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Nawrocka EK, Jadwiszczak M, Leszczyński PJ, Kazimierczuk K. Supporting the assignment of NMR spectra with variable-temperature experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:479-485. [PMID: 38303612 DOI: 10.1002/mrc.5433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful tools in analytical chemistry. An important step in the analysis of NMR data is the assignment of resonance frequencies to the corresponding atoms in the molecule being investigated. The traditional approach considers the spectrum's characteristic parameters: chemical shift values, internuclear couplings, and peak intensities. In this paper, we show how to support the process of assigning a series of spectra of similar organic compounds by using temperature coefficients, that is, the rates of change in chemical shift values associated with given changes in temperature.
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Affiliation(s)
- Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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2
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Romero JA, Kazimierczuk K, Kasprzak P. Optimizing measurements of linear changes of NMR signal parameters. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 360:107632. [PMID: 38382405 DOI: 10.1016/j.jmr.2024.107632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Serial NMR experiments are commonly applied in variable-temperature studies, reaction monitoring, and other tasks. The resonance frequencies often shift linearly over the series, and the shift rates help to characterize the studied system. They can be determined using a classical fitting of peak positions or a more advanced method of Radon transform. However, the optimal procedure for data collection remains to be determined. In this paper, we discuss how to invest experimental time, i.e., whether to measure more scans at the expense of the number of spectra or vice versa. The results indicate that classical fitting provides slightly less error than the Radon transform, although the latter can be the method of choice for a low signal-to-noise ratio. We demonstrate this fact through theoretical consideration, simulations, and an experiment. Finally, we extend our considerations to the linear fitting of peak amplitudes. Interestingly, the optimal setup for measuring peak height changes differs from the one for resonance frequency changes - fewer spectra with more scans provide better results.
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Affiliation(s)
- Javier Agustin Romero
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-097, Poland
| | | | - Paweł Kasprzak
- Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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3
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Shchukina A, Schwarz TC, Nowakowski M, Konrat R, Kazimierczuk K. Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes. JOURNAL OF BIOMOLECULAR NMR 2023; 77:149-163. [PMID: 37237169 PMCID: PMC10406685 DOI: 10.1007/s10858-023-00418-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
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4
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Bruno F, Fiorucci L, Ravera E. Sensitivity considerations on denoising series of spectra by singular value decomposition. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:373-379. [PMID: 36840610 DOI: 10.1002/mrc.5338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/11/2023]
Abstract
When acquiring series of spectra ( T 1 , T 2 , CP buildup curves, etc.) on samples with poor SNR, we are usually faced with choosing between taking a few points with a large number of scans to maximize the SNR or more points with a smaller number of scans to maximize the information content. In this Letter, we show how low-rank decomposition can be used to denoise a series of spectra, reducing the trade-off between the number of scans and the number of experiments.
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Affiliation(s)
- Francesco Bruno
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Letizia Fiorucci
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
- Florence Data Science, University of Florence, Firenze, 50134, Italy
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5
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Gołowicz D, Shchukina A, Kazimierczuk K. Enhanced Nuclear Magnetic Resonance Spectroscopy with Isotropic Mixing as a Pseudodimension. Anal Chem 2022; 94:9114-9121. [PMID: 35695926 PMCID: PMC9244872 DOI: 10.1021/acs.analchem.2c01471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical analysis based on liquid-state nuclear magnetic resonance spectroscopy exploits numerous observables, mainly chemical shifts, relaxation rates, and internuclear coupling constants. Regarding the latter, the efficiencies of internuclear coherence transfers may be encoded in spectral peak intensities. The dependencies of these intensities on the experimental parameter that influences the transfer, for example, mixing time, are an important source of structural information. Yet, they are costly to measure and difficult to analyze. Here, we show that peak intensity build-up curves in two-dimensional total correlation spectroscopy (2D TOCSY) experiments may be quickly measured by employing nonuniform sampling and that their analysis can be effective if supported by quantum mechanical calculations. Thus, such curves can be used to form a new, third pseudodimension of the TOCSY spectrum. Similarly to the other two frequency dimensions, this one also resolves ambiguities and provides characteristic information. We show how the approach supports the analysis of a fragment of protein Tau Repeat-4 domain. Yet, its potential applications are far broader, including the analysis of complex mixtures or other polymers.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Alexandra Shchukina
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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6
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Yang C, Chen J, Zeng Q, Luo Y, Chen Z, Lin Y. Simultaneous acquirement of pure shift 2D homonuclear correlation spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 339:107229. [PMID: 35512441 DOI: 10.1016/j.jmr.2022.107229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/08/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Two dimensional homonuclear correlation spectra like COSY, TOCSY and NOESY are classic two-dimensional spectra for analyzing coupling networks and delivering structural information of molecules. Two main challenges of the homonuclear correlation spectra are resolution and efficiency. Because of the complexity of the molecular structure and the effect of scalar coupling, spectral resolution is still difficult to meet the demand, and a higher resolution is needed to improve the quality of the homonuclear correlation spectrum. On the other hand, although some homonuclear correlation spectra are often used together (such as COSY and TOCSY), they are generally sampled separately, and as the number of sampling points in the indirect dimension increases, experiment time increases dramatically. Here, we propose a scheme that can be used to simultaneously obtain indirect dimension pure shift COSY and TOCSY or indirect dimension pure shift COSY and NOESY to improve the resolution of them, while reducing the sampling time and improving the efficiency.
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Affiliation(s)
- Chuang Yang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Jinyong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Qing Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yao Luo
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
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7
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Nawrocka EK, Urbańczyk M, Koziński K, Kazimierczuk K. Variable-temperature NMR spectroscopy for metabolite identification in biological materials. RSC Adv 2021; 11:35321-35325. [PMID: 35493175 PMCID: PMC9043013 DOI: 10.1039/d1ra05626c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/21/2021] [Indexed: 01/28/2023] Open
Abstract
Nuclear magnetic resonance is a "workhorse technique" used in metabolomics, complementary to mass spectrometry. Unfortunately, only the most basic NMR methods are sensitive enough to allow fast medical screening. The most common of them, a simple 1H NMR, suffers from low dispersion of resonance frequencies, which often hampers the identification of metabolites. In this article we show that 1H NMR spectra contain previously overlooked parameters potentially helpful in metabolite identification, namely the rates of temperature-induced changes of chemical shifts. We prove that they are reproducible between various metabolite mixtures and can be determined quickly when Radon transform is used to process the data.
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Affiliation(s)
- Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
- Faculty of Chemistry, University of Warsaw ul. Pasteura 1 02-093 Warsaw Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Kamil Koziński
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
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8
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Gołowicz D, Kaźmierczak M, Kazimierczuk K. Benefits of time-resolved nonuniform sampling in reaction monitoring: The case of aza-Michael addition of benzylamine and acrylamide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:213-220. [PMID: 33016346 DOI: 10.1002/mrc.5105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/01/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
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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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Magdalena Kaźmierczak
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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9
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Chen J, Zeng Q, Tian D, Lin Y, Chen Z. High-resolution 2-D NMR spectroscopy based on the Radon transform and pure shift technique for studying chemical shifts perturbations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:346-353. [PMID: 31967670 DOI: 10.1002/mrc.5000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/11/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Chemical shift plays an important role in molecular analysis. However, chemical shifts are influenced by temperature, solvent concentration, pressure, and so forth. Therefore, measuring chemical shift perturbations caused by these factors is helpful to molecular studies. A new form of 2-D spectroscopy (projection spectroscopy) has been introduced whose indirect dimension is derived by implementing the Radon transform on a series of conventional 1-D proton spectra and indicates such perturbations. However, signal overlap may exist in the conventional 1-D spectra and hence in the resulting projection spectra, hampering clear multiplet analysis and accurate extraction of perturbations. Here, the pure shift decoupling technique is employed to obtain clearer projection spectrum with higher spectral resolution. The combination of pure shift technique and the Radon transform is helpful to accurately extract chemical shift perturbations. It is believed that this application will open up a vast prospect for molecular analysis.
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Affiliation(s)
- Jinyong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Qing Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Dan Tian
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, China
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10
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Shchukina A, Małecki P, Mateos B, Nowakowski M, Urbańczyk M, Kontaxis G, Kasprzak P, Conrad-Billroth C, Konrat R, Kazimierczuk K. Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy. Chemistry 2021; 27:1753-1767. [PMID: 32985764 DOI: 10.1002/chem.202003678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 11/07/2022]
Abstract
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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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paweł Małecki
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.,Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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11
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Kupče Ē. Perspectives of adiabatic decoupling in liquids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106799. [PMID: 32792146 DOI: 10.1016/j.jmr.2020.106799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
It is shown that adiabatic decoupling is extremely flexible and achieves very high figure of merit (decoupling bandwidth to RF amplitude ratio) exceeding that of the conventional composite pulse decoupling (CPD) methods by more than an order of magnitude. This comes at a price of increasingly intrusive cycling sidebands when the decoupling bandwidth exceeds that of the CPD methods. Following a brief review of the decoupling theory and modes of adiabatic sweeps a particular attention is focused on decoupling sideband suppression techniques. The close to perfect inversion profiles of adiabatic pulses ensure by far fewer cyclic sidebands as compared to the typically complex sideband patterns observed in CPD applications. The coherent sideband suppression techniques eliminate the cycling sidebands by altering their phase in successive scans thus achieving sideband reduction levels by up to four orders of magnitude and leaving a clean baseline. We show that adiabatic decoupling is highly adaptive offering significant power savings in spin systems with smaller J-couplings while in the other extreme enabling 13C decoupling of up to a 1 MHz wide bandwidth potentially satisfying the needs of ultra-high-field NMR for the foreseeable future.
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Affiliation(s)
- Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom.
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12
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Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K. Fast time-resolved NMR with non-uniform sampling. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:40-55. [PMID: 32130958 DOI: 10.1016/j.pnmrs.2019.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is a versatile tool for studying time-dependent processes: chemical reactions, phase transitions or macromolecular structure changes. However, time-resolved NMR is usually based on the simplest among available techniques - one-dimensional spectra serving as "snapshots" of the studied process. One of the reasons is that multidimensional experiments are very time-expensive due to costly sampling of evolution time space. In this review we summarize efforts to alleviate the problem of limited applicability of multidimensional NMR in time-resolved studies. We focus on techniques based on sparse or non-uniform sampling (NUS), which lead to experimental time reduction by omitting a significant part of the data during measurement and reconstructing it mathematically, adopting certain assumptions about the spectrum. NUS spectra are faster to acquire than conventional ones and thus better suited to the role of "snapshots", but still suffer from non-stationarity of the signal i.e. amplitude and frequency variations within a dataset. We discuss in detail how these instabilities affect the spectra, and what are the optimal ways of sampling the non-stationary FID signal. Finally, we discuss related areas of NMR where serial experiments are exploited and how they can benefit from the same NUS-based approaches.
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Affiliation(s)
- Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Paweł Kasprzak
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland; Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Vladislav Orekhov
- Department of Chemistry & Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
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13
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Rytel M, Kasprzak P, Setny P, Kazimierczuk K. Quick temperature-sweep pure-shift NMR: the case of solvent effects in atorvastatin. Phys Chem Chem Phys 2019; 21:19209-19215. [DOI: 10.1039/c9cp03921j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Quick and sensitive serial pseudo-2D pure-shift NMR experiments provide novel insight into the temperature-dependent solvent distribution.
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Affiliation(s)
- Małgorzata Rytel
- Centre of New Technologies
- University of Warsaw
- 02-097 Warsaw
- Poland
| | - Paweł Kasprzak
- Centre of New Technologies
- University of Warsaw
- 02-097 Warsaw
- Poland
- Department of Mathematical Methods in Physics
| | - Piotr Setny
- Centre of New Technologies
- University of Warsaw
- 02-097 Warsaw
- Poland
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14
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Urbańczyk M, Shchukina A, Gołowicz D, Kazimierczuk K. TReNDS-Software for reaction monitoring with time-resolved non-uniform sampling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:4-12. [PMID: 30255516 DOI: 10.1002/mrc.4796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
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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Affiliation(s)
- Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Spektrino Sp. z o.o., Warsaw, Poland
- NMR Research Unit, University of Oulu, Oulu, Finland
| | | | - Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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15
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Koh JJ, Lin S, Bai Y, Sin WWL, Aung TT, Li J, Chandra V, Pervushin K, Beuerman RW, Liu S. Antimicrobial activity profiles of Amphiphilic Xanthone derivatives are a function of their molecular Oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2281-2298. [PMID: 29782818 DOI: 10.1016/j.bbamem.2018.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 01/01/2023]
Abstract
Currently, membrane-targeting small antimicrobial peptidomimetics (SAP) are important in antibiotic development because bacteria appear to develop resistance to these surface-active compounds less readily. However, the molecular membrane-targeting action of SAPs has received little attention. In this study, we investigated the effect of oligomerization of amphiphilic xanthone, a model SAP, on its antimicrobial properties against both Gram-positive and Gram-negative bacteria. First, oligomer formation by an amphiphilic xanthone, compound 2 (also coded as AM052), was investigated via solution-state nuclear magnetic resonance (NMR) spectroscopy. Then, the effects of oligomerization on membrane disruption were further studied via biophysical approaches. The results showed that the antimicrobial activities of SAPs develop in several stages: oligomer formation in aqueous solution, initial binding of oligomers to the membrane-water interface followed by insertion into the membrane bilayer, aggregation of antimicrobial oligomers in the membrane, and induced membrane leakage. Ultimately, the presence of the oligomers in the bacterial membrane leads to decreased membrane fluidity and bacterial cell death. Interestingly, the early formation of large oligomers leads to stronger membrane disruption and more rapid bacterial killing. However, reduced antimicrobial activities against Gram-negative bacteria were observed for compounds that formed larger oligomers because the LPS layer acts as a barrier to large complexes. Taken together, our results suggest that oligomerization of SAPs has a strong impact on their antimicrobial properties.
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Affiliation(s)
- Jun-Jie Koh
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore
| | - Shuimu Lin
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore
| | - Yang Bai
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Wendy Wan Ling Sin
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore
| | - Thet Tun Aung
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore
| | - Jianguo Li
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore; Bioinformatics Institute, 138671, Singapore
| | - Verma Chandra
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore; Bioinformatics Institute, 138671, Singapore
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Roger W Beuerman
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore; Duke-NUS Medical School, SRP Neuroscience and Behavioral Disorders, 169857, Singapore.
| | - Shouping Liu
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, 169856, Singapore; Duke-NUS Medical School, SRP Neuroscience and Behavioral Disorders, 169857, Singapore.
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Dass R, Kasprzak P, Kazimierczuk K. Quick, sensitive serial NMR experiments with Radon transform. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:114-118. [PMID: 28797925 DOI: 10.1016/j.jmr.2017.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/17/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
The Radon transform is a potentially powerful tool for processing the data from serial spectroscopic experiments. It makes it possible to decode the rate at which frequencies of spectral peaks shift under the effect of changing conditions, such as temperature, pH, or solvent. In this paper we show how it also improves speed and sensitivity, especially in multidimensional experiments. This is particularly important in the case of low-sensitivity techniques, such as NMR spectroscopy. As an example, we demonstrate how Radon transform processing allows serial measurements of 15N-HSQC spectra of unlabelled peptides that would otherwise be infeasible.
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Affiliation(s)
- Rupashree Dass
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Paweł Kasprzak
- Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
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