Alternative data processing techniques for serial <scp>NMR</scp> experiments

Shchukina, Alexandra; Urbańczyk, Mateusz; Kasprzak, Paweł; Kazimierczuk, Krzysztof

doi:10.1002/cmr.a.21429

Cited by 12 publications

(10 citation statements)

References 56 publications

(90 reference statements)

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“…The quantitative analysis of NUS spectra is known to be possible [Mayzel et al (2017)] if somewhat challenging [Mobli and Hoch (2014), Shchukina et al(2018), Stetz and Wand(2016)]. In order to verify the extracted quantitative information we compared processing with the SMILE package [Ying et al 2017] with other softwares: SCRUB [Coggins et al(2012)] and MDD , ] using coprocessing with additional spectra measured with the same setup of the spectral resolutions and spectral widths (supplementary information material Figure S4).…”

Section: Resultsmentioning

confidence: 99%

Boosting the resolution of low-field $$^{15}\hbox {N}$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

et al. 2020

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Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of relaxation have, so far, only been based on the recording of one-or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experiment for measurements of protein backbone 15 N amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on 6 different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of δ subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.

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Section: Resultsmentioning

confidence: 99%

Boosting the resolution of low-field $$^{15}\hbox {N}$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

et al. 2020

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“…To measure TCs in a protein, the typical approach is to acquire a series of 2D spectra at different temperatures, either 1 H– 1 H TOCSY for unlabelled samples or 15 N HSQC for 15 N‐labelled proteins. As explained in our recent study, [5] serial measurements of correlation spectra, even those that are 2D, are time‐consuming, due to sampling and sensitivity limitations. These limitations make the measurement of TCs from spectra with more than two dimensions difficult.…”

Section: Introductionmentioning

confidence: 99%

Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy

Shchukina

Małecki

Mateos

et al. 2020

Chemistry A European J

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NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature‐dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature‐swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non‐linearities effectively. Non‐linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.

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“…It is worth mentioning that there exists a variety of alternative sampling methods applicable to cases, when peaks do not shift over the reaction [7,8] or shift according to a simple model [5,32‐35] . These methods are summarized in our recent review [36] . They are, however, not useful in the general case of a process causing potentially complex variations of spectral parameters.…”

Section: Introductionmentioning

confidence: 99%

“…[5,[32][33][34][35] These methods are summarized in our recent review. [36] They are, however, not useful in the general case of a process causing potentially complex variations of spectral parameters.…”

Section: Introductionmentioning

confidence: 99%

Benefits of time‐resolved nonuniform sampling in reaction monitoring: The case of aza‐Michael addition of benzylamine and acrylamide

Gołowicz

Kaźmierczak

Kazimierczuk

2020

Magnetic Reson in Chemistry

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Monitoring of chemical reactions is best carried out using methods that sample the test object at a rate greater than the time scale of the processes taking place. The recently proposed time-resolved nonuniform sampling (TR-NUS) method allows the use of two-dimensional (2D) nuclear magnetic resonance (NMR) spectra for this purpose and provides a time resolution equivalent to that achievable using one-dimensional spectra. Herein, we show that TR-NUS acquired data eliminates 2D spectral line disturbances and enables more accurate signal integration and kinetics conclusions. The considerations are exemplified with a seemingly simple aza-Michael reaction of benzylamine and acrylamide. Surprisingly, the product identification is possible only using 2D spectra, although credible monitoring requires TR-NUS.

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Alternative data processing techniques for serial NMR experiments

Cited by 12 publications

References 56 publications

Boosting the resolution of low-field $$^{15}\hbox {N}$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Boosting the resolution of low-field $$^{15}\hbox {N}$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy

Benefits of time‐resolved nonuniform sampling in reaction monitoring: The case of aza‐Michael addition of benzylamine and acrylamide

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