Nuclear magnetic resonance of rotational mobility of mouse hemoglobin labeled with (2-13C)histidine

Multiple quantum filtered nuclear magnetic resonance of 23Na+ in uniformly stretched and compressed hydrogels

Stretching or compressing hydrogels creates anisotropic environments that lead to motionally averaged alignment of embedded guest quadrupolar nuclear spins such as 23Na+. These distorted hydrogels can elicit a residual quadrupolar coupling that gives an oscillation in the trajectories of single quantum coherences (SQCs) as a function of the evolution time during a spin-echo experiment. We present solutions to equations of motion derived with a Liouvillian superoperator approach, which encompass the coherent quadrupolar interaction in conjunction with relaxation, to give a full analytical description of the evolution trajectories of rank-1 (T^1±1), rank-2 (T^2±1), and rank-3 (T^3±1) SQCs. We performed simultaneous numerical fitting of the experimental 23Na nuclear magnetic resonance (NMR) spectra and rank-2 (T^2±1) and rank-3 (T^3±1) SQC evolution trajectories measured in double and triple quantum filtered experiments, respectively. We estimated values of the quadrupolar coupling constant CQ, rotational correlation time τC, and 3 × 3 Saupe order matrix. We performed simultaneous fitting of the analytical expressions to the experimental data to estimate values of the quadrupolar coupling frequency ωQ/2π, residual quadrupolar coupling ωQ/2π, and corresponding spherical order parameter S0*, which showed a linear dependence on the extent of uniform hydrogel stretching and compression. The analytical expressions were completely concordant with the numerical approach. The insights gained here can be extended to more complicated (biological) systems such as 23Na+ bound to proteins or located inside and outside living cells in high-field NMR experiments and, by extension, to the anisotropic environments found in vivo with 23Na magnetic resonance imaging.

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.

Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses

X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural changes due to radiation damage. Here, we probe the dynamics of dense antibody protein (Ig-PEG) solutions using megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL. By varying the total dose and dose rate, we identify a regime for measuring the motion of proteins in their first coordination shell, quantify XFEL-induced effects such as driven motion, and map out the extent of agglomeration dynamics. The results indicate that for average dose rates below 1.06 kGy μs^-1 in a time window up to 10 μs, it is possible to capture the protein dynamics before the onset of beam induced aggregation. We refer to this approach as correlation before aggregation and demonstrate that MHz-XPCS bridges an important spatio-temporal gap in measurement techniques for biological samples.

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

Dynamical spectroscopy and microscopy of proteins in cells

With a strong understanding of how proteins fold in hand, it is now possible to ask how in-cell environments modulate their folding, binding and function. Studies accessing fast (ns to s) in-cell dynamics have accelerated over the past few years through a combination of in-cell NMR spectroscopy and time-resolved fluorescence microscopies. Here, we discuss this recent work and the emerging picture of protein surfaces as not just hydrophilic coats interfacing the solvent to the protein's core and functional regions, but as critical components in cells controlling protein mobility, function and communication with post-translational modifications.

In-Cell NMR Study of Tau and MARK2 Phosphorylated Tau

The intrinsically disordered protein, Tau, is abundant in neurons and contributes to the regulation of the microtubule (MT) and actin network, while its intracellular abnormal aggregation is closely associated with Alzheimer's disease. Here, using in-cell Nuclear Magnetic Resonance (NMR) spectroscopy, we investigated the conformations of two different isoforms of Tau, Tau40 and k19, in mammalian cells. Combined with immunofluorescence imaging and western blot analyses, we found that the isotope-enriched Tau, which was delivered into the cultured mammalian cells by electroporation, is partially colocalized with MT and actin filaments (F-actin). We acquired the NMR spectrum of Tau in human embryonic kidney 293 (HEK-293T) cells, and compared it with the NMR spectra of Tau added with MT, F-actin, and a variety of crowding agents, respectively. We found that the NMR spectrum of Tau in complex with MT best recapitulates the in-cell NMR spectrum of Tau, suggesting that Tau predominantly binds to MT at its MT-binding repeats in HEK-293T cells. Moreover, we found that disease-associated phosphorylation of Tau was immediately eliminated once phosphorylated Tau was delivered into HEK-293T cells, implying a potential cellular protection mechanism under stressful conditions. Collectively, the results of our study reveal that Tau utilizes its MT-binding repeats to bind MT in mammalian cells and highlight the potential of using in-cell NMR to study protein structures at the residue level in mammalian cells.

In-cell NMR: from metabolites to macromolecules

In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

Comparative NMR and NIRS analysis of oxygen-dependent metabolism in exercising finger flexor muscles

Muscle contraction requires the physiology to adapt rapidly to meet the surge in energy demand. To investigate the shift in metabolic control, especially between oxygen and metabolism, researchers often depend on near-infrared spectroscopy (NIRS) to measure noninvasively the tissue O₂ Because NIRS detects the overlapping myoglobin (Mb) and hemoglobin (Hb) signals in muscle, interpreting the data as an index of cellular or vascular O₂ requires deconvoluting the relative contribution. Currently, many in the NIRS field ascribe the signal to Hb. In contrast, ¹H NMR has only detected the Mb signal in contracting muscle, and comparative NIRS and NMR experiments indicate a predominant Mb contribution. The present study has examined the question of the NIRS signal origin by measuring simultaneously the ¹H NMR, ³¹P NMR, and NIRS signals in finger flexor muscles during the transition from rest to contraction, recovery, ischemia, and reperfusion. The experiment results confirm a predominant Mb contribution to the NIRS signal from muscle. Given the NMR and NIRS corroborated changes in the intracellular O₂, the analysis shows that at the onset of muscle contraction, O₂ declines immediately and reaches new steady states as contraction intensity rises. Moreover, lactate formation increases even under quite aerobic condition.

Magnetic Resonance Spectroscopy as a Tool for Assessing Macromolecular Structure and Function in Living Cells

Investigating the structure, modification, interaction, and function of biomolecules in their native cellular environment leads to physiologically relevant knowledge about their mechanisms, which will benefit drug discovery and design. In recent years, nuclear and electron magnetic resonance (NMR) spectroscopy has emerged as a useful tool for elucidating the structure and function of biomacromolecules, including proteins, nucleic acids, and carbohydrates in living cells at atomic resolution. In this review, we summarize the progress and future of in-cell NMR as it is applied to proteins, nucleic acids, and carbohydrates.

Intracellular pH modulates quinary structure

NMR spectroscopy can provide information about proteins in living cells. pH is an important characteristic of the intracellular environment because it modulates key protein properties such as net charge and stability. Here, we show that pH modulates quinary interactions, the weak, ubiquitous interactions between proteins and other cellular macromolecules. We use the K10H variant of the B domain of protein G (GB1, 6.2 kDa) as a pH reporter in Escherichia coli cells. By controlling the intracellular pH, we show that quinary interactions influence the quality of in-cell (15) N-(1) H HSQC NMR spectra. At low pH, the quality is degraded because the increase in attractive interactions between E. coli proteins and GB1 slows GB1 tumbling and broadens its crosspeaks. The results demonstrate the importance of quinary interactions for furthering our understanding of protein chemistry in living cells.

Labeling strategy and signal broadening mechanism of Protein NMR spectroscopy in Xenopus laevis oocytes

We used Xenopus laevis oocytes, a paradigm for a variety of biological studies, as a eukaryotic model system for in-cell protein NMR spectroscopy. The small globular protein GB1 was one of the first studied in Xenopus oocytes, but there have been few reports since then of high-resolution spectra in oocytes. The scarcity of data is at least partly due to the lack of good labeling strategies and the paucity of information on resonance broadening mechanisms. Here, we systematically evaluate isotope enrichment and labeling methods in oocytes injected with five different proteins with molecular masses of 6 to 54 kDa. (19) F labeling is more promising than (15) N, (13) C, and (2) H enrichment. We also used (19) F NMR spectroscopy to quantify the contribution of viscosity, weak interactions, and sample inhomogeneity to resonance broadening in cells. We found that the viscosity in oocytes is only about 1.2 times that of water, and that inhomogeneous broadening is a major factor in determining line width in these cells.

Protein dynamics in living cells studied by in-cell NMR spectroscopy

Most proteins function in cells where protein concentrations can reach 400 g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions.

Comparative intermolecular cross-relaxation studies of human hemoglobin in red blood cells and bovine serum albumin in solution

Intermolecular cross-relaxation rate (CR) spectra [1/T(IS) (HDO) or 1/T(IS) (H(2) O) vs f(2) (ppm) profiles] for bovine serum albumin [BSA; molecular weight (MW), 66 kDa] solution, partially hydrolyzed BSA gel (BSA*gel) and packed human red blood cells (RBCs) with normal or unstable hemoglobin (Hb; MW, 65 kDa) were studied using f(2) irradiation ranging from - 100 to 100 ppm at γH(2) /2π of 250 Hz. The CR spectra for BSA*gel (pD 4.01, 0.10 M NaCl, 4.83 and 14.39%) exhibited different features in the off-resonance region (below - 2.00 and above 12.0 ppm) relative to that for BSA solution (pD 7.14, 0.10 M NaCl, 14.39%), indicating the association of BSA* molecules in the gel state. The CR spectrum for packed RBCs was compared with those for BSA*gel and BSA solution (14.39%) by correcting for differences in protein concentration. The corrected CR spectrum for packed normal RBCs in the off-resonance region was similar to that for BSA solution, indicating that the physical characteristics of Hb in normal RBCs may be in a solution-like state. Our results on normal RBCs were approximately consistent with the previously reported thermodynamic and hydrodynamic findings that Hb in RBCs and/or in concentrated solution seems to be in a suspension of hard scaled particles.

Comparative analysis of NMR and NIRS measurements of intracellular PO2 in human skeletal muscle

1H NMR has detected both the deoxygenated proximal histidyl NdeltaH signals of myoglobin (deoxyMb) and deoxygenated Hb (deoxyHb) from human gastrocnemius muscle. Exercising the muscle or pressure cuffing the leg to reduce blood flow elicits the appearance of the deoxyMb signal, which increases in intensity as cellular PO2 decreases. The deoxyMb signal is detected with a 45-s time resolution and reaches a steady-state level within 5 min of pressure cuffing. Its desaturation kinetics match those observed in the near-infrared spectroscopy (NIRS) experiments, implying that the NIRS signals are actually monitoring Mb desaturation. That interpretation is consistent with the signal intensity and desaturation of the deoxyHb proximal histidyl NdeltaH signal from the beta-subunit at 73 parts per million. The experimental results establish the feasibility and methodology to observe the deoxyMb and Hb signals in skeletal muscle, help clarify the origin of the NIRS signal, and set a stage for continuing study of O2 regulation in skeletal muscle.

Observing the deoxy myoglobin and hemoglobin signals from rat myocardium in situ

1H NMR proximal histidyl NdeltaH signals of deoxy hemoglobin (Hb) and myoglobin (Mb) are distinguishable in the rat myocardium in situ. In the normoxic resting state, the blood and tissue pO2 is sufficient to saturate both Mb and Hb. No deoxy Mb or Hb signals are detected. Under 12% inspired O2, the erythrocyte Hb is partially desaturated and yields the alpha and beta proximal histidyl NdeltaH signals of deoxy Hb. The detection of the Hb signals clarifies the debate about the NMR visibility of erythrocyte Hb in vivo and augments the strategy to observe tissue pO2.

Myoglobin and hemoglobin rotational diffusion in the cell

The detection of the 1H NMR signal of myoglobin (Mb) in tissue opens an opportunity to examine its cellular diffusion property, which is central to its purported role in facilitating oxygen transport. In perfused myocardium the field-dependent transverse relaxation analysis of the deoxy Mb proximal histidyl NdeltaH indicates that the Mb rotational correlation time in the cell is only approximately 1.4 times longer than it is in solution. Such a mobility is consistent with the theory that Mb facilitates oxygen diffusion from the sarcoplasm to the mitochondria. The microviscosities of the erythrocyte and myocyte environment are different. The hemoglobin (Hb) rotational correlation time is 2.2 longer in the cell than in solution. Because both the overlapping Hb and Mb signals are visible in vivo, a relaxation-based NMR strategy has been developed to discriminate between them.

Anomeric dependence of fluorodeoxyglucose transport in human erythrocytes

The transport of several n-fluoro-n-deoxy-D-glucose derivatives across the human erythrocyte membrane has been studied under equilibrium exchange conditions using one- and two-dimensional nuclear magnetic resonance (NMR) techniques. This approach is based on the intracellular 19F shift, which was found to depend on the anomeric form and on the F/OH substitution position. Since the transport behavior of both glucose anomers can be followed simultaneously, this approach is particularly sensitive to differences in anomeric permeability. For 2-, 3-, 4-, and 6-fluorodeoxyglucose analogs, the alpha anomers permeate more rapidly, and the P alpha/P beta ratio is dependent on the position of fluorination, with values of 1.1, 1.3, 2.5, and 1.6, respectively, obtained at 37 degrees C. These results have been analyzed in terms of a simple alternating conformation model for the glucose transporter. Although mutarotase activity has been reported for red cells, mutarotation behavior for all anomers was found to be completely negligible on the transport and spin-lattice relaxation time scales. Metabolic transformation of the fluorinated glucose analogs, primarily to fluorinated gluconate and sorbitol analogs, is very slow and does not significantly interfere with the transport measurements. A mean ratio of 2.6 was found for the extracellular/intracellular fluorine spin-lattice relaxation rates.

Estimation of the intracellular free ADP concentration by 19F NMR studies of fluorine-labeled yeast phosphoglycerate kinase in vivo

Yeast phosphoglycerate kinase was selectively fluorine-labeled in vivo by inducing enzyme synthesis in stationary phase cells in the presence of 5-fluorotryptophan. Inducible expression was obtained using a galactose-inducible expression vector containing the yeast phosphoglycerate kinase coding sequence. 19F NMR measurements on intact cells showed two resolved resonances, from the two tryptophan residues in the protein, which underwent reversible changes in chemical shift under different metabolic conditions. Measurements in vitro showed that the difference in the chemical shifts of these two resonances was dependent on the adenine nucleotide concentration, in particular the MgADP concentration. A comparison of the spectra obtained in vitro with those obtained from the intact cell indicated that in glucose-fed cells the cytosolic free MgADP concentration was less than 50 microM, which is significantly lower than the concentrations measured in whole-cell extracts.

Cell volume dependence of 1H spin-echo NMR signals in human erythrocyte suspensions. The influence of in situ field gradients

The 1H spin-echo NMR signal amplitudes and intensities of low molecular weight solutes in the cytoplasm and extracellular fluid of suspensions of human erythrocytes were shown to depend on the osmotic pressure of the media. At low osmotic pressure (220 mosM/kg) freeze-thaw lysis of the cells resulted in signal enhancement which was greatest for extracellular molecules, but both intra- and extracellular species were almost equally enhanced at 580 mosM/kg. This effect is due to field gradients formed at cell boundaries as a result of differences in magnetic susceptibility between the medium and the cytoplasm. T2 values measured using the Carr-Purcell-Meiboom-Gill pulse sequence, with tau = 0.0003 s, depended little on cell volume and absolute changes in volume magnetic susceptibility were also small. The mean field gradients, calculated from data obtained on cell suspensions at different osmotic pressures, were in the range 0.25-1.98 G/cm and 0.89-2.09 G/cm for intra- and extracellular compartments, respectively. The maintenance of isotonicity of the extracellular fluid during metabolic studies of cell suspensions is important in order to avoid artefacts in the determination of metabolite concentrations when using the spin-echo technique. Conversely it may be possible to perform transport measurements using spin-echo NMR to monitor the cell volume changes which occur during the transmembrane migration of molecules.

Intra-erythrocyte microviscosity and diffusion of specifically labelled [glycyl-alpha-13C]glutathione by using 13C n.m.r

[alpha-13C]Glycine was incubated with suspensions of human erythrocytes under special buffer conditions to enrich specifically intracellular glutathione with 13C. The metabolically active cells were then subjected to 13C n.m.r. spectroscopy in which the longitudinal relaxation time(s) (T1) and nuclear Overhauser enhancement(s) of the free glycine and glutathione were measured. With the appropriate analysis, assuming the molecules to be isotropic rotors, intracellular rotational correlation times were calculated. Using these data together with the Stokes-Einstein equation, viscosity and translational diffusion coefficients were calculated. The results were compared with those from cell lysates and extracts. The cytosolic microviscosity probed by glutathione was only 1.9 +/- 0.3 times that of saline, suggesting, therefore, that most enzyme reactions involving this solute are not likely to be diffusion-controlled inside the erythrocyte.