Multiple-quantum filtered 17Q and 23Na NMR analysis of mitochondrial suspensions

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.

Sodium MRI: methods and applications

Sodium NMR spectroscopy and MRI have become popular in recent years through the increased availability of high-field MRI scanners, advanced scanner hardware and improved methodology. Sodium MRI is being evaluated for stroke and tumor detection, for breast cancer studies, and for the assessment of osteoarthritis and muscle and kidney functions, to name just a few. In this article, we aim to present an up-to-date review of the theoretical background, the methodology, the challenges, limitations, and current and potential new applications of sodium MRI.

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.

Investigation of water bound to photosystem I with multiquantum filtered 17 O nuclear magnetic resonance

A new analytical approach was developed to characterize the properties of water molecules bound to macromolecules in solution using 17 O nuclear magnetic resonance (NMR) relaxation. A combination of conventional (single-quantum) and triple-quantum filtered Hahn echo and inversion recovery measurements was employed. From measured relaxation rate constants, the fraction and the correlation time of bound H2 17 O molecules and the relaxation rate constant of bulk water in solution were calculated. This was done by solving analytically a set of nonlinear equations describing the overall relaxation rate constants in the presence of chemical exchange between bulk and bound water. The analytical approach shows the uniqueness of the solution for a given set of three relaxation rate constants. This important result sheds light on the data reduction problem from 17 O NMR experiments on biological systems. Water bound in photosystem I isolated from the wild type and rubA variant of the cyanobacterium Synechocystis species PCC 7002 was investigated for the first time. The analysis revealed that photosystem I isolated from the wild type binds 1720+/-110 water molecules, whereas photosystem I isolated from the rubA variant binds only 1310+/-170. The accuracy of the method proposed can be increased by further 17 O enrichment. The methodology, established for the first time in this work, allows the study of a diverse range of biological samples regardless of their size and molecular weight. Applied initially to photosystem I, this novel method has important consequences for the future investigation of the assembly of biological molecules.

Mitochondrial membrane permeabilization produced by PTP, Bax and apoptosis: a 1H-NMR relaxation study

To analyze the involvement of structured water (bound to macromolecules) in apoptosis-induced mitochondrial outer-membrane permeability, we compared the dynamics of water protons from nuclear magnetic resonance (NMR) data in apoptotic liver mitochondria with that of control mitochondria incubated in vitro with free Ca(2+) (opening of the permeability transition pore, PTP) or with Bax alpha. Our results demonstrate that water molecules in apoptotic mitochondria exhibit an accelerated translational motion of structured water common with that induced by the opening of the PTP, but limited in amplitude. On the other hand, no significant quantitative change in structured water was observed in apoptotic mitochondria, a phenomenon also observed with Bax alpha-induced permeability. We conclude that the changes observed in the different water phases differ both quantitatively and qualitatively during the opening of the PTP and the Bax alpha-induced permeability, and that the apoptotic mitochondria exhibit mixed properties between these model situations.

Selecting ordered environments in NMR of spin 3/2 nuclei via frequency-sweep pulses

We demonstrate that frequency-swept pulses can be used for the selective and enhanced detection of quadrupolar nuclei located in anisotropic environments. The primary driving force for this technique development is the field of sodium-MRI, where sodium signals from locally ordered environments are known to be diagnostic of cartilage defects. We demonstrate here simple one-dimensional images of model systems, in which the signals from free sodium ions are suppressed, while ordered sodium is detected via the narrow central transition signal.

Determination of Na+ binding parameters by relaxation analysis of selected 23Na NMR coherences: RNA, BSA and SDS

Nuclear magnetic resonance provides several unique means of investigating the interactions between different inorganic ions and various macromolecules. (23)Na is a quadrupolar nucleus, meaning that relaxation analysis of the various coherences allows the measurement of its binding to biological macromolecules. In this study, we analyzed the quadrupolar relaxation of (23)Na(+) longitudinal magnetization and single- and triple-quantum coherences in aqueous systems containing RNA, bovine serum albumin and sodium dodecyl sulfate micelles. The effectiveness of the James-Noggle method for determining binding constants was evaluated in these systems, and also the applicability of various (23)Na coherences in providing information on the extent and affinity of binding to the three different classes of biomolecules.

Enhancement of Na+ diffusion in a bicontinuous cubic phase by the ionophore monensin

Pulsed field gradient spin-echo NMR diffusion and relaxation measurements were used to investigate how the Na+ ionophore monensin affected the dynamics of sodium ions in a Myverol 18-99/saline bicontinuous Ia3d cubic phase (BCP). The monensin Na+ binding number was estimated from 23Na line widths to be between 3 and 6. The dependence of the apparent Na+ diffusion coefficient on the concentration of monensin revealed monensin-induced Na+ transport. At high monensin concentrations, the enhancement of D(Na+) was offset by Na+-monensin binding. The greatest enhancement was measured at short diffusion times (delta < or = 5 ms), which we explain in terms of the bicontinuous topology of the cubic phase and a combination of tortuosity and bilayer permeability effects. We also propose numerical simulations which would enable the separation of the two effects. To our knowledge, this is the first study of ionophore-mediated cation diffusion in a bicontinuous cubic phase. The approach could be used to study the dynamics of hydrophilic species in the aqueous channels of BCPs and similar structures, as well as to measure the ion-transporting efficiency of ionophores.

Saturation transfer in human red blood cells with normal and unstable hemoglobin

Saturation transfer phenomena from irradiated protein protons to observed water protons in packed human red blood cells (RBCs) with normal or unstable hemoglobin (Hb), i.e. Hb Yokohama and Hb Koeln, were studied using intermolecular cross-relaxation rates [CR; 1/T(IS)(H(2)O)], action spectra [[1-(I(infinity)/I(0))] vs f(2) (ppm), where I(0) and I(infinity) are the longitudinal magnetization of observed water protons before and after long-time f(2)-irradiation, respectively], CR spectra [CR vs f(2) (ppm)] and CR ratio vs f(2) (ppm) with f(2)-irradiation from -100 to 100 ppm at gammaH(2)/2pi of 69 or 250 Hz. RBCs (Hb Yokohama) exhibited many large Heinz bodies and strongly impaired filterability, while RBCs (Hb Koeln) showed few microscopically typical Heinz bodies and virtually normal filterability. However, increases in CR values for RBCs (Hb Koeln) and RBCs (Hb Yokohama), monitored by f(2)-irradiation below approximately -6 and above approximately 14 ppm, clearly indicated marked increases in association or aggregation of unstable Hb in RBCs compared with those in normal RBCs. CR values, monitored between approximately 0 and approximately 10 ppm, were related to not only association or aggregation of unstable Hb but also amounts of water in RBCs. Aggregation or association of unstable Hb exhibited greater effects on CR values compared with those of methemoglobin formation.

A faster way to characterize by triple-quantum-filtered (17)O NMR water molecules strongly bound to macromolecules in solution

The simultaneous use of transverse and longitudinal relaxation rates, together with a transverse triple-quantum-filtering NMR sequence, was estimated for the adequate characterization of (17)O-water relaxation behavior in protein solutions. A complementary contribution to transverse relaxation was found, which was interpreted as chemical exchange of (17)O-water between different sites of the proteins. This contribution was estimated via calibration measurements. Then, for other similar samples, faster experiments could be performed. The analysis of the results obtained in this way gave adequate values of the relaxation rate of water in fast motion, of the fraction of water in slow motion, and of its correlation time. Hence, it permitted the complete characterization of the sample in a reasonable experimental time.

Characterisation by triple-quantum filtered 17O-NMR of water molecules buried in lysozyme and trapped in a lysozyme-inhibitor complex

Triple-quantum filtering NMR sequences were used to study the multiexponential relaxation behaviour of H2 17O in the presence of hen egg white lysozyme. By this means, the fraction and the correlation time of water were determined in slow motion, as well as the relaxation time of water in the extreme narrowing limit. The small number of water molecules in slow motion, which is between four and five per lysozyme, seems to correspond to the 'integral' water, buried or in the cleft inside the protein, whereas water in fast motion corresponds to all other water molecules, interacting or not with the macromolecules. The same experiment was performed after addition of the inhibitor tri-N-acetylglucosamine (NAG)3. For solutions of sufficient viscosity, there were approximately three supplementary water molecules in slow motion per lysozyme, probably trapped between the protein and the inhibitor. The correlation time of these water molecules was estimated at 2 ns, which should correspond to their residence time in the complex.

17O NMR of water in ordered environments

Two NMR experiments are designed for selective excitation of spin I=5/2 nuclei that exhibit residual quadrupolar splittings. The I=5/2 Jeener-Broekaert experiment is preferred to the four-quantum filtration experiment as it is shown to be a more sensitive technique in experimental practice. Both techniques are applied to (17)O-enriched water in biological systems. The occurrence of water which displays a residual (17)O quadrupolar splitting is demonstrated for the first time in a model biological system and an excised tissue sample. The resulting (17)O NMR spectra are shown to have the characteristics predicted in computer-simulated I=5/2 NMR spectra.