Chemical Shift Dispersion Research Articles

Improved efficiency on editing MRS of lactate and γ‐aminobutyric acid by inclusion of frequency offset corrected inversion pulses at high fields

γ-Aminobutyric acid (GABA) and lactate are metabolites which are present in the brain. These metabolites can be indicators of psychiatric disorders or tumor hypoxia, respectively. The measurement of these weakly coupled spin systems can be performed using MRS editing techniques; however, at high field strength, this can be challenging. This is due to the low available B1 (+) field at high fields, which results in narrow-bandwidth refocusing pulses and, consequently, in large chemical shift displacement artifacts. In addition, as a result of the increased chemical shift displacement artifacts and chemical shift dispersion, the efficiency of the MRS method is reduced, even when using adiabatic refocusing pulses. To overcome this limitation, frequency offset corrected inversion (FOCI) pulses have been suggested as a mean to substantially increase the bandwidth of adiabatic pulses. In this study, a Mescher-Garwood semi-localization by adiabatic selection and refocusing (MEGA-sLASER) editing sequence with refocusing FOCI pulses is presented for the measurement of GABA and lactate in the human brain. Metabolite detection efficiencies were improved by 20% and 75% for GABA and lactate, respectively, when compared with editing techniques that employ adiabatic radiofrequency refocusing pulses. The highly efficient MEGA-sLASER sequence with refocusing FOCI pulses is an ideal and robust MRS editing technique for the measurement of weakly coupled metabolites at high field strengths.

Detection of Living Anionic Species in Polymerization Reactions Using Hyperpolarized NMR

Intermediates during the anionic polymerization of styrene were observed using hyperpolarized NMR. Dissolution dynamic nuclear polarization (DNP) of monomers provides a sufficient signal-to-noise ratio for detection of (13)C NMR signals in real time as the reaction progresses. Because of its large chemical shift dispersion, (13)C is well-suited to distinguish and characterize the chemical species that arise during the reaction. At the same time, incorporation of hyperpolarized small-molecule monomers is a unique way to generate polymers that exhibit a transient signal enhancement at the active site. This strategy is applicable despite the decay of the hyperpolarization of the polymer due to rapid spin-lattice relaxation. Real-time measurements on polymerization reactions provide both mechanistic and kinetic information without the need for stable isotope labeling of the molecules of interest. These capabilities are orthogonal to currently established methods that separate synthesis and analysis into two steps, making dissolution DNP an attractive method to study polymerization reactions.

Application of chemical exchange saturation transfer (CEST) MRI for endogenous contrast at 7 Tesla.

Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) indirectly images exchangeable solute protons resonating at frequencies different than bulk water. These solute protons are selectively saturated using low bandwidth RF irradiation and saturation is transferred to bulk water protons via chemical exchange, resulting in an attenuation of the measured water proton signal. CEST MRI is an advanced MRI technique with wide application potential due to the ability to examine complex molecular contributions. CEST MRI at high field (7 Tesla [7 T]) will improve the overall results due to increase in signal, T1 relaxation time, and chemical shift dispersion. Increased field strength translates to enhanced quantification of the metabolite of interest, allowing more fundamental studies on underlying pathophysiology. CEST contrast is affected by several tissue properties, such as the concentrations of exchange partners and their rate of proton exchange, whose effects have been examined and explored in this review. We have highlighted the background of CEST MRI, typical implementation strategy, and complications at 7 T.

Probing Arginine Side‐Chains and Their Dynamics with Carbon‐Detected NMR Spectroscopy: Application to the 42 kDa Human Histone Deacetylase 8 at High pH

Arginine side-chains play a distinct role because of their high pKa and perpetual positive charge. An NMR method is presented, based on carbon-detected 13Cζ–15Ne correlation spectra, which allows probing the arginine side-chains and their dynamics at neutral-to-high pH. The methodology is demonstrated on human histone deacetylase 8.

Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of (13)C(α), is proposed.

Study of near‐symmetric cyclodextrins by compressed sensing 2D NMR

The compressed sensing NMR (CS-NMR) is an approach to processing of nonuniformly sampled NMR data. Its idea is to introduce minimal l(p) -norm (0 < p ≤ 1) constraint to a penalty function used in a reconstruction algorithm. Here, we demonstrate that 2D CS-NMR spectra allow the full spectral assignment of near-symmetric β-cyclodextrin derivatives (mono-modified at the C6 position). The application of CS-NMR ensures experimental time saving and the resolution improvement, necessary because of very low chemical shift dispersion. In the overnight experimental time, the set of properly resolved 2D NMR spectra required for the unambiguous assignment of mono(6-deoxy-6-(1-1,2,3-triazo-4-yl)-1-propane-3-O-(phenyl)) β-cyclodextrin was obtained. The highly resolved HSQC spectrum was reconstructed from 5.12% of the data. Moreover, reconstructed 2D HSQC-TOCSY spectrum yielded information about the correlations within one sugar unit, and 2D HSQC-NOESY technique allowed the sequential assignment of the glucosidic units.

Structural characterization of a peptoid with lysine-like side chains and biological activity using NMR and computational methods

N-substituted glycine oligomers or peptoids with charged side chains are a novel class of cell penetrating peptide mimetics and have been shown to serve as drug delivery agents. Here, we investigated by NMR spectroscopy and quantum chemical calculations whether a Rhodamine B labelled peptoid [RhoB(Spiro)-Ahx]-[But](6A)NH(2) with lysine-like side chains adopts structural motifs similar to regular peptides. Due to a low chemical shift dispersion, high resolution structure determination with conventional NMR-derived distance restraints and J-couplings was not possible. Instead, a combined assignment and structure refinement strategy using the QM/MM force field COSMOS-NMR was developed to interpret the highly ambiguous chemical shift and distance constraints and obtain a medium resolution three-dimensional structural model. This allowed us to select for the all cis-amide conformation of the peptide with a pseudo-helical arrangement of extended side chains as a faithful representative structure of [RhoB(Spiro)-Ahx]-[But](6A)NH(2). We tested the biological activity of the peptoid by live-cell imaging, which showed that the cellular uptake of the peptoid was comparable to conventional cell-penetrating peptides.

An H3K36 Methylation-Engaging Tudor Motif of Polycomb-like Proteins Mediates PRC2 Complex Targeting

Polycomb repressive complex 2 (PRC2) regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. However, the mechanisms that underlie PRC2 recruitment and spreading on chromatin remain unclear. Here we report that histone H3 lysine 36 trimethylation (H3K36me3) binding activity is harbored in the Tudor motifs of PRC2-associated polycomb-like (PCL) proteins PHF1/PCL1 and PHF19/PCL3. Ectopically expressed PHF1 induced Tudor-dependent stabilization of PRC2 complexes on bulk chromatin and mediated spreading of PRC2 and H3K27me3 into H3K36me3-containing chromatin regions. In murine pluripotent stem cells, we identified coexistence of H3K36me3, H3K27me3, and PHF19/PCL3 at a subset of poised developmental genes and demonstrated that PHF19/PCL3 Tudor function is required for optimal H3K27me3 and repression of these loci. Collectively, our data suggest that PCL recognition of H3K36me3 promotes intrusion of PRC2 complexes into active chromatin regions to promote gene silencing and modulate the chromatin landscape during development.

Rapid estimation of nuclear magnetic resonance experiment time in low‐concentration environmental samples

Nuclear magnetic resonance (NMR) spectroscopy is an essential tool for studying environmental samples but is often hindered by low sensitivity, especially for the direct detection of nuclei such as(13) C. In very heterogeneous samples with NMR nuclei at low abundance, such as soils, sediments, and air particulates, it can take days to acquire a conventional(13) C spectrum. The present study describes a prescreening method that permits the rapid prediction of experimental run time in natural samples. The approach focuses the NMR chemical shift dispersion into a single spike, and, even in samples with extremely low carbon content, the spike can be observed in two to three minutes, or less. The intensity of the spike is directly proportional to the total concentration of nuclei of interest in the sample. Consequently, the spike intensity can be used as a powerful prescreening method that answers two key questions: (1) Will this sample produce a conventional NMR spectrum? (2) How much instrument time is required to record a spectrum with a specific signal-to-noise (S/N) ratio? The approach identifies samples to avoid (or pretreat) and permits additional NMR experiments to be performed on samples producing high-quality NMR data. Applications in solid- and liquid-state(13) C NMR are demonstrated, and it is shown that the technique is applicable to a range of nuclei.

Reduced Dimensionality (4,3)D-HN(C)NH for Rapid Assignment of 1HN–15N HSQC Peaks in Proteins: An Analytical Tool for Protein Folding, Proteomics, and Drug Discovery Programs

While nuclear magnetic resonance (NMR) has had commendable success in atomic-level investigation of folded proteins, intrinsically unfolded and partially folded proteins have always posed a great challenge, because of poor chemical shift dispersions. We present here a reduced-dimensionality-based NMR triple resonance pulse sequence, (4,3)D-HN(C)NH, which not only helps to disperse the peaks further by combining (15)N and amide (1)H chemical shifts, but also directly establishes correlations between (1)H(i)(N), (15)N(i), (1)H(i+1)(N), and (15)N(i+1) spins along the F(1)-F(3) planes. The F(2)-F(3) projection planes of this experiment provide unique identification of the check points in amide resonances. An assignment strategy derived by combining information along the F(1)-F(3) planes and in the F(2)-F(3) projection planes of the experiment has been presented and shown to be very useful for both intrinsically disordered/unfolded proteins and folded protein alike. The experiment and the protocol would be valuable for protein folding, proteomics, and drug discovery programs.

In vivo magnetic resonance imaging of glucose – initial experience

A new noninvasive, nonradioactive approach for glucose imaging using spin hyperpolarization technology and stable isotope labeling is presented. A glucose analog labeled with (13)C at all six positions increased the overall hyperpolarized imaging signal; deuteration at all seven directly bonded proton positions prolonged the spin-lattice relaxation time. High-bandwidth (13)C imaging overcame the large glucose carbon chemical shift dispersion. Hyperpolarized glucose images in the live rat showed time-dependent organ distribution patterns. At 8 s after the start of bolus injection, the inferior vena cava was demonstrated at angiographic quality. Distribution of hyperpolarized glucose in the kidneys, vasculature, and heart was demonstrated at 12 and 20 s. The heart-to-vasculature intensity ratio at 20 s suggests myocardial uptake. Cancer imaging, currently performed with (18)F-deoxyglucose positron emission tomography (FDG-PET), warrants further investigation, and glucose imaging could be useful in a vast range of clinical conditions and research fields where the radiation associated with the FDG-PET examination limits its use.

Metabolic imaging of multiple X-nucleus resonances

This study describes a technique for fast imaging of x-nuclei metabolites. Due to increased sensitivity and larger chemical shift dispersion at high magnetic fields, images of multiple metabolites can be obtained simultaneously by selective excitation of their resonances with a multifrequency selective radiofrequency pulse at any desired flip angle. This aim is achieved by combining a three-dimensional gradient echo imaging sequence with a Shinnar-LeRoux optimized excitation pulse. A proper choice of bandwidth, imaging matrix size, and field of view allows using the chemical shift dispersion of the different resonances to completely separate their images within one large field of view. The method of fast metabolic imaging is illustrated with (13)C measurements of a phantom containing a solution of (13)C labeled glucose, lactate, and sodium octanoate and by dynamic measurements of the (31)P metabolites phosphocreatine and β-adenosine triphosphate in human femoral muscle in vivo, both at 7T. With dynamic selective (31)P imaging of the larger part of the upper leg, phosphocreatine signal intensity changes of specific muscles can be studied simultaneously by analyzing the sum of phosphocreatine signals within arbitrarily shaped regions of interest following the muscles' contours. This concept of dynamic metabolic imaging can be applied to other organs and further expanded to other MR-detectable nuclei and metabolites.

Insight into the Dynamics of Lanthanide-DTPA Complexes As Revealed by Oxygen-17 NMR

DTPA chelates of various diamagnetic and paramagnetic lanthanide(III) metal ions, as well as the chemically similar DTPA chelate of Y(3+), were studied in aqueous solution by variable temperature (17)O NMR with the aim of characterizing their internal dynamics. As a consequence of poor chemical shift dispersion and fast quadrupole relaxation, no dynamic exchange process could be detected for the diamagnetic complexes nor for the Sm-DTPA complex. In contrast, the spectra recorded for the Eu-DTPA complex show chemical exchange due to the well-known racemization process and, at high temperature, feature signal broadening that reveals a fluxional process involving the interchange of the coordinated and noncoordinated oxygen atoms of the carboxylate groups. The spectra recorded for the Pr-DTPA complex feature coalescence events due to such a fluxional process, which is ascribable to the rotation of the carboxylate groups. The activation free energy barriers determined experimentally are remarkably lower than the calculated activation barriers recently reported for the rotation of the carboxylate groups of various Ln-DOTA complexes. Furthermore, the smallest activation free energy measured for the Pr-DTPA complex, about 45 kJ mol(-1), is significantly lower than the activation free energy characterizing the racemization process. The fluxional behavior of the carboxylate groups is, however, not expected to significantly affect the residence time of the water molecule coordinated to the metal ion.

Selective lighting up of segments around Gly, Ala and Ser/Thr in proteins

Direct detection of (13) C nucleus can be used as a valuable alternative where (1) H detection poses a challenge due to relaxation effects, chemical exchange and poor chemical shift dispersion. In this context, we have designed a suite of 2D (13) C(α) -detected hNCA experiments that provide sequential correlations of (13) C(α) with (15) N on one hand and efficient spectroscopic labeling of certain groups of residues, namely, Gly, Ala, Ser and Thr, on the other. These residues act as checkpoints in the sequential walk, which in turn offer new possibilities of backbone assignment of small proteins from a set of 2D experiments, thereby providing great economy in terms of spectrometer time. The direct identification of peptide segments around Gly, Ala, Ser and Thr residues along a protein chain will be highly valuable for deriving important information on sites of ligand binding, phosphorylation, inhibitor/substrate binding, understanding protein folding pathways, comprehending local conformational dynamics etc. without having to obtain complete sequence-specific assignments, which can be time consuming and at times formidable, especially in large proteins. We have illustratively demonstrated the multifaceted applications of these variants of 2D experiments on ubiquitin and M-crystallin. We foresee that these 2D hNCA experiments will provide economic and efficient strategies for studying the structure and function of proteins.

Dynamic monitoring of carnitine and acetylcarnitine in the trimethylamine signal after exercise in human skeletal muscle by 7T 1H‐MRS

A trimethylamine (TMA) moiety is present in carnitine and acetylcarnitine, and both molecules play critical roles in muscle metabolism. At 7 T, the chemical shift dispersion was sufficient to routinely resolve the TMA signals from carnitine at 3.20 and from acetylcarnitine at 3.17 ppm in the (1)H-MRS (Magnetic Resonance Spectroscopy) of human soleus muscle with a temporal resolution of about 2 min. In healthy, sedentary adults, the concentration of acetylcarnitine increased nearly 10-fold, to 4.1 ± 1.0 mmol/kg, in soleus muscle after 5 min of calf-raise exercise and recovered to a baseline concentration of 0.5 ± 0.3 mmol/kg. While the half-time for decay of acetylcarnitine was the same whether measured from the TMA signal (18.8 ± 5.6 min) or measured from the methyl signal (19.4 ± 6.1 min), the detection of acetylcarnitine by its TMA signal in soleus has the advantage of higher sensitivity and without overlapping from lipid signals. Although the activity of carnitine acetyltransferase is sufficient to allow equilibrium between carnitine and coenzyme-A pools, the exchange in TMA signal between carnitine and acetylcarnitine is slow in soleus following exercise on 7T (1)H-NMR time scale. The TMA signal provides a simple and direct measure of the relative amounts of carnitine and acetylcarnitine.

Asymmetric Mode of Ca2+-S100A4 Interaction with Nonmuscle Myosin IIA Generates Nanomolar Affinity Required for Filament Remodeling

SummaryFilament assembly of nonmuscle myosin IIA (NMIIA) is selectively regulated by the small Ca2+-binding protein, S100A4, which causes enhanced cell migration and metastasis in certain cancers. Our NMR structure shows that an S100A4 dimer binds to a single myosin heavy chain in an asymmetrical configuration. NMIIA in the complex forms a continuous helix that stretches across the surface of S100A4 and engages the Ca2+-dependent binding sites of each subunit in the dimer. Synergy between these sites leads to a very tight association (KD ∼1 nM) that is unique in the S100 family. Single-residue mutations that remove this synergy weaken binding and ameliorate the effects of S100A4 on NMIIA filament assembly and cell spreading in A431 human epithelial carcinoma cells. We propose a model for NMIIA filament disassembly by S100A4 in which initial binding to the unstructured NMIIA tail initiates unzipping of the coiled coil and disruption of filament packing.

Efficient acquisition of high-resolution 4-D diagonal-suppressed methyl–methyl NOESY for large proteins

The methyl–methyl NOESY experiment plays an important role in determining the global folds of large proteins. Despite the high sensitivity of this experiment, the analysis of methyl–methyl NOEs is frequently hindered by the limited chemical shift dispersion of methyl groups, particularly methyl protons. This makes it difficult to unambiguously assign all of the methyl–methyl NOE crosspeaks using 3-D spectroscopy. The recent development of sparse sampling methods enables highly efficient acquisition of high-resolution 4-D spectra, which provides an excellent solution to resolving the degeneracy of methyl signals. However, many reconstruction algorithms for processing sparsely-sampled NMR data do not provide adequate suppression of aliasing artifacts in the presence of strong NOE diagonal signals. In order to overcome this limitation, we present a 4-D diagonal-suppressed methyl–methyl NOESY experiment specifically optimized for ultrasparse sampling and evaluate it using a deuterated, ILV methyl-protonated sample of the 42kDa Escherichia coli maltose binding protein (MBP). Suppression of diagonal signals removes the dynamic range barrier of the methyl–methyl NOESY experiment such that residual aliasing artifacts in the CLEAN-reconstructed high-resolution 4-D spectrum can be further reduced. At an ultrasparse sampling rate of less than 1%, we were able to identify and unambiguously assign the vast majority of expected NOE crosspeaks between methyl groups separated by less than 5Å and to detect very weak NOE crosspeaks from methyl groups that are over 7Å apart.

Structural Analysis of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Intracellular Domain Reveals a Conserved Interaction Epitope

Plasmodium falciparum-infected red blood cells adhere to endothelial cells, thereby obstructing the microvasculature. Erythrocyte adherence is directly associated with severe malaria and increased disease lethality, and it is mediated by the PfEMP1 family. PfEMP1 clustering in knob-like protrusions on the erythrocyte membrane is critical for cytoadherence, however the molecular mechanisms behind this system remain elusive. Here, we show that the intracellular domains of the PfEMP1 family (ATS) share a unique molecular architecture, which comprises a minimal folded core and extensive flexible elements. A conserved flexible segment at the ATS center is minimally restrained by the folded core. Yeast-two-hybrid data and a novel sequence analysis method suggest that this central segment contains a conserved protein interaction epitope. Interestingly, ATS in solution fails to bind the parasite knob-associated histidine-rich protein (KAHRP), an essential cytoadherence component. Instead, we demonstrate that ATS associates with PFI1780w, a member of the Plasmodium helical interspersed sub-telomeric (PHIST) family. PHIST domains are widespread in exported parasite proteins, however this is the first specific molecular function assigned to any variant of this family. We propose that PHIST domains facilitate protein interactions, and that the conserved ATS epitope may be targeted to disrupt the parasite cytoadherence system.

A solid-state NMR study of C70: A model molecule for amorphous carbons

We show that natural abundance, solid-state MAS-NMR 13C INADEQUATE spectra can be recorded for crystallized C70, using the through-bond J-coupling for the magnetization transfer. The effect of strong J-coupling can be lessened at high magnetic fields, allowing the observation of cross-peaks between close resonances. DFT calculations of the chemical shifts show an excellent agreement with the experimental values. A correlation is observed between the average CCC bond angles and the 13C chemical shift, offering a way to understand the dispersion of 13C chemical shifts in nanoporous activated carbons in terms of local deviations from planarity.

Deuteration of a molecular probe for DNP hyperpolarization – a new approach and validation for choline chloride

The promising dynamic nuclear polarization (DNP) for hyperpolarized (13)C-MRI/MRS of real-time metabolism in vivo is challenged by the limited number of agents with the required physical and biological properties. The physical requirement of a liquid-state T(1) of tens of seconds is mostly found for (13)C-carbons in small molecules that have no direct protons attached, i.e. carbonyl, carboxyl and certain quaternary carbons. Unfortunately, such carbon positions do not exist in a large number of metabolic agents, and chemical shift dispersion often limits detection of their chemical evolution. We have previously shown that direct deuteration of protonated carbon positions significantly prolongs the (13)C T(1) in the liquid state and provides potential (13)C-labeled agents with differential chemical shift with respect to metabolism. The Choline Molecular Probe [1,1,2,2-D(4), 2-(13)C]choline chloride (CMP2) has recently been introduced as a means of studying choline metabolism in a hyperpolarized state. Here, the biophysical properties of CMP2 were characterized and compared with those of [1-(13)C]pyruvate to evaluate the impact of molecular probe deuteration. The CMP2 solid-state polarization build-up time constant (30 min) and polarization level (24%) were comparable to those of [1-(13)C]pyruvate. Both compounds' liquid state T(1) increased with temperature. The high-field T(1) of CMP2 compared favorably with [1-(13)C]pyruvate. Thus, a deuterated agent demonstrated physical properties comparable to a hyperpolarized compound of already proven value, whereas both showed chemical shift dispersion that allowed monitoring of their metabolism. It is expected that the use of deuterated carbon-13 positions as reporting hyperpolarized nuclei will substantially expand the library of agents for DNP-MR.