Analysis of Complex Reacting Mixtures by Time-Resolved 2D NMR

Dass, Rupashree; Koźmiński, Wiktor; Kazimierczuk, Krzysztof

doi:10.1021/ac504114h

Cited by 38 publications

(32 citation statements)

References 36 publications

(50 reference statements)

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“…All peaks are well resolved showing the metabolomic changes occurring in the sample with time. The high signal-to-noise ratio shows that the 128 points frame size kept during NUS processing is optimal (for the discussion of the frame size see Dass et al, 2015). The sample in this case contains 0.01% (0.55 mM) glucose and 0.1% face tonic.…”

Section: Resultsmentioning

confidence: 99%

“…Subsets of data points are formed and each subset is processed using multidimensional decomposition (MDD), a high-dimensional variant of principal component analysis (Orekhov et al, 2017) to reconstruct a spectrum. We have further modified TR-NUS by introducing CS processing, that contrary to MDD, does not require stable peak positions (Bermel et al, 2014; Dass et al, 2015, 2016). The algorithm was used to reconstruct missing points in every overlapping subset and obtain a huge stack of two-dimensional (2D) spectra.…”

Section: Introductionmentioning

confidence: 99%

“…This enables one to see in a “movie-like” manner various chemical changes that occurred in the sample. We have previously applied this method to monitor reactions occurring in natural mixtures (Dass et al, 2015) and the process of protein unfolding with rising temperature (Bermel et al, 2014). Figure 2B presents the concept of TR-NUS with CS processing.…”

Section: Introductionmentioning

confidence: 99%

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Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures

et al. 2017

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The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1 H experiments have been reported in studies of bacterial metabolism monitored in situ. However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes, an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13 C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures

et al. 2017

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“…The application of NMR in reaction monitoring (RM) has recently been attracting growing attention. () In most cases, RM‐NMR relies on one‐dimensional (1D) experiments (usually simple 1 H NMR) repeated in fixed time intervals.…”

Section: Introductionmentioning

confidence: 99%

“…Several examples of TR‐NUS applications have been given in the recent years, studying, for example, biochemical reactions,() protein unfolding,() metabolism of yeasts() and bacteria,() or a coherence transfer. () Up to now, however, the method has existed as a prototype and thus, despite its potential, has not been widely applied.…”

Section: Introductionmentioning

confidence: 99%

TReNDS—Software for reaction monitoring with time‐resolved non‐uniform sampling

Urbańczyk

Shchukina

Gołowicz

2018

Magnetic Reson in Chemistry

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NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods—correlation experiments—are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time‐consuming, and thus, the reaction‐monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single‐scan or fast‐sampling experiments). Recently, the technique of time‐resolved non‐uniform sampling (TR‐NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on‐the‐fly processing during the reaction. In this paper, we introduce TReNDS: free, user‐friendly software kit for acquisition and processing of TR‐NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR‐NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.

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Compressed Sampling in NMR Spectroscopy

Kazimierczuk

eMagRes

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Analysis of Complex Reacting Mixtures by Time-Resolved 2D NMR

Cited by 38 publications

References 36 publications

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures

TReNDS—Software for reaction monitoring with time‐resolved non‐uniform sampling

Compressed Sampling in NMR Spectroscopy

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