri DM, Pelton JG, Sparks SW, Torchia DA
Complete proton and carbon sidechain assignments are...
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[NMR paper] Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding
Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding domain of GAL4.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Complete assignment of the 1H NMR spectrum and secondary structure of the DNA binding domain of GAL4.
FEBS Lett. 1990 Dec 10;276(1-2):49-53
Authors: Gadhavi PL, Raine AR, Alefounder PR, Laue ED
Complete 1H NMR resonance assignments are presented for the cysteine rich region of the DNA binding domain of the yeast...
Complete protein assignment from sets of spectra recorded overnight
Linear Mode
