Pulsed NMR Research Articles

Investigating Different Dynamic pHP1α States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations.

Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in vivo. However, the underlying mechanisms are largely unknown, and elucidating the physicochemical properties of the phase-separated complexes remains technically challenging. In this study, we detected dynamic, viscous, and intermediate components within the phosphorylated heterochromatin protein 1α (pHP1α) phase-separated system by using modified solid-state NMR (SSNMR) pulse sequences. The basis of these sequences relies on the different time scale of motion detected by heteronuclear Overhauser effect (hetNOE), scalar coupling-based, and dipolar coupling-based transfer schemes in NMR. In comparison to commonly utilized scalar coupling-based methods for studying the dynamic components in phase-separated systems, hetNOE offers more direct insight into molecular dynamics. NMR signals from the three different states in the protein gel were selectively excited and individually studied. Combined with molecular dynamics (MD) simulations, our findings indicate that at low KCl concentration (30 mM), the protein gel displays reduced molecular motion. Conversely, an increase in molecular motion was observed at a high KCl concentration (150 mM), which we attribute to the resultant intermolecular electrostatic interactions regulated by KCl.

1H pulsed NMR measurement of reactivity of silane coupling agents for conservation of cultural heritage sites

AbstractThe network structure and reactivity of suitable restoration agent consisting of silane coupling agents (SCAs) of the brittle walls of a cultural heritage site located underground in a desert area in Egypt were investigated using 1H pulsed nuclear magnetic resonance (pulse NMR). It should possess both high coagulation strength and ductility to ensure that it can withstand an earthquake; it should also contain ethoxy rather than methoxy groups, which generate toxic methanol. The solidification rate for the SCA or oligomer with ethoxy groups was lower than those with methoxy groups; however, the final polycondensates showed the same relaxation time (hardness). The difference spectrum was developed newly to analyze the network structure combined higher strength and ductility. The distribution of crosslinking degree of such polycondensates was narrow, and the amount of lower crosslinking degree was small. On the other hand, the distribution was wide in the polycondensates with ductility but lower strength. From the compression tests of model sand solidified with the restoration agent for both methoxy and ethoxy types showed the superior properties combined higher strength and ductility. The pulse NMR experiment was useful for estimating the solidification rate and the network structure.

Development of pea protein nanoparticle/hydrolyzed rice glutelin fibril emulsion gels for encapsulation of curcumin

The potential of using emulsion gels stabilized by binary plant protein nanoparticle mixtures for the encapsulation and delivery of lipophilic nutraceuticals was evaluated. The particle characteristics, physical stability, water diffusivity, microrheology, large amplitude oscillating shear (LAOS) properties, and in vitro digestion of emulsion gels prepared by different ratios of hydrolyzed rice glutelin fibrils (HRGFs) and pea protein nanoparticle (PNP) were characterized. The emulsion gel with P/H = 2:1 (0.84 μm) exhibited the best storage stability and freeze-thaw stability, as seen by the smaller oil droplet size (1.02 and 1.42 μm, respectively). Low-field pulsed NMR indicated that the majority of water in samples was highly mobile. All the samples were predominantly elastic-like materials. The P/H 2:1 emulsion gel had the lowest FI value (6.21 × 10−4 Hz), the highest MVI value (5.57 s/nm2), G′/ G″ values and enclosed area, showing that it had denser 3D network structures, higher stiffness values, and a high sensitivity to changes in strain. Additionally, P/H 2:1 emulsion gel had a relatively high lipid digestibility (96.1 %), curcumin bioaccessibility (58.9 %), and curcumin stability (94.2 %). This study showed that emulsion gels stabilized by binary protein nanoparticle mixtures (PNP/HRGF) have potential as edible delivery systems for lipophilic nutraceuticals.

Molecular localization and exchange kinetics in pharmaceutical liposome and mRNA lipoplex nanoparticle products determined by small angle X-ray scattering and pulsed field gradient NMR diffusion measurements

We have used pulsed field gradient (PFG)-NMR diffusion experiments, also known as DOSY, in combination with small angle X-ray scattering measurements to investigate structure and molecular exchange dynamics between pharmaceutical lipid nanoparticles and the bulk phase. Using liposomes and lipoplexes formed after complexation of the liposomes with messenger mRNA as test systems, information on dynamics of encapsulated water molecules, lipids and excipients was obtained. The encapsulated fraction, having a diffusivity similar to that of the liposomes, could be clearly identified and quantified by the NMR diffusion measurements. The unilamellar liposome membranes allowed a fast exchange of water molecules, while sucrose, used as an osmolyte and model solute, showed very slow exchange. Upon interactions with mRNA a topological transition from a vesicular to a lamellar organization took place, where the mRNA was inserted in repeating lipid bilayer stacks. In the lipoplexes, a small fraction of tightly bound water molecules was present, with a diffusivity that was influenced by the additional presence of sucrose. This extended information on dynamic coherencies inside pharmaceutical nanoparticle products, provided by the combined application of SAXS and PFG-NMR diffusion measurements, can be valuable for evaluation of quality and comparability of nanoscaled pharmaceuticals.

Comparison of methods for the NMR measurement of motionally averaged dipolar couplings

Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods’ strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C–H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.

ATP‐Independent Turnover of Dinitrogen Intermediates Captured on the Nitrogenase Cofactor

AbstractNitrogenase reduces N2 to NH3 at its active‐site cofactor. Previous studies of an N2‐bound Mo‐nitrogenase from Azotobacter vinelandii suggest binding of three N2 species via asymmetric belt‐sulfur displacements in the two cofactors of its catalytic component (designated Av1*), leading to the proposal of stepwise N2 reduction involving all cofactor belt‐sulfur sites; yet, the evidence for the existence of multiple N2 species on Av1* remains elusive. Here we report a study of ATP‐independent, EuII/SO32−‐driven turnover of Av1* using GC‐MS and frequency‐selective pulse NMR techniques. Our data demonstrate incorporation of D2‐derived D by Av1* into the products of C2H2‐ and H+‐reduction, and decreased formation of NH3 by Av1* concomitant with the release of N2 under H2; moreover, they reveal a strict dependence of these activities on SO32−. These observations point to the presence of distinct N2 species on Av1*, thereby providing strong support for our proposed mechanism of stepwise reduction of N2 via belt‐sulfur mobilization.

ATP-Independent Turnover of Dinitrogen Intermediates Captured on the Nitrogenase Cofactor.

Nitrogenase reduces N2 to NH3 at its active-site cofactor. Previous studies of an N2-bound Mo-nitrogenase from Azotobacter vinelandii suggest binding of three N2 species via asymmetric belt-sulfur displacements in the two cofactors of its catalytic component (designated Av1*), leading to the proposal of stepwise N2 reduction involving all cofactor belt-sulfur sites; yet, the evidence for the existence of multiple N2 species on Av1* remains elusive. Here we report a study of ATP-independent, EuII/SO3 2--driven turnover of Av1* using GC-MS and frequency-selective pulse NMR techniques. Our data demonstrate incorporation of D2-derived D by Av1* into the products of C2H2- and H+-reduction, and decreased formation of NH3 by Av1* concomitant with the release of N2 under H2; moreover, they reveal a strict dependence of these activities on SO3 2-. These observations point to the presence of distinct N2 species on Av1*, thereby providing strong support for our proposed mechanism of stepwise reduction of N2 via belt-sulfur mobilization.

The generalized Ernst angle

Though the Ernst angle concept presented in the original paper introducing Fourier NMR spectroscopy was developed for sensitivity optimization in a time-averaged single-pulse experiment it is shown here that its conclusions may be generalized to complex multidimensional experiments. The salient message is to explore (re-)design of NMR pulse sequences to return some of the magnetization to the z axis at the end, so that they can be performed without a relaxation delay. In favorable cases, such pulse sequences can be concatenated in a synergistic way to further enhance sensitivity.

Measuring Protein-Ligand Binding by Hyperpolarized Ultrafast NMR.

Protein-ligand interactions can be detected by observing changes in the transverse relaxation rates of the ligand upon binding. The ultrafast NMR technique, which correlates the chemical shift with the transverse relaxation rate, allows for the simultaneous acquisition of R2 for carbon spins at different positions. In combination with dissolution dynamic nuclear polarization (D-DNP), where the signal intensity is enhanced by thousands of times, the R2 values of several carbon signals from unlabeled benzylamine are observable within a single scan. The hyperpolarized ultrafast chemical shift-R2 correlated experiment separates chemical shift encoding from the readout phase in the NMR pulse sequence, which allows it to beat the fundamental limit on the spectral resolution otherwise imposed by the sampling theorem. Applications enabled by the ability to measure multiple relaxation rates in a single scan include the study of structural properties of protein-ligand interactions.

Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields

NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.

Macrocyclic Ligand Coordinating Amide-Arm Hydrolysis Reaction Activation in Aqueous Solutions: Tetravalent Uranium Does It Better.

Chelation of lanthanide and actinide cations within a suitable macrocyclic ligand often results in a rigid, kinetically inert, and thermodynamically stable complex. A benchmark for such cation-ligand suitability are cyclen-derived macrocyclic ligands, frequently used as large cation hosts for various applications. Herein, a comprehensive study of the 1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane ligand (DOTAM) chelates of UIV and CeIII and their properties in aqueous solutions is presented. By employing multiple analysis techniques, including X-ray crystallography, UV-vis absorbance, 1H NMR, UPLC-MS, cyclic voltammetry, and differential pulse voltammetry, the study has revealed that the two aqueous complexes undergo a spontaneous, gradual, and stepwise hydrolysis of each of the coordinated amides toward carboxylates. The coordination of UIV in the studied reaction has been shown to significantly enhance the reaction rate, leading to an acceleration of up to 6 orders of magnitude compared to the natural process of simple aqueous amides at room temperature. An attempt to describe the unusual chelated metal cation amide-activation feature, based on the relatively lower rigidity of the complex structure, is presented. Additionally, the electrochemical properties of the complex series are discussed in detail, along with the limitations of the analytical methods employed.

Comparative analysis of vegetable oils by 1H NMR in low and high magnetic fields

High-resolution 1H NMR, high-field 1H NMR relaxometry, and low-field (<0.5 T) NMR relaxometry have been applied to study different types of olive and soybean oils. It has been shown that the use of spectral and relaxation information in high-field NMR is an effective tool for the detection of oil adulteration and identification of food oils, including oils with close content. We have also shown that low-field NMR relaxation measurements can be applied for the discrimination between various food oils in the case of a limited group of samples. This work has demonstrated the possibilities of the different types of pulse NMR experimental methods for the analysis of vegetable oils.

Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4

MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion Dtr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP’s conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of Dtr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental Dtr result. These observations are supported by the analyses of the 15N spin relaxation rates. We also tested a number of empirical methods to predict Dtr based on IDP’s coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental Dtr values also prove to be problematic. In this sense, the first-principle calculations of Dtr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.

Nanocomposite Polymer Gel Electrolyte Based on TiO2 Nanoparticles for Lithium Batteries.

In this article, the specific features of competitive ionic and molecular transport in nanocomposite systems based on network membranes synthesized by radical polymerization of polyethylene glycol diacrylate in the presence of LiBF4, 1-ethyl-3-methylimidazolium tetrafluoroborate, ethylene carbonate (EC), and TiO2 nanopowder (d~21 nm) were studied for 1H, 7Li, 11B, 13C, and 19F nuclei using NMR. The membranes obtained were studied through electrochemical impedance, IR-Fourier spectroscopy, DSC, and TGA. The ionic conductivity of the membranes was up to 4.8 m Scm-1 at room temperature. The operating temperature range was from -40 to 100 °C. Two types of molecular and ionic transport (fast and slow) have been detected by pulsed field gradient NMR. From quantum chemical modeling, it follows that the difficulty of lithium transport is due to the strong chemisorption of BF4- anions with counterions on the surface of TiO2 nanoparticles. The theoretical conclusion about the need to increase the proportion of EC in order to reduce the influence of this effect was confirmed by an experimental study of a system with 4 moles of EC. It has been shown that this approach leads to an increase in lithium conductivity in an ionic liquid medium, which is important for the development of thermostable nanocomposite electrolytes for Li//LiFePO4 batteries with a base of lithium salts and aprotonic imidasolium ionic liquid.

Evaluation of the simplified method of fulvic fractions extraction from peat and lignite

Due to numerous and valuable properties of humic substances, preparations produced from alternative organic materials have been widely used in agriculture, bioremediations, dietary supplements and others. In addition to well-known humic acids, fulvic acids (FA) are a valuable product with a wide range of applications. The aim of performed examinations was to assess the thermal and physicochemical properties of FA obtained from lignite and peat using simplified conventional and ultrasound-assisted methods. DSC coupled with TG and MS, 13C NMR, FTIR spectroscopy and differential pulse voltammetry has been used to examine extracted FA. Depending on the source of FA and the extraction method applied, their structure and properties differ. Obtained FA fractions varied for both tested raw materials in terms of analyzed carbon structures, and the highest discrepancy was observed for carbonyl groups (20.2 pp) in fractions obtained by conventional extraction. The use of the ultrasound-assisted extraction (UAE), in comparison with the traditional method, lowered the ratio of carbon in carbonyl groups by 8.4 pp and increased the ratio of aromatic and aliphatic carbon by 3.5 and 4.9 pp, respectively, for FA obtained from lignite. As for FA obtained from peat, the UAE effect appeared to be less impactful in terms of structural changes. Thermal analysis showed that the products were thermally stable up to 100 °C, and the simplified extraction resulted in the creation of mineral-organic structures that decomposed at unusually high temperatures. Simplifying the extraction process, by excluding inorganic purification and protonation of obtained FA fractions, greatly affects product quality and limits its possible application.

Probing Water Diffusion Inside Crystals of AlPO‐5 by PFG NMR and IRM for Heat Storage Applications

AbstractDiffusion of water in the aluminophosphates AlPO‐5 is studied using a combination of pulsed field gradient NMR and IR microimaging. The concentration profiles measured by the latter allowed to visualize the process of water sorption and propagation into the crystals of AlPO‐5. The self‐diffusion coefficients obtained by NMR were one order of magnitude higher values compared to corrected ones from the IR microimaging study. The concentration profiles allowed to visualize the process of water sorption and propagation into the crystals of AlPO‐5. The obtained results are compared with experimental and simulation data for the water/AlPO‐5 system for the literature and discussed in the context of its potential use for heat storage applications.

Spatiotemporal 1H NMR Spectroscopy of 3D Cell Models

The emergence of three-dimensional cell cultures representing tissue features closely, that are weakly reproduced by standard two-dimensional systems, requires adapting established analytical techniques to investigate these challenging new models. It is especially desired to obtain spatially resolved data for living organoids giving insight into transport processes and biochemical characteristics of domains differently provided with nutrition supply and waste product removal. Within this work we present an NMR-based approach to dynamically obtained radial metabolite profiles for cell spheroids, one of the most frequently used 3D models. Our approach combines an easy to reproduce custom-made measurement design maintaining incubator conditions without inhibition of the NMR experiment, with a spatial selective NMR pulse sequence. To overcome the inherently low sensitivity of NMR spectroscopy we modified the selective sequence to achieve faster acquisition and employed a commercially available cryo NMR probe. Finally, radial metabolite profiles could be obtained via double Abel inversion of the measured one‑dimensional intensity profiles. Applying this method to Ty82 cancer cell spheroids clearly demonstrates the spatial resolution, for instance confirming exceedingly high lactate and strongly decreased glucose concentrations in the oxygen-depleted core of the spheroid. Furthermore, we dynamically investigate the process of cell death and metabolite degradation after maintaining a spheroid under incubator conditions for several days.

Effects of Homogeneous and Heterogeneous Crowding on Translational Diffusion of Rigid Bovine Serum Albumin and Disordered Alfa-Casein.

Intracellular environment includes proteins, sugars, and nucleic acids interacting in restricted media. In the cytoplasm, the excluded volume effect takes up to 40% of the volume available for occupation by macromolecules. In this work, we tested several approaches modeling crowded solutions for protein diffusion. We experimentally showed how the protein diffusion deviates from conventional Brownian motion in artificial conditions modeling the alteration of medium viscosity and rigid spatial obstacles. The studied tracer proteins were globular bovine serum albumin and intrinsically disordered α-casein. Using the pulsed field gradient NMR, we investigated the translational diffusion of protein probes of different structures in homogeneous (glycerol) and heterogeneous (PEG 300/PEG 6000/PEG 40,000) solutions as a function of crowder concentration. Our results showed fundamentally different effects of homogeneous and heterogeneous crowded environments on protein self-diffusion. In addition, the applied "tracer on lattice" model showed that smaller crowding obstacles (PEG 300 and PEG 6000) create a dense net of restrictions noticeably hindering diffusing protein probes, whereas the large-sized PEG 40,000 creates a "less restricted" environment for the diffusive motion of protein molecules.

Water and Molecular Exchange in Biological Cells Studied Using 1H Pulsed Field Gradient NMR.

This review presents the results of studies of molecular exchange processes in various biological systems (erythrocytes, yeast, liposomes, etc.) performed using pulsed field gradient NMR (PFG NMR). The main theory of processing necessary for the analysis of experimental data is briefly presented: the extraction of self-diffusion coefficients, calculation of cell sizes, and permeability of cell membranes. Attention is paid to the results of assessing the permeability of biological membranes for water molecules and biologically active compounds. The results for other systems are also presented: yeast, chlorella, and plant cells. The results of studies of the lateral diffusion of lipid and cholesterol molecules in model bilayers are also presented.

Hydration and Mobility of Alkaline Metal Cations in Sulfonic Cation Exchange Membranes.

The interconnection of ionogenic channel structure, cation hydration, water and ionic translational mobility was revealed in Nafion and MSC membranes based on polyethylene and grafted sulfonated polystyrene. A local mobility of Li+, Na+ and Cs+ cations and water molecules was estimated via the 1H, 7Li, 23Na and 133Cs spin relaxation technique. The calculated cation and water molecule self-diffusion coefficients were compared with experimental values measured using pulsed field gradient NMR. It was shown that macroscopic mass transfer is controlled by molecule and ion motion near sulfonate groups. Lithium and sodium cations whose hydrated energy is higher than water hydrogen bond energy move together with water molecules. Cesium cations in possession of low hydrated energy are directly jumping between neighboring sulfonate groups. Cation Li+, Na+ and Cs+ hydration numbers (h) in membranes were calculated from 1H chemical shift water molecule temperature dependences. The values calculated from the Nernst-Einstein equation and the experimental conductivity values were close to each other in Nafion membranes. In MSC membranes, calculated conductivities were one order of magnitude more compared to the experimental ones, which is explained by the heterogeneity of the membrane pore and channel system.