In vivo absolute quantification of hepatic γ-ATP concentration in mice using 31 P MRS at 11.7 T.

Measurement of ATP concentrations and synthesis in humans indicated abnormal hepatic energy metabolism in obesity, non-alcoholic fatty liver disease (NAFLD) and Type 2 diabetes. Further mechanistic studies on energy metabolism require the detailed phenotyping of specific mouse models. Thus, this study aimed to establish and evaluate a robust and fast single voxel 31 P MRS method to quantify hepatic γ-ATP concentrations at 11.7 T in three mouse models with different insulin sensitivities and liver fat contents (72-week-old C57BL/6 control mice, 72-week-old insulin resistant sterol regulatory-element binding protein-1c overexpressing (SREBP-1c+ ) mice and 10-12-week-old prediabetic non-obese diabetic (NOD) mice). Absolute quantification was performed by employing an external reference and a matching replacement ATP phantom with 3D image selected in vivo spectroscopy 31 P MRS. This single voxel 31 P MRS method non-invasively quantified hepatic γ-ATP within 17 min and the repeatability tests provided a coefficient of variation of 7.8 ± 1.1%. The mean hepatic γ-ATP concentrations were markedly lower in SREBP-1c+ mice (1.14 ± 0.10 mM) than in C57BL/6 mice (2.15 ± 0.13 mM; p < 0.0002) and NOD mice (1.78 ± 0.13 mM; p < 0.006, one-way ANOVA test). In conclusion, this method allows us to rapidly and precisely measure hepatic γ-ATP concentrations, and thereby to non-invasively detect abnormal hepatic energy metabolism in mice with different degrees of insulin resistance and NAFLD. Thus, this 31 P MRS will also be useful for future mechanistic as well as therapeutic translational studies in other murine models.

1H detection of heteronuclear dipolar oscillations with water suppression in single crystal peptide and oriented protein samples.

Oriented sample solid-state NMR is a complementary approach to protein structure determination with the distinct advantage that it can be applied to supramolecular assemblies, such as viruses and membrane proteins, under near-native conditions, which generally include high levels of hydration as found in living systems. Thus, in order to perform 1H detected versions of multi-dimensional experiments water suppression techniques must be integrated into the pulse sequences. For example, 1H-windowed detection of 1H-15N dipolar couplings enable multi-dimensional NMR experiments to be performed. Here we show that the addition of a solvent suppression pulse during the z-filter interval greatly improves the sensitivity of the experiments by suppressing the 1H signals from water present. This is demonstrated here with a crystal sample submerged in water and then extended to proteins. The combination of solvent-suppressed 1H detected PISEMO and the use of a strip shield-solenoid coil probe configuration provides a two-fold sensitivity enhancement in both the crystal sample and Pf1 coat protein sample compared to the 15N direct detection method. Here we also examine protein NMR line-widths and sensitivity enhancements in the context of window detected separated local field experiments for protein samples.

Determining Binding Kinetics of Intrinsically Disordered Proteins by NMR Spectroscopy.

The unique structural flexibility of intrinsically disordered proteins (IDPs) is central to their diverse functions in cellular processes. Protein-protein interactions involving IDPs are frequently transient and dynamic in nature. Nuclear magnetic resonance (NMR) spectroscopy is an especially powerful tool for characterizing the structural propensities, dynamics, and interactions of IDPs. Here we describe applications of the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment in combination with NMR titrations to characterize the kinetics and mechanisms of interactions between intrinsically disordered proteins and their targets. We illustrate the method with reference to interactions between the activation domain of the human T-cell leukemia virus type-I (HTLV-1) basic leucine zipper protein (HBZ) and its cellular binding partner, the KIX domain of the transcriptional coactivator CBP.

Multiple Site-Specific Phosphorylation of IDPs Monitored by NMR.

In line with their high accessibility, disordered proteins are exquisite targets of kinases. Eukaryotic organisms use the so-called intrinsically disordered proteins (IDPs) or intrinsically disordered regions of proteins (IDRs) as molecular switches carrying intracellular information tuned by reversible phosphorylation schemes. Solvent-exposed serines and threonines are abundant in IDPs, and, consistently, kinases often modify disordered regions of proteins at multiple sites. In this context, nuclear magnetic resonance (NMR) spectroscopy provides quantitative, residue-specific information that permits mapping of phosphosites and monitoring of their individual kinetics. Hence, NMR monitoring emerges as an in vitro approach, complementary to mass-spectrometry or immuno-blotting, to characterize IDP phosphorylation comprehensively. Here, we describe in detail generic protocols for carrying out NMR monitoring of IDP phosphorylation, and we provide a number of practical insights that improve handiness and reproducibility of this method.

Effects of deuteration on solid-state NMR spectra of single peptide crystals and oriented protein samples.

Extensive deuteration can be used to simplify NMR spectra by "diluting" and minimizing the effects of the abundant 1H nuclei. In solution-state NMR and magic angle spinning solid-state NMR of proteins, perdeuteration has been widely applied and its effects are well understood. Oriented sample solid-state NMR of proteins, however, is at a much earlier stage of development. In spite of the promise of the approach, the effects of sample deuteration are largely unknown. Here we map out the effects of perdeuteration on solid-state NMR spectra of aligned samples by closely examining differences in results obtained on fully protiated and perdeuterated samples, where all of the carbon sites have either 1H or 2H bonded to them, respectively. The 2H and 15N labeled samples are back-exchanged in 1H2O solution so that the amide 15N sites have a bonded 1H. Line-widths in the 15N chemical shift, 1H chemical shift, and 1H-15N dipolar coupling frequency dimensions were compared for peptide single crystals as well as membrane proteins aligned along with the phospholipids in bilayers with their normals perpendicular to the direction of the magnetic field. Remarkably, line-width differences were not found between fully protiated and perdeuterated samples. However, in the absence of effective 1H-1H homonuclear decoupling, the line-widths in the 1H-15N heteronuclear dipolar coupling frequency dimension were greatly narrowed in the perdeuterated samples. In proton-driven spin diffusion (PDSD) experiments, no effects of perdeuteration were observed. In contrast, in mismatched Hartmann-Hahn experiments, perdeuteration enhances cross-peak intensities by allowing more efficient spin-exchange with less polarization transfer back to the carbon-bound 1H. Here we show that in oriented sample solid-state NMR, the effects of perdeuteration can be exploited in experiments where 1H-1H homonuclear decoupling cannot be applied. These data also provide evidence for the possible contribution of direct 15N-15N dilute-spin mixing mechanism in proton-driven spin diffusion experiments.

DNP NMR of biomolecular assemblies.

Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins. Since then, DNP has experienced tremendous advances, with the development of extremely efficient polarizing agents or with the introduction of new microwaves sources, suitable for NMR experiments at very high magnetic fields (currently up to 900 MHz). After a brief introduction, several experimental aspects of DNP enhanced NMR spectroscopy applied to biomolecular assemblies are discussed. Recent demonstration experiments of the method on viral capsids, the type III and IV bacterial secretion systems, ribosome and membrane proteins are then described.

(15)N CSA tensors and (15)N-(1)H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR.

In this work, we assess the usefulness of static (15)N NMR techniques for the determination of the (15)N chemical shift anisotropy (CSA) tensor parameters and (15)N-(1)H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone (15)N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the (15)N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the (15)N CSA parameters, a more advanced approach based on the "magic sandwich" SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the (15)N-(1)H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

Looking into Living Cell Systems: Planar Waveguide Microfluidic NMR Detector for in Vitro Metabolomics of Tumor Spheroids.

The complex cell metabolism and its link to oncogenic signaling pathways have received huge interest within the last few years. But the lack of advanced analytical tools for the investigation of living cell metabolism is still a challenge to be faced. Therefore, we designed and fabricated a novel miniaturized microslot NMR detector with on-board heater integrated with a microfluidic device as NMR sample holder. For the first time, a tumor spheroid of 500 µm diameter and consisting of 9000 cells has been studied noninvasively and online for 24 h. The dynamic processes of production and degradation of 23 intra- and extracellular metabolites were monitored. Remarkably high concentrations of lactate and alanine were observed, being an indicator for a shift from oxidative to glycolytic metabolism. In summary, this methodical development has proven to be a successful analytical tool for the elucidation of cellular functions and their corresponding biochemical pathways. Additionally, the planar geometry of the microslot NMR detector allows the hyphenation with versatile lab-on-a chip (LOC) technology. This opens a new window for metabolomics studies on living cells and can be implemented into new application fields in biotechnology and life sciences.

Dynamic UltraFast 2D EXchange SpectroscopY (UF-EXSY) of hyperpolarized substrates.

In this work, we present a new ultrafast method for acquiring dynamic 2D EXchange SpectroscopY (EXSY) within a single acquisition. This technique reconstructs two-dimensional EXSY spectra from one-dimensional spectra based on the phase accrual during echo times. The Ultrafast-EXSY acquisition overcomes long acquisition times typically needed to acquire 2D NMR data by utilizing sparsity and phase dependence to dramatically undersample in the indirect time dimension. This allows for the acquisition of the 2D spectrum within a single shot. We have validated this method in simulations and hyperpolarized enzyme assay experiments separating the dehydration of pyruvate and lactate-to-pyruvate conversion. In a renal cell carcinoma cell (RCC) line, bidirectional exchange was observed. This new technique revealed decreased conversion of lactate-to-pyruvate with high expression of monocarboxylate transporter 4 (MCT4), known to correlate with aggressive cancer phenotypes. We also showed feasibility of this technique in vivo in a RCC model where bidirectional exchange was observed for pyruvate-lactate, pyruvate-alanine, and pyruvate-hydrate and were resolved in time. Broadly, the technique is well suited to investigate the dynamics of multiple exchange pathways and applicable to hyperpolarized substrates where chemical exchange has shown great promise across a range of disciplines.

A system for accurate and automated injection of hyperpolarized substrate with minimal dead time and scalable volumes over a large range.

Over recent years hyperpolarization by dissolution dynamic nuclear polarization has become an established technique for studying metabolism in vivo in animal models. Temporal signal plots obtained from the injected metabolite and daughter products, e.g. pyruvate and lactate, can be fitted to compartmental models to estimate kinetic rate constants. Modeling and physiological parameter estimation can be made more robust by consistent and reproducible injections through automation. An injection system previously developed by us was limited in the injectable volume to between 0.6 and 2.4ml and injection was delayed due to a required syringe filling step. An improved MR-compatible injector system has been developed that measures the pH of injected substrate, uses flow control to reduce dead volume within the injection cannula and can be operated over a larger volume range. The delay time to injection has been minimized by removing the syringe filling step by use of a peristaltic pump. For 100µl to 10.000ml, the volume range typically used for mice to rabbits, the average delivered volume was 97.8% of the demand volume. The standard deviation of delivered volumes was 7µl for 100µl and 20µl for 10.000ml demand volumes (mean S.D. was 9 ul in this range). In three repeat injections through a fixed 0.96mm O.D. tube the coefficient of variation for the area under the curve was 2%. For in vivo injections of hyperpolarized pyruvate in tumor-bearing rats, signal was first detected in the input femoral vein cannula at 3-4s post-injection trigger signal and at 9-12s in tumor tissue. The pH of the injected pyruvate was 7.1±0.3 (mean±S.D., n=10). For small injection volumes, e.g. less than 100µl, the internal diameter of the tubing contained within the peristaltic pump could be reduced to improve accuracy. Larger injection volumes are limited only by the size of the receiving vessel connected to the pump.

Broadband finite-pulse radio-frequency-driven recoupling (fp-RFDR) with (XY8)4(1) super-cycling for homo-nuclear correlations in very high magnetic fields at fast and ultra-fast MAS frequencies.

We demonstrate that inter-residue (13)C-(13)C proximities (of about 380 pm) in uniformly (13)C-labeled proteins can be probed by applying robust first-order recoupling during several milliseconds in single-quantum single-quantum dipolar homo-nuclear correlation (SQ-SQ D-HOMCOR) 2D experiments. We show that the intensity of medium-range homo-nuclear correlations in these experiments is enhanced using broadband first-order finite-pulse radio-frequency-driven recoupling (fp-RFDR) NMR sequence with a nested (XY8)4(1) super-cycling. The robustness and the efficiency of the fp-RFDR-(XY8)4(1) method is demonstrated at high magnetic field (21.1T) and high Magic-Angle Spinning (MAS) speeds (up to 60 kHz). The introduced super-cycling, formed by combining phase inversion and a global four-quantum phase cycle, improves the robustness of fp-RFDR to (i) chemical shift anisotropy (CSA), (ii) spread in isotropic chemical shifts, (iii) rf-inhomogeneity and (iv) hetero-nuclear dipolar couplings for long recoupling times. We show that fp-RFDR-(XY8)4(1) is efficient sans (1)H decoupling, which is beneficial for temperature-sensitive biomolecules. The efficiency and the robustness of fp-RFDR-(XY8)4(1) is investigated by spin dynamics numerical simulations as well as solid-state NMR experiments on [U-(13)C]-L-histidine·HCl, a tetra-peptide (Fmoc-[U-(13)C,(15)N]-Val-[U-(13)C,(15)N]-Ala-[U-(13)C,(15)N]-Phe-Gly-t-Boc) and Al(PO(3))(3).

Magnetic resonance spectroscopy of cancer metabolism and response to therapy.

Magnetic resonance spectroscopy allows noninvasive in vivo measurements of biochemical information from living systems, ranging from cultured cells through experimental animals to humans. Studies of biopsies or extracts offer deeper insights by detecting more metabolites and resolving metabolites that cannot be distinguished in vivo. The pharmacokinetics of certain drugs, especially fluorinated drugs, can be directly measured in vivo. This review briefly describes these methods and their applications to cancer metabolism, including glycolysis, hypoxia, bioenergetics, tumor pH, and tumor responses to radiotherapy and chemotherapy.

Electron paramagnetic resonance imaging of tumor pO2.

Electron paramagnetic resonance imaging (EPRI) can be used to noninvasively and quantitatively obtain three-dimensional maps of tumor pO2. The paramagnetic tracer triarylmethyl (TAM), a substituted trityl radical moiety, is not toxic to animals and provides narrow isotropic spectra, which is ideal for in vivo EPR imaging experiments. From the oxygen-induced spectral broadening of TAM, pO2 maps can be derived using EPRI. The instrumentation consists of an EPRI spectrometer and 7T magnetic resonance imaging (MRI) system both operating at a common radiofrequency of 300 MHz. Anatomic images obtained by MRI can be overlaid with pO2 maps obtained from EPRI. With imaging times of less than 3 min, it was possible to monitor the dynamics of oxygen changes in tumor and distinguish chronically hypoxic regions from acutely hypoxic regions. In this article, the principles of pO2 imaging with EPR and some relevant examples of tumor imaging are reviewed.

Diagnosis of early stage ovarian cancer by 1H NMR metabonomics of serum explored by use of a microflow NMR probe.

We show that (1)H NMR based metabonomicsof serum allows the diagnosis of early stage I/II epithelial ovarian cancer (EOC) required for successful treatment. Because patient specimens are highly precious, we conducted an exploratory study using a microflow probe requiring only 20 µL of serum. By use of logistic regression on principal components (PCs) of the NMR profiles, we built a 4-variable model for early stage EOC prediction (training set: 69 EOC specimens, 84 healthy controls; test set: 40 EOC, 44 controls) with operating characteristics estimated for the test set at 80% specificity [95% confidence interval (CI): 65-90%], 63% sensitivity (95% CI: 46-77%), and an area under the Receiver Operator Characteristic Curve (AUC) of 0.796. Independent validation (50 EOC, 50 controls) of the model yielded 95% specificity (95% CI: 86-99.5%), 68% sensitivity (95% CI: 53-80%) and an AUC of 0.949. A test on cancer type specificity showed that women diseased with renal cell carcinoma were not incorrectly diagnosed with EOC, indicating that metabonomics bears significant potential for cancer type-specific diagnosis. Our model can potentially be applied for women at high risk for EOC, and our study promises to contribute to developing a screening protocol for the general population.

Pyridazine-based Schiff base ligands with N4OxS2 (x=2, 4) donor set atoms: synthesis, characterization, spectral studies and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies.

Six pyridazine-based Schiff base ligands, H(2)L(n) (n=1-5) and H(4)L, with N(4)O(2)S(2) and N(4)O(4)S(2) donor set atoms, respectively, were prepared by condensation reaction of 3,6-bis-((2-aminoethyl)thio)pyridazine with various salicyladehyde derivatives in ethanol and under solvent-free polyphosphate ester catalyzed conditions. The acid-base properties of H(2)L(2) and H(2)L(3) in DMSO/water (1:1) solution have been studied by spectrophotometric method at 25 degrees C. Optimized geometries of all compounds were also obtained at the B3LYP level of theory. Additionally, the (13)C chemical shielding of gas phase H(2)L(1) and H(2)L(2) were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The 6-311++G* basis set was utilized for all of the atoms.

The T-lock: automated compensation of radio-frequency induced sample heating.

Modern high-field NMR spectrometers can stabilize the nominal sample temperature at a precision of less than 0.1 K. However, the actual sample temperature may differ from the nominal value by several degrees because the sample heating caused by high-power radio frequency pulses is not readily detected by the temperature sensors. Without correction, transfer of chemical shifts between different experiments causes problems in the data analysis. In principle, the temperature differences can be corrected by manual procedures but this is cumbersome and not fully reliable. Here, we introduce the concept of a "T-lock", which automatically maintains the sample at the same reference temperature over the course of different NMR experiments. The T-lock works by continuously measuring the resonance frequency of a suitable spin and simultaneously adjusting the temperature control, thus locking the sample temperature at the reference value. For three different nuclei, 13C, 17O and 31P in the compounds alanine, water, and phosphate, respectively, the T-lock accuracy was found to be <0.1 K. The use of dummy scan periods with variable lengths allows a reliable establishment of the thermal equilibrium before the acquisition of an experiment starts.

Evidence of multiexponential T2 in rat glioblastoma.

The aim of this study was to characterize multiexponential T(2) (MET(2)) relaxation in a rat C6 glioblastoma tumor model. To do this, rats (n = 11) were inoculated with the C6 cells via stereotaxic injection into the brain. Ten days later, MET(2) measurements were performed in vivo using a single-slice, multi-echo spin-echo sequence at 7.0 T. Tumor signal was biexponential in eight animals with a short-lived T(2) component (T(2) = 20.7 +/- 5.4 ms across samples) representing 6.8 +/- 6.2% of the total signal and a long-lived T(2) component (T(2) = 76.4 +/- 9.3 ms) representing the remaining signal fraction. In contrast, signal from contralateral grey matter was consistently monoexponential (T(2) = 48.8 +/- 2.3 ms). Additional ex vivo studies (n = 3) and Monte Carlo simulations showed that the in vivo results were not significantly corrupted by partial volume averaging or noise. The underlying physiological origin of the observed MET(2) components is unknown; however, MET(2) analysis may hold promise as a non-invasive tool for characterizing tumor microenvironment in vivo on a sub-voxel scale.

Detecting colorectal cancer by 1H magnetic resonance spectroscopy of fecal extracts.

Colorectal cancer is one of the most common cancers in the western world. Its early detection has been found to improve the prognosis of the patient, providing a wide window of opportunity for successful therapeutic interventions. However, current diagnostic techniques all have some limitations; there is a need to develop a better technique for routine screening purposes. We present a new methodology based on magnetic resonance spectroscopy of fecal extracts for the non-invasive detection of colorectal cancer. Five hundred twenty-three human subjects (412 with no colonic neoplasia and 111 with colorectal cancer, who were scheduled for colonoscopy or surgery) were recruited to donate a single sample of stool. One-dimensional (1)H magnetic resonance spectroscopy (MRS) experiments were performed on the supernatant of aqueous dispersions of the stool samples. Using a statistical classification strategy, several multivariate classifiers were developed. Applying the preprocessing, feature selection and classifier development stages of the Statistical Classification Strategy led to approximately 87% average balanced sensitivity and specificity for both training and monitoring sets, improving to approximately 92% when only crisp results, i.e. class assignment probabilities > or =75%, are considered. These results indicate that (1)H magnetic resonance spectroscopy of human fecal extracts, combined with appropriate data analysis methodology, has the potential to detect colorectal neoplasia accurately and reliably, and could be a useful addition to the current screening tools.

New methods for calibration of the RF field strength for indirectly observed nuclei.

Two novel pulse sequences, CALIS-1 and CALIS-2, for accurate calibration of the RF field strength for an indirectly observed spin are introduced. CALIS-2 is intended for calibration of e.g., (13)C or (15)N pulses on natural abundance samples whilst CALIS-1 is recommended primarily for enriched samples. Both experiments can be performed without prior knowledge or guess of the RF field strength and no delays in the pulse sequences are critically dependent on coupling constants.

NMR difference spectroscopy with a dual saddle-coil difference probe.

A new difference probe for nuclear magnetic resonance (NMR) spectroscopy is presented. The difference probe uses two saddle-shaped coils to excite and detect two samples simultaneously. The samples are held in a specially modified 3-mm NMR tube with an Ultem plastic disk to separate the samples. The probe's resonant circuit contains two crossed diodes that passively switch the relative phase of each coil during the NMR experiment. The result is a difference spectrum from the two samples. The degree of cancellation of common signals was determined to be approximately 90%, and the application of the probe to relaxation-edited difference spectroscopy for identifying protein-ligand interactions was demonstrated using glutathione and glutathione S-transferase binding protein.