Chemical Shift Differences Research Articles

Backbone resonance assignments of monomeric SOD1 in dilute and crowded environments

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to movement disorders. In motor neurons of ALS patients, intracellular aggregates of superoxide dismutase 1 (SOD1) have often been observed. To elucidate the aggregation mechanism, it is important to analyze the folding equilibrium of SOD1 between folded and aggregation-prone unfolded states. However, in most cases, this folding equilibrium has been studied in dilute solution even though the aggregate formation occurs in a highly crowded intracellular environment. Indeed, a recent study reported that the folding stability of SOD1 decreased in an environment containing protein crowder molecules. To understand such a destabilization effect due to protein crowders, it is necessary to obtain more precise structural information on SOD1 in the presence of protein crowders. Here, we report the 1H, 13C, and 15N backbone resonance assignments of monomeric SOD1 in the absence and presence of the protein crowder lysozyme. The chemical shift differences caused by addition of lysozyme suggest that SOD1 associated with lysozyme via negatively charged surfaces. Based on the assigned chemical shifts, the presence of lysozyme has a limited influence on the secondary structure of SOD1. We anticipate that our assignments will provide an important basis for elucidation of the crowding-induced folding destabilization of SOD1.

Structure and absolute configuration of hydroxy-bis-dihydrofarinosin from Encelia farinosa.

The structure of the dimeric eudesmanolide hydroxy-bis-dihydrofarinosin (1) from Encelia farinosa followed after contrasting their 1 H and 13 C NMR spectra with those of encelin (6), hydroxy-bis-dihydroencelin (3), and farinosin (4). Structure1 was verified by single-crystal X-ray diffraction analysis, which further provided the stereochemistry of the hydroxy group at C-4. Comparison of the experimental vibrational circular dichroism spectrum of its derived diacetate 2 with that calculated by density functional theory provided the absolute configuration, which resulted the same as that of its biogenetic precursor 4. Evaluation of several chemical shift differences between the two eudesmanolide fragments of 1 and 3 allows also ascertaining the yet not reported absolute configuration of the C-4 stereogenic center of 3. Copyright © 2016 John Wiley & Sons, Ltd.

“Molecular” MR imaging at high fields

Magnetic resonance imaging (MRI) and spectroscopy (MRS) have contributed considerably to clinical radiology, and a variety of MR techniques have been developed to evaluate pathological processes as well as normal tissue biology at the cellular and molecular level. However, in comparison to nuclear imaging, MRI has relatively poor sensitivity for detecting true molecular changes or for detecting the presence of targeted contrast agents, though these remain under active development. In recent years very high field (7T and above) MRI systems have been developed for human studies and these provide new opportunities and technical challenges for molecular imaging. We identify 5 types of intrinsic contrast mechanisms that do not require the use of exogenous agents but which can provide molecular and cellular information. We can derive information on tissue composition by (i) imaging different nuclei, especially sodium (ii) exploiting chemical shift differences as in MRS (iii) exploiting specific relaxation mechanisms (iv) exploiting tissue differences in the exchange rates of molecular species such as amides or hydroxyls and (v) differences in susceptibility. The increased signal strength at higher fields enables higher resolution images to be acquired, along with increased sensitivity to detecting subtle effects caused by molecular changes in tissues.

Ionization of Cellobiose in Aqueous Alkali and the Mechanism of Cellulose Dissolution.

Cellulose, one of the most abundant renewable resources, is insoluble in most common solvents but dissolves in aqueous alkali under a narrow range of conditions. To elucidate the solubilization mechanism, we performed electrophoretic NMR on cellobiose, a subunit of cellulose, showing that cellobiose acts as an acid with two dissociation steps at pH 12 and 13.5. Chemical shift differences between cellobiose in NaOH and NaCl were estimated using 2D NMR and compared to DFT shift differences upon deprotonation. The dissociation steps are the deprotonation of the hemiacetal OH group and the deprotonation of one of four OH groups on the nonreducing anhydroglucose unit. MD simulations reveal that aggregation is suppressed upon charging cellulose chains in solution. Our findings strongly suggest that cellulose is to a large extent charged in concentrated aqueous alkali, a seemingly crucial factor for solubilization. This insight, overlooked in the current literature, is important for understanding cellulose dissolution and for synthesis of new sustainable materials.

Accelerating proton spin diffusion in perdeuterated proteins at 100kHz MAS.

Fast magic-angle spinning (>60kHz) has many advantages but makes spin-diffusion-type proton-proton long-range polarization transfer inefficient and highly dependent on chemical-shift offset. Using 100%-HN-[2H,13C,15N]-ubiquitin as a model substance, we quantify the influence of the chemical-shift difference on the spin diffusion between proton spins and compare two experiments which lead to an improved chemical-shift compensation of the transfer: rotating-frame spin diffusion and a new experiment, reverse amplitude-modulated MIRROR. Both approaches enable broadband spin diffusion, but the application of the first variant is limited due to fast spin relaxation in the rotating frame. The reverse MIRROR experiment, in contrast, is a promising candidate for the determination of structurally relevant distance restraints. The applied tailored rf-irradiation schemes allow full control over the range of recoupled chemical shifts and efficiently drive spin diffusion. Here, the relevant relaxation time is the larger longitudinal relaxation time, which leads to a higher signal-to-noise ratio in the spectra.

Low-bandwidth space/frequency component separation for quantitative imaging.

Quantitative MRI is often used to analyse multicomponent systems. The analysis requires the contributions from different species to be isolated. Species with distinct chemical shifts can be separated by using a low acquisition bandwidth, which is easy to achieve in common quantitative imaging protocols. The bandwidth reduction leads to separation of NMR contributions from different species in the image space. This new method was implemented and tested on two multicomponent systems containing several spectrally and spatially unresolved components with both distinctly different and similar diffusion coefficients and relaxation times. Separation was achieved with routine MRI diffusion and relaxation measurement pulse sequences in a microimaging environment for water/polyethylene glycol solution and for chloroform/TMS/polyethylene glycol solution. Conventional monoexponential fitting was used to determine diffusion coefficients and relaxation times from the spectrally separated data, whereas biexponential or triexponential fitting was required in the unseparated reference experiments. In the two-component sample, the variation in the determined fast diffusing components was on the same order of magnitude for all experiments, while the variation in the slow diffusing polyethylene glycol was larger when no separation was present. The separation technique provided lower variability for all the determined diffusion coefficients and relaxation times in the three-component sample. The low-bandwidth separation method can provide separation of multicomponent systems based on the chemical shift difference between the species. The accuracy of the technique is comparable with the commonly used methods for bicomponent system analysis and surpasses those when there are more than two components in the sample. Copyright © 2016 John Wiley & Sons, Ltd.

Recent developments in muscle imaging of neuromuscular disorders

In this update, we describe recent findings on imaging techniques used for the analysis and quantification of affected muscles, advances in pattern recognition, and quantitative muscle imaging in clinical studies. Whole-body muscle MRI and meta-analytical approaches, so-called (hierarchical) heat maps of affected muscles are promising advances compared with commonly applied lower leg pattern recognition approaches. Muscle fat fraction assessments measuring chemical shift differences and T2-relaxation times of separated fat and water components in skeletal muscle are currently the most reliable quantitative muscle imaging techniques. Quantitative muscle MRI detects subclinical disease progression in muscular dystrophies and is a powerful surrogate outcome measure in clinical trials. Diagnostic and quantitative muscular imaging techniques are increasingly important for diagnostic workup and for interventional studies in patients with inherited myopathies.

Molecular Determinants of Tubulin's C-Terminal Tail Conformational Ensemble.

Tubulin is important for a wide variety of cellular processes including cell division, ciliogenesis, and intracellular trafficking. To perform these diverse functions, tubulin is regulated by post-translational modifications (PTM), primarily at the C-terminal tails of both the α- and β-tubulin heterodimer subunits. The tubulin C-terminal tails are disordered segments that are predicted to extend from the ordered tubulin body and may regulate both intrinsic properties of microtubules and the binding of microtubule associated proteins (MAP). It is not understood how either interactions with the ordered tubulin body or PTM affect tubulin's C-terminal tails. To probe these questions, we developed a method to isotopically label tubulin for C-terminal tail structural studies by NMR. The conformational changes of the tubulin tails as a result of both proximity to the ordered tubulin body and modification by mono- and polyglycine PTM were determined. The C-terminal tails of the tubulin dimer are fully disordered and, in contrast with prior simulation predictions, exhibit a propensity for β-sheet conformations. The C-terminal tails display significant chemical shift differences as compared to isolated peptides of the same sequence, indicating that the tubulin C-terminal tails interact with the ordered tubulin body. Although mono- and polyglycylation affect the chemical shift of adjacent residues, the conformation of the C-terminal tail appears insensitive to the length of polyglycine chains. Our studies provide important insights into how the essential disordered domains of tubulin function.

Long-lived nuclear spin states in rapidly rotating CH2D groups

Although monodeuterated methyl groups support proton long-lived states, hindering of the methyl rotation limits the singlet relaxation time. We demonstrate an experimental case in which the rapid rotation of the CH2D group extends the singlet lifetime but does not quench the chemical shift difference between the CH2D protons, induced by the chiral environment. Proton singlet order is accessed using Spin-Lock Induced Crossing (SLIC) experiments, showing that the singlet relaxation time TS is over 2min, exceeding the longitudinal relaxation time T1 by a factor of more than 10. This result shows that proton singlet states may be accessible and long-lived in rapidly rotating CH2D groups.

Reaction monitoring using hyperpolarized NMR with scaling of heteronuclear couplings by optimal tracking

Off-resonance decoupling using the method of Scaling of Heteronuclear Couplings by Optimal Tracking (SHOT) enables determination of heteronuclear correlations of chemical shifts in single scan NMR spectra. Through modulation of J-coupling evolution by shaped radio frequency pulses, off resonance decoupling using SHOT pulses causes a user-defined dependence of the observed J-splitting, such as the splitting of 13C peaks, on the chemical shift offset of coupled nuclei, such as 1H. Because a decoupling experiment requires only a single scan, this method is suitable for characterizing on-going chemical reactions using hyperpolarization by dissolution dynamic nuclear polarization (D-DNP). We demonstrate the calculation of [13C, 1H] chemical shift correlations of the carbanionic active sites from hyperpolarized styrene polymerized using sodium naphthalene as an initiator. While off resonance decoupling by SHOT pulses does not enhance the resolution in the same way as a 2D NMR spectrum would, the ability to obtain the correlations in single scans makes this method ideal for determination of chemical shifts in on-going reactions on the second time scale. In addition, we present a novel SHOT pulse that allows to scale J-splittings 50% larger than the respective J-coupling constant. This feature can be used to enhance the resolution of the indirectly detected chemical shift and reduce peak overlap, as demonstrated in a model reaction between p-anisaldehyde and isobutylamine. For both pulses, the accuracy is evaluated under changing signal-to-noise ratios (SNR) of the peaks from reactants and reaction products, with an overall standard deviation of chemical shift differences compared to reference spectra of 0.02ppm when measured on a 400MHz NMR spectrometer. Notably, the appearance of decoupling side-bands, which scale with peak intensity, appears to be of secondary importance.

Helical Conformation in the CA-SP1 Junction of the Immature HIV-1 Lattice Determined from Solid-State NMR of Virus-like Particles.

Maturation of HIV-1 requires disassembly of the Gag polyprotein lattice, which lines the viral membrane in the immature state, and subsequent assembly of the mature capsid protein lattice, which encloses viral RNA in the mature state. Metastability of the immature lattice has been proposed to depend on the existence of a structurally ordered, α-helical segment spanning the junction between capsid (CA) and spacer peptide 1 (SP1) subunits of Gag, a segment that is dynamically disordered in the mature capsid lattice. We report solid state nuclear magnetic resonance (ssNMR) measurements on the immature lattice in noncrystalline, spherical virus-like particles (VLPs) derived from Gag. The ssNMR data provide definitive evidence for this critical α-helical segment in the VLPs. Differences in ssNMR chemical shifts and signal intensities between immature and mature lattice assemblies also support a major rearrangement of intermolecular interactions in the maturation process, consistent with recent models from electron cryomicroscopy and X-ray crystallography.

Quantitative produced water analysis using mobile 1H NMR

Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1–30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

13C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)

Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14-Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D (13)C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically (13)C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14-Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m c14 and m c38). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 α-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for (13)C relaxation dispersion experiments was obtained through the carbon line-shape profile. With respect to the m c38 isomerization, the (1)H-(13)C signals at the β-position of the minor state were resolved from the major peaks and detected by exchange experiments at a low temperature.

MRS of pilocytic astrocytoma: The peak at 2 ppm may not be NAA.

To determine whether the chemical shift of residual N-acetylaspartate (NAA) signal in pilocytic astrocytomas (PA) is consistent with the position of the NAA peak in controls. MR spectra from 27 pediatric World Health Organization (WHO) grade I pilocytic astrocytoma patients, fifteen patients with WHO grade II and high-grade (III-IV) astrocytomas, and 36 controls were analyzed. All spectra were acquired with a short echo time (35 ms), single voxel point-resolved spectroscopy sequence on clinical 3 tesla scanners. Fully automated LCModel software was used for processing, which included the fitting of peak positions for NAA and creatine (Cr). The chemical shift difference between the NAA and Cr peaks was significantly smaller (by 0.016 ± 0.005 parts per million, P < 1e-10) in PAs than in controls and was also smaller than what was observed in infiltrative astrocytomas. The chemical shift position of the residual NAA peak in PAs is not consistent with NAA. The signal likely originates from an N-acetyl group of one or more other chemicals such as N-acetylated sugars. Magn Reson Med 78:452-456, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Total synthesis, structural, and biological evaluation of stylissatin A and related analogs

The natural product cyclic peptide stylissatin A (1a) was reported to inhibit nitric oxide production in LPS-stimulated murine macrophage RAW 264.7 cells. In the current study, solid-phase total synthesis of stylissatin A was performed by using a safety-catch linker and yielded the peptide with a trans-Phe(7) -Pro(6) linkage, whereas the natural product is the cis rotamer at this position as evidenced by a marked difference in NMR chemical shifts. In order to preclude the possibility of 1b being an epimer of the natural product, we repeated the synthesis using d-allo-Ile in place of l-Ile and a different site for macrocyclization. The resulting product (d-allo-Ile(2) )-stylissatin A (1c) was also found to have the trans-Phe(7) -Pro(6) peptide conformations like rotamer 1b. Applying the second route to the synthesis of stylissatin A itself, we obtained stylissatin A natural rotamer 1a accompanied by rotamer 1b as the major product. Rotamers 1a, 1b, and the epimer 1c were separable by HPLC, and 1a was found to match the natural product in structure and biological activity. Six related analogs 2-7 of stylissatin A were synthesized on Wang resin and characterized by spectral analysis. The natural product (1a), the rotamer (1b), and (d-allo-Ile(2) )-stylissatin A (1c) exhibited significant inhibition of NO(.) . Further investigations were focused on 1b, which also inhibited proliferation of T-cells and inflammatory cytokine IL-2 production. The analogs 2-7 weakly inhibited NO(.) production, but strongly inhibited IL-2 cytokine production compared with synthetic peptide 1b. All analogs inhibited the proliferation of T-cells, with analog 7 having the strongest effect. In the analogs, the Pro(6) residue was replaced by Glu/Ala, and the SAR indicates that the nature of this residue plays a role in the biological function of these peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400–500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU.

An Approach for Determining the Absolute Configuration of C-2 in 2-Oxygenated Phenylethanoid Glycosides by (1)H NMR Spectroscopy.

The absolute configurations of 2-oxygenated phenylethanoid glycosides were conveniently determined by (1)H NMR spectroscopy. A comparison of the chemical shift differences (Δδ) of the diastereotopic methylene protons (H-1) demonstrate that a large chemical shift difference corresponds to an R configuration and a small chemical shift difference indicates S for the 2-alkoxy form. However, the situation is contrary to that of the 2-hydroxy form. Furthermore, the mechanism underlying this result is discussed based on the visualized conformations of such compounds.

Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the 13Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

Mapping the interactions and bioactivity of quercetin⿿(2-hydroxypropyl)-β-cyclodextrin complex

Natural products have served as a rich source for drug discovery and development. In the last decade their fruitful integration in the drug discovery pipeline declined due to their reduced bioavailability, mainly attributed to their poor aqueous solubility. We synthesized a quercetin (QUE)⿿(2-hydroxypropyl)-β-cyclodextrin (HP-β-CD) complex that enabled amplification of its solubility and in the same time retained its bioactivity in T24 human bladder cancer cell line. The stability of the complex and the molecular basis of the interactions developed in this host-guest complex were assayed by incorporating an array of analytical techniques and Molecular Dynamics (MD) experiments. 2D DOSY NMR experiment revealed that the diffusion coefficient of free HP-β-CD was 3.55ÿ10⿿10m2s⿿1 while that of QUE⿿HP-β-CD inclusion complex 3.09ÿ10⿿10m2s⿿1, indicating the formation of a complex. Solid and liquid high resolution NMR spectroscopy data showed that the most pronounced differences in chemical shifts at carbons and protons correspondingly during complexation occur in the aromatic ring ο (bearing the two phenolic hydroxyl groups meta to each other). The chemical shift differences in the aromatic ring ο (bearing the two phenolic hydroxyl groups ortho to each other) were less pronounced. The MD results confirmed the experimental data.

ChemInform Abstract: Chiral Derivatizing Agents, Macrocycles, Metal Complexes, and Liquid Crystals for Enantiomer Differentiation in NMR Spectroscopy

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