Wiktor Koźmiński's NMR group

Biological and Chemical Research Centre, University of Warsaw

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Wiktor Koźmiński's NMR Group

Best poster at SMASH

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Mateusz Urbańczyk was awarded with best poster award at SMASH NMR!

 

New Article in Angewandte Chemie International Edition

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Accelerating Diffusion-Ordered NMR Spectroscopy by Joint Sparse Sampling of Diffusion and Time Dimensions

Mateusz Urbańczyk, Wiktor Koźmiński, Krzysztof Kazimierczuk


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Diffusion-ordered multidimensional NMR spectroscopy is a valuable technique for the analysis of complex chemical mixtures. However, this method is very time-consuming because of the costly sampling of a multidimensional signal. Various sparse sampling techniques have been proposed to accelerate such measurements, but they have always been limited to frequency dimensions of NMR spectra. It is now revealed how sparse sampling can be extended to diffusion dimensions.

 

New Article in Journal of Biomolecular NMR

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High-dimensionality 13C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins

Wolfgang Bermel, Isabella C. Felli, Leonardo Gonelli, Wiktor Koźmiński, Alessandro Piai, Roberta Pierratelli, Anna Zawadzka-Kazimierczuk


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We present three novel exclusively heteronuclear 5D 13C direct-detected NMR experiments, namely (HN-flipN)CONCACON, (HCA)CONCACON and (H)CACON(CA)CON, designed for easy sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The experiments proposed have been optimized to overcome the drawbacks which may dramatically complicate the characterization of IDPs by NMR, namely the small dispersion of chemical shifts and the fast exchange of the amide protons with the solvent. A fast and reliable automatic assignment of α-synuclein chemical shifts was obtained with the Tool for SMFT-based Assignment of Resonances (TSAR) program based on the information provided by these experiments.

 

New Article in Journal of Structural Biology

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NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme

Mariusz Jaremko, Łukasz Jaremko, Michał Nowakowski, Marek Wojciechowski, Roman H. Szczepanowski, Renata Panecka, Igor Zhukov, Matthias Bochtlerd, Andrzej Ejchart


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We report a high resolution NMR structure and 15N relaxation studies of the first catalytic cysteine half-domain (FCCH) of the mouse ubiquitin-activating enzyme E1, together with interaction studies of FCCH and the other catalytic E1 subdomain – SCCH (second catalytic cysteine half-domain). In solution, mouse FCCH forms a well-defined six-stranded antiparallel β-barrel structure, a common fold for many proteins with a variety of cellular functions. 15N relaxation data reveal FCCH complex backbone dynamics and indicate which residues experience slow intramolecular motions. Some of these residues make contacts with the polar face of ubiquitin in the co-crystal structure of yeast E1 and ubiquitin. However, the titration of FCCH with ubiquitin does not show any visible chemical shift changes in the 2D 1H/15N HSQC spectra of the FCCH. The 2D 1H/15N HSQC experiments performed both for each catalytic half-domain individually and for their equimolar mixture in the milimolar concentration range display no detectable chemical shift perturbation, suggesting a lack of interaction between the two subdomains unless they are covalently linked via the adenylation domain.

 

New Article in Journal of Biomolecular NMR

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4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C,15N-labeled RNAs

Jan Stanek, Peter Podbevšek, Wiktor Koźmiński, Janez Plavec, Mirko Cevec


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A 4D 13C(aromatic),13C(ribose)-edited NOESY experiment is introduced to improve sequential assignment of non-coding RNA, often hampered by a limited dispersion of 1H and 13C chemical shifts. The 13C-labeling of RNA is fully utilized by inclusion of two 13C evolution periods. These dimensions provide enhanced dispersion of resonances in the 4D spectrum. High spectral resolution is obtained using random non-uniform sampling in three indirect dimensions. The autocorrelation peaks are efficiently suppressed using band-selective pulses. Since the dynamic range of observed resonances is significantly decreased, the reconstruction of the 4D spectrum is greatly simplified. The experiment can replace two conventionally sampled 3D NOESY spectra (either ribose-13C- or aromatic-13C-separated), and remove most ambiguities encountered during sequential walks. The assignment strategy based on a homonuclear and 4D C,C-edited NOESY experiments is proposed and verified on a 34-nt RNA showing typical structure elements.

 


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