23Na multiple quantum filtered NMR characterisation of Na+ binding and dynamics in animal cells: a comparative study and effect of Na+/Li+ competition

Sodium Dynamics in the Cellular Environment

Sodium ions are essential for the functions of biological cells, and they are maintained at the balance between intra- and extracellular environments. The quantitative assessment of intra- and extracellular sodium as well as its dynamics can provide crucial physiological information on a living system. ²³Na nuclear magnetic resonance (NMR) is a powerful and noninvasive technique to probe the local environment and dynamics of sodium ions. However, due to the complex relaxation behavior of the quadrupolar nucleus in the intermediate-motion regime and because of the heterogeneous compartments and diverse molecular interactions in the cellular environment, the understanding of the ²³Na NMR signal in biological systems is still at the early stage. In this work, we characterize the relaxation and diffusion of sodium ions in the solutions of proteins and polysaccharides, as well as in the in vitro samples of living cells. The multi-exponential behavior of ²³Na transverse relaxation has been analyzed according to the relaxation theory to derive the crucial information related to the ionic dynamics and molecular binding in the solutions. The bi-compartment model of transverse relaxation and diffusion measurements can corroborate each other to quantify the fractions of intra- and extracellular sodium. We show that ²³Na relaxation and diffusion can be used to monitor the viability of human cells, which offers versatile NMR metrics for in vivo studies.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Protein conformational changes affect the sodium triple-quantum MR signal

The aim of this study was to investigate possible sodium triple-quantum (TQ) signal dependence on pH variation and protein unfolding which may happen in vivo. The model system, composed of bovine serum albumin (BSA), was investigated over a wide pH range of 0.70 to 13.05 and during urea-induced unfolding. In both experimental series, the sodium and BSA concentration were kept constant so that TQ signal changes solely arose from an environmental change. The experiments were performed using unique potential to detect weak TQ signals by implementing a TQ time proportional phase increment pulse sequence. At a pH of 0.70, in which case the effect of the negatively charged groups was minimized, the minimum TQ percentage relative to single-quantum of 1.34% ± 0.05% was found. An increase of the pH up to 13.05 resulted in an increase of the sodium TQ signal by 225%. Urea-induced unfolding of BSA, without changes in pH, led to a smaller increase in the sodium TQ signal of up to 40%. The state of BSA unfolding was verified by fluorescence microscopy. Results of both experiments were well fitted by sigmoid functions. Both TQ signal increases were in agreement with an increase of the availability of negatively charged groups. The results point to vital contributions of the biochemical environment to the TQ MR signals. The sodium TQ signal in vivo could be a valuable biomarker of cell viability, and therefore possible effects of pH and protein unfolding need to be considered for a proper interpretation of changes in sodium TQ signals.

Development of a bioreactor system for cytotoxic evaluation of pharmacological compounds in living cells using NMR spectroscopy

INTRODUCTION

The evaluation of drug's cytotoxicity is a crucial step in the development of new pharmacological compounds. ³¹P NMR can be a tool for toxicological screening, as it enables the study of drugs' cytotoxicity and their effect on cell energy metabolism in a real-time, in a non- invasive and non-destructive way. This paper details a step-by-step protocol to implement a bioreactor system able to maintain cell viability during NMR acquisitions, at high cell densities and for several hours, enabling toxicological evaluation of pharmacological compounds in living cells.

METHOD

HeLa cells were immobilized in agarose gel threads and continuously perfused with oxygenated medium inside a 5 mm NMR tube. Signals corresponding to intracellular high-energy phosphorous compounds were continuously monitored by ³¹P NMR to assess cell energy levels, intracellular pH and intracellular free Mg²⁺ concentrations ([Mg²⁺]_f) under control and in the presence of two different cytotoxic drugs, calix-NH₂ or 5-fluorouracil (5-FU).

RESULTS

The bioreactor system was effective in maintaining cell energy levels as well as intracellular pH and [Mg²⁺]_f along time, with a good ³¹P NMR signal to noise ratio. Calix-NH₂ and 5-FU decreased cell energy levels by 35% and 39%, respectively, with a negligible increase in intracellular [Mg²⁺]_f, and without affecting intracellular pH.

DISCUSSION

The immobilization and perfusion system here detailed, along with ³¹P NMR, is useful in toxicological evaluation of new pharmacological compounds, enabling the continuous assessment of drugs' effect on energy levels, intracellular pH and [Mg²⁺]_f in intact cells, for several hours without compromising cell viability.

The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling

Traditional biochemical research has resulted in a good understanding of many aspects of metabolism. However, this reductionist approach is time consuming and requires substantial resources, thus raising the question whether modern metabolomics and genomics should take over and replace the targeted experiments of old. We proffer that such a replacement is neither feasible not desirable and propose instead the tight integration of modern, system-wide omics with traditional experimental bench science and dedicated computational approaches. This integration is an important prerequisite toward the optimal acquisition of knowledge regarding metabolism and physiology in health and disease. The commentary describes advantages and drawbacks of current approaches to assessing metabolism and highlights the challenges to be overcome as we strive to achieve a deeper level of metabolic understanding in the future.

Tracking protein function with sodium multi quantum spectroscopy in a 3D-tissue culture based on microcavity arrays

The aim of this study was to observe the effects of strophanthin induced inhibition of the Na-/K-ATPase in liver cells using a magnetic resonance (MR) compatible bioreactor. A microcavity array with a high density three-dimensional cell culture served as a functional magnetic resonance imaging (MRI) phantom for sodium multi quantum (MQ) spectroscopy. Direct contrast enhanced (DCE) MRI revealed the homogenous distribution of biochemical substances inside the bioreactor. NMR experiments using advanced bioreactors have advantages with respect to having full control over a variety of physiological parameters such as temperature, gas composition and fluid flow. Simultaneous detection of single quantum (SQ) and triple quantum (TQ) MR signals improves accuracy and was achieved by application of a pulse sequence with a time proportional phase increment (TQTPPI). The time course of the Na-/K-ATPase inhibition in the cell culture was demonstrated by the corresponding alterations of sodium TQ/SQ MR signals.

Effects of instrumental artifacts on triple quantum filtered NMR spectra for spin I=3/2

In this work, the effects of various instrumental artifacts on the triple quantum filtered NMR spectra for spin I=3/2 nuclei are investigated. The studied artifacts include finite pulse widths, phase errors, radio frequency field inhomogeneity and pulse transients, which are commonly encountered in practice. The triple quantum filtered spectra are numerically simulated, based on the evolution of the spin density operator under the Hamiltonian for the artifacts. The results show that the presence of the artifacts introduces a shape distortion in the spectrum as well as a variation in the peak intensity, compared with the spectrum without any artifacts. This work indicates that the existence of the instrumental artifacts may cause a misunderstanding of the triple quantum filtered NMR spectra in experiments. The results suggest that one be aware of the instrumental artifacts when performing the triple quantum filtered NMR experiments.

Spatial Mapping of Flow-Induced Molecular Alignment in a Noncrystalline Biopolymer Fluid Using Double Quantum Filtered (DQF) (23)Na MRI

Flow-induced molecular alignment was observed experimentally in a non-liquid-crystalline bioplymeric fluid during developed tubular flow. The fluid was comprised of rigid rods of the polysaccharide xanthan and exhibited shear-thinning behavior. Without a requirement for optical transparency or the need for an added tracer, (23)Na magic angle (MA) double quantum filtered (DQF) magnetic resonance imaging (MRI) enabled the mapping of the anisotropic molecular arrangement under flow conditions. A regional net molecular alignment was found in areas of high shear values in the vicinity of the tube wall. Furthermore, the xanthan molecules resumed random orientations after the cessation of flow. The observed flow-induced molecular alignment was correlated with the rheological properties of the fluid. The work demonstrates the ability of (23)Na MA DQF magnetic resonance to provide a valuable molecular-mechanical link.