Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-09-02

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

Non-invasive analysis of swelling in polymer dispersions by means of time-domain(TD)-NMR.

PubMed

Nestle, Nikolaus; Häberle, Karl

2009-11-03

In this contribution, we discuss the potential of low-field time-domain(TD)-NMR to study the swelling of (aqueous) polymer dispersions by a volatile solvent. Due to the sensitivity of transverse relaxation times (T2) to swelling-induced changes in the molecular dynamics of the polymer component, the effects of swelling can be measured without spectral resolution. The measurement is performed on polymer dispersions in native state with solids contents around 50% in a non-invasive way without separating the polymeric phase and the water phase from each other. Using acetone in two polyurethane (PU) dispersions with different hard phase contents, we explore the sensitivity of the method and present a data evaluation strategy based on multicomponent fitting and proton balancing. Furthermore, we report exchange continualization as a further effect that needs to be taken into account for correct interpretation of the data.

Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell

PubMed Central

Charlier, Cyril; Alderson, T. Reid; Courtney, Joseph M.; Ying, Jinfa; Anfinrud, Philip

2018-01-01

In general, small proteins rapidly fold on the timescale of milliseconds or less. For proteins with a substantial volume difference between the folded and unfolded states, their thermodynamic equilibrium can be altered by varying the hydrostatic pressure. Using a pressure-sensitized mutant of ubiquitin, we demonstrate that rapidly switching the pressure within an NMR sample cell enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions. This approach makes it possible to record 2D and 3D NMR spectra of the unfolded protein at atmospheric pressure, providing residue-specific information on the folding process. 15N and 13C chemical shifts measured immediately after dropping the pressure from 2.5 kbar (favoring unfolding) to 1 bar (native) are close to the random-coil chemical shifts observed for a large, disordered peptide fragment of the protein. However, 15N relaxation data show evidence for rapid exchange, on a ∼100-μs timescale, between the unfolded state and unstable, structured states that can be considered as failed folding events. The NMR data also provide direct evidence for parallel folding pathways, with approximately one-half of the protein molecules efficiently folding through an on-pathway kinetic intermediate, whereas the other half fold in a single step. At protein concentrations above ∼300 μM, oligomeric off-pathway intermediates compete with folding of the native state. PMID:29666248

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

PubMed

Chen, Jianhan; Im, Wonpil; Brooks, Charles L

2004-12-15

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.

Achievement of a 920-MHz High Resolution NMR

NASA Astrophysics Data System (ADS)

Hashi, Kenjiro; Shimizu, Tadashi; Goto, Atsushi; Kiyoshi, Tsukasa; Matsumoto, Shinji; Wada, Hitoshi; Fujito, Teruaki; Hasegawa, Ken-ichi; Yoshikawa, Masatoshi; Miki, Takashi; Ito, Satoshi; Hamada, Mamoru; Hayashi, Seiji

2002-06-01

We have developed a 920-MHz NMR system and performed the proton NMR measurement of H 2O and ethylbenzene using the superconducting magnet operating at 21.6 T (920 MHz for proton), which is the highest field produced by a superconducting NMR magnet in the persistent mode. From the NMR measurements, it is verified that both homogeneity and stability of the magnet have a specification sufficient for a high resolution NMR.

High-resolution magnetic resonance spectroscopy using a solid-state spin sensor

NASA Astrophysics Data System (ADS)

Glenn, David R.; Bucher, Dominik B.; Lee, Junghyun; Lukin, Mikhail D.; Park, Hongkun; Walsworth, Ronald L.

2018-03-01

Quantum systems that consist of solid-state electronic spins can be sensitive detectors of nuclear magnetic resonance (NMR) signals, particularly from very small samples. For example, nitrogen–vacancy centres in diamond have been used to record NMR signals from nanometre-scale samples, with sensitivity sufficient to detect the magnetic field produced by a single protein. However, the best reported spectral resolution for NMR of molecules using nitrogen–vacancy centres is about 100 hertz. This is insufficient to resolve the key spectral identifiers of molecular structure that are critical to NMR applications in chemistry, structural biology and materials research, such as scalar couplings (which require a resolution of less than ten hertz) and small chemical shifts (which require a resolution of around one part per million of the nuclear Larmor frequency). Conventional, inductively detected NMR can provide the necessary high spectral resolution, but its limited sensitivity typically requires millimetre-scale samples, precluding applications that involve smaller samples, such as picolitre-volume chemical analysis or correlated optical and NMR microscopy. Here we demonstrate a measurement technique that uses a solid-state spin sensor (a magnetometer) consisting of an ensemble of nitrogen–vacancy centres in combination with a narrowband synchronized readout protocol to obtain NMR spectral resolution of about one hertz. We use this technique to observe NMR scalar couplings in a micrometre-scale sample volume of approximately ten picolitres. We also use the ensemble of nitrogen–vacancy centres to apply NMR to thermally polarized nuclear spins and resolve chemical-shift spectra from small molecules. Our technique enables analytical NMR spectroscopy at the scale of single cells.

Micromixer-based time-resolved NMR: applications to ubiquitin protein conformation.

PubMed

Kakuta, Masaya; Jayawickrama, Dimuthu A; Wolters, Andrew M; Manz, Andreas; Sweedler, Jonathan V

2003-02-15

Time-resolved NMR spectroscopy is used to studychanges in protein conformation based on the elapsed time after a change in the solvent composition of a protein solution. The use of a micromixer and a continuous-flow method is described where the contents of two capillary flows are mixed rapidly, and then the NMR spectra of the combined flow are recorded at precise time points. The distance after mixing the two fluids and flow rates define the solvent-protein interaction time; this method allows the measurement of NMR spectra at precise mixing time points independent of spectral acquisition time. Integration of a micromixer and a microcoil NMR probe enables low-microliter volumes to be used without losing significant sensitivity in the NMR measurement. Ubiquitin, the model compound, changes its conformation from native to A-state at low pH and in 40% or higher methanol/water solvents. Proton NMR resonances of the His-68 and the Tyr-59 of ubiquitin are used to probe the conformational changes. Mixing ubiquitin and methanol solutions under low pH at microliter per minute flow rates yields both native and A-states. As the flow rate decreases, yielding longer reaction times, the population of the A-state increases. The micromixer-NMR system can probe reaction kinetics on a time scale of seconds.

High resolution NMR measurements using a 400MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR.

PubMed

Piao, R; Iguchi, S; Hamada, M; Matsumoto, S; Suematsu, H; Saito, A T; Li, J; Nakagome, H; Takao, T; Takahashi, M; Maeda, H; Yanagisawa, Y

2016-02-01

Use of high-temperature superconducting (HTS) inner coils in combination with conventional low-temperature superconducting (LTS) outer coils for an NMR magnet, i.e. a LTS/HTS NMR magnet, is a suitable option to realize a high-resolution NMR spectrometer with operating frequency >1GHz. From the standpoint of creating a compact magnet, (RE: Rare earth) Ba2Cu3O7-x (REBCO) HTS inner coils which can tolerate a strong hoop stress caused by a Lorentz force are preferred. However, in our previous work on a first-generation 400MHz LTS/REBCO NMR magnet, the NMR resolution and sensitivity were about ten times worse than that of a conventional LTS NMR magnet. The result was caused by a large field inhomogeneity in the REBCO coil itself and the shielding effect of a screening current induced in that coil. In the present paper, we describe the operation of a modified 400MHz LTS/REBCO NMR magnet with an advanced field compensation technology using a combination of novel ferromagnetic shimming and an appropriate procedure for NMR spectrum line shape optimization. We succeeded in obtaining a good NMR line shape and 2D NOESY spectrum for a lysozyme aqueous sample. We believe that this technology is indispensable for the realization of a compact super-high-field high-resolution NMR. Copyright © 2016 Elsevier Inc. All rights reserved.

NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer.

PubMed

Bocian, Wojciech; Borowicz, Piotr; Mikołajczyk, Jerzy; Sitkowski, Jerzy; Tarnowska, Anna; Bednarek, Elzbieta; Głabski, Tadeusz; Tejchman-Małecka, Bozena; Bogiel, Monika; Kozerski, Lech

2008-10-01

A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. (c) 2008 Wiley Periodicals, Inc.

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

Development of a superconducting bulk magnet for NMR and MRI.

PubMed

Nakamura, Takashi; Tamada, Daiki; Yanagi, Yousuke; Itoh, Yoshitaka; Nemoto, Takahiro; Utumi, Hiroaki; Kose, Katsumi

2015-10-01

A superconducting bulk magnet composed of six vertically stacked annular single-domain c-axis-oriented Eu-Ba-Cu-O crystals was energized to 4.74 T using a conventional superconducting magnet for high-resolution NMR spectroscopy. Shim coils, gradient coils, and radio frequency coils for high resolution NMR and MRI were installed in the 23 mm-diameter room-temperature bore of the bulk magnet. A 6.9 ppm peak-to-peak homogeneous region suitable for MRI was achieved in the central cylindrical region (6.2 mm diameter, 9.1 mm length) of the bulk magnet by using a single layer shim coil. A 21 Hz spectral resolution that can be used for high resolution NMR spectroscopy was obtained in the central cylindrical region (1.3 mm diameter, 4 mm length) of the bulk magnet by using a multichannel shim coil. A clear 3D MR image dataset of a chemically fixed mouse fetus with (50 μm)(3) voxel resolution was obtained in 5.5 h. We therefore concluded that the cryogen-free superconducting bulk magnet developed in this study is useful for high-resolution desktop NMR, MRI and mobile NMR device. Copyright © 2015 Elsevier Inc. All rights reserved.

Denaturant-Dependent Conformational Changes in a [beta]-Trefoil Protein: Global and Residue-Specific Aspects of an Equilibrium Denaturation Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Latypov, Ramil F.; Liu, Dingjiang; Jacob, Jaby

2010-01-12

Conformational properties of the folded and unfolded ensembles of human interleukin-1 receptor antagonist (IL-1ra) are strongly denaturant-dependent as evidenced by high-resolution two-dimensional nuclear magnetic resonance (NMR), limited proteolysis, and small-angle X-ray scattering (SAXS). The folded ensemble was characterized in detail in the presence of different urea concentrations by 1H-15N HSQC NMR. The {beta}-trefoil fold characteristic of native IL-1ra was preserved until the unfolding transition region beginning at 4 M urea. At the same time, a subset of native resonances disappeared gradually starting at low denaturant concentrations, indicating noncooperative changes in the folded state. Additional evidence of structural perturbations came frommore » the chemical shift analysis, nonuniform and bell-shaped peak intensity profiles, and limited proteolysis. In particular, the following nearby regions of the tertiary structure became progressively destabilized with increasing urea concentrations: the {beta}-hairpin interface of trefoils 1 and 2 and the H2a-H2 helical region. These regions underwent small-scale perturbations within the native baseline region in the absence of populated molten globule-like states. Similar regions were affected by elevated temperatures known to induce irreversible aggregation of IL-1ra. Further evidence of structural transitions invoking near-native conformations came from an optical spectroscopy analysis of its single-tryptophan variant W17A. The increase in the radius of gyration was associated with a single equilibrium unfolding transition in the case of two different denaturants, urea and guanidine hydrochloride (GuHCl). However, the compactness of urea- and GuHCl-unfolded molecules was comparable only at high denaturant concentrations and deviated under less denaturing conditions. Our results identified the role of conformational flexibility in IL-1ra aggregation and shed light on the nature of structural transitions within the folded ensembles of other {beta}-trefoil proteins, such as IL-1{beta} and hFGF-1.« less

Enhancing the resolution of 1H and 13C solid-state NMR spectra by reduction of anisotropic bulk magnetic susceptibility broadening.

PubMed

Hanrahan, Michael P; Venkatesh, Amrit; Carnahan, Scott L; Calahan, Julie L; Lubach, Joseph W; Munson, Eric J; Rossini, Aaron J

2017-10-25

We demonstrate that natural isotopic abundance 2D heteronuclear correlation (HETCOR) solid-state NMR spectra can be used to significantly reduce or eliminate the broadening of 1 H and 13 C solid-state NMR spectra of organic solids due to anisotropic bulk magnetic susceptibility (ABMS). ABMS often manifests in solids with aromatic groups, such as active pharmaceutical ingredients (APIs), and inhomogeneously broadens the NMR peaks of all nuclei in the sample. Inhomogeneous peaks with full widths at half maximum (FWHM) of ∼1 ppm typically result from ABMS broadening and the low spectral resolution impedes the analysis of solid-state NMR spectra. ABMS broadening of solid-state NMR spectra has previously been eliminated using 2D multiple-quantum correlation experiments, or by performing NMR experiments on diluted materials or single crystals. However, these experiments are often infeasible due to their poor sensitivity and/or provide limited gains in resolution. 2D 1 H- 13 C HETCOR experiments have previously been applied to reduce susceptibility broadening in paramagnetic solids and we show that this strategy can significantly reduce ABMS broadening in diamagnetic organic solids. Comparisons of 1D solid-state NMR spectra and 1 H and 13 C solid-state NMR spectra obtained from 2D 1 H- 13 C HETCOR NMR spectra show that the HETCOR spectrum directly increases resolution by a factor of 1.5 to 8. The direct gain in resolution is determined by the ratio of the inhomogeneous 13 C/ 1 H linewidth to the homogeneous 1 H linewidth, with the former depending on the magnitude of the ABMS broadening and the strength of the applied field and the latter on the efficiency of homonuclear decoupling. The direct gains in resolution obtained using the 2D HETCOR experiments are better than that obtained by dilution. For solids with long proton longitudinal relaxation times, dynamic nuclear polarization (DNP) was applied to enhance sensitivity and enable the acquisition of 2D 1 H- 13 C HETCOR NMR spectra. 2D 1 H- 13 C HETCOR experiments were applied to resolve and partially assign the NMR signals of the form I and form II polymorphs of aspirin in a sample containing both forms. These findings have important implications for ultra-high field NMR experiments, optimization of decoupling schemes and assessment of the fundamental limits on the resolution of solid-state NMR spectra.

High resolution NMR imaging using a high field yokeless permanent magnet.

PubMed

Kose, Katsumi; Haishi, Tomoyuki

2011-01-01

We measured the homogeneity and stability of the magnetic field of a high field (about 1.04 tesla) yokeless permanent magnet with 40-mm gap for high resolution nuclear magnetic resonance (NMR) imaging. Homogeneity was evaluated using a 3-dimensional (3D) lattice phantom and 3D spin-echo imaging sequences. In the central sphere (20-mm diameter), peak-to-peak magnetic field inhomogeneity was about 60 ppm, and the root-mean-square was 8 ppm. We measured room temperature, magnet temperature, and NMR frequency of the magnet simultaneously every minute for about 68 hours with and without the thermal insulator of the magnet. A simple mathematical model described the magnet's thermal property. Based on magnet performance, we performed high resolution (up to [20 µm](2)) imaging with internal NMR lock sequences of several biological samples. Our results demonstrated the usefulness of the high field small yokeless permanent magnet for high resolution NMR imaging.

Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls.

PubMed

Wang, Tuo; Hong, Mei

2016-01-01

Until recently, the 3D architecture of plant cell walls was poorly understood due to the lack of high-resolution techniques for characterizing the molecular structure, dynamics, and intermolecular interactions of the wall polysaccharides in these insoluble biomolecular mixtures. We introduced multidimensional solid-state NMR (SSNMR) spectroscopy, coupled with (13)C labelling of whole plants, to determine the spatial arrangements of macromolecules in near-native plant cell walls. Here we review key evidence from 2D and 3D correlation NMR spectra that show relatively few cellulose-hemicellulose cross peaks but many cellulose-pectin cross peaks, indicating that cellulose microfibrils are not extensively coated by hemicellulose and all three major polysaccharides exist in a single network rather than two separate networks as previously proposed. The number of glucan chains in the primary-wall cellulose microfibrils has been under active debate recently. We show detailed analysis of quantitative (13)C SSNMR spectra of cellulose in various wild-type (WT) and mutant Arabidopsis and Brachypodium primary cell walls, which consistently indicate that primary-wall cellulose microfibrils contain at least 24 glucan chains. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

Overview of the development of high-resolution 920 MHz NMR in NIMS

NASA Astrophysics Data System (ADS)

Shimizu, Tadashi; Hashi, Kenjiro; Goto, Atsushi; Tansyo, Masataka; Kiyoshi, Tsukasa; Matsumoto, Shinji; Wada, Hitoshi; Fujito, Teruaki; Hasegawa, Ken-ichi; Kirihara, Noriaki; Suematsu, Hiroto; Kida, Yoshiki; Yoshikawa, Masatoshi; Miki, Takashi; Ito, Satoshi; Hamada, Mamoru; Hayashi, Seiji

2004-04-01

We have developed a 920 MHz NMR system and performed the proton NMR measurement of ethylbenzene and water using the superconducting magnet operating at 21.6 T ( 920 MHz for proton), which is the highest field produced by a superconducting NMR magnet in the persistent mode. From the NMR measurements, it is verified that both homogeneity and stability of the magnet have a specification sufficient for a high-resolution NMR. The sensitivity has been examined by 1H NMR of 0.1% ethylbenzene in Wilmad 555 tube and obtained the signal-to-noise ratio as S/ N=2981, which is the highest record, to our knowledge, among the room temperature measurements.

Enzymatic and acidic degradation of high molecular weight dextran into low molecular weight and its characterizations using novel Diffusion-ordered NMR spectroscopy.

PubMed

Iqbal, Samina; Marchetti, Roberta; Aman, Afsheen; Silipo, Alba; Qader, Shah Ali Ul; Molinaro, Antonio

2017-10-01

Low molecular weight fractions were derived from native high molecular weight dextran produced by Leuconostoc mesenteroides KIBGE-IB26. Structural characterization of native and low molecular weight fractions obtained after acidic and enzymatic hydrolysis was done using FTIR and NMR spectroscopy. The molecular weight was estimated using Diffusion Ordered NMR spectroscopy. Native dextran (892kDa) is composed of α-(1→6) glycosidic linkage along with α-(1→3) branching. Major proportion of 528kDa dextran was obtained after prolong enzymatic hydrolysis however, an effective acidic treatment at pH-1.4 up to 02 and 04h of exposure resulted in the formation of 77kDa and 57kDa, respectively. The increment in pH from 1.4 to 1.8 lowered the hydrolysis efficiency and resulted in the formation of 270kDa dextran fraction. The results suggest that derived low molecular weight water soluble fractions can be utilized as a drug delivery carrier along with multiple application relating pharmaceutical industries. Copyright © 2017 Elsevier B.V. All rights reserved.

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, A.; Samoson, A.

1990-02-06

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimalmore » frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.« less

Earth field NMR with chemical shift spectral resolution: theory and proof of concept.

PubMed

Katz, Itai; Shtirberg, Lazar; Shakour, Gubrail; Blank, Aharon

2012-06-01

A new method for obtaining an NMR signal in the Earth's magnetic field (EF) is presented. The method makes use of a simple pulse sequence with only DC fields which is much less demanding than previous approaches in terms of the pulses' rise and fall times. Furthermore, it offers the possibility of obtaining NMR data with enough spectral resolution to allow retrieving high resolution molecular chemical shift (CS) information - a capability that was not considered possible in EF NMR until now. Details of the pulse sequence, the experimental system, and our specially tailored EF NMR probe are provided. The experimental results demonstrate the capability to differentiate between three types of samples made of common fluorine compounds, based on their CS data. Copyright © 2012 Elsevier Inc. All rights reserved.

Establishing resolution-improved NMR spectroscopy in high magnetic fields with unknown spatiotemporal variations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zhiyong; Cai, Shuhui; Zheng, Zhenyao

A half-century quest for higher magnetic fields has been an integral part of the progress undergone in the Nuclear Magnetic Resonance (NMR) study of materials’ structure and dynamics. Because 2D NMR relies on systematic changes in coherences’ phases as a function of an encoding time varied over a series of independent experiments, it generally cannot be applied in temporally unstable fields. This precludes most NMR methods from being used to characterize samples situated in hybrid or resistive magnets that are capable of achieving extremely high magnetic field strength. Recently, “ultrafast” NMR has been developed into an effective and widely applicablemore » methodology enabling the acquisition of a multidimensional NMR spectrum in a single scan; it can therefore be used to partially mitigate the effects of temporally varying magnetic fields. Nevertheless, the strong interference of fluctuating fields with the spatial encoding of ultrafast NMR still severely restricts measurement sensitivity and resolution. Here, we introduce a strategy for obtaining high resolution NMR spectra that exploits the immunity of intermolecular zero-quantum coherences (iZQCs) to field instabilities and inhomogeneities. The spatial encoding of iZQCs is combined with a J-modulated detection scheme that removes the influence of arbitrary field inhomogeneities during acquisition. This new method can acquire high-resolution one-dimensional NMR spectra in large inhomogeneous and fluctuating fields, and it is tested with fields experimentally modeled to mimic those of resistive and resistive-superconducting hybrid magnets.« less

Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins

NASA Astrophysics Data System (ADS)

Koroloff, Sophie N.; Nevzorov, Alexander A.

2017-01-01

Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the 1H-15N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the 15N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.

Photo-CIDNP NMR spectroscopy of amino acids and proteins.

PubMed

Kuhn, Lars T

2013-01-01

Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.

Synthesis and Resolution of the Atropisomeric 1,1'-Bi-2-Naphthol: An Experiment in Organic Synthesis and 2-D NMR Spectroscopy

ERIC Educational Resources Information Center

Mak, Kendrew K. W.

2004-01-01

NMR spectroscopy is presented. It is seen that the experiment regarding the synthesis and resolution of 1,1'-Bi-2-naphtol presents a good experiment for teaching organic synthesis and NMR spectroscopy and provides a strategy for obtaining enantiopure compounds from achiral starting materials.

Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

PubMed

Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

2012-01-01

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

A Simple Approach for Obtaining High Resolution, High Sensitivity ¹H NMR Metabolite Spectra of Biofluids with Limited Mass Supply

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian Zhi; Rommereim, Donald N.; Wind, Robert A.

2006-11-01

A simple approach is reported that yields high resolution, high sensitivity ¹H NMR spectra of biofluids with limited mass supply. This is achieved by spinning a capillary sample tube containing a biofluid at the magic angle at a frequency of about 80Hz. A 2D pulse sequence called ¹H PASS is then used to produce a high-resolution ¹H NMR spectrum that is free from magnetic susceptibility induced line broadening. With this new approach a high resolution ¹H NMR spectrum of biofluids with a volume less than 1.0 µl can be easily achieved at a magnetic field strength as low as 7.05T.more » Furthermore, the methodology facilitates easy sample handling, i.e., the samples can be directly collected into inexpensive and disposable capillary tubes at the site of collection and subsequently used for NMR measurements. In addition, slow magic angle spinning improves magnetic field shimming and is especially suitable for high throughput investigations. In this paper first results are shown obtained in a magnetic field of 7.05T on urine samples collected from mice using a modified commercial NMR probe.« less

6-carboxydihydroresveratrol 3-O-β-glucopyranoside--a novel natural product from the Cretaceous relict Metasequoia glyptostroboides.

PubMed

Nguyen, Xuan Hong Thy; Juvik, Ole Johan; Øvstedal, Dag Olav; Fossen, Torgils

2014-06-01

Metasequoia glyptostroboides, a tree native to China, is described as a living fossil and has existed for millions of years. The oldest fossils recorded have been dated to the late Cretaceous era. During the time of its existence, the molecular defence system of the tree has apparently resisted millions of generations of pathogens, which encouraged search for novel natural product from this source. Eight compounds have been characterised from needles of M. glyptostroboides, including the novel natural product 6-carboxydihydroresveratrol 3-O-β-glucopyranoside. The structure determinations were based on extensive use of 2D NMR spectroscopic techniques and high-resolution mass spectrometry. Copyright © 2014 Elsevier B.V. All rights reserved.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Characterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopy

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2008-01-01

A recently described plant cell wall dissolution system has been modified to use perdeuterated solvents to allow direct in-NMR-tube dissolution and high-resolution solution-state NMR of the whole cell wall without derivatization. Finely ground cell wall material dissolves in a solvent system containing dimethylsulfoxide-d6 and 1-methylimidazole-d6 in a ratio of 4:1 (v/...

NMR Microscopy - Micron-Level Resolution.

NASA Astrophysics Data System (ADS)

Kwok, Wing-Chi Edmund

1990-01-01

Nuclear Magnetic Resonance Imaging (MRI) has been developed into a powerful and widely used diagnostic tool since the invention of techniques using linear magnetic field gradients in 1973. The variety of imaging contrasts obtainable in MRI, such as spin density, relaxation times and flow rate, gives MRI a significant advantage over other imaging techniques. For common diagnostic applications, image resolutions have been in the order of millimeters with slice thicknesses in centimeters. For many research applications, however, resolutions in the order of tens of microns or smaller are needed. NMR Imaging in these high resolution disciplines is known as NMR microscopy. Compared with conventional microscopy, NMR microscopy has the advantage of being non-invasive and non-destructive. The major obstacles of NMR microscopy are low signal-to-noise ratio and effects due to spin diffusion. To overcome these difficulties, more sensitive RF probes and very high magnetic field gradients have to be used. The most effective way to increase sensitivity is to build smaller probes. Microscope probes of different designs have been built and evaluated. Magnetic field gradient coils that can produce linear field gradients up to 450 Gauss/cm were also assembled. In addition, since microscope probes often employ remote capacitors for RF tuning, the associated signal loss in the transmission line was studied. Imaging experiments have been carried out in a 2.1 Tesla small bore superconducting magnet using the typical two-dimensional spin warp imaging technique. Images have been acquired for both biological and non-biological samples. The highest resolution was obtained in an image of a nerve bundle from the spinal cord of a racoon and has an in-plane resolution of 4 microns. These experiments have demonstrated the potential application of NMR microscopy to pathological research, nervous system study and non -destructive testings of materials. One way to further improve NMR microscopy is to implement a higher static magnetic field which will increase signal strength. In the future, NMR microscopy should prove to be useful in the studies of cell linings, T1 & T2 relaxation mechanisms and NMR contrast agents.

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

PubMed Central

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-01

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix. PMID:25550503

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR.

PubMed

Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

2015-01-13

Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.

NMR and mass spectrometry of phosphorus in wetlands

USGS Publications Warehouse

El-Rifai, H.; Heerboth, M.; Gedris, T.E.; Newman, S.; Orem, W.; Cooper, W.T.

2008-01-01

There is at present little information on the long-term stability of phosphorus sequestered in wetlands. Phosphorus sequestered during high loading periods may be relatively unstable and easily remobilized following changes in nutrient status or hydrological regime, but the chemical forms of sequestered phosphorus that do remobilize are largely unknown at this time. A lack of suitable analytical techniques has contributed to this dearth of knowledge regarding the stability of soil organic phosphorus. We analysed phosphorus in soils from the 'head' of Rescue Strand tree island and an adjacent marsh in the Florida Everglades by 31P nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry. Tree islands are important areas of biodiversity within the Everglades and offer a unique opportunity to study phosphorus sequestration because they are exposed to large phosphorus loads and appear to be natural nutrient sinks. The 31P NMR profiling of extracts from surface and sediment samples in the tree island indicates that phosphorus input to Rescue Strand tree island soils is mostly in the form of inorganic ortho-phosphate and is either refractory when deposited or rapidly recycled by the native vegetation into a stable phosphorus pool largely resistant to re-utilization by plants or microbes. Mass spectrometry revealed the presence of inositol hexakisphosphate, a common organic monophosphate ester not previously observed in Everglades' soils. ?? 2008 The Authors.

Novel NMR tools to study structure and dynamics of biomembranes.

PubMed

Gawrisch, Klaus; Eldho, Nadukkudy V; Polozov, Ivan V

2002-06-01

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

PubMed Central

Zook, James D.; Molugu, Trivikram R.; Jacobsen, Neil E.; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra

2013-01-01

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

MULTIVARIATE CURVE RESOLUTION OF NMR SPECTROSCOPY METABONOMIC DATA

EPA Science Inventory

Sandia National Laboratories is working with the EPA to evaluate and develop mathematical tools for analysis of the collected NMR spectroscopy data. Initially, we have focused on the use of Multivariate Curve Resolution (MCR) also known as molecular factor analysis (MFA), a tech...

Partial homogeneity based high-resolution nuclear magnetic resonance spectra under inhomogeneous magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Zhiliang; Lin, Liangjie; Lin, Yanqin, E-mail: linyq@xmu.edu.cn, E-mail: chenz@xmu.edu.cn

2014-09-29

In nuclear magnetic resonance (NMR) technique, it is of great necessity and importance to obtain high-resolution spectra, especially under inhomogeneous magnetic fields. In this study, a method based on partial homogeneity is proposed for retrieving high-resolution one-dimensional NMR spectra under inhomogeneous fields. Signals from series of small voxels, which characterize high resolution due to small sizes, are recorded simultaneously. Then, an inhomogeneity correction algorithm is developed based on pattern recognition to correct the influence brought by field inhomogeneity automatically, thus yielding high-resolution information. Experiments on chemical solutions and fish spawn were carried out to demonstrate the performance of the proposedmore » method. The proposed method serves as a single radiofrequency pulse high-resolution NMR spectroscopy under inhomogeneous fields and may provide an alternative of obtaining high-resolution spectra of in vivo living systems or chemical-reaction systems, where performances of conventional techniques are usually degenerated by field inhomogeneity.« less

High-Resolution Solid-State NMR Spectroscopy: Characterization of Polymorphism in Cimetidine, a Pharmaceutical Compound

ERIC Educational Resources Information Center

Pacilio, Julia E.; Tokarski, John T.; Quiñones, Rosalynn; Iuliucci, Robbie J.

2014-01-01

High-resolution solid-state NMR (SSNMR) spectroscopy has many advantages as a tool to characterize solid-phase material that finds applications in polymer chemistry, nanotechnology, materials science, biomolecular structure determination, and others, including the pharmaceutical industry. The technology associated with achieving high resolution…

The Impact of Focus on Pronoun Resolution in Native and Non-Native Sentence Comprehension

ERIC Educational Resources Information Center

Patterson, Clare; Esaulova, Yulia; Felser, Claudia

2017-01-01

Non-native speakers' sensitivity to discourse-level cues in pronoun interpretation has not been widely researched. We carried out three antecedent-choice questionnaire experiments which investigate the impact of focus on within-sentence pronoun resolution in native and non-native speakers of German and native speakers of Russian. Focus was…

A fast field-cycling device for high-resolution NMR: Design and application to spin relaxation and hyperpolarization experiments

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Pravdivtsev, Andrey N.; Ivanov, Konstantin L.; Grishin, Yuri A.; Vieth, Hans-Martin; Yurkovskaya, Alexandra V.

2016-02-01

A device for performing fast magnetic field-cycling NMR experiments is described. A key feature of this setup is that it combines fast switching of the external magnetic field and high-resolution NMR detection. The field-cycling method is based on precise mechanical positioning of the NMR probe with the mounted sample in the inhomogeneous fringe field of the spectrometer magnet. The device enables field variation over several decades (from 100 μT up to 7 T) within less than 0.3 s; progress in NMR probe design provides NMR linewidths of about 10-3 ppm. The experimental method is very versatile and enables site-specific studies of spin relaxation (NMRD, LLSs) and spin hyperpolarization (DNP, CIDNP, and SABRE) at variable magnetic field and at variable temperature. Experimental examples of such studies are demonstrated; advantages of the experimental method are described and existing challenges in the field are outlined.

Challenges and perspectives in quantitative NMR.

PubMed

Giraudeau, Patrick

2017-01-01

This perspective article summarizes, from the author's point of view at the beginning of 2016, the major challenges and perspectives in the field of quantitative NMR. The key concepts in quantitative NMR are first summarized; then, the most recent evolutions in terms of resolution and sensitivity are discussed, as well as some potential future research directions in this field. A particular focus is made on methodologies capable of boosting the resolution and sensitivity of quantitative NMR, which could open application perspectives in fields where the sample complexity and the analyte concentrations are particularly challenging. These include multi-dimensional quantitative NMR and hyperpolarization techniques such as para-hydrogen-induced polarization or dynamic nuclear polarization. Because quantitative NMR cannot be dissociated from the key concepts of analytical chemistry, i.e. trueness and precision, the methodological developments are systematically described together with their level of analytical performance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Compressed NMR: Combining compressive sampling and pure shift NMR techniques.

PubMed

Aguilar, Juan A; Kenwright, Alan M

2017-12-26

Historically, the resolution of multidimensional nuclear magnetic resonance (NMR) has been orders of magnitude lower than the intrinsic resolution that NMR spectrometers are capable of producing. The slowness of Nyquist sampling as well as the existence of signals as multiplets instead of singlets have been two of the main reasons for this underperformance. Fortunately, two compressive techniques have appeared that can overcome these limitations. Compressive sensing, also known as compressed sampling (CS), avoids the first limitation by exploiting the compressibility of typical NMR spectra, thus allowing sampling at sub-Nyquist rates, and pure shift techniques eliminate the second issue "compressing" multiplets into singlets. This paper explores the possibilities and challenges presented by this combination (compressed NMR). First, a description of the CS framework is given, followed by a description of the importance of combining it with the right pure shift experiment. Second, examples of compressed NMR spectra and how they can be combined with covariance methods will be shown. Copyright © 2017 John Wiley & Sons, Ltd.

Scalable NMR spectroscopy with semiconductor chips

PubMed Central

Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

2014-01-01

State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm2 silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes.

PubMed

Wittig, Ilka; Karas, Michael; Schägger, Hermann

2007-07-01

Clear native electrophoresis and blue native electrophoresis are microscale techniques for the isolation of membrane protein complexes. The Coomassie Blue G-250 dye, used in blue native electrophoresis, interferes with in-gel fluorescence detection and in-gel catalytic activity assays. This problem can be overcome by omitting the dye in clear native electrophoresis. However, clear native electrophoresis suffers from enhanced protein aggregation and broadening of protein bands during electrophoresis and therefore has been used rarely. To preserve the advantages of both electrophoresis techniques we substituted Coomassie dye in the cathode buffer of blue native electrophoresis by non-colored mixtures of anionic and neutral detergents. Like Coomassie dye, these mixed micelles imposed a charge shift on the membrane proteins to enhance their anodic migration and improved membrane protein solubility during electrophoresis. This improved clear native electrophoresis offers a high resolution of membrane protein complexes comparable to that of blue native electrophoresis. We demonstrate the superiority of high resolution clear native electrophoresis for in-gel catalytic activity assays of mitochondrial complexes I-V. We present the first in-gel histochemical staining protocol for respiratory complex III. Moreover we demonstrate the special advantages of high resolution clear native electrophoresis for in-gel detection of fluorescent labeled proteins labeled by reactive fluorescent dyes and tagged by fluorescent proteins. The advantages of high resolution clear native electrophoresis make this technique superior for functional proteomics analyses.

High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids

PubMed Central

Nucci, Nathaniel V.; Valentine, Kathleen G.; Wand, A. Joshua

2014-01-01

High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (< 25 kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the ‘slow tumbling problem’ can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100 kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics. PMID:24656086

Crocus sativus Petals: Waste or Valuable Resource? The Answer of High-Resolution and High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.

PubMed

Righi, Valeria; Parenti, Francesca; Tugnoli, Vitaliano; Schenetti, Luisa; Mucci, Adele

2015-09-30

Intact Crocus sativus petals were studied for the first time by high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, revealing the presence of kinsenoside (2) and goodyeroside A (3), together with 3-hydroxy-γ-butyrolactone (4). These findings were confirmed by HR-NMR analysis of the ethanol extract of fresh petals and showed that, even though carried out rapidly, partial hydrolysis of glucopyranosyloxybutanolides occurs during extraction. On the other hand, kaempferol 3-O-sophoroside (1), which is "NMR-silent" in intact petals, is present in extracts. These results suggest to evaluate the utilization of saffron petals for phytopharmaceutical and nutraceutical purposes to exploit a waste product of massive production of commercial saffron and point to the application of HR-MAS NMR for monitoring bioactive compounds directly on intact petals, avoiding the extraction procedure and the consequent hydrolysis reaction.

High-resolution detection of 13C multiplets from the conscious mouse brain by ex vivo NMR spectroscopy

PubMed Central

Marin-Valencia, Isaac; Good, Levi B.; Ma, Qian; Jeffrey, F. Mark; Malloy, Craig R.; Pascual, Juan M.

2011-01-01

Glucose readily supplies the brain with the majority of carbon needed to sustain neurotransmitter production and utilization., The rate of brain glucose metabolism can be computed using 13C nuclear magnetic resonance (NMR) spectroscopy by detecting changes in 13C contents of products generated by cerebral metabolism. As previously observed, scalar coupling between adjacent 13C carbons (multiplets) can provide additional information to 13C contents for the computation of metabolic rates. Most NMR studies have been conducted in large animals (often under anesthesia) because the mass of the target organ is a limiting factor for NMR. Yet, despite the challengingly small size of the mouse brain, NMR studies are highly desirable because the mouse constitutes a common animal model for human neurological disorders. We have developed a method for the ex vivo resolution of NMR multiplets arising from the brain of an awake mouse after the infusion of [1,6-13C2]glucose. NMR spectra obtained by this method display favorable signal-to-noise ratios. With this protocol, the 13C multiplets of glutamate, glutamine, GABA and aspartate achieved steady state after 150 min. The method enables the accurate resolution of multiplets over time in the awake mouse brain. We anticipate that this method can be broadly applicable to compute brain fluxes in normal and transgenic mouse models of neurological disorders. PMID:21946227

High-resolution solution-state NMR of unfractionated plant cell walls

Treesearch

John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom

2009-01-01

Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

High-resolution NMR study of light and heavy crude oils: “structure-property” analysis

NASA Astrophysics Data System (ADS)

Rakhmatullin, I.; Efimov, S.; Varfolomeev, M.; Klochkov, V.

2018-05-01

Measurements of three light and one heavy crude oil samples were carried out by high-resolution nuclear magnetic resonance (NMR) spectroscopy methods. Quantitative fractions of aromatic molecules and functional groups constituting oil hydrocarbons were determined, and comparative analysis of the oil samples of different viscosity and origin was done.

Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide.

PubMed

Koukos, Panagiotis I; Glykos, Nicholas M

2014-08-28

Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, and (c) the structure of the mutant is an irregular β-hairpin with a non-glycine β-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small β-hairpin-like population for the native peptide but surprisingly indicate that this population is structurally more similar to the structure of the native peptide as observed in the vammin protein than to the NMR structure of the isolated mutant peptide. We conclude that, at least for the given system, force field, and simulation protocol, folding molecular dynamics simulations appear to be successful in reproducing the experimentally accessible physical reality to a satisfactory level of detail and accuracy.

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and "hidden" dimensions.

PubMed

Meng, Xi; Nguyen, Bao D; Ridge, Clark; Shaka, A J

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to "reduced-dimensionality" strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the filter diagonalization method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra-dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths.

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and “hidden” dimensions

PubMed Central

Meng, Xi; Nguyen, Bao D.; Ridge, Clark; Shaka, A. J.

2009-01-01

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to “reduced-dimensionality” strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the Filter Diagonalization Method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths. PMID:18926747

Proton-Based Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy.

PubMed

Zhang, Rongchun; Mroue, Kamal H; Ramamoorthy, Ayyalusamy

2017-04-18

Protons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution using solid-state NMR (ssNMR) spectroscopy. Unfortunately, the high signal sensitivity, afforded by the high natural-abundance and high gyromagnetic ratio of protons, is greatly compromised by severe line broadening due to the very strong 1 H- 1 H dipolar couplings. As a result, protons are rarely used, in spite of the desperate need for enhancing the sensitivity of ssNMR to study a variety of systems that are not amenable for high resolution investigation using other techniques including X-ray crystallography, cryo-electron microscopy, and solution NMR spectroscopy. Thanks to the remarkable improvement in proton spectral resolution afforded by the significant advances in magic-angle-spinning (MAS) probe technology, 1 H ssNMR spectroscopy has recently attracted considerable attention in the structural and dynamics studies of various molecular systems. However, it still remains a challenge to obtain narrow 1 H spectral lines, especially from proteins, without resorting to deuteration. In this Account, we review recent proton-based ssNMR strategies that have been developed in our laboratory to further improve proton spectral resolution without resorting to chemical deuteration for the purposes of gaining atomistic-level insights into molecular structures of various crystalline solid systems, using small molecules and peptides as illustrative examples. The proton spectral resolution enhancement afforded by the ultrafast MAS frequencies up to 120 kHz is initially discussed, followed by a description of an ensemble of multidimensional NMR pulse sequences, all based on proton detection, that have been developed to obtain in-depth information from dipolar couplings and chemical shift anisotropy (CSA). Simple single channel multidimensional proton NMR experiments could be performed to probe the proximity of protons for structure determination using 1 H- 1 H dipolar couplings and to evaluate the changes in chemical environments as well as the relative orientation to the external magnetic field using proton CSA. Due to the boost in signal sensitivity enabled by proton detection under ultrafast MAS, by virtue of high proton natural abundance and gyromagnetic ratio, proton-detected multidimensional experiments involving low-γ nuclei can now be accomplished within a reasonable time, while the higher dimension also offers additional resolution enhancement. In addition, the application of proton-based ssNMR spectroscopy under ultrafast MAS in various challenging and crystalline systems is also presented. Finally, we briefly discuss the limitations and challenges pertaining to proton-based ssNMR spectroscopy under ultrafast MAS conditions, such as the presence of high-order dipolar couplings, friction-induced sample heating, and limited sample volume. Although there are still a number of challenges that must be circumvented by further developments in radio frequency pulse sequences, MAS probe technology and approaches to prepare NMR-friendly samples, proton-based ssNMR has already gained much popularity in various research domains, especially in proteins where uniform or site-selective deuteration can be relatively easily achieved. In addition, implementation of the recently developed fast data acquisition approaches would also enable further developments in the design and applications of proton-based ultrafast MAS multidimensional ssNMR techniques.

Long-lived coherences: Improved dispersion in the frequency domain using continuous-wave and reduced-power windowed sustaining irradiation

NASA Astrophysics Data System (ADS)

Sadet, A.; Fernandes, L.; Kateb, F.; Balzan, R.; Vasos, P. R.

2014-08-01

Long-lived coherences (LLC's) are detectable magnetisation modes with favourable relaxation times that translate as sharp resonances upon Fourier transform. The frequency domain of LLC's was previously limited to the range of J-couplings within pairs of homonuclear spins. LLC evolution at high magnetic fields needs to be sustained by radio-frequency irradiation. We show that LLC-based spectral dispersion can be extended beyond the J-couplings domain using adapted carrier offsets and introduce a new reduced-power sustaining method to preserve LLC's within the required range of offsets. Spectral resolution is enhanced as the natively narrow lines of LLC's are further dispersed, making them potential probes for the study of biomolecules featuring strong resonance overlap and for media where NMR spectroscopy is commonly hindered by line broadening.

Pressure-resisting cell for high-pressure, high-resolution nuclear magnetic resonance measurements at very high magnetic fields

NASA Astrophysics Data System (ADS)

Yamada, H.; Nishikawa, K.; Honda, M.; Shimura, T.; Akasaka, K.; Tabayashi, K.

2001-02-01

A pressure-resisting cell system has been developed for high-pressure high-resolution nuclear magnetic resonance (NMR) measurements up to a maximum pressure of 600 MPa. This cell system is capable of performing high-pressure experiments with any standard spectrometer, including modern high field NMR machines. A full description of the high-pressure NMR assembly mounted on a 750 MHz spectrometer is presented along with a detailed explanation of the procedure for preparing the pressure-resisting quartz and glass cells.

Hydraulic Conductivity Calibration of Logging NMR in a Granite Aquifer, Laramie Range, Wyoming.

PubMed

Ren, Shuangpo; Parsekian, Andrew D; Zhang, Ye; Carr, Bradley J

2018-05-15

In granite aquifers, fractures can provide both storage volume and conduits for groundwater. Characterization of fracture hydraulic conductivity (K) in such aquifers is important for predicting flow rate and calibrating models. Nuclear magnetic resonance (NMR) well logging is a method to quickly obtain near-borehole hydraulic conductivity (i.e., K NMR ) at high-vertical resolution. On the other hand, FLUTe flexible liner technology can produce a K profile at comparable resolution but requires a fluid driving force between borehole and formation. For three boreholes completed in a fractured granite, we jointly interpreted logging NMR data and FLUTe K estimates to calibrate an empirical equation for translating borehole NMR data to K estimates. For over 90% of the depth intervals investigated from these boreholes, the estimated K NMR are within one order of magnitude of K FLUTe . The empirical parameters obtained from calibrating the NMR data suggest that "intermediate diffusion" and/or "slow diffusion" during the NMR relaxation time may occur in the flowing fractures when hydraulic aperture are sufficiently large. For each borehole, "intermediate diffusion" dominates the relaxation time, therefore assuming "fast diffusion" in the interpretation of NMR data from fractured rock may lead to inaccurate K NMR estimates. We also compare calibrations using inexpensive slug tests that suggest reliable K NMR estimates for fractured rock may be achieved using limited calibration against borehole hydraulic measurements. © 2018, National Ground Water Association.

Angstrom-Resolution Magnetic Resonance Imaging of Single Molecules via Wave-Function Fingerprints of Nuclear Spins

NASA Astrophysics Data System (ADS)

Ma, Wen-Long; Liu, Ren-Bao

2016-08-01

Single-molecule sensitivity of nuclear magnetic resonance (NMR) and angstrom resolution of magnetic resonance imaging (MRI) are the highest challenges in magnetic microscopy. Recent development in dynamical-decoupling- (DD) enhanced diamond quantum sensing has enabled single-nucleus NMR and nanoscale NMR. Similar to conventional NMR and MRI, current DD-based quantum sensing utilizes the "frequency fingerprints" of target nuclear spins. The frequency fingerprints by their nature cannot resolve different nuclear spins that have the same noise frequency or differentiate different types of correlations in nuclear-spin clusters, which limit the resolution of single-molecule MRI. Here we show that this limitation can be overcome by using "wave-function fingerprints" of target nuclear spins, which is much more sensitive than the frequency fingerprints to the weak hyperfine interaction between the targets and a sensor under resonant DD control. We demonstrate a scheme of angstrom-resolution MRI that is capable of counting and individually localizing single nuclear spins of the same frequency and characterizing the correlations in nuclear-spin clusters. A nitrogen-vacancy-center spin sensor near a diamond surface, provided that the coherence time is improved by surface engineering in the near future, may be employed to determine with angstrom resolution the positions and conformation of single molecules that are isotope labeled. The scheme in this work offers an approach to breaking the resolution limit set by the "frequency gradients" in conventional MRI and to reaching the angstrom-scale resolution.

High-resolution nuclear magnetic resonance studies of proteins.

PubMed

Jonas, Jiri

2002-03-25

The combination of advanced high-resolution nuclear magnetic resonance (NMR) techniques with high-pressure capability represents a powerful experimental tool in studies of protein folding. This review is organized as follows: after a general introduction of high-pressure, high-resolution NMR spectroscopy of proteins, the experimental part deals with instrumentation. The main section of the review is devoted to NMR studies of reversible pressure unfolding of proteins with special emphasis on pressure-assisted cold denaturation and the detection of folding intermediates. Recent studies investigating local perturbations in proteins and the experiments following the effects of point mutations on pressure stability of proteins are also discussed. Ribonuclease A, lysozyme, ubiquitin, apomyoglobin, alpha-lactalbumin and troponin C were the model proteins investigated.

High-resolution NMR in magnetic fields with unknown spatiotemporal variations.

PubMed

Pelupessy, Philippe; Rennella, Enrico; Bodenhausen, Geoffrey

2009-06-26

Nuclear magnetic resonance (NMR) experiments are usually carried out in homogeneous magnetic fields. In many cases, however, high-resolution spectra are virtually impossible to obtain because of the inherent heterogeneity of the samples or living organisms under investigation, as well as the poor homogeneity of the magnets (particularly when bulky samples must be placed outside their bores). Unstable power supplies and vibrations arising from cooling can lead to field fluctuations in time as well as space. We show how high-resolution NMR spectra can be obtained in inhomogeneous fields with unknown spatiotemporal variations. Our method, based on coherence transfer between spins, can accommodate spatial inhomogeneities of at least 11 gauss per centimeter and temporal fluctuations slower than 2 hertz.

(14)N overtone transition in double rotation solid-state NMR.

PubMed

Haies, Ibraheem M; Jarvis, James A; Brown, Lynda J; Kuprov, Ilya; Williamson, Philip T F; Carravetta, Marina

2015-10-07

Solid-state NMR transitions involving outer energy levels of the spin-1 (14)N nucleus are immune, to first order in perturbation theory, to the broadening caused by the nuclear quadrupole interaction. The corresponding overtone spectra, when acquired in conjunction with magic-angle sample spinning, result in lines, which are just a few kHz wide, permitting the direct detection of nitrogen compounds without the need for labeling. Despite the success of this technique, "overtone" resonances are still broadened due to indirect, second order effects arising from the large quadrupolar interaction. Here we demonstrate that another order of magnitude in spectral resolution may be gained by using double rotation. This brings the width of the (14)N solid-state NMR lines much closer to the region commonly associated with high-resolution solid-state NMR spectroscopy of (15)N and demonstrates the improvements in resolution that may be possible through the development of pulsed methodologies to suppress these second order effects.

Quantum memory enhanced nuclear magnetic resonance of nanometer-scale samples with a single spin in diamond

NASA Astrophysics Data System (ADS)

Aslam, Nabeel; Pfender, Matthias; Zaiser, Sebastian; Favaro de Oliveira, Felipe; Momenzadeh, S. Ali; Denisenko, Andrej; Isoya, Junichi; Neumann, Philipp; Wrachtrup, Joerg

Recently nuclear magnetic resonance (NMR) of nanoscale samples at ambient conditions has been achieved with nitrogen-vacancy (NV) centers in diamond. So far the spectral resolution in the NV NMR experiments was limited by the sensor's coherence time, which in turn prohibited revealing the chemical composition and dynamics of the system under investigation. By entangling the NV electron spin sensor with a long-lived memory spin qubit we increase the spectral resolution of NMR measurement sequences for the detection of external nuclear spins. Applying the latter sensor-memory-couple it is particularly easy to track diffusion processes, to identify the molecules under study and to deduce the actual NV center depth inside the diamond. We performed nanoscale NMR on several liquid and solid samples exhibiting unique NMR response. Our method paves the way for nanoscale identification of molecule and protein structures and dynamics of conformational changes.

Cell signaling, post-translational protein modifications and NMR spectroscopy

PubMed Central

Theillet, Francois-Xavier; Smet-Nocca, Caroline; Liokatis, Stamatios; Thongwichian, Rossukon; Kosten, Jonas; Yoon, Mi-Kyung; Kriwacki, Richard W.; Landrieu, Isabelle; Lippens, Guy

2016-01-01

Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy. PMID:23011410

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani

2009-10-21

One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based onmore » these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.« less

Applications of solid-state NMR to membrane proteins.

PubMed

Ladizhansky, Vladimir

2017-11-01

Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Solution state NMR of lignins

Treesearch

John Ralph; Jane M. Marita; Sally A. Ralph; Ronald D. Hatfield; Fachuang Lu; Richard M. Ede; Junpeng Peng; Larry L. Landucci

1999-01-01

Despite the rather random and heterogeneous nature of isolated lignins, many of their intimate structural details are revealed by diagnostic NMR experiments. 13C-NMR was recognized early-on as a high-resolution method for detailed structural characterization, aided by the almost exact agreement between chemical shifts of carbons in good low-molecular...

New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Junfeng; Isern, Nancy G.; Ewing, R James

An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequencymore » of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.« less

The structural basis of the difference in sensitivity for PNGase F in the de-N-glycosylation of the native bovine pancreatic ribonucleases B and BS.

PubMed

Blanchard, Véronique; Frank, Martin; Leeflang, Bas R; Boelens, Rolf; Kamerling, Johannis P

2008-03-18

In glycoanalysis protocols, N-glycans from glycoproteins are most frequently released with peptide- N (4)-( N-acetyl-beta-glucosaminyl)asparagine amidase F (PNGase F). As the enzyme is an amidase, it cleaves the NH-CO linkage between the Asn side chain and the Asn-bound GlcNAc residue. Usually, the enzyme has a low activity, or is not active at all, on native glycoproteins. A typical example is native bovine pancreatic ribonuclease B (RNase B) with oligomannose-type N-glycans at Asn-34. However, native RNase BS, generated by subtilisin digestion of native RNase B, which comprises amino acid residues 21-124 of RNase B, is sensitive to PNGase F digestion. The same holds for carboxymethylated RNase B (RNase B (cm)). In this study, NMR spectroscopy and molecular modeling have been used to explain the differences in PNGase F activity for native RNase B, native RNase BS, and RNase B (cm). NMR analysis combined with literature data clearly indicated that the N-glycan at Asn-34 is more mobile in RNase BS than in RNase B. MD simulations showed that the region around Asn-34 in RNase B is not very flexible, whereby the alpha-helix of the amino acid residues 1-20 has a stabilizing effect. In RNase BS, the alpha-helix formed by amino acid residues 23-32 is significantly more flexible. Using these data, the possibilities for complex formation of both RNase B and RNase BS with PNGase F were studied, and a model for the RNase BS-PNGase F complex is proposed.

Reduced native state stability in crowded cellular environment due to protein-protein interactions.

PubMed

Harada, Ryuhei; Tochio, Naoya; Kigawa, Takanori; Sugita, Yuji; Feig, Michael

2013-03-06

The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.

Development and application of high-resolution solid- state NMR dipolar recovery techniques for spin-1/2 nuclei

NASA Astrophysics Data System (ADS)

Joers, James M.

The use of magic angle spinning to obtain high resolution solid state spectra has been well documented. This resolution occurs by coherently averaging the chemical shift anisotropy and dipolar interactions to zero over the period of a full rotation. While this allows for higher resolution, the structural information is seemingly lost to the spectrometer eye. Thus, high resolution spectra and structural information appear to be mutually exlusive. Recently, the push in solid state NMR is the development of recoupling techniques which afford both high resolution and structural information. The following dissertation demonstrates the feasibility of implementing such experiments in solving real world problems, and is centered on devising a method to recover homonuclear dipolar interactions in the high resolution regime.

Spider Gland Fluids: From Protein-Rich Isotropic Liquid to Insoluble Super Fiber

DTIC Science & Technology

2013-09-17

natural gland fluids with solid-state NMR can be used to guide the production of synthetic spider silk fibers that more closely match native spider silk...duct contents in combination with micro -imaging. An ability to conduct NMR spectroscopy in combination with MRI will provide us with a structural...NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Arizona State University,Tempe,AZ,85281 8. PERFORMING ORGANIZATION

Enzymatic Resolution of 1-Phenylethanol and Formation of a Diastereomer: An Undergraduate [superscript 1]H NMR Experiment to Introduce Chiral Chemistry

ERIC Educational Resources Information Center

Faraldos, Juan A.; Giner, Jos-Luis; Smith, David H.; Wilson, Mark; Ronhovde, Kyla; Wilson, Erin; Clevette, David; Holmes, Andrea E.; Rouhier, Kerry

2011-01-01

This organic laboratory experiment introduces students to stereoselective enzyme reactions, resolution of enantiomers, and NMR analysis of diastereomers. The reaction between racemic 1-phenylethanol and vinyl acetate in hexane to form an ester is catalyzed by acylase I. The unreacted alcohol is then treated with a chiral acid and the resulting…

High resolution NMR study of T{sub 1} magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L., E-mail: ivanov@tomo.nsc.ru

2014-10-21

Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I–III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T{sub 1}-relaxation timesmore » at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.« less

Nanoscale NMR spectroscopy and imaging of multiple nuclear species.

PubMed

DeVience, Stephen J; Pham, Linh M; Lovchinsky, Igor; Sushkov, Alexander O; Bar-Gill, Nir; Belthangady, Chinmay; Casola, Francesco; Corbett, Madeleine; Zhang, Huiliang; Lukin, Mikhail; Park, Hongkun; Yacoby, Amir; Walsworth, Ronald L

2015-02-01

Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) provide non-invasive information about multiple nuclear species in bulk matter, with wide-ranging applications from basic physics and chemistry to biomedical imaging. However, the spatial resolution of conventional NMR and MRI is limited to several micrometres even at large magnetic fields (>1 T), which is inadequate for many frontier scientific applications such as single-molecule NMR spectroscopy and in vivo MRI of individual biological cells. A promising approach for nanoscale NMR and MRI exploits optical measurements of nitrogen-vacancy (NV) colour centres in diamond, which provide a combination of magnetic field sensitivity and nanoscale spatial resolution unmatched by any existing technology, while operating under ambient conditions in a robust, solid-state system. Recently, single, shallow NV centres were used to demonstrate NMR of nanoscale ensembles of proton spins, consisting of a statistical polarization equivalent to ∼100-1,000 spins in uniform samples covering the surface of a bulk diamond chip. Here, we realize nanoscale NMR spectroscopy and MRI of multiple nuclear species ((1)H, (19)F, (31)P) in non-uniform (spatially structured) samples under ambient conditions and at moderate magnetic fields (∼20 mT) using two complementary sensor modalities.

Squid detected NMR and MRI at ultralow fields

DOEpatents

Clarke, John [Berkeley, CA; McDermott, Robert [Louisville, CO; Pines, Alexander [Berkeley, CA; Trabesinger, Andreas Heinz [CH-8006 Zurich, CH

2007-05-15

Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

Squid detected NMR and MRI at ultralow fields

DOEpatents

Clarke, John; McDermott, Robert; Pines, Alexander; Trabesinger, Andreas Heinz

2006-05-30

Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

Squid detected NMR and MRI at ultralow fields

DOEpatents

Clarke, John [Berkeley, CA; Pines, Alexander [Berkeley, CA; McDermott, Robert F [Monona, WI; Trabesinger, Andreas H [London, GB

2008-12-16

Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

SQUID detected NMR and MRI at ultralow fields

DOEpatents

Clarke, John; McDermott, Robert; Pines, Alexander; Trabesinger, Andreas Heinz

2006-10-03

Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

Displacement of native white-spotted charr Salvelinus leucomaenis by non-native brown trout Salmo trutta after resolution of habitat fragmentation by a migration barrier.

PubMed

Hasegawa, K

2017-06-01

After resolution of habitat fragmentation by an erosion-control dam, non-native brown trout Salmo trutta invaded the upstream side of the dam and displaced native white-spotted charr Salvelinus leucomaenis in Monbetsu stream, Hokkaido, northern Japan. © 2017 The Fisheries Society of the British Isles.

Nuclear magnetic resonance imaging at microscopic resolution

NASA Astrophysics Data System (ADS)

Johnson, G. Allan; Thompson, Morrow B.; Gewalt, Sally L.; Hayes, Cecil E.

Resolution limits in NMR imaging are imposed by bandwidth considerations, available magnetic gradients for spatial encoding, and signal to noise. This work reports modification of a clinical NMR imaging device with picture elements of 500 × 500 × 5000 μm to yield picture elements of 50 × 50 × 1000 μm. Resolution has been increased by using smaller gradient coils permitting gradient fields >0.4 mT/cm. Significant improvements in signal to noise are achieved with smaller rf coils, close attention to choice of bandwidth, and signal averaging. These improvements permit visualization of anatomical structures in the rat brain with an effective diameter of 1 cm with the same definition as is seen in human imaging. The techniques and instrumentation should open a number of basic sciences such as embryology, plant sciences, and teratology to the potentials of NMR imaging.

Magic Angle Spinning NMR of Viruses

PubMed Central

Quinn, Caitlin; Lu, Manman; Suiter, Christopher L.; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

2015-01-01

Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies. PMID:25919197

Selective observation of charge storing ions in supercapacitor electrode materials.

PubMed

Forse, Alexander C; Griffin, John M; Grey, Clare P

2018-02-01

Nuclear magnetic resonance (NMR) spectroscopy has emerged as a useful technique for probing the structure and dynamics of the electrode-electrolyte interface in supercapacitors, as ions inside the pores of the carbon electrodes can be studied separately from bulk electrolyte. However, in some cases spectral resolution can limit the information that can be obtained. In this study we address this issue by showing how cross polarisation (CP) NMR experiments can be used to selectively observe the in-pore ions in supercapacitor electrode materials. We do this by transferring magnetisation from 13 C nuclei in porous carbons to nearby nuclei in the cations ( 1 H) or anions ( 19 F) of an ionic liquid. Two-dimensional NMR experiments and CP kinetics measurements confirm that in-pore ions are located within Ångströms of sp 2 -hybridised carbon surfaces. Multinuclear NMR experiments hold promise for future NMR studies of supercapacitor systems where spectral resolution is limited. Copyright © 2017 University of Cambridge. Published by Elsevier Inc. All rights reserved.

A chiral BINOL-based Gemini amphiphilic gelator and its specific discrimination of native arginine by gelation in water.

PubMed

Jia, Lihua; Yin, Jianxin; Guo, Xiangfeng; Cao, Guangzhou; Tian, Xuhua; Zhu, Bo; Pu, Lin

2017-08-16

A novel axially chiral cationic Gemini amphiphile gelator (S1) derived from (S)-BINOL has been synthesized and characterized by 1 H NMR, 13 C NMR, ESI-MS and FT-IR analyses. The critical micelle concentration (CMC) of S1 was determined to be 0.21 mM in water at room temperature. A transparent hydrogel with S1 at 43 mM was obtained at room temperature and characterized using various methods including SEM, CD, fluorescence, 1 H NMR, FT-IR, and XRD. The results indicate that the hydrophobic effect of long alkyl chains, π-π stacking of naphthalene rings, and intermolecular hydrogen-bonding of the amide groups of S1 should be responsible for the hydrogel formation. Moreover, an 8.5 mM aqueous solution of S1 could gel by the addition of l-arginine, whereas it failed to gel in the presence of other 15 amino acids, respectively. It is suggested that S1 could discriminate native arginine by hydrogel formation, mainly due to the electrostatic interaction and hydrogen bonding effects between S1 and l-arginine molecules.

Method and apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise oreintationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions is zero.

NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

PubMed

Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

2018-04-01

Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity

PubMed Central

Anderson, Janet S.; Hernández, Griselda; LeMaster, David M.

2012-01-01

Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. PMID:23182463

NMR analysis of a kinetically trapped intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Noda, Yasuo; Segawa, Shin-ichi

2011-09-16

A thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase refolds into a kinetically trapped metastable intermediate when subjected to a rapid lowering of temperature. We attempted to characterise this intermediate using multidimensional NMR spectroscopy. The (1)H-(15)N heteronuclear single quantum coherence spectrum after a rapid temperature decrease (the spectrum of the intermediate) showed good chemical shift dispersion but was significantly different from that of the native state, suggesting that the intermediate adopts a nonnative but well-structured conformation. Large chemical shift changes for the backbone amide protons between the native and the intermediate states were observed for residues in the β-sheet consisting of strands 2, 3, 5, 6, and 7 as well as in the C-terminal region. These residues were found to be in close proximity to aromatic residues, suggesting that the chemical shift changes are mainly due to ring current shifts caused by the aromatic residues. The two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy experiments showed that the intermediate contained substantial, native-like NOE connectivities, although there were fewer cross peaks in the spectrum of the intermediate compared with that of the native state. It was also shown that there were native-like interresidue NOEs for residues buried in the protein, whereas many of the NOE cross peaks were lost for the residues involved in a surface-exposed aromatic cluster. These results suggest that, in the intermediate, the aromatic cluster at the surface is structurally less organised, whereas the interior of the protein has relatively rigid, native-like side-chain packing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

PubMed Central

Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

2015-01-01

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

Velocity distributions in a micromixer measured by NMR imaging.

PubMed

Ahola, Susanna; Telkki, Ville-Veikko; Stapf, Siegfried

2012-04-24

Velocity distributions (so-called propagators) with two-dimensional spatial resolution inside a chemical micromixer were measured by pulsed-field-gradient spin-echo (PGSE) nuclear magnetic resonance (NMR). A surface coil matching the volume of interest was built to enhance the signal-to-noise ratio. This enabled the acquisition of velocity maps with a very high spatial resolution of 29 μm × 39 μm. The measured propagators are compared with theoretical distributions and a good agreement is found. The results show that the propagator data provide much richer information about flow behaviour than conventional NMR velocity imaging and the information is essential for understanding the performance of a micromixer. It reveals, for example, deviations in the shape and size of the channel structures and multicomponent flow velocity distribution of overlapping channels. Propagator data efficiently compensate lost information caused by insufficient 3D resolution in conventional velocity imaging.

Starch-based xerogels: Effect of acetylation on Physicochemical and rheological properties.

PubMed

Kemas, Chinwe U; Ngwuluka, Ndidi C; Ochekpe, Nelson A; Nep, Elijah I

2017-05-01

This study was aimed at evaluating the physicochemical and rheological properties of starch-based xerogels. The starch from the shoots of Borassus aethiopium was physically modified by xerogelization, and chemically by acetylation, and combination of acetylation and xerogelization. The solubility, swelling and syneresis of the starches were determined by gravimetric techniques. Evaluation of the native starch and derivatives was done using microscopy, Fourier transform infra-red (FTIR), x-ray diffractometry (XRD), and 1 H NMR spectroscopy. Rheological evaluation was done on 10%w/v dispersions using a Bohlin Gemini rheometer (fitted with a 55mm and 2° cone and plate geometry with gap of 70). The diffractograms displayed three peaks, centered on 2θ=15.3, 17.2 and 23.1° for the native and the starch acetate while the xerogel and the starch acetate xerogel were amorphous. The 1 H NMR and FTIR confirmed the presence of acetyl groups at about 2.05ppm and 1720cm -1 , respectively. Acetylation of the native starch resulted in improvement of solubility. The starch acetate-xerogel sample formed viscoelastic gels without the need for heating. Acetylation and/or xerogelization of the native starch inhibited syneresis. Starch acetate-xerogels, may find application as stabilizer or suspending agent in liquid food and pharmaceutical formulations. Copyright © 2017 Elsevier B.V. All rights reserved.

NMR relaxometry study of cement hydration in the presence of different oxidic fine fraction materials.

PubMed

Nestle, Nikolaus

2004-01-01

NMR relaxometry has been applied to study hydrating cements for about 25 years now. The most important advantage over other experimental approaches is the possibility to conduct non-destructive measurements with a time resolution of minutes. NMR relaxometry data thus can help to identify details in the time course of cement hydration that possibly would be overlooked in other experiments with lower temporal resolution. Time-resolved information on cement hydration kinetics can provide interesting insights into the impact of oxidic additive materials on cement hydration. For PbO, a very strong delay was observed which then was systematically studied. An explanation for this delay is suggested.

NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA.

PubMed

Ma, Dejian; Tillman, Tommy S; Tang, Pei; Meirovitch, Eva; Eckenhoff, Roderic; Carnini, Anna; Xu, Yan

2008-10-28

Structural studies of polytopic membrane proteins are often hampered by the vagaries of these proteins in membrane mimetic environments and by the difficulties in handling them with conventional techniques. Designing and creating water-soluble analogues with preserved native structures offer an attractive alternative. We report here solution NMR studies of WSK3, a water-soluble analogue of the potassium channel KcsA. The WSK3 NMR structure (PDB ID code 2K1E) resembles the KcsA crystal structures, validating the approach. By more stringent comparison criteria, however, the introduction of several charged residues aimed at improving water solubility seems to have led to the possible formations of a few salt bridges and hydrogen bonds not present in the native structure, resulting in slight differences in the structure of WSK3 relative to KcsA. NMR dynamics measurements show that WSK3 is highly flexible in the absence of a lipid environment. Reduced spectral density mapping and model-free analyses reveal dynamic characteristics consistent with an isotropically tumbling tetramer experiencing slow (nanosecond) motions with unusually low local ordering. An altered hydrogen-bond network near the selectivity filter and the pore helix, and the intrinsically dynamic nature of the selectivity filter, support the notion that this region is crucial for slow inactivation. Our results have implications not only for the design of water-soluble analogues of membrane proteins but also for our understanding of the basic determinants of intrinsic protein structure and dynamics.

Method and sample spinning apparatus for measuring the NMR spectrum of an orientationally disordered sample

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR apparatus and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus spins the sample about an axis. The angle of the axis is mechanically varied such that the time average of two or more Legendre polynomials are zero.

Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-..cap alpha..-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers ofmore » the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz /sup 1/H and 125-MHz /sup 13/C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent ..beta..-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants.« less

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model

PubMed Central

Heisel, Kurt A.; Krishnan, V. V.

2014-01-01

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex (NPC) is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on 13Cα, 1Hα, and 1HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

PubMed Central

2018-01-01

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. PMID:29488756

NMR reaction monitoring in flow synthesis

PubMed Central

Gomez, M Victoria

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed. PMID:28326137

Beyond Fourier

NASA Astrophysics Data System (ADS)

Hoch, Jeffrey C.

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.

NMR reaction monitoring in flow synthesis.

PubMed

Gomez, M Victoria; de la Hoz, Antonio

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

NMR and MRI apparatus and method

DOEpatents

Clarke, John; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Myers, Whittier; McDermott, Robert; ten Haken, Bernard; Pines, Alexander; Trabesinger, Andreas

2007-03-06

Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. Additional signal to noise benefits are obtained by use of a low noise polarization coil, comprising litz wire or superconducting materials. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

Towards Single Biomolecule Imaging via Optical Nanoscale Magnetic Resonance Imaging.

PubMed

Boretti, Alberto; Rosa, Lorenzo; Castelletto, Stefania

2015-09-09

Nuclear magnetic resonance (NMR) spectroscopy is a physical marvel in which electromagnetic radiation is charged and discharged by nuclei in a magnetic field. In conventional NMR, the specific nuclei resonance frequency depends on the strength of the magnetic field and the magnetic properties of the isotope of the atoms. NMR is routinely utilized in clinical tests by converting nuclear spectroscopy in magnetic resonance imaging (MRI) and providing 3D, noninvasive biological imaging. While this technique has revolutionized biomedical science, measuring the magnetic resonance spectrum of single biomolecules is still an intangible aspiration, due to MRI resolution being limited to tens of micrometers. MRI and NMR have, however, recently greatly advanced, with many breakthroughs in nano-NMR and nano-MRI spurred by using spin sensors based on an atomic impurities in diamond. These techniques rely on magnetic dipole-dipole interactions rather than inductive detection. Here, novel nano-MRI methods based on nitrogen vacancy centers in diamond are highlighted, that provide a solution to the imaging of single biomolecules with nanoscale resolution in-vivo and in ambient conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 112th Congress

Sen. Akaka, Daniel K. [D-HI

2012-09-19

Senate - 09/22/2012 Resolution agreed to in Senate without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

ALS-causing profilin-1-mutant forms a non-native helical structure in membrane environments.

PubMed

Lim, Liangzhong; Kang, Jian; Song, Jianxing

2017-11-01

Despite having physiological functions completely different from superoxide dismutase 1 (SOD1), profilin 1 (PFN1) also carries mutations causing amyotrophic lateral sclerosis (ALS) with a striking similarity to that triggered by SOD1 mutants. Very recently, the C71G-PFN1 has been demonstrated to cause ALS by a gain of toxicity and the acceleration of motor neuron degeneration preceded the accumulation of its aggregates. Here by atomic-resolution NMR determination of conformations and dynamics of WT-PFN1 and C71G-PFN1 in aqueous buffers and in membrane mimetics DMPC/DHPC bicelle and DPC micelle, we deciphered that: 1) the thermodynamic destabilization by C71G transforms PFN1 into coexistence with the unfolded state, which is lacking of any stable tertiary/secondary structures as well as restricted ps-ns backbone motions, thus fundamentally indistinguishable from ALS-causing SOD1 mutants. 2) Most strikingly, while WT-PFN1 only weakly interacts with DMPC/DHPC bicelle without altering the native structure, C71G-PFN1 acquires abnormal capacity in strongly interacting with DMPC/DHPC bicelle and DPC micelle, energetically driven by transforming the highly disordered unfolded state into a non-native helical structure, similar to what has been previously observed on ALS-causing SOD1 mutants. Our results imply that one potential mechanism for C71G-PFN1 to initiate ALS might be the abnormal interaction with membranes as recently established for SOD1 mutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2, Non-catalyzed reactions with the wood cell wall

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2011-01-01

Solution-state NMR provides a powerful tool to observe the presence or absence of covalent bonds between wood and adhesives. Finely ground wood can be dissolved in an NMR compatible solvent system containing dimethylsulfoxide-d6 and N-methylimidazole-d6, in which the wood polymers remain largely intact. High-resolution...

Effect of molecular exchange on water droplet size analysis as determined by diffusion NMR: The W/O/W double emulsion case.

PubMed

Vermeir, Lien; Sabatino, Paolo; Balcaen, Mathieu; Declerck, Arnout; Dewettinck, Koen; Martins, José C; Guthausen, Gisela; Van der Meeren, Paul

2016-08-01

The accuracy of the inner water droplet size determination of W/O/W emulsions upon water diffusion measurement by diffusion NMR was evaluated. The resulting droplet size data were compared to the results acquired from the diffusion measurement of a highly water soluble marker compound with low permeability in the oil layer of a W/O/W emulsion, which provide a closer representation of the actual droplet size. Differences in droplet size data obtained from water and the marker were ascribed to extra-droplet water diffusion. The diffusion data of the tetramethylammonium cation marker were measured using high-resolution pulsed field gradient NMR, whereas the water diffusion was measured using both low-resolution and high-resolution NMR. Different data analysis procedures were evaluated to correct for the effect of extra-droplet water diffusion on the accuracy of water droplet size analysis. Using the water diffusion data, the use of a low measurement temperature and diffusion delay Δ could reduce the droplet size overestimation resulting from extra-droplet water diffusion, but this undesirable effect was inevitable. Detailed analysis of the diffusion data revealed that the extra-droplet diffusion effect was due to an exchange between the inner water phase and the oil phase, rather than by exchange between the internal and external aqueous phase. A promising data analysis procedure for retrieving reliable size data consisted of the application of Einstein's diffusion law to the experimentally determined diffusion distances. This simple procedure allowed determining the inner water droplet size of W/O/W emulsions upon measurement of water diffusion by low-resolution NMR at or even above room temperature. Copyright © 2016 Elsevier Inc. All rights reserved.

Boundaries of mass resolution in native mass spectrometry.

PubMed

Lössl, Philip; Snijder, Joost; Heck, Albert J R

2014-06-01

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.

Beyond Fourier.

PubMed

Hoch, Jeffrey C

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

DOE PAGES

Perras, Frederic A.

2015-12-15

Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vourtsis, Dionysios J.; Chasapis, Christos T.; Pairas, George

2014-07-18

Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successfulmore » overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.« less

Para-hydrogen raser delivers sub-millihertz resolution in nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Suefke, Martin; Lehmkuhl, Sören; Liebisch, Alexander; Blümich, Bernhard; Appelt, Stephan

2017-06-01

The precision of nuclear magnetic resonance spectroscopy (NMR) is limited by the signal-to-noise ratio, the measurement time Tm and the linewidth Δν = 1/(πT2). Overcoming the T 2 limit is possible if the nuclear spins of a molecule emit continuous radio waves. Lasers and masers are self-organized systems which emit coherent radiation in the optical and micro-wave regime. Both are based on creating a population inversion of specific energy states. Here we show continuous oscillations of proton spins of organic molecules in the radiofrequency regime (raser). We achieve this by coupling a population inversion created through signal amplification by reversible exchange (SABRE) to a high-quality-factor resonator. For the case of 15N labelled molecules, we observe multi-mode raser activity, which reports different spin quantum states. The corresponding 1H-15N J-coupled NMR spectra exhibit unprecedented sub-millihertz resolution and can be explained assuming two-spin ordered quantum states. Our findings demonstrate a substantial improvement in the frequency resolution of NMR.

Micro-scale NMR Screening of New Detergents for Membrane Protein Structural Biology

PubMed Central

Zhang, Qinghai; Horst, Reto; Geralt, Michael; Ma, Xingquan; Hong, Wen-Xu; Finn, M. G.; Stevens, Raymond C.; Wüthrich, Kurt

2008-01-01

The rate limiting step in biophysical characterization of membrane proteins is often the availability of suitable amounts of protein material. It was therefore of interest to demonstrate that micro-coil nuclear magnetic resonance (NMR) technology can be used to screen microscale quantities of membrane proteins for proper folding in samples destined for structural studies. Micoscale NMR was then used to screen a series of newly designed zwitterionic phosphocholine detergents for their ability to reconstitute membrane proteins, using the previously well characterized β-barrel E.coli outer membrane protein OmpX as a test case. Fold screening was thus achieved with μg-amounts of uniformly 2H,15N-labeld OmpX and affordable amounts of the detergents, and prescreening with SDS-gel electrophoresis ensured efficient selection of the targets for NMR studies. A systematic approach to optimize the phosphocholine motif for membrane protein refolding led to the identification of two new detergents, 138-Fos and 179-Fos, that yield 2D [15N,1H]-TROSY correlation NMR spectra of natively folded reconstituted OmpX. PMID:18479092

Random phase detection in multidimensional NMR.

PubMed

Maciejewski, Mark W; Fenwick, Matthew; Schuyler, Adam D; Stern, Alan S; Gorbatyuk, Vitaliy; Hoch, Jeffrey C

2011-10-04

Despite advances in resolution accompanying the development of high-field superconducting magnets, biomolecular applications of NMR require multiple dimensions in order to resolve individual resonances, and the achievable resolution is typically limited by practical constraints on measuring time. In addition to the need for measuring long evolution times to obtain high resolution, the need to distinguish the sign of the frequency constrains the ability to shorten measuring times. Sign discrimination is typically accomplished by sampling the signal with two different receiver phases or by selecting a reference frequency outside the range of frequencies spanned by the signal and then sampling at a higher rate. In the parametrically sampled (indirect) time dimensions of multidimensional NMR experiments, either method imposes an additional factor of 2 sampling burden for each dimension. We demonstrate that by using a single detector phase at each time sample point, but randomly altering the phase for different points, the sign ambiguity that attends fixed single-phase detection is resolved. Random phase detection enables a reduction in experiment time by a factor of 2 for each indirect dimension, amounting to a factor of 8 for a four-dimensional experiment, albeit at the cost of introducing sampling artifacts. Alternatively, for fixed measuring time, random phase detection can be used to double resolution in each indirect dimension. Random phase detection is complementary to nonuniform sampling methods, and their combination offers the potential for additional benefits. In addition to applications in biomolecular NMR, random phase detection could be useful in magnetic resonance imaging and other signal processing contexts.

A highly versatile automatized setup for quantitative measurements of PHIP enhancements

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Sauer, Grit; Hadjiali, Sara; Yurkovskaya, Alexandra V.; Breitzke, Hergen; Buntkowsky, Gerd

2017-12-01

The design and application of a versatile and inexpensive experimental extension to NMR spectrometers is described that allows to carry out highly reproducible PHIP experiments directly in the NMR sample tube, i.e. under PASADENA condition, followed by the detection of the NMR spectra of hyperpolarized products with high spectral resolution. Employing this high resolution it is feasible to study kinetic processes in the solution with high accuracy. As a practical example the dissolution of hydrogen gas in the liquid and the PHIP kinetics during the hydrogenation reaction of Fmoc-O-propargyl-L-tyrosine in acetone-d6 are monitored. The timing of the setup is fully controlled by the pulse-programmer of the NMR spectrometer. By flushing with an inert gas it is possible to efficiently quench the hydrogenation reaction in a controlled fashion and to detect the relaxation of hyperpolarization without a background reaction. The proposed design makes it possible to carry out PHIP experiments in an automatic mode and reliably determine the enhancement of polarized signals.

Mycosporine-like Amino Acids and Other Phytochemicals Directly Detected by High-Resolution NMR on Klamath (Aphanizomenon flos-aquae) Blue-Green Algae.

PubMed

Righi, Valeria; Parenti, Francesca; Schenetti, Luisa; Mucci, Adele

2016-09-07

This study describes for the first time the use of high-resolution nuclear magnetic resonance (NMR) on Klamath (Aphanizomenon flos-aquae, AFA) blue-green algae directly on powder suspension. These algae are considered to be a "superfood", due to their complete nutritional profile that has proved to have important therapeutic effects. The main advantage of NMR spectroscopy is that it permits the detection of a number of metabolites all at once. The Klamath alga metabolome was revealed to be quite complex, and the most peculiar phytochemicals that can be detected directly on algae by NMR are mycosporine-like amino acids (porphyra-334, P334; shinorine, Shi) and low molecular weight glycosides (glyceryl β-d-galactopyranoside, GalpG; glyceryl 6-amino-6-deoxy-α-d-glucopyranoside, ADG), all compounds with a high nutraceutical value. The presence of cis-3,4-DhLys was revealed for the first time. This molecule could be involved in the anticancer properties ascribed to AFA.

Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning.

PubMed

Jaudzems, Kristaps; Bertarello, Andrea; Chaudhari, Sachin R; Pica, Andrea; Cala-De Paepe, Diane; Barbet-Massin, Emeline; Pell, Andrew J; Akopjana, Inara; Kotelovica, Svetlana; Gajan, David; Ouari, Olivier; Tars, Kaspars; Pintacuda, Guido; Lesage, Anne

2018-06-18

Dynamic nuclear polarization (DNP) is a powerful way to overcome the sensitivity limitation of magic-angle-spinning (MAS) NMR experiments. However, the resolution of the DNP NMR spectra of proteins is compromised by severe line broadening associated with the necessity to perform experiments at cryogenic temperatures and in the presence of paramagnetic radicals. High-quality DNP-enhanced NMR spectra of the Acinetobacter phage 205 (AP205) nucleocapsid can be obtained by combining high magnetic field (800 MHz) and fast MAS (40 kHz). These conditions yield enhanced resolution and long coherence lifetimes allowing the acquisition of resolved 2D correlation spectra and of previously unfeasible scalar-based experiments. This enables the assignment of aromatic resonances of the AP205 coat protein and its packaged RNA, as well as the detection of long-range contacts, which are not observed at room temperature, opening new possibilities for structure determination. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct determination of phosphate sugars in biological material by (1)H high-resolution magic-angle-spinning NMR spectroscopy.

PubMed

Diserens, Gaëlle; Vermathen, Martina; Gjuroski, Ilche; Eggimann, Sandra; Precht, Christina; Boesch, Chris; Vermathen, Peter

2016-08-01

The study aim was to unambiguously assign nucleotide sugars, mainly UDP-X that are known to be important in glycosylation processes as sugar donors, and glucose-phosphates that are important intermediate metabolites for storage and transfer of energy directly in spectra of intact cells, as well as in skeletal muscle biopsies by (1)H high-resolution magic-angle-spinning (HR-MAS) NMR. The results demonstrate that sugar phosphates can be determined quickly and non-destructively in cells and biopsies by HR-MAS, which may prove valuable considering the importance of phosphate sugars in cell metabolism for nucleic acid synthesis. As proof of principle, an example of phosphate-sugar reaction and degradation kinetics after unfreezing the sample is shown for a cardiac muscle, suggesting the possibility to follow by HR-MAS NMR some metabolic pathways. Graphical abstract Glucose-phosphate sugars (Glc-1P and Glc-6P) detected in muscle by 1H HR-MAS NMR.

Comprehensive MS and Solid-State NMR Metabolomic Profiling Reveals Molecular Variations in Native Periderms from Four Solanum tuberosum Potato Cultivars.

PubMed

Huang, Wenlin; Serra, Olga; Dastmalchi, Keyvan; Jin, Liqing; Yang, Lijia; Stark, Ruth E

2017-03-15

The potato (Solanum tuberosum L.) ranks third in worldwide consumption among food crops. Whereas disposal of potato peels poses significant challenges for the food industry, secondary metabolites in these tissues are also bioactive and essential to crop development. The diverse primary and secondary metabolites reported in whole tubers and wound-healing tissues prompted a comprehensive profiling study of native periderms from four cultivars with distinctive skin morphologies and commercial food uses. Polar and nonpolar soluble metabolites were extracted concurrently, analyzed chromatographically, and characterized with mass spectrometry; the corresponding solid interfacial polymeric residue was examined by solid-state 13 C NMR. In total, 112 secondary metabolites were found in the phellem tissues; multivariate analysis identified 10 polar and 30 nonpolar potential biomarkers that distinguish a single cultivar among Norkotah Russet, Atlantic, Chipeta, and Yukon Gold cultivars which have contrasting russeting features. Compositional trends are interpreted in the context of periderm protective function.

A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

PubMed

Cassaignau, Anaïs M E; Launay, Hélène M M; Karyadi, Maria-Evangelia; Wang, Xiaolin; Waudby, Christopher A; Deckert, Annika; Robertson, Amy L; Christodoulou, John; Cabrita, Lisa D

2016-08-01

During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome.

Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

PubMed

Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

2013-04-03

Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

NMR comparison of the native energy landscapes of DLC8 dimer and monomer.

PubMed

Krishna Mohan, P M; Barve, Maneesha; Chatterjee, Amarnath; Ghosh-Roy, Anindya; Hosur, Ramakrishna V

2008-04-01

Characterization of the low energy excited states on the energy landscape of a protein is one of the exciting and challenging problems in structural biology today. In this context, we present here residue level NMR description of the low energy excited states representing locally different alternative conformations in the dynein light chain protein, in its dimeric as well as monomeric forms. Important differences have been observed between the two cases and these are not necessarily restricted to the dimer interface. Simulations indicate that the low energy excited states are within a free energy of 2-3 kcal/mol above the native state. In both the monomer and the dimer the energy landscape is very sensitive to small pH perturbations. Nearly 25% of the residues (total of residues at pH 3.0 and 3.5 for the monomer, and at pH 7.0 and 6.0 for the dimer) access alternative conformations. The observations have been rationalized on the basis of protonation-deprotonation equilibria in the side chains; histidines in the case of the dimer and aspartates/glutamates in the case of the monomer. The possible relationship of the observed ruggedness of the native energy landscape with the protein structure, and its implications to protein adaptability and unfolding have been discussed.

Structure and hydration of membranes embedded with voltage-sensing domains.

PubMed

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

2009-11-26

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

Combined NMR and EPR Spectroscopy to Determine Structures of Viral Fusion Domains in Membranes

PubMed Central

Tamm, Lukas K.; Lai, Alex L.; Li, Yinling

2008-01-01

Methods are described to determine the structures of viral membrane fusion domains in detergent micelles by NMR and in lipid bilayers by site-directed spin labeling and EPR spectroscopy. Since in favorable cases, the lower-resolution spin label data obtained in lipid bilayers fully support the higher-resolution structures obtained by solution NMR, it is possible to graft the NMR structural coordinates into membranes using the EPR-derived distance restraints to the lipid bilayer. Electron paramagnetic dynamics and distance measurements in bilayers support conclusions drawn from NMR in detergent micelles. When these methods are applied to a structure determination of the influenza virus fusion domain and four point mutations with different functional phenotypes, it is evident that a fixed-angle boomerang structure with a glycine edge on the outside of the N-terminal arm is both necessary and sufficient to support membrane fusion. The human immunodeficiency virus fusion domain forms a straight helix with a flexible C-terminus. While EPR data for this fusion domain are not yet available, it is tentatively speculated that, because of its higher hydrophobicity, a critically tilted insertion may occur even in the absence of a kinked boomerang structure in this case. PMID:17963720

Schemes of detecting nuclear spin correlations by dynamical decoupling based quantum sensing

NASA Astrophysics Data System (ADS)

Ma, Wen-Long Ma; Liu, Ren-Bao

Single-molecule sensitivity of nuclear magnetic resonance (NMR) and angstrom resolution of magnetic resonance imaging (MRI) are the highest challenges in magnetic microscopy. Recent development in dynamical decoupling (DD) enhanced diamond quantum sensing has enabled NMR of single nuclear spins and nanoscale NMR. Similar to conventional NMR and MRI, current DD-based quantum sensing utilizes the frequency fingerprints of target nuclear spins. Such schemes, however, cannot resolve different nuclear spins that have the same noise frequency or differentiate different types of correlations in nuclear spin clusters. Here we show that the first limitation can be overcome by using wavefunction fingerprints of target nuclear spins, which is much more sensitive than the ''frequency fingerprints'' to weak hyperfine interaction between the targets and a sensor, while the second one can be overcome by a new design of two-dimensional DD sequences composed of two sets of periodic DD sequences with different periods, which can be independently set to match two different transition frequencies. Our schemes not only offer an approach to breaking the resolution limit set by ''frequency gradients'' in conventional MRI, but also provide a standard approach to correlation spectroscopy for single-molecule NMR.

Neuronal current detection with low-field magnetic resonance: simulations and methods.

PubMed

Cassará, Antonino Mario; Maraviglia, Bruno; Hartwig, Stefan; Trahms, Lutz; Burghoff, Martin

2009-10-01

The noninvasive detection of neuronal currents in active brain networks [or direct neuronal imaging (DNI)] by means of nuclear magnetic resonance (NMR) remains a scientific challenge. Many different attempts using NMR scanners with magnetic fields >1 T (high-field NMR) have been made in the past years to detect phase shifts or magnitude changes in the NMR signals. However, the many physiological (i.e., the contemporarily BOLD effect, the weakness of the neuronal-induced magnetic field, etc.) and technical limitations (e.g., the spatial resolution) in observing the weak signals have led to some contradicting results. In contrast, only a few attempts have been made using low-field NMR techniques. As such, this paper was aimed at reviewing two recent developments in this front. The detection schemes discussed in this manuscript, the resonant mechanism (RM) and the DC method, are specific to NMR instrumentations with main fields below the earth magnetic field (50 microT), while some even below a few microteslas (ULF-NMR). However, the experimental validation for both techniques, with differentiating sensitivity to the various neuronal activities at specific temporal and spatial resolutions, is still in progress and requires carefully designed magnetic field sensor technology. Additional care should be taken to ensure a stringent magnetic shield from the ambient magnetic field fluctuations. In this review, we discuss the characteristics and prospect of these two methods in detecting neuronal currents, along with the technical requirements on the instrumentation.

Solution structure of a small protein containing a fluorinated side chain in the core

PubMed Central

Cornilescu, Gabriel; Hadley, Erik B.; Woll, Matthew G.; Markley, John L.; Gellman, Samuel H.; Cornilescu, Claudia C.

2007-01-01

We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe → F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe → F5-Phe mutations are interesting because aryl–perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl–aryl or perfluoroaryl–perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 → F5-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by ∼1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe → F5-Phe mutations offer the possibility of greater tertiary structural stability from side chain–side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability. PMID:17123960

Detection of tannins in modern and fossil barks and in plant residues by high-resolution solid-state 13C nuclear magnetic resonance

USGS Publications Warehouse

Wilson, M.A.; Hatcher, P.G.

1988-01-01

Bark samples isolated from brown coal deposits in Victoria, Australia, and buried wood from Rhizophora mangle have been studies by high-resolution solid-state nuclear magnetic resonance (NMR) techniques. Dipolar dephasing 13C NMR appears to be a useful method of detecting the presence of tannins in geochemical samples including barks, buried woods, peats and leaf litter. It is shown that tannins are selectively preserved in bark during coalification to the brown coal stage. ?? 1988.

1H, 15N and 13C assignments of domain 5 of Dictyostelium discoideum gelation factor (ABP-120) in its native and 8M urea-denatured states.

PubMed

Hsu, Shang-Te Danny; Cabrita, Lisa D; Christodoulou, John; Dobson, Christopher M

2009-06-01

The gelation factor from Dictyostelium discoideum (ABP-120) is an actin binding protein consisting of six immunoglobulin (Ig) domains in the C-terminal rod domain. We have recently used the pair of domains 5 and 6 of ABP-120 as a model system for studying multi-domain nascent chain folding on the ribosome. Here we present the NMR assignments of domain 5 in its native and 8M urea-denatured states.

Application of random coherence order selection in gradient-enhanced multidimensional NMR

NASA Astrophysics Data System (ADS)

Bostock, Mark J.; Nietlispach, Daniel

2016-03-01

Development of multidimensional NMR is essential to many applications, for example in high resolution structural studies of biomolecules. Multidimensional techniques enable separation of NMR signals over several dimensions, improving signal resolution, whilst also allowing identification of new connectivities. However, these advantages come at a significant cost. The Fourier transform theorem requires acquisition of a grid of regularly spaced points to satisfy the Nyquist criterion, while frequency discrimination and acquisition of a pure phase spectrum require acquisition of both quadrature components for each time point in every indirect (non-acquisition) dimension, adding a factor of 2 N -1 to the number of free- induction decays which must be acquired, where N is the number of dimensions. Compressed sensing (CS) ℓ 1-norm minimisation in combination with non-uniform sampling (NUS) has been shown to be extremely successful in overcoming the Nyquist criterion. Previously, maximum entropy reconstruction has also been used to overcome the limitation of frequency discrimination, processing data acquired with only one quadrature component at a given time interval, known as random phase detection (RPD), allowing a factor of two reduction in the number of points for each indirect dimension (Maciejewski et al. 2011 PNAS 108 16640). However, whilst this approach can be easily applied in situations where the quadrature components are acquired as amplitude modulated data, the same principle is not easily extended to phase modulated (P-/N-type) experiments where data is acquired in the form exp (iωt) or exp (-iωt), and which make up many of the multidimensional experiments used in modern NMR. Here we demonstrate a modification of the CS ℓ 1-norm approach to allow random coherence order selection (RCS) for phase modulated experiments; we generalise the nomenclature for RCS and RPD as random quadrature detection (RQD). With this method, the power of RQD can be extended to the full suite of experiments available to modern NMR spectroscopy, allowing resolution enhancements for all indirect dimensions; alone or in combination with NUS, RQD can be used to improve experimental resolution, or shorten experiment times, of considerable benefit to the challenging applications undertaken by modern NMR.

High-field 95 Mo and 183 W static and MAS NMR study of polyoxometalates.

PubMed

Haouas, Mohamed; Trébosc, Julien; Roch-Marchal, Catherine; Cadot, Emmanuel; Taulelle, Francis; Martineau-Corcos, Charlotte

2017-10-01

The potential of high-field NMR to measure solid-state 95 Mo and 183 W NMR in polyoxometalates (POMs) is explored using some archetypical structures like Lindqvist, Keggin and Dawson as model compounds that are well characterized in solution. NMR spectra in static and under magic angle spinning (MAS) were obtained, and their analysis allowed extraction of the NMR parameters, including chemical shift anisotropy and quadrupolar coupling parameters. Despite the inherent difficulties of measurement in solid state of these low-gamma NMR nuclei, due mainly to the low spectral resolution and poor signal-to-noise ratio, the observed global trends compare well with the solution-state NMR data. This would open an avenue for application of solid-state NMR to POMs, especially when liquid-state NMR is not possible, e.g., for poorly soluble or unstable compounds in solution, and for giant molecules with slow tumbling motion. This is the case of Keplerate where we provide here the first NMR characterization of this class of POMs in the solid state. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A (13)C NMR analysis of the effects of electron radiation on graphite/polyetherimide composites

NASA Technical Reports Server (NTRS)

Ferguson, Milton W.

1989-01-01

Initial investigations have been made into the use of high resolution nuclear magnetic resonance (NMR) for the characterization of radiation effects in graphite and Kevlar fibers, polymers, and the fiber/matrix interface in graphite/polyetherimide composites. Sample preparation techniques were refined. Essential equipment has been procured. A new NMR probe was constructed to increase the proton signal-to-noise ratio. Problem areas have been identified and plans developed to resolve them.

- and Cross-Polarization 13C NMR Evidence of Alterations in Molecular Composition of Humic Substances Following Afforestation with Eucalypt in Distinct Brazilian Biomes

NASA Astrophysics Data System (ADS)

Silva, I. R.; Soares, E. M.; Schmidt-Rohr, K.; Novais, R.; Barros, N.; Fernandes, S.

2010-12-01

The effect of planting fast growing tree species on SOM quality in tropical regions has been overlooked. In the present study 13C-NMR approaches were used to evaluate the impact of eucalypt cultivation on humic and fulvic acids molecular composition. The results indicate that the replacement of native vegetation by eucalypt plantations increased the relative contribution of aliphatic groups in HA from soils previously under Atlantic Forest, Grassland, and the Cerrado (Curvelo site only). The same trend was observed for FA, except in the Curvelo site. A trend for degradation and smaller contribution of O-alkyl C (carbohydrates) in HA was observed in soils under eucalyptus in Atlantic Forest and Cerrado. For FA such decreases were seen in Cerrado and Grassland biomes after eucalypt planting. In the area cultivated with pasture in the Atlantic Forest biome and in the Grassland soil, the largest contributions of lignin-derived compounds were detected in HA. The HA from the Cerrado at the Curvelo site, where the woody vegetation is virtually devoid of grassy species, showed the lowest intensity of lignin signal then those from the Cerrado sensu stricto in Itacambira, where grass species are more abundant. At our study sites, charred material are most likely derived from burning of the native vegetation, as naturally occurs in the Cerrado region, or anthropogenic fires in the Grassland biome. Burning of harvest residues in eucalypt fields was also a common practice in the early rotations. The replacement of native vegetation by eucalypt plantations increases the relative contribution of nonpolar alkyl groups in HA from soils previously under Atlantic Forest, Grassland, and the Cerrado (Curvelo site only) biomes. There is evidence of substantial contribution of lignin-derived C to HA and FA, especially in sites planted with Brachiaria sp pastures. Eucalypt introduction decreases the relative contribution of carbohydrates in HA and FA. 13C DP/MAS NMR functional groups in the humic and fulvic acid samples from the Eucalypt and native vegetation soils in the Atlantic Forest, Cerrado and Grassland biomes

Modulation of dimerization by residues distant from the interface in bovine neurophysin-II.

PubMed

Zheng, C; Peyton, D; Breslow, E

1997-09-01

The crystal structure of bovine neurophysin-II in its liganded state (Chen et al. [1991] Proc. Natl. Acad. Sci. USA 88, 4240-4244) indicates that the 1-6 sequence has a disordered conformation, lacks noncovalent contacts to other regions of the protein and is distant from the monomer-monomer interface. Cleavage of the 1-6 sequence by Staphylococcus protease V8 yielded a protein that, for the first time, crystallized in both liganded and unliganded states. Insights into the role of the 1-6 sequence in the unliganded state were obtained by NMR and related biophysical comparisons of the native and des-1-6 proteins. NMR spectra demonstrated that the environment and/or conformation of residues in the 1-6 sequence differed in liganded and unliganded states. Additionally, the unliganded des-1-6 protein exhibited a dimerization constant four to five times that of the native protein, potentially accounting for the observation that its peptide affinity was also increased. NMR studies further indicated that the increased dimerization constant of the des-1-6 protein correlated with the presence in the native protein of two isoenergetic forms of the monomer, in contrast to only a single form in the des-1-6 protein, as evidenced by signals from an internal dimerization-sensitive alpha-proton. Thus, the 1-6 sequence reduces the dimerization constant by stabilization of an alternative monomer conformation. A second product of Staphylococcus protease V8 digestion of the native protein was identified as the des-1-6 protein with an internal clip after binding site residue Glu-47, the clip presumably breaking the short 3,10 helix that most directly connects the interface to the interface to the binding site. This product, although unable to bind peptide, retained the dimerization constant of the des-1-6 protein, suggesting a lack of importance of the helix in dimerization and contrasting with the effects of the 1-6 sequence. A model is proposed in which the 1-6 sequence stabilizes the second conformation of the unliganded monomer via interactions affecting the loop region that separates the two neurophysin domains and which has been shown to influence neurophysin self-association.

Solid-state NMR covariance of homonuclear correlation spectra.

PubMed

Hu, Bingwen; Amoureux, Jean-Paul; Trebosc, Julien; Deschamps, Michael; Tricot, Gregory

2008-04-07

Direct covariance NMR spectroscopy, which does not involve a Fourier transformation along the indirect dimension, is demonstrated to obtain homonuclear correlation two-dimensional (2D) spectra in the solid state. In contrast to the usual 2D Fourier transform (2D-FT) NMR, in a 2D covariance (2D-Cov) spectrum the spectral resolution in the indirect dimension is determined by the resolution along the detection dimension, thereby largely reducing the time-consuming indirect sampling requirement. The covariance method does not need any separate phase correction or apodization along the indirect dimension because it uses those applied in the detection dimension. We compare in detail the specifications obtained with 2D-FT and 2D-Cov, for narrow and broad resonances. The efficiency of the covariance data treatment is demonstrated in organic and inorganic samples that are both well crystallized and amorphous, for spin -1/2 nuclei with 13C, 29Si, and 31P through-space or through-bond homonuclear 2D correlation spectra. In all cases, the experimental time has been reduced by at least a factor of 10, without any loss of resolution and signal to noise ratio, with respect to what is necessary with the 2D-FT NMR. According to this method, we have been able to study the silicate network of glasses by 2D NMR within reasonable experimental time despite the very long relaxation time of the 29Si nucleus. The main limitation of the 2D-Cov data treatment is related to the introduction of autocorrelated peaks onto the diagonal, which does not represent any actual connectivity.

Study of the interactions between a proline-rich protein and a flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands.

PubMed

Pascal, Christine; Paté, Franck; Cheynier, Véronique; Delsuc, Marc-André

2009-09-01

Astringency is one of the major organoleptic properties of food and beverages that are made from plants, such as tea, chocolate, beer, or red wine. This sensation is thought to be due to interactions between tannins and salivary proline-rich proteins, which are natively unfolded proteins. A human salivary proline-rich protein, namely IB-5, was produced by the recombinant method. Its interactions with a model tannin, epigallocatechin gallate (EGCG), the major flavan-3-ol in green tea, were studied here. Circular dichroism experiments showed that IB-5 presents residual structures (PPII helices) when the ionic strength is close to that in saliva. In the presence of these residual structures, IB-5 undergoes an increase in structural content upon binding to EGCG. NMR data corroborated the presence of preformed structural elements within the protein prior to binding and a partial assignment was proposed, showing partial structuration. TOCSY experiments showed that amino acids that are involved in PPII helices are more likely to interact with EGCG than those in random coil regions, as if they were anchorage points for the ligand. The signal from IB-5 in the DOSY NMR spectrum revealed an increase in polydispersity upon addition of EGCG while the mean hydrodynamic radius remained unchanged. This strongly suggests the formation of IB-5/EGCG aggregates.

Toward high-resolution NMR spectroscopy of microscopic liquid samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, Mark C.; Mehta, Hardeep S.; Chen, Ying

A longstanding limitation of high-resolution NMR spectroscopy is the requirement for samples to have macroscopic dimensions. Commercial probes, for example, are designed for volumes of at least 5 mL, in spite of decades of work directed toward the goal of miniaturization. Progress in miniaturizing inductive detectors has been limited by a perceived need to meet two technical requirements: (1) minimal separation between the sample and the detector, which is essential for sensitivity, and (2) near-perfect magnetic-field homogeneity at the sample, which is typically needed for spectral resolution. The first of these requirements is real, but the second can be relaxed,more » as we demonstrate here. By using pulse sequences that yield high-resolution spectra in an inhomogeneous field, we eliminate the need for near-perfect field homogeneity and the accompanying requirement for susceptibility matching of microfabricated detector components. With this requirement removed, typical imperfections in microfabricated components can be tolerated, and detector dimensions can be matched to those of the sample, even for samples of volume << 5 uL. Pulse sequences that are robust to field inhomogeneity thus enable small-volume detection with optimal sensitivity. We illustrate the potential of this approach to miniaturization by presenting spectra acquired with a flat-wire detector that can easily be scaled to subnanoliter volumes. In particular, we report high-resolution NMR spectroscopy of an alanine sample of volume 500 pL.« less

Spatially resolved D-T(2) correlation NMR of porous media.

PubMed

Zhang, Yan; Blümich, Bernhard

2014-05-01

Within the past decade, 2D Laplace nuclear magnetic resonance (NMR) has been developed to analyze pore geometry and diffusion of fluids in porous media on the micrometer scale. Many objects like rocks and concrete are heterogeneous on the macroscopic scale, and an integral analysis of microscopic properties provides volume-averaged information. Magnetic resonance imaging (MRI) resolves this spatial average on the contrast scale set by the particular MRI technique. Desirable contrast parameters for studies of fluid transport in porous media derive from the pore-size distribution and the pore connectivity. These microscopic parameters are accessed by 1D and 2D Laplace NMR techniques. It is therefore desirable to combine MRI and 2D Laplace NMR to image functional information on fluid transport in porous media. Because 2D Laplace resolved MRI demands excessive measuring time, this study investigates the possibility to restrict the 2D Laplace analysis to the sum signals from low-resolution pixels, which correspond to pixels of similar amplitude in high-resolution images. In this exploratory study spatially resolved D-T2 correlation maps from glass beads and mortar are analyzed. Regions of similar contrast are first identified in high-resolution images to locate corresponding pixels in low-resolution images generated with D-T2 resolved MRI for subsequent pixel summation to improve the signal-to-noise ratio of contrast-specific D-T2 maps. This method is expected to contribute valuable information on correlated sample heterogeneity from the macroscopic and the microscopic scales in various types of porous materials including building materials and rock. Copyright © 2014 Elsevier Inc. All rights reserved.

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide.

PubMed

Sardo, Mariana; Siegel, Renée; Santos, Sérgio M; Rocha, João; Gomes, José R B; Mafra, Luis

2012-06-28

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.

Solution structure of an artificial Fe8S8 ferredoxin: the D13C variant of Bacillus schlegelii Fe7S8 ferredoxin.

PubMed

Aono, S; Bentrop, D; Bertini, I; Cosenza, G; Luchinat, C

1998-12-01

The solution structure of the D13C variant of the thermostable Fe7S8 ferredoxin from Bacillus schlegelii has been determined by 1H-NMR spectroscopy in its oxidized form. In a variable-temperature NMR study the D13C variant was as thermostable (up to 90 degrees C) as the wild-type protein (WT). Seventy-five out of 77 amino acid residues and 81% of all theoretically expected proton resonances in the D13C Fe8S8 protein have been assigned. Its structure was determined through torsion angle dynamics calculations with the program DYANA, using 935 meaningful NOEs (from a total of 1251), hydrogen bond constraints, and NMR-derived dihedral angle constraints for the cluster-ligating cysteines. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.055 nm for the backbone atoms and of 0.099 nm for all heavy atoms. The overall folding of the WT is maintained in the mutant, except for the immediate vicinity of the new cysteine, which becomes much more similar to native Fe8S8 proteins. The two residues at positions 11 and 12, which constitute an insertion with respect to all known Fe8S8 proteins, assume a conformation that does not prevent the preceding and following residues from folding like in native Fe8S8 proteins. Clear evidence for the existence of two conformations involving almost half of the amino acid residues was found. The two conformations are structurally indistinguishable. Temperature-dependent NMR experiments show that one of them is thermodynamically more stable than the other.

Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations

PubMed Central

Deng, Hua

2017-01-01

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis. PMID:24018325

The application of NMR and MS methods for detection of adulteration of wine, fruit juices, and olive oil. A review.

PubMed

Ogrinc, N; Kosir, I J; Spangenberg, J E; Kidric, J

2003-06-01

This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration.

A simple and low-cost permanent magnet system for NMR

NASA Astrophysics Data System (ADS)

Chonlathep, K.; Sakamoto, T.; Sugahara, K.; Kondo, Y.

2017-02-01

We have developed a simple, easy to build, and low-cost magnet system for NMR, of which homogeneity is about 4 ×10-4 at 57 mT, with a pair of two commercially available ferrite magnets. This homogeneity corresponds to about 90 Hz spectral resolution at 2.45 MHz of the hydrogen Larmor frequency. The material cost of this NMR magnet system is little more than 100. The components can be printed by a 3D printer.

Online monitoring of fermentation processes via non-invasive low-field NMR.

PubMed

Kreyenschulte, Dirk; Paciok, Eva; Regestein, Lars; Blümich, Bernhard; Büchs, Jochen

2015-09-01

For the development of biotechnological processes in academia as well as in industry new techniques are required which enable online monitoring for process characterization and control. Nuclear magnetic resonance (NMR) spectroscopy is a promising analytical tool, which has already found broad applications in offline process analysis. The use of online monitoring, however, is oftentimes constrained by high complexity of custom-made NMR bioreactors and considerable costs for high-field NMR instruments (>US$200,000). Therefore, low-field (1) H NMR was investigated in this study in a bypass system for real-time observation of fermentation processes. The new technique was validated with two microbial systems. For the yeast Hansenula polymorpha glycerol consumption could accurately be assessed in spite of the presence of high amounts of complex constituents in the medium. During cultivation of the fungal strain Ustilago maydis, which is accompanied by the formation of several by-products, the concentrations of glucose, itaconic acid, and the relative amount of glycolipids could be quantified. While low-field spectra are characterized by reduced spectral resolution compared to high-field NMR, the compact design combined with the high temporal resolution (15 s-8 min) of spectra acquisition allowed online monitoring of the respective processes. Both applications clearly demonstrate that the investigated technique is well suited for reaction monitoring in opaque media while at the same time it is highly robust and chemically specific. It can thus be concluded that low-field NMR spectroscopy has a great potential for non-invasive online monitoring of biotechnological processes at the research and practical industrial scales. © 2015 Wiley Periodicals, Inc.

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE PAGES

Foston, Marcus B.; Samuel, Reichel; He, Jian; ...

2016-01-19

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A review of whole cell wall NMR by the direct-dissolution of biomass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foston, Marcus B.; Samuel, Reichel; He, Jian

To fully realize the potential of lignocellulosic biomass as a renewable resource for the production of fuels, chemicals, and materials, an improved understanding of the chemical and molecular structures within biomass and how those structures are formed during biosynthesis and transformed during (thermochemical and biological) conversion must be developed. This effort will require analytical techniques which are not only in-depth, rapid, and cost-effective, but also leave native cell wall features intact. Whole plant cell wall nuclear magnetic resonance (NMR) analysis facilitates unparalleled structural characterization of lignocellulosic biomass without causing (or with minimal) structural modification. The objective of this review ismore » to summarize research pertaining to solution- or gel-state whole plant cell wall NMR analysis of biomass, demonstrating the capability of NMR to delineate the structural features and transformations of biomass. In particular, this review will focus on the application of a two-dimensional solution-state NMR technique and perdeuterated ionic liquid based organic electrolyte solvents for the direct dissolution and analysis of biomass. Furthermore, we believe this type of analysis will be critical to advancing biofuel research, improving bioprocessing methodology, and enhancing plant bioengineering efforts.« less

A nuclear magnetic resonance spectrometer concept for hermetically sealed magic angle spinning investigations on highly toxic, radiotoxic, or air sensitive materials.

PubMed

Martel, L; Somers, J; Berkmann, C; Koepp, F; Rothermel, A; Pauvert, O; Selfslag, C; Farnan, I

2013-05-01

A concept to integrate a commercial high-resolution, magic angle spinning nuclear magnetic resonance (MAS-NMR) probe capable of very rapid rotation rates (70 kHz) in a hermetically sealed enclosure for the study of highly radiotoxic materials has been developed and successfully demonstrated. The concept centres on a conventional wide bore (89 mm) solid-state NMR magnet operating with industry standard 54 mm diameter probes designed for narrow bore magnets. Rotor insertion and probe tuning take place within a hermetically enclosed glovebox, which extends into the bore of the magnet, in the space between the probe and the magnet shim system. Oxygen-17 MAS-NMR measurements demonstrate the possibility of obtaining high quality spectra from small sample masses (~10 mg) of highly radiotoxic material and the need for high spinning speeds to improve the spectral resolution when working with actinides. The large paramagnetic susceptibility arising from actinide paramagnetism in (Th(1-x)U(x))O2 solid solutions gives rise to extensive spinning sidebands and poor resolution at 15 kHz, which is dramatically improved at 55 kHz. The first (17)O MAS-NMR measurements on NpO(2+x) samples spinning at 55 kHz are also reported. The glovebox approach developed here for radiotoxic materials can be easily adapted to work with other hazardous or even air sensitive materials.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR

PubMed Central

Mobli, Mehdi; Hoch, Jeffrey C.

2017-01-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. PMID:25456315

Towards native-state imaging in biological context in the electron microscope

PubMed Central

Weston, Anne E.; Armer, Hannah E. J.

2009-01-01

Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context. PMID:19916039

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melchior, Jan-Patrick; Frick, Bernhard

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE PAGES

Melchior, Jan-Patrick; Frick, Bernhard

2017-09-22

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

New mechanistic insights regarding Pd/Cu catalysts for the Sonogashira reaction: HRMAS NMR studies of silica-immobilized systems.

PubMed

Posset, Tobias; Blümel, Janet

2006-07-05

The title technique, high-resolution magic angle spinning NMR of suspensions, constitutes a powerful new tool for investigating the structures and mobilities of immobilized species and, thus, for optimizing heterobimetallic catalyst systems, such as the Sonogashira coupling of terminal alkynes and aryl halides.

Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC.

PubMed

Meier, Sebastian; Petersen, Bent O; Duus, Jens Ø; Sørensen, Ole W

2009-11-02

The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of (13)C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the (1)H spins, all in a single spectrum with good resolution and non-informative diagonal-type peaks suppressed. Clean HMBC is a remedy for the ubiquitous problem of strong coupling induced one-bond correlation artifacts in HMBC spectra of carbohydrates. Both experiments work well for one of the largest carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.

Solid-state NMR adiabatic TOBSY sequences provide enhanced sensitivity for multidimensional high-resolution magic-angle-spinning 1H MR spectroscopy

NASA Astrophysics Data System (ADS)

Andronesi, Ovidiu C.; Mintzopoulos, Dionyssios; Struppe, Jochem; Black, Peter M.; Tzika, A. Aria

2008-08-01

We propose a solid-state NMR method that maximizes the advantages of high-resolution magic-angle-spinning (HRMAS) applied to intact biopsies when compared to more conventional liquid-state NMR approaches. Theoretical treatment, numerical simulations and experimental results on intact human brain biopsies are presented. Experimentally, it is proven that an optimized adiabatic TOBSY (TOtal through Bond correlation SpectroscopY) solid-state NMR pulse sequence for two-dimensional 1H- 1H homonuclear scalar-coupling longitudinal isotropic mixing provides a 20%-50% improvement in signal-to-noise ratio relative to its liquid-state analogue TOCSY (TOtal Correlation SpectroscopY). For this purpose we have refined the C9151 symmetry-based 13C TOBSY pulse sequence for 1H MRS use and compared it to MLEV-16 TOCSY sequence. Both sequences were rotor-synchronized and implemented using WURST-8 adiabatic inversion pulses. As discussed theoretically and shown in simulations, the improved magnetization-transfer comes from actively removing residual dipolar couplings from the average Hamiltonian. Importantly, the solid-state NMR techniques are tailored to perform measurements at low temperatures where sample degradation is reduced. This is the first demonstration of such a concept for HRMAS metabolic profiling of disease processes, including cancer, from biopsies requiring reduced sample degradation for further genomic analysis.

NMR of thin layers using a meanderline surface coil

DOEpatents

Cowgill, Donald F.

2001-01-01

A miniature meanderline sensor coil which extends the capabilities of nuclear magnetic resonance (NMR) to provide analysis of thin planar samples and surface layer geometries. The sensor coil allows standard NMR techniques to be used to examine thin planar (or curved) layers, extending NMRs utility to many problems of modern interest. This technique can be used to examine contact layers, non-destructively depth profile into films, or image multiple layers in a 3-dimensional sense. It lends itself to high resolution NMR techniques of magic angle spinning and thus can be used to examine the bonding and electronic structure in layered materials or to observe the chemistry associated with aging coatings. Coupling this sensor coil technology with an arrangement of small magnets will produce a penetrator probe for remote in-situ chemical analysis of groundwater or contaminant sediments. Alternatively, the sensor coil can be further miniaturized to provide sub-micron depth resolution within thin films or to orthoscopically examine living tissue. This thin-layer NMR technique using a stationary meanderline coil in a series-resonant circuit has been demonstrated and it has been determined that the flat meanderline geometry has about he same detection sensitivity as a solenoidal coil, but is specifically tailored to examine planar material layers, while avoiding signals from the bulk.

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

High-resolution proton nuclear magnetic resonance characterization of seminolipid from bovine spermatozoa.

PubMed

Alvarez, J G; Storey, B T; Hemling, M L; Grob, R L

1990-06-01

The high-resolution one- and two-dimensional proton nuclear magnetic resonance (1H-NMR) characterization of seminolipid from bovine spermatozoa is presented. The 1H-NMR data was confirmed by gas-liquid chromatography-mass spectrometric analysis of the partially methylated alditol acetates of the sugar unit, mild alkaline methanolysis of the glyceryl ester, mobility on normal phase and diphasic thin-layer chromatography (HPTLC), and fast atom bombardment mass spectrometry (FAB-MS). The structure of the molecule corresponds to 1-O-hexadecyl-2-O-hexadecanoyl-3-O-beta-D-(3'-sulfo)-galactopyranosyl- sn-glycerol.

Multi-crystal native SAD analysis at 6 keV.

PubMed

Liu, Qun; Guo, Youzhong; Chang, Yanqi; Cai, Zheng; Assur, Zahra; Mancia, Filippo; Greene, Mark I; Hendrickson, Wayne A

2014-10-01

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

Evaluation of the separation performance of polyvinylpyrrolidone as a virtual stationary phase for chromatographic NMR.

PubMed

Huang, Shaohua; Wu, Rui; Bai, Zhengwu; Yang, Ying; Li, Suying; Dou, Xiaowei

2014-09-01

Polyvinylpyrrolidone (PVP) was used as a virtual stationary phase to separate p-xylene, benzyl alcohol, and p-methylphenol by the chromatographic NMR technique. The effects of concentration and weight-average molecular weight (Mw) of PVP, solvent viscosity, solvent polarity, and sample temperature on the resolution of these components were investigated. It was found that both higher PVP concentration and higher PVP Mw caused the increase of diffusion resolution for the three components. Moreover, the diffusion resolution did not change at viscosity-higher solvents. Moreover, the three components showed different resolution at different solvents. As temperature increased, the diffusion resolution between p-xylene and benzyl alcohol gradually increased, and the one between p-xylene and p-methylphenol slightly increased from 278 to 298 K and then decreased above 298 K. It was also found that the polarity of the analytes played an important role for the separation by affecting the diffusion coefficient. Copyright © 2014 John Wiley & Sons, Ltd.

Susceptibility-matched plugs for microcoil NMR probes

NASA Astrophysics Data System (ADS)

Kc, Ravi; Gowda, Yashas N.; Djukovic, Danijel; Henry, Ian D.; Park, Gregory H. J.; Raftery, Daniel

2010-07-01

For mass-limited samples, the residual sample volume outside the detection coil is an important concern, as is good base line resolution. Here, we present the construction and evaluation of magnetic susceptibility-matched plugs for microcoil NMR sample cells which address these issues. Mixed-epoxy glue and ultem tube plugs that have susceptibility values close to those of perfluorocarbon FC-43 (fluorinert) and copper were used in small volume (0.5-2 μL) and larger volume (15-20 μL) thin glass capillary sample cells. Using these plugs, the sample volume efficiency (i.e. ratio of active volume to total sample volume in the microcoil NMR cell) was improved by 6-12-fold without sensitivity and resolution trade-offs. Comparison with laser etched or heat etched microcoil sample cells is provided. The approaches described are potentially useful in metabolomics for biomarkers detection in mass limited biological samples.

Susceptibility-matched plugs for microcoil NMR probes.

PubMed

Kc, Ravi; Gowda, Yashas N; Djukovic, Danijel; Henry, Ian D; Park, Gregory H J; Raftery, Daniel

2010-07-01

For mass-limited samples, the residual sample volume outside the detection coil is an important concern, as is good base line resolution. Here, we present the construction and evaluation of magnetic susceptibility-matched plugs for microcoil NMR sample cells which address these issues. Mixed-epoxy glue and ultem tube plugs that have susceptibility values close to those of perfluorocarbon FC-43 (fluorinert) and copper were used in small volume (0.5-2 microL) and larger volume (15-20 microL) thin glass capillary sample cells. Using these plugs, the sample volume efficiency (i.e. ratio of active volume to total sample volume in the microcoil NMR cell) was improved by 6-12-fold without sensitivity and resolution trade-offs. Comparison with laser etched or heat etched microcoil sample cells is provided. The approaches described are potentially useful in metabolomics for biomarkers detection in mass limited biological samples. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

13C and 1H NMR (Nuclear Magnetic Resonance) studies of solid polyolefines

NASA Technical Reports Server (NTRS)

Cudby, M. E. A.; Harris, R. K.; Metcalfe, K.; Packer, K. J.; Smith, P. W. R.

1983-01-01

The basis of H-1 and C-13 high-resolution NMR investigations of solid polymers is outlined. The C-13 NMR spectra of solid syndiotactic and isotactic polypropene are discussed and their interpretation in terms of conformation and chain-packing effects are reviewed. The effects of decreasing temperature on the C-13 high-resolution spectrum of an annealed sample of isotactic polypropene is described and interpreted in terms of the crystal structure. The question of the proportion of the sample giving rise to C-13 signals is addressed and some results reported. The main cause for observing only part of the total sample is shown to be the H-1 rotating frame spin-lattice relaxation behavior. The H-1 spin-lattice relaxation and spectral characteristics of a number of polyolefin samples are summarized and the role of spin-diffusion discussed.

Susceptibility-matched plugs for microcoil NMR probes

PubMed Central

Kc, Ravi; Gowda, Yashas N.; Djukovic, Danijel; Henry, Ian D; Park, Gregory H J; Raftery, Daniel

2010-01-01

For mass limited samples, the residual sample volume outside the detection coil is an important concern, as is good base line resolution. Here, we present the construction and evaluation of magnetic susceptibility-matched plugs for microcoil NMR sample cells which address these issues. Mixed-epoxy glue and ultem tube plugs that have susceptibility values close to those of perfluorocarbon FC-43 (fluorinert) and copper were used in small volume (0.5 to 2 μL) and larger volume (15 to 20 μL) thin glass capillary sample cells. Using these plugs, the sample volume efficiency (i.e. ratio of active volume to total sample volume in the microcoil NMR cell) was improved by 6 to 12 fold without sensitivity and resolution trade-offs. Comparison with laser etched or heat etched microcoil sample cells is provided. The approaches described are potentially useful in metabolomics for biomarkers detection in mass limited biological samples. PMID:20510638

Video Toroid Cavity Imager

DOEpatents

Gerald, II, Rex E.; Sanchez, Jairo; Rathke, Jerome W.

2004-08-10

A video toroid cavity imager for in situ measurement of electrochemical properties of an electrolytic material sample includes a cylindrical toroid cavity resonator containing the sample and employs NMR and video imaging for providing high-resolution spectral and visual information of molecular characteristics of the sample on a real-time basis. A large magnetic field is applied to the sample under controlled temperature and pressure conditions to simultaneously provide NMR spectroscopy and video imaging capabilities for investigating electrochemical transformations of materials or the evolution of long-range molecular aggregation during cooling of hydrocarbon melts. The video toroid cavity imager includes a miniature commercial video camera with an adjustable lens, a modified compression coin cell imager with a fiat circular principal detector element, and a sample mounted on a transparent circular glass disk, and provides NMR information as well as a video image of a sample, such as a polymer film, with micrometer resolution.

Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure.

PubMed

Fuglestad, Brian; Stetz, Matthew A; Belnavis, Zachary; Wand, A Joshua

2017-12-01

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately -115mlmol -1 and an average pressure dependent change in compressibility of approximately 30mlmol -1 kbar -1 . In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state. Copyright © 2017 Elsevier B.V. All rights reserved.

Studies of organic paint binders by NMR spectroscopy

NASA Astrophysics Data System (ADS)

Spyros, A.; Anglos, D.

2006-06-01

Nuclear magnetic resonance spectroscopy is applied to the study of aged binding media used in paintings, namely linseed oil, egg tempera and an acrylic medium. High resolution 1D and 2D NMR experiments establish the state of hydrolysis and oxidation of the linseed and egg tempera binders after five years of aging, by determining several markers sensitive to the hydrolytic and oxidative processes of the binder lipid fraction. The composition of the acrylic binder co-polymer is determined by 2D NMR spectroscopy, while the identification of a surfactant, poly(ethylene glycol), found in greater amounts in aged acrylic medium, is reported. The non-destructive nature of the proposed analytical NMR methodology, and minimization of the amount of binder material needed through the use of sophisticated cryoprobes and hyphenated LC-NMR techniques, make NMR attractive for the arts analyst, in view of its rapid nature and experimental simplicity.

Screening of Small Molecule Interactor Library by Using In-Cell NMR Spectroscopy (SMILI-NMR)

PubMed Central

Xie, Jingjing; Thapa, Rajiv; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander

2011-01-01

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP–FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast. PMID:19422228

High-field EPR on membrane proteins - crossing the gap to NMR.

PubMed

Möbius, Klaus; Lubitz, Wolfgang; Savitsky, Anton

2013-11-01

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

PubMed

Wang, Guanbo; Kaltashov, Igor A

2014-08-05

Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

High-sensitivity NMR beyond 200,000 atmospheres of pressure

NASA Astrophysics Data System (ADS)

Meier, T.; Reichardt, S.; Haase, J.

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. 1 H NMR of water shows sensitivity and resolution obtained with the cells, and 63 Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. 115 In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry.

NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

PubMed

Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

2017-09-13

NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations.

PubMed

Webber, Amy L; Elena, Bénédicte; Griffin, John M; Yates, Jonathan R; Pham, Tran N; Mauri, Francesco; Pickard, Chris J; Gil, Ana M; Stein, Robin; Lesage, Anne; Emsley, Lyndon; Brown, Steven P

2010-07-14

A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.

State Legislation Relating to Native Americans, 1991.

ERIC Educational Resources Information Center

Reed, James B.

1991-01-01

This report summarizes legislative activities in states that enacted bills and resolutions relating to Native Americans in 1991. Conflicts between states and the Indian tribes within their borders were the subject of significant legislation in 1991. In all, 220 bills and resolutions were introduced in state legislatures; 77 passed and 20 are still…

Detergent Optimized Membrane Protein Reconstitution in Liposomes for Solid State NMR

PubMed Central

2015-01-01

For small helical membrane proteins, their structures are highly sensitive to their environment, and solid state NMR is a structural technique that can characterize these membrane proteins in native-like lipid bilayers and proteoliposomes. To date, a systematic method by which to evaluate the effect of the solubilizing detergent on proteoliposome preparations for solid state NMR of membrane proteins has not been presented in the literature. A set of experiments are presented aimed at determining the conditions most amenable to dialysis mediated reconstitution sample preparation. A membrane protein from M. tuberculosis is used to illustrate the method. The results show that a detergent that stabilizes the most protein is not always ideal and sometimes cannot be removed by dialysis. By focusing on the lipid and protein binding properties of the detergent, proteoliposome preparations can be readily produced, which provide double the signal-to-noise ratios for both the oriented sample and magic angle spinning solid state NMR. The method will allow more membrane protein drug targets to be structurally characterized in lipid bilayer environments. PMID:24665863

Simultaneous 19F-1H medium resolution NMR spectroscopy for online reaction monitoring

NASA Astrophysics Data System (ADS)

Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

2014-12-01

Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02 mm) was used as a flow cell in combination with a 5 mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a 1H Larmor frequency of 43.32 MHz and 40.68 MHz for 19F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating 19F and 1H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500 MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02 mm was characterised regarding the limit of detection (LOQ (1H) = 0.335 mol L-1 and LOQ (19F) = 0.130 mol L-1 for trifluoroethanol in D2O (single scan)) and maximum quantitative flow rates up to 0.3 mL min-1. Thus, a series of single scan 19F and 1H NMR spectra acquired with this simple set-up already presents a valuable basis for quantitative reaction monitoring.

Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Ju; Isern, Nancy G.; Burton, Sarah D.

2013-10-31

NMR metabolomics, consisting of solid state high resolution (hr) magic angle spinning (MAS) 1H NMR (1H hr-MAS), liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver . The melanoma group can be differentiated from its control group by PCA analysis of the absolute concentrations or by the absolute peak intensities of metabolites from either 1H hr-MAS NMR data on intact liver tissues or liquid state 1H-NMR spectra on liver tissue extracts. In particular, we found that the absolute concentrations of alanine, glutamate, creatine, creatinine, fumarate andmore » cholesterol are elevated in the melanoma group as compared to controls, while the absolute concentrations of succinate, glycine, glucose, and the family of linear lipids including long chain fatty acids, total choline and acylglycerol are decreased. The ratio of glycerophosphocholine to phosphocholine is increased by about 1.5 fold in the melanoma group, while the absolute concentration of total choline is actually lower in melanoma mice. These results suggest the following picture in secondary melanoma metastasis: Linear lipid levels are decreased by beta oxidation in the melanoma group, which contributes to an increase in the synthesis of cholesterol, and also provides an energy source input for TCA cycle. These findings suggest a link between lipid oxidation, the TCA cycle and the hypoxia-inducible factors (HIF) signal pathway in tumor metastases. Thus this study indicates that the metabolic profile derived from NMR analysis can provide a valuable bio-signature of malignancy and cell hypoxia in metastatic melanoma.« less

A simple and low-cost permanent magnet system for NMR.

PubMed

Chonlathep, K; Sakamoto, T; Sugahara, K; Kondo, Y

2017-02-01

We have developed a simple, easy to build, and low-cost magnet system for NMR, of which homogeneity is about 4×10 -4 at 57mT, with a pair of two commercially available ferrite magnets. This homogeneity corresponds to about 90Hz spectral resolution at 2.45MHz of the hydrogen Larmor frequency. The material cost of this NMR magnet system is little more than $100. The components can be printed by a 3D printer. Copyright © 2016 Elsevier Inc. All rights reserved.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

PubMed

Mobli, Mehdi; Hoch, Jeffrey C

2014-11-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

Band selective small flip angle COSY: a simple experiment for the analyses of 1H NMR spectra of small chiral molecules.

PubMed

Prabhu, Uday Ramesh; Suryaprakash, N

2008-12-01

The NMR spectroscopic discrimination of enantiomers in the chiral liquid crystalline solvent is more often carried out using (2)H detection in its natural abundance. The employment of (1)H detection for such a purpose is severely hampered due to significant loss of resolution in addition to indistinguishable overlap of the spectra from the two enantiomers. This study demonstrates that the band selected small flip angle homonuclear correlation experiment is a simple and robust technique that provides unambiguous discrimination, very high spectral resolution, reduced multiplicity of transitions, relative signs of the couplings and enormous saving of instrument time.

Edible seaweed as future functional food: Identification of α-glucosidase inhibitors by combined use of high-resolution α-glucosidase inhibition profiling and HPLC-HRMS-SPE-NMR.

PubMed

Liu, Bingrui; Kongstad, Kenneth T; Wiese, Stefanie; Jäger, Anna K; Staerk, Dan

2016-07-15

Crude chloroform, ethanol and acetone extracts of nineteen seaweed species were screened for their antioxidant and α-glucosidase inhibitory activity. Samples showing more than 60% α-glucosidase inhibitory activity, at a concentration of 1 mg/ml, were furthermore investigated using high-resolution α-glucosidase inhibition profiling combined with high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy (HR-bioassay/HPLC-HRMS-SPE-NMR). The results showed Ascophyllum nodosum and Fucus vesicolosus to be rich in antioxidants, equaling a Trolox equivalent antioxidant capacity of 135 and 108 mM Troloxmg(-1) extract, respectively. HR-bioassay/HPLC-HRMS-SPE-NMR showed the α-glucosidase inhibitory activity of A. nodosum, F. vesoculosus, Laminaria digitata, Laminaria japonica and Undaria pinnatifida to be caused by phlorotannins as well as fatty acids - with oleic acid, linoleic acid and eicosapentaenoic acid being the most potent with IC50 values of 0.069, 0.075 and 0.10 mM, respectively, and showing a mixed-type inhibition mode. Copyright © 2016 Elsevier Ltd. All rights reserved.

Alaska Natives & the Land.

ERIC Educational Resources Information Center

Arnold, Robert D.; And Others

Pursuant to the Native land claims within Alaska, this compilation of background data and interpretive materials relevant to a fair resolution of the Alaska Native problem seeks to record data and information on the Native peoples; the land and resources of Alaska and their uses by the people in the past and present; land ownership; and future…

Quantitative analysis of NMR spectra with chemometrics

NASA Astrophysics Data System (ADS)

Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

2008-01-01

The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

PubMed

Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

2015-08-24

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Masquerade of Plesiomonas shigelloides Strain CNCTC 78/89 O-Antigen-High-Resolution Magic Angle Spinning NMR Reveals the Modified d-galactan I of Klebsiella pneumoniae.

PubMed

Ucieklak, Karolina; Koj, Sabina; Pawelczyk, Damian; Niedziela, Tomasz

2017-11-29

The high-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR) analysis of Plesiomonas shigelloides 78/89 lipopolysaccharide directly on bacteria revealed the characteristic structural features of the O -acetylated polysaccharide in the NMR spectra. The O -antigen profiles were unique, yet the pattern of signals in the, spectra along with their ¹H, 13 C chemical shift values, resembled these of d-galactan I of Klebsiella pneumoniae . The isolated O- specific polysaccharide (O-PS) of P. shigelloides strain CNCTC 78/89 was investigated by ¹H and 13 C NMR spectroscopy, mass spectrometry and chemical methods. The analyses demonstrated that the P. shigelloides 78/89 O- PS is composed of →3)-α-d-Gal p -(1→3)-β-d-Gal f 2OAc-(1→ disaccharide repeating units. The O- acetylation was incomplete and resulted in a microheterogeneity of the O- antigen. This O- acetylation generates additional antigenic determinants within the O- antigen, forms a new chemotype, and contributes to the epitopes recognized by the O- serotype specific antibodies. The serological cross-reactivities further confirmed the inter-specific structural similarity of these O- antigens.

Analysis of commercial proanthocyanidins. Part 4: solid state (13)C NMR as a tool for in situ analysis of proanthocyanidin tannins, in heartwood and bark of quebracho and acacia, and related species.

PubMed

Reid, David G; Bonnet, Susan L; Kemp, Gabre; van der Westhuizen, Jan H

2013-10-01

(13)C NMR is an effective method of characterizing proanthocyanidin (PAC) tannins in quebracho (Schinopsis lorentzii) heartwood and black wattle (Acacia mearnsii) bark, before and after commercial extraction. The B-rings of the constituent flavan-3-ols, catechols (quebracho) or pyrogallols (wattle), are recognized in unprocessed source materials by "marker" signals at ca. 118 or 105ppm, respectively. NMR allows the minimum extraction efficiency to be calculated; ca. 30%, and ca. 80%, for quebracho heartwood and black wattle bark, respectively. NMR can also identify PAC tannin (predominantly robinetinidin), and compare tannin content, in bark from other acacia species; tannin content decreases in the order A. mearnsii, Acacia pycnantha (87% of A. mearnsii), Acacia dealbata and Acacia decurrens (each 74%) and Acacia karroo (30%). Heartwood from an underexploited PAC tannin source, Searsia lancea, taxonomically close to quebracho, shows abundant profisetinidin and catechin PACs. NMR offers the advantage of being applicable to source materials in their native state, and has potential applications in optimizing extraction processes, identification of tannin sources, and characterization of tannin content in cultivar yield improvement programmes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Grafting C8-C16 alkyl groups altered the self-assembly and curcumin -loading properties of sodium caseinate in water.

PubMed

Zhang, Yaqiong; Yang, Puyu; Yao, Fangyi; Liu, Jie; Yu, Liangli Lucy

2018-02-01

The data presented here are related to the research article entitled "Synthesis and characterization of alkylated caseinate, and its structure-curcumin loading property relationship in water" (Zhang et al., 2018) [1]. This data article reports the detailed spectra information for 1 H NMR, 13 C NMR and UPLC-Q-TOF MS of the N-succinimidyl fatty acid esters with various alkyl chain lengths (Cn-NHSs, n = 8, 12, 14 and 16). 1 H NMR, 13 C NMR and UPLC-Q-TOF MS spectra for C16-NHS are shown as an example. Then the stacked 1 H NMR spectra of the obtained alkylated caseinates (Cn-caseinates, n = 8, 12, 14 and 16) are provided. The surface hydrophobicity index (S 0 ) of Cn-caseinates with different substitution degrees (SD) of alkyl groups is shown. Additionally, Visual appearances for the formed aqueous dispersions of curcumin-loaded native caseinate (NaCas) and Cn-caseinates self-assemblies are shown. X-ray diffraction patterns of curcumin, C16-caseinate, its physical mixture and curcumin-loaded C16-caseinate self-assemblies are examined. The re-dispersibility and short-term storage stability of the curcumin-loaded NaCas and C16-caseinate self-assemblies are also studied.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Reducing seed dependent variability of non-uniformly sampled multidimensional NMR data

NASA Astrophysics Data System (ADS)

Mobli, Mehdi

2015-07-01

The application of NMR spectroscopy to study the structure, dynamics and function of macromolecules requires the acquisition of several multidimensional spectra. The one-dimensional NMR time-response from the spectrometer is extended to additional dimensions by introducing incremented delays in the experiment that cause oscillation of the signal along "indirect" dimensions. For a given dimension the delay is incremented at twice the rate of the maximum frequency (Nyquist rate). To achieve high-resolution requires acquisition of long data records sampled at the Nyquist rate. This is typically a prohibitive step due to time constraints, resulting in sub-optimal data records to the detriment of subsequent analyses. The multidimensional NMR spectrum itself is typically sparse, and it has been shown that in such cases it is possible to use non-Fourier methods to reconstruct a high-resolution multidimensional spectrum from a random subset of non-uniformly sampled (NUS) data. For a given acquisition time, NUS has the potential to improve the sensitivity and resolution of a multidimensional spectrum, compared to traditional uniform sampling. The improvements in sensitivity and/or resolution achieved by NUS are heavily dependent on the distribution of points in the random subset acquired. Typically, random points are selected from a probability density function (PDF) weighted according to the NMR signal envelope. In extreme cases as little as 1% of the data is subsampled. The heavy under-sampling can result in poor reproducibility, i.e. when two experiments are carried out where the same number of random samples is selected from the same PDF but using different random seeds. Here, a jittered sampling approach is introduced that is shown to improve random seed dependent reproducibility of multidimensional spectra generated from NUS data, compared to commonly applied NUS methods. It is shown that this is achieved due to the low variability of the inherent sensitivity of the random subset chosen from a given PDF. Finally, it is demonstrated that metrics used to find optimal NUS distributions are heavily dependent on the inherent sensitivity of the random subset, and such optimisation is therefore less critical when using the proposed sampling scheme.

Oligomerization of a molecular chaperone modulates its activity

PubMed Central

Kawagoe, Soichiro; Ishimori, Koichiro

2018-01-01

Molecular chaperones alter the folding properties of cellular proteins via mechanisms that are not well understood. Here, we show that Trigger Factor (TF), an ATP-independent chaperone, exerts strikingly contrasting effects on the folding of non-native proteins as it transitions between a monomeric and a dimeric state. We used NMR spectroscopy to determine the atomic resolution structure of the 100 kDa dimeric TF. The structural data show that some of the substrate-binding sites are buried in the dimeric interface, explaining the lower affinity for protein substrates of the dimeric compared to the monomeric TF. Surprisingly, the dimeric TF associates faster with proteins and it exhibits stronger anti-aggregation and holdase activity than the monomeric TF. The structural data show that the dimer assembles in a way that substrate-binding sites in the two subunits form a large contiguous surface inside a cavity, thus accounting for the observed accelerated association with unfolded proteins. Our results demonstrate how the activity of a chaperone can be modulated to provide distinct functional outcomes in the cell. PMID:29714686

Purification and biophysical characterization of the core protease domain of anthrax lethal factor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gkazonis, Petros V.; Dalkas, Georgios A.; Chasapis, Christos T.

2010-06-04

Anthrax lethal toxin (LeTx) stands for the major virulence factor of the anthrax disease. It comprises a 90 kDa highly specific metalloprotease, the anthrax lethal factor (LF). LF possesses a catalytic Zn{sup 2+} binding site and is highly specific against MAPK kinases, thus representing the most potent native biomolecule to alter and inactivate MKK [MAPK (mitogen-activated protein kinase) kinases] signalling pathways. Given the importance of the interaction between LF and substrate for the development of anti-anthrax agents as well as the potential treatment of nascent tumours, the analysis of the structure and dynamic properties of the LF catalytic site aremore » essential to elucidate its enzymatic properties. Here we report the recombinant expression and purification of a C-terminal part of LF (LF{sub 672-776}) that harbours the enzyme's core protease domain. The biophysical characterization and backbone assignments ({sup 1}H, {sup 13}C, {sup 15}N) of the polypeptide revealed a stable, well folded structure even in the absence of Zn{sup 2+}, suitable for high resolution structural analysis by NMR.« less

Reconstruction of full high-resolution HSQC using signal split in aliased spectra.

PubMed

Foroozandeh, Mohammadali; Jeannerat, Damien

2015-11-01

Resolution enhancement is a long-sought goal in NMR spectroscopy. In conventional multidimensional NMR experiments, such as the (1) H-(13) C HSQC, the resolution in the indirect dimensions is typically 100 times lower as in 1D spectra because it is limited by the experimental time. Reducing the spectral window can significantly increase the resolution but at the cost of ambiguities in frequencies as a result of spectral aliasing. Fortunately, this information is not completely lost and can be retrieved using methods in which chemical shifts are encoded in the aliased spectra and decoded after processing to reconstruct high-resolution (1) H-(13) C HSQC spectrum with full spectral width and a resolution similar to that of 1D spectra. We applied a new reconstruction method, RHUMBA (reconstruction of high-resolution using multiplet built on aliased spectra), to spectra obtained from the differential evolution for non-ambiguous aliasing-HSQC and the new AMNA (additional modulation for non-ambiguous aliasing)-HSQC experiments. The reconstructed spectra significantly facilitate both manual and automated spectral analyses and structure elucidation based on heteronuclear 2D experiments. The resolution is enhanced by two orders of magnitudes without the usual complications due to spectral aliasing. Copyright © 2015 John Wiley & Sons, Ltd.

Glycerol dehydration of native and diabetic animal tissues studied by THz-TDS and NMR methods

PubMed Central

Smolyanskaya, O. A.; Schelkanova, I. J.; Kulya, M. S.; Odlyanitskiy, E. L.; Goryachev, I. S.; Tcypkin, A. N.; Grachev, Ya. V.; Toropova, Ya. G.; Tuchin, V. V.

2018-01-01

The optical clearing method has been widely used for different spectral ranges where it provides tissue transparency. In this work, we observed the enhanced penetration of the terahertz waves inside biological samples (skin, kidney, and cornea) treated with glycerol solutions inducing changes of optical and dielectric properties. It was supported by the observed trend of free-to-bound water ratio measured by the nuclear magnetic resonance (NMR) method. The terahertz clearing efficiency was found to be less for diabetic samples than for normal ones. Results of the numerical simulation proved that pulse deformation is due to bigger penetration depth caused by the reduction of absorption and refraction at optical clearing. PMID:29541513

Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold*S⃞

PubMed Central

Wang, Conan K.; Hu, Shu-Hong; Martin, Jennifer L.; Sjögren, Tove; Hajdu, Janos; Bohlin, Lars; Claeson, Per; Göransson, Ulf; Rosengren, K. Johan; Tang, Jun; Tan, Ning-Hua; Craik, David J.

2009-01-01

Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 Å. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design. PMID:19211551

Investigations on the Crystal-Chemical Behavior of Transition-Metal-Bearing Aluminosilicate Garnet Solid Solutions Using 27Al and 29Si NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Palke, A. C.; Geiger, C. A.; Stebbins, J. F.

2015-12-01

The petrological importance of silicate garnet is derived from the presence of three distinct cation sites of varying size and coordination number. This allows for a wide range of trace, minor, and major element substitutions. However, a full and precise crystal-chemical understanding of the nature of transition metals in garnet is not at hand. Possible mechanisms of various charge-balanced substitutions (e.g. octahedral Ti4+ or tetrahedral Al3+) and the structural state of solid solutions (i.e. short- to long-range ordering) need study. We report on ongoing efforts in these directions using 27Al and 29Si Magic-Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) spectroscopy. Early work on synthetic and natural Fe- and Mn-bearing pyrope- and grossular-rich garnets focused on the effect these paramagnetic transition metals have in measuring and interpreting NMR spectra. These results have been expanded with NMR measurements on synthetic pyrope-rich garnets containing other paramagnetic transition metals including Cr3+, V3+, Co2+, and Ni2+ as well as diamagnetic Ti4+. NMR peaks are severely broadened in the presence of even small concentrations of Cr3+, Mn2+, and Fe3+ leading to a loss of spectral resolution. On the other hand, the spectra of garnet containing V3+, Fe2+, Co2+, and Ni2+ have better resolution and show separate paramagnetically shifted NMR peaks. In some cases, crystal-chemical information can be obtained because of the large frequency separations between the NMR peaks that can be assigned to various local atomic configurations around Al and Si. Furthermore, the 27Al NMR spectrum of a synthetic pyrope garnet with about 2% diamagnetic Ti4+ on the octahedral site showed the absence of any tetrahedral Al3+, which rules out the substitution mechanism VITi + IVAl = VIAl + IVSi in the solid solution. Our NMR investigations on garnet are now being made at the exploratory level. We think that NMR spectra of diamagnetic garnet can provide information on a number of crystal-chemical properties. Spectra of garnet containing various paramagnetic transition elements can also, in some cases, give local structural information. With a better understanding of paramagnetic effects in NMR spectroscopy, this type of study can possibly be expanded to other geologically important paramagnetic minerals and phases.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

High-sensitivity NMR beyond 200,000 atmospheres of pressure.

PubMed

Meier, T; Reichardt, S; Haase, J

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. (1)H NMR of water shows sensitivity and resolution obtained with the cells, and (63)Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. (115)In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry. Copyright © 2015 Elsevier Inc. All rights reserved.

An overview of tools for the validation of protein NMR structures.

PubMed

Vuister, Geerten W; Fogh, Rasmus H; Hendrickx, Pieter M S; Doreleijers, Jurgen F; Gutmanas, Aleksandras

2014-04-01

Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).

13C-NMR spectra and contact time experiment for Skjervatjern fulvic and humic acids

USGS Publications Warehouse

Malcolm, R.L.

1992-01-01

The T(CP) and T(1p) time constants for Skjervatjern fulvic and humic acids were determined to be short with T(CP) values ranging from 0.14 ms to 0.53 ms and T(1p) values ranging from 3.3 ms to 5.9 ms. T(CP) or T(1p) time constants at a contact time of 1 ms are favorable for quantification of 13C-NMR spectra. Because of the short T(CP) values, correction factors for signal intensity for various regions of the 13C-NMR spectra would be necessary at contact times greater than 1.1 ms or less than 0.9 ms. T(CP) and T(1p) values have a limited non-homogeneity within Skjervatjern fulvic and humic acids. A pulse delay or repeat time of 700 ms is more than adequate for quantification of these 13C-NMR spectra. Paramagnetic effects in these humic substances are precluded due to low inorganic ash contents, low contents of Fe, Mn, and Co, and low organic free-radical contents. The observed T(CP) values suggest that all the carbon types in Skjervatjern fulvic and humic acids are fully cross-polarized before significant proton relaxation occurs. The 13C-NMR spectra for Skjervatjern fulvic acid is similar to most aquatic fulvic acids as it is predominantly aliphatic, low in aromaticity (fa1 = 24), low in phenolic content, high in carboxyl content, and has no resolution of a methoxyl peak. The 13C-NMR spectra for Skjervatjern humic acid is also similar to most other aquatic humic acids in that it is also predominantly aliphatic, high in aromaticity (fa1 = 38), moderate in phenolic content, moderate in carboxyl content, and has a clear resolution of a methoxyl carbon region. After the consideration of the necessary 13C-NMR experimental conditions, these spectra are considered to be quantitative. With careful consideration of the previously determined 13C-NMR experimental conditions, quantitative spectra can be obtained for humic substances in the future from the HUMEX site. Possible changes in humic substances due to acidification should be determined from 13C-NMR data.

A biofilm microreactor system for simultaneous electrochemical and nuclear magnetic resonance techniques.

PubMed

Renslow, R S; Babauta, J T; Majors, P D; Mehta, H S; Ewing, R J; Ewing, T W; Mueller, K T; Beyenal, H

2014-01-01

Nuclear magnetic resonance (NMR) techniques are ideally suited for the study of biofilms and for probing their microenvironments because these techniques allow for noninvasive interrogation and in situ monitoring with high resolution. By combining NMR with simultaneous electrochemical techniques, it is possible to sustain and study live biofilms respiring on electrodes. Here, we describe a biofilm microreactor system, including a reusable and a disposable reactor, that allows for simultaneous electrochemical and NMR techniques (EC-NMR) at the microscale. Microreactors were designed with custom radio frequency resonator coils, which allowed for NMR measurements of biofilms growing on polarized gold electrodes. For an example application of this system we grew Geobacter sulfurreducens biofilms on electrodes. EC-NMR was used to investigate growth medium flow velocities and depth-resolved acetate concentration inside the biofilm. As a novel contribution we used Monte Carlo error analysis to estimate the standard deviations of the acetate concentration measurements. Overall, we found that the disposable EC-NMR microreactor provided a 9.7 times better signal-to-noise ratio over the reusable reactor. The EC-NMR biofilm microreactor system can ultimately be used to correlate extracellular electron transfer rates with metabolic reactions and explore extracellular electron transfer mechanisms.

Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

PubMed

Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

2012-11-25

The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

Determination of dipole coupling constants using heteronuclear multiple quantum NMR

NASA Astrophysics Data System (ADS)

Weitekamp, D. P.; Garbow, J. R.; Pines, A.

1982-09-01

The problem of extracting dipole couplings from a system of N spins I = 1/2 and one spin S by NMR techniques is analyzed. The resolution attainable using a variety of single quantum methods is reviewed. The theory of heteronuclear multiple quantum (HMQ) NMR is developed, with particular emphasis being placed on the superior resolution available in HMQ spectra. Several novel pulse sequences are introduced, including a two-step method for the excitation of HMQ coherence. Experiments on partially oriented [1-13C] benzene demonstrate the excitation of the necessary HMQ coherence and illustrate the calculation of relative line intensities. Spectra of high order HMQ coherence under several different effective Hamiltonians achievable by multiple pulse sequences are discussed. A new effective Hamiltonian, scalar heteronuclear recoupled interactions by multiple pulse (SHRIMP), achieved by the simultaneous irradiation of both spin species with the same multiple pulse sequence, is introduced. Experiments are described which allow heteronuclear couplings to be correlated with an S-spin spreading parameter in spectra free of inhomogeneous broadening.

Extended Czjzek model applied to NMR parameter distributions in sodium metaphosphate glass

NASA Astrophysics Data System (ADS)

Vasconcelos, Filipe; Cristol, Sylvain; Paul, Jean-François; Delevoye, Laurent; Mauri, Francesco; Charpentier, Thibault; Le Caër, Gérard

2013-06-01

The extended Czjzek model (ECM) is applied to the distribution of NMR parameters of a simple glass model (sodium metaphosphate, NaPO3) obtained by molecular dynamics (MD) simulations. Accurate NMR tensors, electric field gradient (EFG) and chemical shift anisotropy (CSA) are calculated from density functional theory (DFT) within the well-established PAW/GIPAW framework. The theoretical results are compared to experimental high-resolution solid-state NMR data and are used to validate the considered structural model. The distributions of the calculated coupling constant CQ ∝ |Vzz| and the asymmetry parameter ηQ that characterize the quadrupolar interaction are discussed in terms of structural considerations with the help of a simple point charge model. Finally, the ECM analysis is shown to be relevant for studying the distribution of CSA tensor parameters and gives new insight into the structural characterization of disordered systems by solid-state NMR.

Extended Czjzek model applied to NMR parameter distributions in sodium metaphosphate glass.

PubMed

Vasconcelos, Filipe; Cristol, Sylvain; Paul, Jean-François; Delevoye, Laurent; Mauri, Francesco; Charpentier, Thibault; Le Caër, Gérard

2013-06-26

The extended Czjzek model (ECM) is applied to the distribution of NMR parameters of a simple glass model (sodium metaphosphate, NaPO3) obtained by molecular dynamics (MD) simulations. Accurate NMR tensors, electric field gradient (EFG) and chemical shift anisotropy (CSA) are calculated from density functional theory (DFT) within the well-established PAW/GIPAW framework. The theoretical results are compared to experimental high-resolution solid-state NMR data and are used to validate the considered structural model. The distributions of the calculated coupling constant C(Q) is proportional to |V(zz)| and the asymmetry parameter η(Q) that characterize the quadrupolar interaction are discussed in terms of structural considerations with the help of a simple point charge model. Finally, the ECM analysis is shown to be relevant for studying the distribution of CSA tensor parameters and gives new insight into the structural characterization of disordered systems by solid-state NMR.

NMR-based diffusion pore imaging by double wave vector measurements.

PubMed

Kuder, Tristan Anselm; Laun, Frederik Bernd

2013-09-01

One main interest of nuclear magnetic resonance (NMR) diffusion experiments is the investigation of boundaries such as cell membranes hindering the diffusion process. NMR diffusion measurements allow collecting the signal from the whole sample. This mainly eliminates the problem of vanishing signal at increasing resolution. It has been a longstanding question if, in principle, the exact shape of closed pores can be determined by NMR diffusion measurements. In this work, we present a method using short diffusion gradient pulses only, which is able to reveal the shape of arbitrary closed pores without relying on a priori knowledge. In comparison to former approaches, the method has reduced demands on relaxation times due to faster convergence to the diffusion long-time limit and allows for a more flexible NMR sequence design, because, e.g., stimulated echoes can be used. Copyright © 2012 Wiley Periodicals, Inc.

Continuous-wave Submillimeter-wave Gyrotrons

PubMed Central

Han, Seong-Tae; Griffin, Robert G.; Hu, Kan-Nian; Joo, Chan-Gyu; Joye, Colin D.; Mastovsky, Ivan; Shapiro, Michael A.; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Torrezan, Antonio C.; Woskov, Paul P.

2007-01-01

Recently, dynamic nuclear polarization enhanced nuclear magnetic resonance (DNP/NMR) has emerged as a powerful technique to obtain significant enhancements in spin spectra from biological samples. For DNP in modern NMR systems, a high power continuous-wave source in the submillimeter wavelength range is necessary. Gyrotrons can deliver tens of watts of CW power at submillimeter wavelengths and are well suited for use in DNP/NMR spectrometers. To date, 140 GHz and 250 GHz gyrotrons are being employed in DNP spectrometer experiments at 200 MHz and 380 MHz at MIT. A 460 GHz gyrotron, which has operated with 8 W of CW output power, will soon be installed in a 700 MHz NMR spectrometer. High power radiation with good spectral and spatial resolution from these gyrotrons should provide NMR spectrometers with high signal enhancement through DNP. Also, these tubes operating at submillimeter wavelengths should have important applications in research in physics, chemistry, biology, materials science and medicine. PMID:17404605

Parahydrogen-enhanced zero-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Theis, T.; Ganssle, P.; Kervern, G.; Knappe, S.; Kitching, J.; Ledbetter, M. P.; Budker, D.; Pines, A.

2011-07-01

Nuclear magnetic resonance, conventionally detected in magnetic fields of several tesla, is a powerful analytical tool for the determination of molecular identity, structure and function. With the advent of prepolarization methods and detection schemes using atomic magnetometers or superconducting quantum interference devices, interest in NMR in fields comparable to the Earth's magnetic field and below (down to zero field) has been revived. Despite the use of superconducting quantum interference devices or atomic magnetometers, low-field NMR typically suffers from low sensitivity compared with conventional high-field NMR. Here we demonstrate direct detection of zero-field NMR signals generated through parahydrogen-induced polarization, enabling high-resolution NMR without the use of any magnets. The sensitivity is sufficient to observe spectra exhibiting 13C-1H scalar nuclear spin-spin couplings (known as J couplings) in compounds with 13C in natural abundance, without the need for signal averaging. The resulting spectra show distinct features that aid chemical fingerprinting.

Structure of the exopolysaccharide produced by Enterobacter amnigenus.

PubMed

Cescutti, Paola; Kallioinen, Anne; Impallomeni, Giuseppe; Toffanin, Renato; Pollesello, Piero; Leisola, Matti; Eerikäinen, Tero

2005-02-28

The bacterial species Enterobacter amnigenus was isolated from sugar beets harvested in Finland. It produced an exopolysaccharide rich in l-fucose, which gave viscous water solutions. Its primary structure was determined mainly by NMR spectroscopy and ESIMS of oligosaccharides and a polysaccharide with decreased molecular weight, obtained by Smith degradation of the O-deacetylated native polymer [carbohydrate structure: see text

integrating Solid State NMR and Computations in Membrane Protein Science

NASA Astrophysics Data System (ADS)

Cross, Timothy

2015-03-01

Helical membrane protein structures are influenced by their native environment. Therefore the characterization of their structure in an environment that models as closely as possible their native environment is critical for achieving not only structural but functional understanding of these proteins. Solid state NMR spectroscopy in liquid crystalline lipid bilayers provides an excellent tool for such characterizations. Two classes of restraints can be obtained - absolute restraints that constrain the structure to a laboratory frame of reference when using uniformly oriented samples (approximately 1° of mosaic spread) and relative restraints that restrain one part of the structure with respect to another part such as torsional and distance restraints. Here, I will discuss unique restraints derived from uniformly oriented samples and the characterization of initial structures utilizing both restraint types, followed by restrained molecular dynamics refinement in the same lipid bilayer environment as that used for the experimental restraint collection. Protein examples will be taken from Influenza virus and Mycobacterium tuberculosis. When available comparisons of structures to those obtained using different membrane mimetic environments will be shown and the causes for structural distortions explained based on an understanding of membrane biophysics and its sophisticated influence on membrane proteins.

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

The NMR phased array.

PubMed

Roemer, P B; Edelstein, W A; Hayes, C E; Souza, S P; Mueller, O M

1990-11-01

We describe methods for simultaneously acquiring and subsequently combining data from a multitude of closely positioned NMR receiving coils. The approach is conceptually similar to phased array radar and ultrasound and hence we call our techniques the "NMR phased array." The NMR phased array offers the signal-to-noise ratio (SNR) and resolution of a small surface coil over fields-of-view (FOV) normally associated with body imaging with no increase in imaging time. The NMR phased array can be applied to both imaging and spectroscopy for all pulse sequences. The problematic interactions among nearby surface coils is eliminated (a) by overlapping adjacent coils to give zero mutual inductance, hence zero interaction, and (b) by attaching low input impedance preamplifiers to all coils, thus eliminating interference among next nearest and more distant neighbors. We derive an algorithm for combining the data from the phased array elements to yield an image with optimum SNR. Other techniques which are easier to implement at the cost of lower SNR are explored. Phased array imaging is demonstrated with high resolution (512 x 512, 48-cm FOV, and 32-cm FOV) spin-echo images of the thoracic and lumbar spine. Data were acquired from four-element linear spine arrays, the first made of 12-cm square coils and the second made of 8-cm square coils. When compared with images from a single 15 x 30-cm rectangular coil and identical imaging parameters, the phased array yields a 2X and 3X higher SNR at the depth of the spine (approximately 7 cm).

Toward MRI microimaging of single biological cells

NASA Astrophysics Data System (ADS)

Seeber, Derek Allan

There is a great advantage in signal to noise ratio (SNR) that can be obtained in nuclear magnetic resonance (NMR) on very small samples (having spatial dimensions ˜100 mum or less) if one employs NMR "microcoils" that are of similarly small dimensions. These gains in SNR could enable magnetic resonance imaging (MRI) microscopy with spatial resolutions of ˜1--2 mum, much better than currently available. We report the design and testing of a NMR microcoil receiver apparatus, employing solenoidal microcoils of dimensions of tens to hundreds of microns, using an applied field of 9 Tesla (proton frequency 383 MHz). For the smallest receiver coils we attain sensitivity sufficient to observe proton NMR with SNR one in a single scan applied to ˜10 mum3 (10 fl) water sample, containing 7 x 1011 total proton spins. In addition to the NMR applications, microcoils have been applied to MRI producing images with spatial resolutions as low as 2 mum x 3.5 mum x 14.8 mum on phantom images of rods and beads. This resolution can be further improved. MRI imaging of small sample volumes requires significant hardware modifications and improvements, all of which are discussed. Specifically, MRI microscopy requires very strong (>10 T/m), rapidly switchable triaxial magnetic field gradients. We report the design and construction of such a triaxial gradient system, producing gradient substantially greater than 15 T/m in all three directions, x, y, and z (as high as 50 T/m for the x direction). The gradients are power by a custom designed power supply capable of providing currents in excess of 200 amps and switching times of less than 5 mus corresponding to slew rates of greater that 107 T/m/s. The gradients are adequately uniform (within 5% over a volume of 600 mum3) and sufficient for microcoil MRI of small samples.

Molecular ordering and molecular dynamics in isotactic-polypropylene characterized by solid state NMR.

PubMed

Miyoshi, Toshikazu; Mamun, Al; Hu, Wei

2010-01-14

The order-disorder phenomenon of local packing structures, space heterogeneity, and molecular dynamics and average lamellar thickness, , of the alpha form of isotactic polypropylene (iPP) crystallized at various supercooling temperatures, DeltaT, are investigated by solid-state (SS) NMR and SAXS, respectively. increases with lowering DeltaT, and extrapolations of (-1) versus averaged melting point, , gives an equilibrium melting temperature, T(m)(0) = 457 +/- 4 K. High-power TPPM decoupling with a field strength of 110 kHz extremely improves (13)C high-resolution SS-NMR spectral resolution of the ordered crystalline signals at various DeltaT. A high-resolution (13)C SS-NMR spectrum combined with a conventional spin-lattice relaxation time in the rotating frame (T(1rhoH)) filter easily accesses an order-disorder phenomenon for upward and downward orientations of stems and their packing in the crystalline region. It is found that ordered packing fraction, f(order), increases with lowering DeltaT and reaches a maximum value of 62% at DeltaT = 34 K. The ordering phenomenon of stem packing indicates that chain-folding direction changes from random in the disordered packing to order in the ordered packing along the a sin theta axis under a hypothesis of adjacent re-entry structures. It is also found that f(order) significantly increases prior to enhancement of lamellar thickness. Additionally, annealing experiments indicate that is significantly enhanced after a simultaneous process of partial melting and recrystallization/reorganization into the ordered packing at annealing temperature >/=423 K. Furthermore, the center-bands only detection of exchange (CODEX) NMR method demonstrates that time-kinetic parameters of helical jump motions are highly influenced by DeltaT. These dynamic constraints are interpreted in terms of increment of and packing ordering. Through these new results related to molecular structures and dynamics, roles of polymer chain trajectory and molecular dynamics for the lamellar thickening process are discussed.

Coupling HPLC-SPE-NMR with a microplate-based high-resolution antioxidant assay for efficient analysis of antioxidants in food--validation and proof-of-concept study with caper buds.

PubMed

Wiese, Stefanie; Wubshet, Sileshi G; Nielsen, John; Staerk, Dan

2013-12-15

This work describes the coupling of a microplate-based antioxidant assay with a hyphenated system consisting of high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HPLC-SPE-NMR/high-resolution antioxidant assay, for the analysis of complex food extracts. The applicability of the microplate-based antioxidant assay for high-resolution screening of common food phenolics as well as parameters related to their trapping efficiency, elution behavior, and recovery on/from SPE cartridges are described. It was found that the microplate-based high-resolution antioxidant assay is an attractive and easy implementable alternative to direct on-line screening methods. Furthermore, it was shown that Resin SH and Resin GP SPE material are superior to RP C18HD for trapping of phenolic compounds. Proof-of-concept study was performed with caper bud extract, revealing the most important antioxidants to be quercetin, kaempferol, rutin, kaempferol-3-O-β-rutinoside and N(1),N(5),N(10)-triphenylpropenoyl spermidine amides. Targeted isolation of the latter, and comprehensive NMR experiments showed them to be N(1),N(10)-di-(E)-caffeoyl-N(5)-p-(E)-coumaroyl spermidine, N(1)-(E)-caffeoyl-N(5),N(10)-di-p-(E)-coumaroyl spermidine, N(10)-(E)-caffeoyl-N(1),N(5)-di-p-(E)-coumaroyl spermidine, and N(1),N(5),N(10)-tri-p-(E)-coumaroyl spermidine amides. Copyright © 2013 Elsevier Ltd. All rights reserved.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

NASA Astrophysics Data System (ADS)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA.

PubMed

Mroue, Kamal H; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H; Morris, Michael D; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans. Copyright © 2014 Elsevier Inc. All rights reserved.

Unilateral NMR applied to the conservation of works of art.

PubMed

Del Federico, Eleonora; Centeno, Silvia A; Kehlet, Cindie; Currier, Penelope; Stockman, Denise; Jerschow, Alexej

2010-01-01

In conventional NMR, samples from works of art in sizes above those considered acceptable in the field of art conservation would have to be removed to place them into the bore of large superconducting magnets. The portable permanent-magnet-based systems, by contrast, can be used in situ to study works of art, in a noninvasive manner. One of these portable NMR systems, NMR-MOUSE(R), measures the information contained in one pixel in an NMR image from a region of about 1 cm(2), which can be as thin as 2-3 microm. With such a high depth resolution, profiles through the structures of art objects can be measured to characterize the materials, the artists' techniques, and the deterioration processes. A novel application of the technique to study a deterioration process and to follow up a conservation treatment is presented in which micrometer-thick oil stains on paper are differentiated and characterized. In this example, the spin-spin relaxation T (2) of the stain is correlated to the iodine number and to the degree of cross-linking of the oil, parameters that are crucial in choosing an appropriate conservation treatment to remove them. It is also shown that the variation of T (2) over the course of treatments with organic solvents can be used to monitor the progress of the conservation interventions. It is expected that unilateral NMR in combination with multivariate data analysis will fill a gap within the set of high-spatial-resolution techniques currently available for the noninvasive analysis of materials in works of art, where procedures to study the inorganic components are currently far more developed than those suitable for the study of the organic components.

Development of DNP-Enhanced High-Resolution Solid-State NMR System for the Characterization of the Surface Structure of Polymer Materials

NASA Astrophysics Data System (ADS)

Horii, Fumitaka; Idehara, Toshitaka; Fujii, Yutaka; Ogawa, Isamu; Horii, Akifumi; Entzminger, George; Doty, F. David

2012-07-01

A dynamic nuclear polarization (DNP)-enhanced cross-polarization/magic-angle spinning (DNP/CP/MAS) NMR system has been developed by combining a 200 MHz Chemagnetics CMX-200 spectrometer operating at 4.7 T with a high-power 131.5 GHz Gyrotron FU CW IV. The 30 W sub-THz wave generated in a long pulse TE _{{41}}^{{(1)}} mode with a frequency of 5 Hz was successfully transmitted to the modified Doty Scientific low-temperature CP/MAS probe through copper smooth-wall circular waveguides. Since serious RF noises on NMR signals by arcing in the electric circuit of the probe and undesired sample heating were induced by the continuous sub-THz wave pulse irradiation with higher powers, the on-off sub-THz wave pulse irradiation synchronized with the NMR detection was developed and the appropriate setting of the irradiation time and the cooling time corresponding to the non-irradiation time was found to be very effective for the suppression of the arcing and the sample heating. The attainable maximum DNP enhancement was more than 30 folds for C1 13 C-enriched D-glucose dissolved in the frozen medium containing mono-radical 4-amino-TEMPO. The first DNP/CP/MAS 13 C NMR spectra of poly(methyl methacrylate) (PMMA) sub-micron particles were obtained at the dispersed state in the same frozen medium, indicating that DNP-enhanced 1H spins effectively diffuse from the medium to the PMMA particles through their surface and are detected as high-resolution 13 C spectra in the surficial region to which the 1H spins reach. On the basis of these results, the possibility of the DNP/CP/MAS NMR characterization of the surface structure of nanomaterials including polymer materials was discussed.

High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance of Intact Zebrafish Embryos Detects Metabolic Changes Following Exposure to Teratogenic Polymethoxyalkenes from Algae

PubMed Central

Roy, Upasana; Jaja-Chimedza, Asha; Sanchez, Kristel; Matysik, Joerg

2016-01-01

Abstract Techniques based on nuclear magnetic resonance (NMR) for imaging and chemical analyses of in vivo, or otherwise intact, biological systems are rapidly emerging and finding diverse applications within a wide range of fields. Very recently, several NMR-based techniques have been developed for the zebrafish as a model animal system. In the current study, the novel application of high-resolution magic angle spinning (HR-MAS) NMR is presented as a means of metabolic profiling of intact zebrafish embryos. Toward investigating the utility of HR-MAS NMR as a toxicological tool, these studies specifically examined metabolic changes of embryos exposed to polymethoxy-1-alkenes (PMAs)—a recently identified family of teratogenic compounds from freshwater algae—as emerging environmental contaminants. One-dimensional and two-dimensional HR-MAS NMR analyses were able to effectively identify and quantify diverse metabolites in early-stage (≤36 h postfertilization) embryos. Subsequent comparison of the metabolic profiles between PMA-exposed and control embryos identified several statistically significant metabolic changes associated with subacute exposure to the teratogen, including (1) elevated inositol as a recognized component of signaling pathways involved in embryo development; (2) increases in several metabolites, including inositol, phosphoryl choline, fatty acids, and cholesterol, which are associated with lipid composition of cell membranes; (3) concomitant increase in glucose and decrease in lactate; and (4) decreases in several biochemically related metabolites associated with central nervous system development and function, including γ-aminobutyric acid, glycine, glutamate, and glutamine. A potentially unifying model/hypothesis of PMA teratogenicity based on the data is presented. These findings, taken together, demonstrate that HR-MAS NMR is a promising tool for metabolic profiling in the zebrafish embryo, including toxicological applications. PMID:27348393

Cell-Free Protein Synthesis Enhancement from Real-Time NMR Metabolite Kinetics: Redirecting Energy Fluxes in Hybrid RRL Systems.

PubMed

Panthu, Baptiste; Ohlmann, Théophile; Perrier, Johan; Schlattner, Uwe; Jalinot, Pierre; Elena-Herrmann, Bénédicte; Rautureau, Gilles J P

2018-01-19

A counterintuitive cell-free protein synthesis (CFPS) strategy, based on reducing the ribosomal fraction in rabbit reticulocyte lysate (RRL), triggers the development of hybrid systems composed of RRL ribosome-free supernatant complemented with ribosomes from different mammalian cell-types. Hybrid RRL systems maintain translational properties of the original ribosome cell types, and deliver protein expression levels similar to RRL. Here, we show that persistent ribosome-associated metabolic activity consuming ATP is a major obstacle for maximal protein yield. We provide a detailed picture of hybrid CFPS systems energetic metabolism based on real-time nuclear magnetic resonance (NMR) investigation of metabolites kinetics. We demonstrate that protein synthesis capacity has an upper limit at native ribosome concentration and that lower amounts of the ribosomal fraction optimize energy fluxes toward protein translation, consequently increasing CFPS yield. These results provide a rationalized strategy for further mammalian CFPS developments and reveal the potential of real-time NMR metabolism phenotyping for optimization of cell-free protein expression systems.

Investigating the reactivity of pMDI with wood cell walls using high-resolution solution-state NMR spectroscopy

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2009-01-01

The objectives of this study are the following: (1) Use solution-state NMR to assign contours in HSQC spectra of the reaction products between pMDI model compounds and: (a) lignin model compounds, (b) milled-wood lignin, (c) ball-milled wood, (d) microtomed loblolly pine; (2) Determine where and to what degree urethane formation occurs with loblolly pine cell wall...

Enhanced detection of aldehydes in Extra-Virgin Olive Oil by means of band selective NMR spectroscopy

NASA Astrophysics Data System (ADS)

Dugo, Giacomo; Rotondo, Archimede; Mallamace, Domenico; Cicero, Nicola; Salvo, Andrea; Rotondo, Enrico; Corsaro, Carmelo

2015-02-01

High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a very powerful tool for comprehensive food analyses and especially for Extra-Virgin Olive Oils (EVOOs). We use the NMR technique to study the spectral region of aldehydes (8-10 ppm) for EVOOs coming from the south part of Italy. We perform novel experiments by using mono and bidimensional band selective spin-echo pulse sequences and identify four structural classes of aldehydes in EVOOs. For the first time such species are identified in EVOOs without any chemical treatment; only dilution with CDCl3 is employed. This would allow the discrimination of different EVOOs for the aldehydes content increasing the potentiality of the NMR technique in the screening of metabolites for geographical characterization of EVOOs.

NMR Studies of Dynamic Biomolecular Conformational Ensembles

PubMed Central

Torchia, Dennis A.

2015-01-01

Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. PMID:25669739

Liquid- and solid-state high-resolution NMR methods for the investigation of aging processes of silicone breast implants.

PubMed

Birkefeld, Anja Britta; Bertermann, Rüdiger; Eckert, Hellmut; Pfleiderer, Bettina

2003-01-01

To investigate aging processes of silicone gel breast implants, which may include migration of free unreacted material from the gel and rubber to local (e.g. connective tissue capsule) or distant sites in the body, chemical alteration of the polymer and infiltration of body compounds, various approaches of multinuclear nuclear magnetic resonance (NMR) experiments (29Si, 13C, 1H) were evaluated. While 29Si, 13C, and 1H solid-state magic angle spinning (MAS) NMR techniques performed on virgin and explanted envelopes of silicone prostheses provided only limited information, high-resolution liquid-state NMR techniques of CDCl(3) extracts were highly sensitive analytical tools for the detection of aging related changes in the materials. Using 2D 1H, 1H correlation spectroscopy (COSY) and 29Si, 1H heteronuclear multiple bond coherence (HMBC) experiments with gradient selection, it was possible to detect lipids (mainly phospholipids) as well as silicone oligomer species in explanted envelopes and gels. Silicone oligomers were also found in connective tissue capsules, indicating that cyclic polysiloxanes can migrate from intact implants to adjacent and distant sites. Furthermore, lipids can permeate the implant and modify its chemical composition. Copyright 2002 Elsevier Science Ltd.

Recombinant expression of Ixolaris, a Kunitz-type inhibitor from the tick salivary gland, for NMR studies.

PubMed

De Paula, V S; Silva, F H S; Francischetti, I M B; Monteiro, R Q; Valente, A P

2017-11-01

Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy. Although numerous functional studies of Ixolaris exist, three-dimensional structure of Ixolaris has not been obtained at atomic resolution. Using the pET32 vector, we successfully expressed a TRX-His 6 -Ixolaris fusion protein. By combining Ni-NTA chromatography, enterokinase protease cleavage, and reverse phase HPLC (RP-HPLC), we purified isotopically labeled Ixolaris for NMR studies. 1D 1 H and 2D 15 N- 1 H NMR analysis yielded high quality 2D 15 N- 1 H HSQC spectra revealing that the recombinant protein is folded. These studies represent the first steps in obtaining high-resolution structural information by NMR for Ixolaris enabling the investigation of the molecular basis for Ixolaris-coagulation factors interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

High-Resolution Magic-Angle-Spinning NMR and Magnetic Resonance Imaging Spectroscopies Distinguish Metabolome and Structural Properties of Maize Seeds from Plants Treated with Different Fertilizers and Arbuscular mycorrhizal fungi.

PubMed

Mazzei, Pierluigi; Cozzolino, Vincenza; Piccolo, Alessandro

2018-03-21

Both high-resolution magic-angle-spinning (HRMAS) and magnetic resonance imaging (MRI) NMR spectroscopies were applied here to identify the changes of metabolome, morphology, and structural properties induced in seeds (caryopses) of maize plants grown at field level under either mineral or compost fertilization in combination with the inoculation by arbuscular mycorrhizal fungi (AMF). The metabolome of intact caryopses was examined by HRMAS-NMR, while the morphological aspects, endosperm properties and seed water distribution were investigated by MRI. Principal component analysis (PCA) was applied to evaluate 1 H CPMG (Carr-Purcel-Meiboom-Gill) HRMAS spectra as well as several MRI-derived parameters ( T 1 , T 2 , and self-diffusion coefficients) of intact maize caryopses. PCA score-plots from spectral results indicated that both seeds metabolome and structural properties depended on the specific field treatment undergone by maize plants. Our findings show that a combination of multivariate statistical analyses with advanced and nondestructive NMR techniques, such as HRMAS and MRI, enables the evaluation of the effects induced on maize caryopses by different fertilization and management practices at field level. The spectroscopic approach adopted here may become useful for the objective appraisal of the quality of seeds produced under a sustainable agriculture.

(1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins.

PubMed

Wu, Chin H; Das, Bibhuti B; Opella, Stanley J

2010-02-01

(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples. Copyright 2009 Elsevier Inc. All rights reserved.

A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

NASA Astrophysics Data System (ADS)

Gao, Ya; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong

2017-07-01

We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A.

PubMed

Pereverzev, A Y; Boyarkin, O V

2017-02-01

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Time domain para hydrogen induced polarization.

PubMed

Ratajczyk, Tomasz; Gutmann, Torsten; Dillenberger, Sonja; Abdulhussaein, Safaa; Frydel, Jaroslaw; Breitzke, Hergen; Bommerich, Ute; Trantzschel, Thomas; Bernarding, Johannes; Magusin, Pieter C M M; Buntkowsky, Gerd

2012-01-01

Para hydrogen induced polarization (PHIP) is a powerful hyperpolarization technique, which increases the NMR sensitivity by several orders of magnitude. However the hyperpolarized signal is created as an anti-phase signal, which necessitates high magnetic field homogeneity and spectral resolution in the conventional PHIP schemes. This hampers the application of PHIP enhancement in many fields, as for example in food science, materials science or MRI, where low B(0)-fields or low B(0)-homogeneity do decrease spectral resolution, leading to potential extinction if in-phase and anti-phase hyperpolarization signals cannot be resolved. Herein, we demonstrate that the echo sequence (45°-τ-180°-τ) enables the acquisition of low resolution PHIP enhanced liquid state NMR signals of phenylpropiolic acid derivatives and phenylacetylene at a low cost low-resolution 0.54 T spectrometer. As low field TD-spectrometers are commonly used in industry or biomedicine for the relaxometry of oil-water mixtures, food, nano-particles, or other systems, we compare two variants of para-hydrogen induced polarization with data-evaluation in the time domain (TD-PHIP). In both TD-ALTADENA and the TD-PASADENA strong spin echoes could be detected under conditions when usually no anti-phase signals can be measured due to the lack of resolution. The results suggest that the time-domain detection of PHIP-enhanced signals opens up new application areas for low-field PHIP-hyperpolarization, such as non-invasive compound detection or new contrast agents and biomarkers in low-field Magnetic Resonance Imaging (MRI). Finally, solid-state NMR calculations are presented, which show that the solid echo (90y-τ-90x-τ) version of the TD-ALTADENA experiment is able to convert up to 10% of the PHIP signal into visible magnetization. Copyright © 2012 Elsevier Inc. All rights reserved.

The Native Production of the Sesquiterpene Isopterocarpolone by Streptomyces sp. RM-14-6

PubMed Central

Shaaban, Khaled A.; Singh, Shanteri; Elshahawi, Sherif I.; Wang, Xiachang; Ponomareva, Larissa V.; Sunkara, Manjula; Copley, Gregory C.; Hower, James C.; Morris, Andrew J.; Kharel, Madan K.; Thorson, Jon S.

2013-01-01

We report the production, isolation and structure elucidation of the sesquiterpene isopterocarpolone from an Appalachian isolate Streptomyces species RM-14-6. While isopterocarpolone was previously put forth as a putative plant metabolite, the current study highlights the first native bacterial production of isopterocarpolone and the first full characterization of isopterocarpolone using 1D and 2D NMR spectroscopy and HR-ESI mass spectrometry. Considering the biosynthesis of closely related metabolites (geosmin or 5-epiaristolochene), the structure of isopterocarpolone also suggests the potential participation of one or more unique enzymatic transformations. In this context, this work also sets the stage for the elucidation of potentially novel bacterial biosynthetic machinery. PMID:24237421

Automatic NMR field-frequency lock-pulsed phase locked loop approach.

PubMed

Kan, S; Gonord, P; Fan, M; Sauzade, M; Courtieu, J

1978-06-01

A self-contained deuterium frequency-field lock scheme for a high-resolution NMR spectrometer is described. It is based on phase locked loop techniques in which the free induction decay signal behaves as a voltage-controlled oscillator. By pulsing the spins at an offset frequency of a few hundred hertz and using a digital phase-frequency discriminator this method not only eliminates the usual phase, rf power, offset adjustments needed in conventional lock systems but also possesses the automatic pull-in characteristics that dispense with the use of field sweeps to locate the NMR line prior to closure of the lock loop.

MEMS-Based Force-Detected Nuclear Magnetic Resonance (FDNMR) Spectrometer

NASA Technical Reports Server (NTRS)

Lee, Choonsup; Butler, Mark C.; Elgammal, Ramez A.; George, Thomas; Hunt, Brian; Weitekamp, Daniel P.

2006-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy allows assignment of molecular structure by acquiring the energy spectrum of nuclear spins in a molecule, and by interpreting the symmetry and positions of resonance lines in the spectrum. As such, NMR has become one of the most versatile and ubiquitous spectroscopic methods. Despite these tremendous successes, NMR experiments suffer from inherent low sensitivity due to the relatively low energy of photons in the radio frequency (rt) region of the electromagnetic spectrum. Here, we describe a high-resolution spectroscopy in samples with diameters in the micron range and below. We have reported design and fabrication of force-detected nuclear magnetic resonance (FDNMR).

High-field dynamic nuclear polarization in aqueous solutions.

PubMed

Prandolini, M J; Denysenkov, V P; Gafurov, M; Endeward, B; Prisner, T F

2009-05-06

Unexpected high DNP enhancements of more than 10 have been achieved in liquid water samples at room temperature and magnetic fields of 9.2 T (corresponding to 400 MHz (1)H NMR frequency and 260 GHz EPR frequency). The liquid samples were polarized in situ using a double-resonance structure, which allows simultaneous excitation of NMR and EPR transitions and achieves significant DNP enhancements at very low incident microwave power of only 45 mW. These results demonstrate the first important step toward the application of DNP to high-resolution NMR, increasing the sensitivity on biomolecules with small sample volumes and at physiologically low concentrations.

In-pore exchange and diffusion of carbonate solvent mixtures in nanoporous carbon

DOE PAGES

Alam, Todd M.; Osborn Popp, Thomas M.

2016-06-04

High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy has been used to resolve different surface and in-pore solvent environments of ethylene carbonate (EC) and dimethyl carbonate (DMC) mixtures absorbed within nanoporous carbon (NPC). Two dimensional (2D) 1H HRMAS NMR exchange measurements revealed that the inhomogeneous broadened in-pore resonances have pore-to-pore exchange rates on the millisecond timescale. Pulsed-field gradient (PFG) NMR diffusometry revealed the in-pore self-diffusion constants for both EC and DMC were reduced by up to a factor of five with respect to the diffusion in the non-absorbed solvent mixtures.

Recent progress and future directions in protein-protein docking.

PubMed

Ritchie, David W

2008-02-01

This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of efficient search and scoring strategies, including e.g. fast Fourier transform correlations, geometric hashing, and Monte Carlo techniques. These approaches can often produce a relatively small list of up to a few thousand orientations, amongst which a near-native binding mode is often observed. However, despite the use of improved scoring functions which typically include models of desolvation, hydrophobicity, and electrostatics, current algorithms still have difficulty in identifying the correct solution from the list of false positives, or decoys. Nonetheless, significant progress is being made through better use of bioinformatics, biochemical, and biophysical information such as e.g. sequence conservation analysis, protein interaction databases, alanine scanning, and NMR residual dipolar coupling restraints to help identify key binding residues. Promising new approaches to incorporate models of protein flexibility during docking are being developed, including the use of molecular dynamics snapshots, rotameric and off-rotamer searches, internal coordinate mechanics, and principal component analysis based techniques. Some investigators now use explicit solvent models in their docking protocols. Many of these approaches can be computationally intensive, although new silicon chip technologies such as programmable graphics processor units are beginning to offer competitive alternatives to conventional high performance computer systems. As cryo-EM techniques improve apace, docking NMR and X-ray protein structures into low resolution EM density maps is helping to bridge the resolution gap between these complementary techniques. The use of symmetry and fragment assembly constraints are also helping to make possible docking-based predictions of large multimeric protein complexes. In the near future, the closer integration of docking algorithms with protein interface prediction software, structural databases, and sequence analysis techniques should help produce better predictions of protein interaction networks and more accurate structural models of the fundamental molecular interactions within the cell.

Determination of Structural Topology of a Membrane Protein in Lipid -Bilayers using Polarization Optimized Experiments (POE) for Static and MAS Solid State NMR Spectroscopy

PubMed Central

Mote, Kaustubh R.; Gopinath, T.; Veglia, Gianluigi

2013-01-01

The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments (POE), for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ∼ 0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional O-ssNMR and MAS-ssNMR. PMID:23963722

High-resolution α-amylase assay combined with high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy for expedited identification of α-amylase inhibitors: proof of concept and α-amylase inhibitor in cinnamon.

PubMed

Okutan, Leyla; Kongstad, Kenneth T; Jäger, Anna K; Staerk, Dan

2014-11-26

Type 2 diabetes affects millions of people worldwide, and new improved drugs or functional foods containing selective α-amylase inhibitors are needed for improved management of blood glucose. In this article the development of a microplate-based high-resolution α-amylase inhibition assay with direct photometric measurement of α-amylase activity is described. The inhibition assay is based on porcine pancreatic α-amylase with 2-chloro-4-nitrophenyl-α-D-maltotriose as substrate, which this gives a stable, sensitive, and cheap inhibition assay as requested for high-resolution purposes. In combination with HPLC-HRMS-SPE-NMR, this provides an analytical platform that allows simultaneous chemical and biological profiling of α-amylase inhibitors in plant extracts. Proof-of-concept with an artificial mixture of six compounds-of which three are known α-amylase inhibitors-showed that the high-resolution α-amylase inhibition profiles allowed detection of sub-microgram amounts of the α-amylase inhibitors. Furthermore, the high-resolution α-amylase inhibition assay/HPLC-HRMS-SPE-NMR platform allowed identification of cinnamaldehyde as the α-amylase inhibitor in cinnamon (Cinnamomum verum Presl.).

Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS 1 approach: Hybrid 1D 1 H NMR/ESI MS 1 metabolomics method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Lawrence R.; Hoyt, David W.; Walker, S. Michael

We present a novel approach to improve accuracy of metabolite identification by combining direct infusion ESI MS1 with 1D 1H NMR spectroscopy. The new approach first applies standard 1D 1H NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in metabolomics library. This generates a list of candidate metabolites. The list contains false positive and ambiguous identifications. Next, we constrained the list with the chemical formulas derived from high-resolution direct infusion ESI MS1 spectrum of the same sample. Detection of the signals of a metabolitemore » both in NMR and MS significantly improves the confidence of identification and eliminates false positive identification. 1D 1H NMR and direct infusion ESI MS1 spectra of a sample can be acquired in parallel in several minutes. This is highly beneficial for rapid and accurate screening of hundreds of samples in high-throughput metabolomics studies. In order to make this approach practical, we developed a software tool, which is integrated to Chenomx NMR Suite. The approach is demonstrated on a model mixture, tomato and Arabidopsis thaliana metabolite extracts, and human urine.« less

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: Utility in exploration of endangered plants

Treesearch

Joonseok Oh; John J. Bowling; Amar G. Chittiboyina; Robert J. Doerksen; Daneel Ferreira; Theodor D. Leininger; Mark T. Hamann

2013-01-01

Endangered plant species are an important resource for new chemistry. Lindera melissifolia is native to the Southeastern U.S. and scarcely populates the edges of lakes and ponds. Quantum mechanics (QM) used in combination with NMR/ECD is a powerful tool for the assignment of absolute configuration in lieu of X-ray crystallography. Methods: The EtOAc extract of L....

Intermediate couplings: NMR at the solids-liquids interface

NASA Astrophysics Data System (ADS)

Spence, Megan

2006-03-01

Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics.

Coal liquefaction process streams characterization and evaluation: Analysis of Black Thunder coal and liquefaction products from HRI Bench Unit Run CC-15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pugmire, R.J.; Solum, M.S.

This study was designed to apply {sup 13}C-nuclear magnetic resonance (NMR) spectrometry to the analysis of direct coal liquefaction process-stream materials. {sup 13}C-NMR was shown to have a high potential for application to direct coal liquefaction-derived samples in Phase II of this program. In this Phase III project, {sup 13}C-NMR was applied to a set of samples derived from the HRI Inc. bench-scale liquefaction Run CC-15. The samples include the feed coal, net products and intermediate streams from three operating periods of the run. High-resolution {sup 13}C-NMR data were obtained for the liquid samples and solid-state CP/MAS {sup 13}C-NMR datamore » were obtained for the coal and filter-cake samples. The {sup 1}C-NMR technique is used to derive a set of twelve carbon structural parameters for each sample (CONSOL Table A). Average molecular structural descriptors can then be derived from these parameters (CONSOL Table B).« less

Modeling an in-register, parallel "iowa" aβ fibril structure using solid-state NMR data from labeled samples with rosetta.

PubMed

Sgourakis, Nikolaos G; Yau, Wai-Ming; Qiang, Wei

2015-01-06

Determining the structures of amyloid fibrils is an important first step toward understanding the molecular basis of neurodegenerative diseases. For β-amyloid (Aβ) fibrils, conventional solid-state NMR structure determination using uniform labeling is limited by extensive peak overlap. We describe the characterization of a distinct structural polymorph of Aβ using solid-state NMR, transmission electron microscopy (TEM), and Rosetta model building. First, the overall fibril arrangement is established using mass-per-length measurements from TEM. Then, the fibril backbone arrangement, stacking registry, and "steric zipper" core interactions are determined using a number of solid-state NMR techniques on sparsely (13)C-labeled samples. Finally, we perform Rosetta structure calculations with an explicitly symmetric representation of the system. We demonstrate the power of the hybrid Rosetta/NMR approach by modeling the in-register, parallel "Iowa" mutant (D23N) at high resolution (1.2Å backbone rmsd). The final models are validated using an independent set of NMR experiments that confirm key features. Copyright © 2015 Elsevier Ltd. All rights reserved.

On the Analytical Superiority of 1D NMR for Fingerprinting the Higher Order Structure of Protein Therapeutics Compared to Multidimensional NMR Methods.

PubMed

Poppe, Leszek; Jordan, John B; Rogers, Gary; Schnier, Paul D

2015-06-02

An important aspect in the analytical characterization of protein therapeutics is the comprehensive characterization of higher order structure (HOS). Nuclear magnetic resonance (NMR) is arguably the most sensitive method for fingerprinting HOS of a protein in solution. Traditionally, (1)H-(15)N or (1)H-(13)C correlation spectra are used as a "structural fingerprint" of HOS. Here, we demonstrate that protein fingerprint by line shape enhancement (PROFILE), a 1D (1)H NMR spectroscopy fingerprinting approach, is superior to traditional two-dimensional methods using monoclonal antibody samples and a heavily glycosylated protein therapeutic (Epoetin Alfa). PROFILE generates a high resolution structural fingerprint of a therapeutic protein in a fraction of the time required for a 2D NMR experiment. The cross-correlation analysis of PROFILE spectra allows one to distinguish contributions from HOS vs protein heterogeneity, which is difficult to accomplish by 2D NMR. We demonstrate that the major analytical limitation of two-dimensional methods is poor selectivity, which renders these approaches problematic for the purpose of fingerprinting large biological macromolecules.

Feasibility of high-resolution one-dimensional relaxation imaging at low magnetic field using a single-sided NMR scanner applied to articular cartilage

NASA Astrophysics Data System (ADS)

Rössler, Erik; Mattea, Carlos; Stapf, Siegfried

2015-02-01

Low field Nuclear Magnetic Resonance increases the contrast of the longitudinal relaxation rate in many biological tissues; one prominent example is hyaline articular cartilage. In order to take advantage of this increased contrast and to profile the depth-dependent variations, high resolution parameter measurements are carried out which can be of critical importance in an early diagnosis of cartilage diseases such as osteoarthritis. However, the maximum achievable spatial resolution of parameter profiles is limited by factors such as sensor geometry, sample curvature, and diffusion limitation. In this work, we report on high-resolution single-sided NMR scanner measurements with a commercial device, and quantify these limitations. The highest achievable spatial resolution on the used profiler, and the lateral dimension of the sensitive volume were determined. Since articular cartilage samples are usually bent, we also focus on averaging effects inside the horizontally aligned sensitive volume and their impact on the relaxation profiles. Taking these critical parameters into consideration, depth-dependent relaxation time profiles with the maximum achievable vertical resolution of 20 μm are discussed, and are correlated with diffusion coefficient profiles in hyaline articular cartilage in order to reconstruct T2 maps from the diffusion-weighted CPMG decays of apparent relaxation rates.

Comprehensive analysis of commercial willow bark extracts by new technology platform: combined use of metabolomics, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy and high-resolution radical scavenging assay.

PubMed

Agnolet, Sara; Wiese, Stefanie; Verpoorte, Robert; Staerk, Dan

2012-11-02

Here, proof-of-concept of a new analytical platform used for the comprehensive analysis of a small set of commercial willow bark products is presented, and compared with a traditional standardization solely based on analysis of salicin and salicin derivatives. The platform combines principal component analysis (PCA) of two chemical fingerprints, i.e., HPLC and (1)H NMR data, and a pharmacological fingerprint, i.e., high-resolution 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS(+)) reduction profile, with targeted identification of constituents of interest by hyphenated HPLC-solid-phase extraction-tube transfer NMR, i.e., HPLC-SPE-ttNMR. Score plots from PCA of HPLC and (1)H NMR fingerprints showed the same distinct grouping of preparations formulated as capsules of Salix alba bark and separation of S. alba cortex. Loading plots revealed this to be due to high amount of salicin in capsules and ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba cortex, respectively. PCA of high-resolution radical scavenging profiles revealed clear separation of preparations along principal component 1 due to the major radical scavengers (+)-catechin and ampelopsin. The new analytical platform allowed identification of 16 compounds in commercial willow bark extracts, and identification of ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba bark extract is reported for the first time. The detection of the novel compound, ethyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, is also described. Copyright © 2012 Elsevier B.V. All rights reserved.

Cr{sub 2}O{sub 5} as new cathode for rechargeable sodium ion batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Xu-Yong; Chien, Po-Hsiu; Rose, Alyssa M.

2016-10-15

Chromium oxide, Cr{sub 2}O{sub 5}, was synthesized by pyrolyzing CrO{sub 3} at 350 °C and employed as a new cathode in rechargeable sodium ion batteries. Cr{sub 2}O{sub 5}/Na rechargeable batteries delivered high specific capacities up to 310 mAh/g at a current density of C/16 (or 20 mA/g). High-resolution solid-state {sup 23}Na NMR both qualitatively and quantitatively revealed the reversible intercalation of Na ions into the bulk electrode and participation of Na ions in the formation of the solid-electrolyte interphase largely at low potentials. Amorphization of the electrode structure occurred during the first discharge revealed by both NMR and X-ray diffractionmore » data. CrO{sub 3}-catalyzed electrolyte degradation and loss in electronic conductivity led to gradual capacity fading. The specific capacity stabilized at >120 mAh/g after 50 charge-discharge cycles. Further improvement in electrochemical performance is possible via electrode surface modification, polymer binder incorporation, or designs of new morphologies. - Graphical abstract: Electrochemical profile of a Cr{sub 2}O{sub 5}/Na battery cell and high-resolution solid-state {sup 23}Na MAS NMR spectrum of a Cr{sub 2}O{sub 5} electrode discharged to 2 V. - Highlights: • Cr{sub 2}O{sub 5} was synthesized and used as a new cathode in rechargeable Na ion batteries. • A high capacity of 310 mAh/g and an energy density of 564 Wh/kg were achieved. • High-resolution solid-state {sup 23}Na NMR was employed to follow the reaction mechanisms.« less

High field NMR Spectroscopy and FTICR Mass Spectrometry: Powerful Discovery Tools for the Characterization of Marine Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

2012-04-01

High-field NMR and FTMS of SPE-derived marine dissolved organic matter (SPE-DOM) from the South Atlantic Ocean provided molecular level information of complex unknowns with unprecedented coverage of carbon and resolution. SPE-DOM represented major oceanic regimes of general significance: 5 m (near surface photic zone), 48 m (fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 1H NMR spectra showed rather smooth bulk NMR envelopes with a few percent of visibly resolved signatures. 1H NMR spectra of SPE-DOM indicated considerable variance in abundance for all major chemical environments. Two-dimensional NMR spectra of SPE-DOM displayed exceptional resolution. JRES (sensitive but limited resolution), COSY (highly resolved) and HMBC NMR (informative but limited S/N ratio) spectra depicted resolved molecular signatures in excess of a certain minimum abundance. COSY cross peaks were most diverse for sample FMAX and conformed to >1,500 molecules present. Classical methyl groups terminating aliphatic chains represented only ~ 15 % of total methyl in all marine DOM investigated; 2 % of methyl was bound to olefinic carbon. Methyl ethers were abundant in surface marine DOM, and the chemical diversity of carbohydrates was larger than that of freshwater and soil DOM. TOCSY and HSQC cross peaks enabled unprecedented depiction of sp2-hybridized carbon chemical environments in marine SPE-DOM with discrimination of isolated and conjugated olefins as well as ?,?-unsaturated double bonds. Olefinic protons were more abundant than aromatic protons; relative HSQC cross peak integrals indicated more abundant olefinic carbon than aromatic carbon in all marine DOM as well. Furan, pyrrol and thiophene derivatives were marginal. Benzene derivatives and phenols as well as six-membered nitrogen heterocycles were prominent. Various key polycyclic aromatic hydrocarbon substructures suggested the presence of thermogenic organic matter (TMOC) in marine DOM at all water depths. Eventually, olefinic unsaturation in marine DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation. The conformity of key NMR signatures suggests the presence of a numerous set of identical molecules throughout the entire ocean column even if the investigated water masses belonged to different oceanic regimes and currents. High field (12 T) negative electrospray ionization FTICR mass spectra showed abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks and average mass from surface to bottom SPE-DOM. The proportion of CHO and CHNO molecular series increased from surface to depth whereas CHOS and especially CHNOS molecular series markedly declined. The exhaustive characterization of complex unknowns in marine DOM will enable a meaningful assessment of individual marine biogeosignatures which carry the holistic memory of the oceanic water masses.

Affinity analysis and application of dipeptides derived from l-tyrosine in plasmid purification.

PubMed

Ferreira, Soraia; Carvalho, Josué; Valente, Joana F A; Corvo, Marta C; Cabrita, Eurico J; Sousa, Fani; Queiroz, João A; Cruz, Carla

2015-12-01

The developments in the use of plasmid DNA (pDNA) in gene therapy and vaccines have motivated the search and improvement of optimized purification processes. In this context, dipeptides l-tyrosine-l-tyrosine and l-tyrosine-l-arginine are synthetized to explore their application as affinity ligands for supercoiled (sc) plasmid DNA (pDNA) purification. The synthesis is based on the protection of N-Boc-l-tyrosine, followed by condensation with l-tyrosine or l-arginine methyl esters in the presence of dicyclohexylcarbodiimide (DCC), which after hydrolysis and acidification give the afforded dipeptides. The supports are then obtained by coupling l-tyrosine, l-tyrosine-l-tyrosine and l-tyrosine-l-arginine to epoxy-activated Sepharose and are characterized by high resolution magic angle spinning (HR-MAS) NMR and Fourier transform infrared spectroscopy (FTIR). Surface plasmon resonance (SPR) biosensor is used to establish the promising ligand to be used in the chromatographic experiments and ascertain experimental conditions. Sc isoform showed the highest affinity to the dipeptides, followed by linear (ln) pDNA, being the open circular (oc) the one that promoted the lowest affinity to l-tyrosine-l-arginine. Saturation transfer difference (STD)-NMR experiments show that the interaction is mainly hydrophobic with the majority of the 5'-mononucleotides, except for 5'-GMP with l-tyrosine-l-arginine Sepharose that is mainly electrostatic. The support l-tyrosine Sepharose used in chromatographic experiments promotes the separation of native pVAX1-LacZ and pcDNA3-FLAG-p53 samples (oc+sc) by decreasing the salt concentration. The results suggest that it is possible to purify different plasmids with the l-tyrosine Sepharose, with slight adjustments in the gradient conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Validated ¹H and 13C Nuclear Magnetic Resonance Methods for the Quantitative Determination of Glycerol in Drug Injections.

PubMed

Lu, Jiaxi; Wang, Pengli; Wang, Qiuying; Wang, Yanan; Jiang, Miaomiao

2018-05-15

In the current study, we employed high-resolution proton and carbon nuclear magnetic resonance spectroscopy (¹H and 13 C NMR) for quantitative analysis of glycerol in drug injections without any complex pre-treatment or derivatization on samples. The established methods were validated with good specificity, linearity, accuracy, precision, stability, and repeatability. Our results revealed that the contents of glycerol were convenient to calculate directly via the integration ratios of peak areas with an internal standard in ¹H NMR spectra, while the integration of peak heights were proper for 13 C NMR in combination with an external calibration of glycerol. The developed methods were both successfully applied in drug injections. Quantitative NMR methods showed an extensive prospect for glycerol determination in various liquid samples.

A modularized pulse programmer for NMR spectroscopy

NASA Astrophysics Data System (ADS)

Mao, Wenping; Bao, Qingjia; Yang, Liang; Chen, Yiqun; Liu, Chaoyang; Qiu, Jianqing; Ye, Chaohui

2011-02-01

A modularized pulse programmer for a NMR spectrometer is described. It consists of a networked PCI-104 single-board computer and a field programmable gate array (FPGA). The PCI-104 is dedicated to translate the pulse sequence elements from the host computer into 48-bit binary words and download these words to the FPGA, while the FPGA functions as a sequencer to execute these binary words. High-resolution NMR spectra obtained on a home-built spectrometer with four pulse programmers working concurrently demonstrate the effectiveness of the pulse programmer. Advantages of the module include (1) once designed it can be duplicated and used to construct a scalable NMR/MRI system with multiple transmitter and receiver channels, (2) it is a totally programmable system in which all specific applications are determined by software, and (3) it provides enough reserve for possible new pulse sequences.

Moissanite anvil cell design for Giga-Pascal nuclear magnetic resonance.

PubMed

Meier, Thomas; Herzig, Tobias; Haase, Jürgen

2014-04-01

A new design of a non-magnetic high-pressure anvil cell for nuclear magnetic resonance (NMR) experiments at Giga-Pascal pressures is presented, which uses a micro-coil inside the pressurized region for high-sensitivity NMR. The comparably small cell has a length of 22 mm and a diameter of 18 mm, so it can be used with most NMR magnets. The performance of the cell is demonstrated with external-force vs. internal-pressure experiments, and the cell is shown to perform well at pressures up to 23.5 GPa using 800 μm 6H-SiC large cone Boehler-type anvils. (1)H, (23)Na, (27)Al, (69)Ga, and (71)Ga NMR test measurements are presented, which show a resolution of better than 4.5 ppm, and an almost maximum possible signal-to-noise ratio.

Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

PubMed

Goodrich, Katheryn M; Neilson, Andrew P

2014-05-01

Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds, primarily monomers and dimers, in the cecum and colon. Metabolite data indicate the progressive nature of microbial metabolism as the digesta moves through the lower GI tract. This method facilitates the high-throughput, sensitive, and simultaneous analysis of both native compounds and their microbial metabolites in biological samples and provides a more efficient means of extraction and analysis than previous methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Isotope labeling for studying RNA by solid-state NMR spectroscopy.

PubMed

Marchanka, Alexander; Kreutz, Christoph; Carlomagno, Teresa

2018-04-12

Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion. Isotope labeling, either as nucleotide-specific, atom-specific or segmental labeling, can resolve resonance overlaps and reduce the line width, thus allowing ssNMR studies of RNA domains as part of large biomolecules or complexes. In this review we discuss the methods for RNA production and purification as well as numerous approaches for isotope labeling of RNA. Furthermore, we give a few examples that emphasize the instrumental role of isotope labeling and ssNMR for studying RNA as part of large ribonucleoprotein complexes.

Authentication of animal origin of heparin and low molecular weight heparin including ovine, porcine and bovine species using 1D NMR spectroscopy and chemometric tools.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Fareed, Jawed

2018-02-05

High resolution (600MHz) nuclear magnetic resonance (NMR) spectroscopy is used to distinguish heparin and low-molecular weight heparins (LMWHs) produced from porcine, bovine and ovine mucosal tissues as well as their blends. For multivariate analysis several statistical methods such as principal component analysis (PCA), factor discriminant analysis (FDA), partial least squares - discriminant analysis (PLS-DA), linear discriminant analysis (LDA) were utilized for the modeling of NMR data of more than 100 authentic samples. Heparin and LMWH samples from the independent test set (n=15) were 100% correctly classified according to its animal origin. Moreover, by using 1 H NMR coupled with chemometrics and several batches of bovine heparins from two producers were differentiated. Thus, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of animal origin and process based manufacturing difference in heparin products. Copyright © 2017 Elsevier B.V. All rights reserved.

Anvil cell gasket design for high pressure nuclear magnetic resonance experiments beyond 30 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, Thomas; Haase, Jürgen

2015-12-15

Nuclear magnetic resonance (NMR) experiments are reported at up to 30.5 GPa of pressure using radiofrequency (RF) micro-coils with anvil cell designs. These are the highest pressures ever reported with NMR, and are made possible through an improved gasket design based on nano-crystalline powders embedded in epoxy resin. Cubic boron-nitride (c-BN), corundum (α-Al{sub 2}O{sub 3}), or diamond based composites have been tested, also in NMR experiments. These composite gaskets lose about 1/2 of their initial height up to 30.5 GPa, allowing for larger sample quantities and preventing damages to the RF micro-coils compared to precipitation hardened CuBe gaskets. It ismore » shown that NMR shift and resolution are less affected by the composite gaskets as compared to the more magnetic CuBe. The sensitivity can be as high as at normal pressure. The new, inexpensive, and simple to engineer gaskets are thus superior for NMR experiments at high pressures.« less

PSYCHE Pure Shift NMR Spectroscopy.

PubMed

Foroozandeh, Mohammadali; Morris, Gareth; Nilsson, Mathias

2018-03-13

Broadband homodecoupling techniques in NMR, also known as "pure shift" methods, aim to enhance spectral resolution by suppressing the effects of homonuclear coupling interactions to turn multiplet signals into singlets. Such techniques typically work by selecting a subset of "active" nuclear spins to observe, and selectively inverting the remaining, "passive", spins to reverse the effects of coupling. Pure Shift Yielded by Chirp Excitation (PSYCHE) is one such method; it is relatively recent, but has already been successfully implemented in a range of different NMR experiments. Paradoxically, PSYCHE is one of the trickiest of pure shift NMR techniques to understand but one of the easiest to use. Here we offer some insights into theoretical and practical aspects of the method, and into the effects and importance of the experimental parameters. Some recent improvements that enhance the spectral purity of PSYCHE spectra will be presented, and some experimental frameworks including examples in 1D and 2D NMR spectroscopy, for the implementation of PSYCHE will be introduced. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Applications of high-resolution 1H solid-state NMR.

PubMed

Brown, Steven P

2012-02-01

This article reviews the large increase in applications of high-resolution (1)H magic-angle spinning (MAS) solid-state NMR, in particular two-dimensional heteronuclear and homonuclear (double-quantum and spin-diffusion NOESY-like exchange) experiments, in the last five years. These applications benefit from faster MAS frequencies (up to 80 kHz), higher magnetic fields (up to 1 GHz) and pulse sequence developments (e.g., homonuclear decoupling sequences applicable under moderate and fast MAS). (1)H solid-state NMR techniques are shown to provide unique structural insight for a diverse range of systems including pharmaceuticals, self-assembled supramolecular structures and silica-based inorganic-organic materials, such as microporous and mesoporous materials and heterogeneous organometallic catalysts, for which single-crystal diffraction structures cannot be obtained. The power of NMR crystallography approaches that combine experiment with first-principles calculations of NMR parameters (notably using the GIPAW approach) are demonstrated, e.g., to yield quantitative insight into hydrogen-bonding and aromatic CH-π interactions, as well as to generate trial three-dimensional packing arrangements. It is shown how temperature-dependent changes in the (1)H chemical shift, linewidth and DQ-filtered signal intensity can be analysed to determine the thermodynamics and kinetics of molecular level processes, such as the making and breaking of hydrogen bonds, with particular application to proton-conducting materials. Other applications to polymers and biopolymers, inorganic compounds and bioinorganic systems, paramagnetic compounds and proteins are presented. The potential of new technological advances such as DNP methods and new microcoil designs is described. Copyright © 2011 Elsevier Inc. All rights reserved.

Staging research of human lung cancer tissues by high-resolution magic angle spinning proton nuclear magnetic resonance spectroscopy (HRMAS 1 H NMR) and multivariate data analysis.

PubMed

Chen, Wenxue; Lu, Shaohua; Wang, Guifang; Chen, Fener; Bai, Chunxue

2017-10-01

High-resolution magic-angle spinning proton nuclear magnetic resonance (HRMAS 1 H NMR) spectroscopy technique was employed to analyze the metabonomic characterizations of lung cancer tissues in hope to identify potential diagnostic biomarkers for malignancy detection and staging research of lung tissues. HRMAS 1 H NMR spectroscopy technique can rapidly provide important information for accurate diagnosis and staging of cancer tissues owing to its noninvasive nature and limited requirement for the samples, and thus has been acknowledged as an excellent tool to investigate tissue metabolism and provide a more realistic insight into the metabonomics of tissues when combined with multivariate data analysis (MVDA) such as component analysis and orthogonal partial least squares-discriminant analysis in particular. HRMAS 1 H NMR spectra displayed the metabonomic differences of 32 lung cancer tissues at the different stages from 32 patients. The significant changes (P < 0.05) of some important metabolites such as lipids, aspartate and choline-containing compounds in cancer tissues at the different stages had been identified. Furthermore, the combination of HRMAS 1 H NMR spectroscopy and MVDA might potentially and precisely provided for a high sensitivity, specificity, prediction accuracy in the positive identification of the staging for the cancer tissues in contrast with the pathological data in clinic. This study highlighted the potential of metabonomics in clinical settings so that the techniques might be further exploited for the diagnosis and staging prediction of lung cancer in future. © 2016 John Wiley & Sons Australia, Ltd.

Detection of Potential TNA and RNA Nucleoside Precursors in a Prebiotic Mixture by Pure Shift Diffusion-Ordered NMR Spectroscopy

PubMed Central

Islam, Saidul; Aguilar, Juan A; Powner, Matthew W; Nilsson, Mathias; Morris, Gareth A; Sutherland, John D

2013-01-01

In the context of prebiotic chemistry, one of the characteristics of mixed nitrogenous-oxygenous chemistry is its propensity to give rise to highly complex reaction mixtures. There is therefore an urgent need to develop improved spectroscopic techniques if onerous chromatographic separations are to be avoided. One potential avenue is the combination of pure shift methodology, in which NMR spectra are measured with greatly improved resolution by suppressing multiplet structure, with diffusion-ordered spectroscopy, in which NMR signals from different species are distinguished through their different rates of diffusion. Such a combination has the added advantage of working with intact mixtures, allowing analyses to be carried out without perturbing mixtures in which chemical entities are part of a network of reactions in equilibrium. As part of a systems chemistry approach towards investigating the self-assembly of potentially prebiotic small molecules, we have analysed the complex mixture arising from mixing glycolaldehyde and cyanamide, in a first application of pure shift DOSY NMR to the characterisation of a partially unknown reaction composition. The work presented illustrates the potential of pure shift DOSY to be applied to chemistries that give rise to mixtures of compounds in which the NMR signal resolution is poor. The direct formation of potential RNA and TNA nucleoside precursors, amongst other adducts, was observed. These preliminary observations may have implications for the potentially prebiotic assembly chemistry of pyrimidine threonucleotides, and therefore of TNA, by using recently reported chemistries that yield the activated pyridimidine ribonucleotides. PMID:23371787

Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

PubMed Central

Sekhar, Ashok; Rumfeldt, Jessica AO; Broom, Helen R; Doyle, Colleen M; Bouvignies, Guillaume; Meiering, Elizabeth M; Kay, Lewis E

2015-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization. DOI: http://dx.doi.org/10.7554/eLife.07296.001 PMID:26099300

Chaperone-client complexes: A dynamic liaison

NASA Astrophysics Data System (ADS)

Hiller, Sebastian; Burmann, Björn M.

2018-04-01

Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.

Metabolomics by Proton High-Resolution Magic-Angle-Spinning Nuclear Magnetic Resonance of Tomato Plants Treated with Two Secondary Metabolites Isolated from Trichoderma.

PubMed

Mazzei, Pierluigi; Vinale, Francesco; Woo, Sheridan Lois; Pascale, Alberto; Lorito, Matteo; Piccolo, Alessandro

2016-05-11

Trichoderma fungi release 6-pentyl-2H-pyran-2-one (1) and harzianic acid (2) secondary metabolites to improve plant growth and health protection. We isolated metabolites 1 and 2 from Trichoderma strains, whose different concentrations were used to treat seeds of Solanum lycopersicum. The metabolic profile in the resulting 15 day old tomato leaves was studied by high-resolution magic-angle-spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy directly on the whole samples without any preliminary extraction. Principal component analysis (PCA) of HRMAS NMR showed significantly enhanced acetylcholine and γ-aminobutyric acid (GABA) content accompanied by variable amount of amino acids in samples treated with both Trichoderma secondary metabolites. Seed germination rates, seedling fresh weight, and the metabolome of tomato leaves were also dependent upon doses of metabolites 1 and 2 treatments. HRMAS NMR spectroscopy was proven to represent a rapid and reliable technique for evaluating specific changes in the metabolome of plant leaves and calibrating the best concentration of bioactive compounds required to stimulate plant growth.

Structure of shock compressed model basaltic glass: Insights from O K-edge X-ray Raman scattering and high-resolution 27Al NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Sung Keun; Park, Sun Young; Kim, Hyo-Im; Tschauner, Oliver; Asimow, Paul; Bai, Ligang; Xiao, Yuming; Chow, Paul

2012-03-01

The detailed atomic structures of shock compressed basaltic glasses are not well understood. Here, we explore the structures of shock compressed silicate glass with a diopside-anorthite eutectic composition (Di64An36), a common Fe-free model basaltic composition, using oxygen K-edge X-ray Raman scattering and high- resolution 27Al solid-state NMR spectroscopy and report previously unknown details of shock-induced changes in the atomic configurations. A topologically driven densification of the Di64An36 glass is indicated by the increase in oxygen K-edge energy for the glass upon shock compression. The first experimental evidence of the increase in the fraction of highly coordinated Al in shock compressed glass is found in the 27Al NMR spectra. This unambiguous evidence of shock-induced changes in Al coordination environments provides atomistic insights into shock compression in basaltic glasses and allows us to microscopically constrain the magnitude of impact events or relevant processes involving natural basalts on Earth and planetary surfaces.

Dynamic Nuclear Polarization NMR in Human Cells Using Fluorescent Polarizing Agents.

PubMed

Albert, Brice J; Gao, Chukun; Sesti, Erika L; Saliba, Edward P; Alaniva, Nicholas; Scott, Faith J; Sigurdsson, Snorri Th; Barnes, Alexander B

2018-06-20

Solid-state nuclear magnetic resonance (NMR) enables atomic resolution characterization of molecular structure and dynamics within complex heterogeneous samples, but it is typically insensitive. Dynamic nuclear polarization (DNP) increases NMR signal intensity by orders of magnitude and can be performed in combination with magic angle spinning (MAS) for sensitive, high-resolution spectroscopy. Here we report MAS DNP experiments, for the first time, within intact human cells with >40-fold DNP enhancement and a sample temperature below 6 K. In addition to cryogenic MAS results below 6 K, we also show in-cell DNP enhancements of 57-fold at 90 K. In-cell DNP is demonstrated using biradicals and sterically-shielded monoradicals as polarizing agents. A novel trimodal polarizing agent is introduced for DNP, which contains a nitroxide biradical, a targeting peptide for cell penetration, and a fluorophore for subcellular localization with confocal microscopy. The fluorescent polarizing agent provides in-cell DNP enhancements of 63-fold at a concentration of 2.7 mM. These experiments pave the way for structural characterization of biomolecules in an endogenous cellular context.

Structural investigations of Pu{sup III} phosphate by X-ray diffraction, MAS-NMR and XANES spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popa, Karin; Raison, Philippe E., E-mail: philippe.raison@ec.europa.eu; Martel, Laura

2015-10-15

PuPO{sub 4} was prepared by a solid state reaction method and its crystal structure at room temperature was solved by powder X-ray diffraction combined with Rietveld refinement. High resolution XANES measurements confirm the +III valence state of plutonium, in agreement with valence bond derivation. The presence of the americium (as β{sup −} decay product of plutonium) in the +III oxidation state was determined based on XANES spectroscopy. High resolution solid state {sup 31}P NMR agrees with the XANES results and the presence of a solid-solution. - Graphical abstract: A full structural analysis of PuPO{sub 4} based on Rietveld analysis ofmore » room temperature X-ray diffraction data, XANES and MAS NMR measurements was performed. - Highlights: • The crystal structure of PuPO{sub 4} monazite is solved. • In PuPO{sub 4} plutonium is strictly trivalent. • The presence of a minute amount of Am{sup III} is highlighted. • We propose PuPO{sub 4} as a potential reference material for spectroscopic and microscopic studies.« less

Low resolution 1H NMR assignment of proton populations in pound cake and its polymeric ingredients.

PubMed

Luyts, A; Wilderjans, E; Waterschoot, J; Van Haesendonck, I; Brijs, K; Courtin, C M; Hills, B; Delcour, J A

2013-08-15

Based on a model system approach, five different proton populations were distinguished in pound cake crumb using one dimensional low resolution (1)H NMR spectroscopy. In free induction decay (FID) measurements, proton populations were assigned to (i) non-exchanging CH protons of crystalline starch, proteins and crystalline fat and (ii) non-exchanging CH protons of amorphous starch and gluten, which are in little contact with water. In Carr-Purcell-Meiboom-Gill (CPMG) measurements, three proton populations were distinguished. The CPMG population with the lowest mobility and the FID population with the highest mobility represent the same proton population. The two CPMG proton populations with the highest mobility were assigned to exchanging protons (i.e., protons of water, starch, gluten, egg proteins and sugar) and protons of lipids (i.e., protons of egg yolk lipids and amorphous lipid fraction of margarine) respectively. Based on their spin-lattice relaxation times (T1), two dimensional (1)H NMR spectroscopy further resolved the two proton populations with the highest mobility into three and two proton populations, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stiffening of flexible SUMO1 protein upon peptide-binding: Analysis with anisotropic network model.

PubMed

Sarkar, Ranja

2018-01-01

SUMO (small ubiquitin-like modifier) proteins interact with a large number of target proteins via a key regulatory event called sumoylation that encompasses activation, conjugation and ligation of SUMO proteins through specific E1, E2, and E3-type enzymes respectively. Single-molecule atomic force microscopic (AFM) experiments performed to unravel bound SUMO1 along its NC termini direction reveal that E3-ligases (in the form of small peptides) increase mechanical stability (along the axis) of the flexible protein upon binding. The experimental results are expected to correlate with the intrinsic flexibility of bound SUMO1 protein in the native state i.e., the bound conformation of SUMO1 without the binding peptide. The native protein flexibility/stiffness can be measured as a spring constant by normal mode analysis. In the present study, protein normal modes are computed from the protein structural data (as input from protein databank) via a simple anisotropic network model (ANM). ANM is computationally inexpensive and hence, can be explored to investigate and compare the native conformational dynamics of unbound and bound (without the binding partner) structures, if the corresponding structural data (NMR/X-ray) are available. The paper illustrates that SUMO1 stiffens (native flexibility decreases) along the NC termini (end-to-end) direction of the protein upon binding to small peptides; however, the degree of stiffening is peptide sequence-specific. The theoretical results are demonstrated for NMR structures of unbound SUMO1 and that bound to two peptides having short amino acid motifs and of similar size, one being an M-IR2 peptide derived from RanBP2 protein and the other one derived from PIASX protein. The peptide derived from PIASX stiffens SUMO1 remarkably which is evident from an atomic-level normal mode analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

In vivo two-dimensional NMR correlation spectroscopy

NASA Astrophysics Data System (ADS)

Kraft, Robert A.

1999-10-01

The poor resolution of in-vivo one- dimensional nuclear magnetic resonance spectroscopy (NMR) has limited its clinical potential. Currently, only the large singlet methyl resonances arising from N-acetyl aspartate (NAA), choline, and creatine are quantitated in a clinical setting. Other metabolites such as myo- inositol, glutamine, glutamate, lactate, and γ- amino butyric acid (GABA) are of clinical interest but quantitation is difficult due to the overlapping resonances and limited spectral resolution. To improve the spectral resolution and distinguish between overlapping resonances, a series of two- dimensional chemical shift correlation spectroscopy experiments were developed for a 1.5 Tesla clinical imaging magnet. Two-dimensional methods are attractive for in vivo spectroscopy due to their ability to unravel overlapping resonances with the second dimension, simplifying the interpretation and quantitation of low field NMR spectra. Two-dimensional experiments acquired with mix-mode line shape negate the advantages of the second dimension. For this reason, a new experiment, REVOLT, was developed to achieve absorptive mode line shape in both dimensions. Absorptive mode experiments were compared to mixed mode experiments with respect to sensitivity, resolution, and water suppression. Detailed theoretical and experimental calculations of the optimum spin lock and radio frequency power deposition were performed. Two-dimensional spectra were acquired from human bone marrow and human brain tissue. The human brain tissue spectra clearly reveal correlations among the coupled spins of NAA, glutamine, glutamate, lactate, GABA, aspartate and myo-inositol obtained from a single experiment of 23 minutes from a volume of 59 mL. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

A novel in situ electrochemical NMR cell with a palisade gold film electrode

NASA Astrophysics Data System (ADS)

Ni, Zu-Rong; Cui, Xiao-Hong; Cao, Shuo-Hui; Chen, Zhong

2017-08-01

In situ electrochemical nuclear magnetic resonance (EC-NMR) has attracted considerable attention because of its ability to directly observe real-time electrochemical processes. Therefore, minimizing the incompatibility between the electrochemical device and NMR detection has become an important challenge. A circular thin metal film deposited on the outer surface of a glass tube with a thickness considerably less than the metal skin depth is considered to be the ideal working electrode. In this study, we demonstrate that such a thin film electrode still has a great influence on the radio frequency field homogeneity in the detective zone of the NMR spectrometer probe and provide theoretical and experimental confirmation of its electromagnetic shielding. Furthermore, we propose a novel palisade gold film device to act as the working electrode. The NMR nutation behavior of protons shows that the uniformity of the radio frequency field is greatly improved, increasing the sensitivity in NMR detection. Another advantage of the proposed device is that an external reference standard adapted to the reaction compound can be inserted as a probe to determine the fluctuation of the physico-chemical environment and achieve high-accuracy quantitative NMR analysis. A three-chamber electrochemical device based on the palisade gold film design was successfully fabricated and the in situ electrochemical NMR performance was validated in a standard 5 mm NMR probe by acquiring voltammograms and high-resolution NMR spectra to characterize the electrochemically generated species. The evolution of in situ EC-NMR spectrum monitoring of the redox transformation between p-benzoquinone and hydroquinone demonstrates the ability of the EC-NMR device to simultaneously quantitatively determine the reactants and elucidate the reaction mechanism at the molecular level.

SABRE hyperpolarization enables high-sensitivity 1H and 13C benchtop NMR spectroscopy.

PubMed

Richardson, Peter M; Parrott, Andrew J; Semenova, Olga; Nordon, Alison; Duckett, Simon B; Halse, Meghan E

2018-06-19

Benchtop NMR spectrometers operating with low magnetic fields of 1-2 T at sub-ppm resolution show great promise as analytical platforms that can be used outside the traditional laboratory environment for industrial process monitoring. One current limitation that reduces the uptake of benchtop NMR is associated with the detection fields' reduced sensitivity. Here we demonstrate how para-hydrogen (p-H2) based signal amplification by reversible exchange (SABRE), a simple to achieve hyperpolarization technique, enhances agent detectability within the environment of a benchtop (1 T) NMR spectrometer so that informative 1H and 13C NMR spectra can be readily recorded for low-concentration analytes. SABRE-derived 1H NMR signal enhancements of up to 17 000-fold, corresponding to 1H polarization levels of P = 5.9%, were achieved for 26 mM pyridine in d4-methanol in a matter of seconds. Comparable enhancement levels can be achieved in both deuterated and protio solvents but now the SABRE-enhanced analyte signals dominate due to the comparatively weak thermally-polarized solvent response. The SABRE approach also enables the acquisition of 13C NMR spectra of analytes at natural isotopic abundance in a single scan as evidenced by hyperpolarized 13C NMR spectra of tens of millimolar concentrations of 4-methylpyridine. Now the associated signal enhancement factors are up to 45 500 fold (P = 4.0%) and achieved in just 15 s. Integration of an automated SABRE polarization system with the benchtop NMR spectrometer framework produces renewable and reproducible NMR signal enhancements that can be exploited for the collection of multi-dimensional NMR spectra, exemplified here by a SABRE-enhanced 2D COSY NMR spectrum.

Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan.

PubMed

Bozzi, Manuela; Bianchi, Marzia; Sciandra, Francesca; Paci, Maurizio; Giardina, Bruno; Brancaccio, Andrea; Cicero, Daniel O

2003-11-25

Dystroglycan (DG) is an adhesion molecule playing a crucial role for tissue stability during both early embriogenesis and adulthood and is composed by two tightly interacting subunits: alpha-DG, membrane-associated and highly glycosylated, and the transmembrane beta-DG. Recently, by solid-phase binding assays and NMR experiments, we have shown that the C-terminal domain of alpha-DG interacts with a recombinant extracellular fragment of beta-DG (positions 654-750) independently from glycosylation and that the linear binding epitope is located between residues 550 and 565 of alpha-DG. In order to elucidate which moieties of beta-DG are specifically involved in the complex with alpha-DG, the ectodomain has been recombinantly expressed and purified in a labeled ((13)C,(15)N) form and studied by multidimensional NMR. Although it represents a natively unfolded protein domain, we obtained an almost complete backbone assignment. Chemical shift index, (1)H-(15)N heteronuclear single-quantum coherence and nuclear Overhauser effect (HSQC-NOESY) spectra and (3)J(HN,H)(alpha) coupling constant values confirm that this protein is highly disordered, but (1)H-(15)N steady-state NOE experiments indicate that the protein presents two regions of different mobility. The first one, between residues 659 and 722, is characterized by a limited degree of mobility, whereas the C-terminal portion, containing about 30 amino acids, is highly flexible. The binding of beta-DG(654-750) to the C-terminal region of the alpha subunit, alpha-DG(485-620), has been investigated, showing that the region of beta-DG(654-750) between residues 691 and 719 is involved in the interaction.

Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion

PubMed Central

Meinhold, Derrick W.; Wright, Peter E.

2011-01-01

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of R2 dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s-1) and MG → I1 (26 s-1), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from R2 dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process. PMID:21562212

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

PubMed

Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

2012-03-07

Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

[Imaging of alloplastic ligament implant. An in vivo and in vitro study exemplified by Kevlar].

PubMed

Wening, J V; Katzer, A; Nicolas, V; Hahn, M; Jungbluth, K H; Kratzer A [corrected to Katzer, A

1994-04-01

Neither native X-ray nor CT or NMR allow to evaluate intraarticular implantation results of Kevlar -49 directly. In animal trials, the course of an artificial ligament may only be presumed from connective tissue ingrowth. Although soft tissue structure appears much better in NMR than in CT, direct proof of ligament continuity is still impossible. As soon as the connective tissue becomes continuous, it appears clearly and allows indirect evaluation of the prosthesis, as integrity can be judged by its shape like in natural cruciate ligament. Anatomic preparations show that connective tissue fills up the small space between the two cords of a Kevlar -49 two bundle prosthesis eight weeks after implantation, so that imaging systems show only one intraarticular bundle.

Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy

PubMed Central

Sborgi, Lorenzo; Ravotti, Francesco; Dandey, Venkata P.; Dick, Mathias S.; Mazur, Adam; Reckel, Sina; Chami, Mohamed; Scherer, Sebastian; Huber, Matthias; Böckmann, Anja; Egelman, Edward H.; Stahlberg, Henning; Broz, Petr; Meier, Beat H.; Hiller, Sebastian

2015-01-01

Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms. PMID:26464513

On the Observation of Discrete Fluorine NMR Spectra for Uridine 5′-β,γ-Fluoromethylenetriphosphate Diastereomers at Basic pH

PubMed Central

2015-01-01

Jakeman et al. recently reported the inability to distinguish the diastereomers of uridine 5′-β,γ-fluoromethylenetriphosphate (β,γ-CHF-UTP, 1) by 19F NMR under conditions we previously prescribed for the resolution of the corresponding β,γ-CHF-dGTP spectra, stating further that 1 decomposed under these basic conditions. Here we show that the 19F NMR spectra of 1 (∼1:1 diastereomer mixture prepared by coupling of UMP-morpholidate with fluoromethylenebis(phosphonic acid)) in D2O at pH 10 are indeed readily distinguishable. 1 in this solution was stable for 24 h at rt. PMID:24819695

A novel alkaloid isolated from Crotalaria paulina and identified by NMR and DFT calculations

NASA Astrophysics Data System (ADS)

Oliveira, Ramon Prata; Demuner, Antonio Jacinto; Alvarenga, Elson Santiago; Barbosa, Luiz Claudio Almeida; de Melo Silva, Thiago

2018-01-01

Pyrrolizidine alkaloids (PAs) are secondary metabolites found in Crotalaria genus and are known to have several biological activities. A novel macrocycle bislactone alkaloid, coined ethylcrotaline, was isolated and purified from the aerial parts of Crotalaria paulina. The novel macrocycle was identified with the aid of high resolution mass spectrometry and advanced nuclear magnetic resonance techniques. The relative stereochemistry of the alkaloid was defined by comparing the calculated quantum mechanical hydrogen and carbon chemical shifts of eight candidate structures with the experimental NMR data. The best fit between the eight candidate structures and the experimental NMR chemical shifts was defined by the DP4 statistical analyses and the Mean Absolute Error (MAE) calculations.

1H NMR Spectroscopy and MVA Analysis of Diplodus sargus Eating the Exotic Pest Caulerpa cylindracea.

PubMed

De Pascali, Sandra A; Del Coco, Laura; Felline, Serena; Mollo, Ernesto; Terlizzi, Antonio; Fanizzi, Francesco P

2015-06-05

The green alga Caulerpa cylindracea is a non-autochthonous and invasive species that is severely affecting the native communities in the Mediterranean Sea. Recent researches show that the native edible fish Diplodus sargus actively feeds on this alga and cellular and physiological alterations have been related to the novel alimentary habits. The complex effects of such a trophic exposure to the invasive pest are still poorly understood. Here we report on the metabolic profiles of plasma from D. sargus individuals exposed to C. cylindracea along the southern Italian coast, using 1H NMR spectroscopy and multivariate analysis (Principal Component Analysis, PCA, Orthogonal Partial Least Square, PLS, and Orthogonal Partial Least Square Discriminant Analysis, OPLS-DA). Fish were sampled in two seasonal periods from three different locations, each characterized by a different degree of algal abundance. The levels of the algal bisindole alkaloid caulerpin, which is accumulated in the fish tissues, was used as an indicator of the trophic exposure to the seaweed and related to the plasma metabolic profiles. The profiles appeared clearly influenced by the sampling period beside the content of caulerpin, while the analyses also supported a moderate alteration of lipid and choline metabolism related to the Caulerpa-based diet.

A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: amyloid fibrils of human CA150.WW2.

PubMed

Becker, Johanna; Ferguson, Neil; Flinders, Jeremy; van Rossum, Barth-Jan; Fersht, Alan R; Oschkinat, Hartmut

2008-08-11

The second WW domain (WW2) of CA150, a human transcriptional activator, forms amyloid fibrils in vitro under physiological conditions. Based on experimental constraints from MAS NMR spectroscopy experiments, alanine scanning and electron microscopy, a structural model of CA150.WW2 amyloid fibrils was calculated earlier. Here, the assignment strategy is presented and suggested as a general approach for proteins that show intermediate line width. The (13)C,(13)C correlation experiments were recorded on fully or partially (13)C-labelled fibrils. The earlier (13)C assignment (26 residues) was extended to 34 of the 40 residues by direct (13)C-excitation experiments by using a deuterated sample that showed strongly improved line width. A 3D HNC-TEDOR (transferred-echo double-resonance) experiment with deuterated CA150.WW2 fibrils yielded 14 amide nitrogen and proton resonance assignments. The obtained chemical shifts were compared with the chemical shifts determined with the natively folded WW domain. TALOS (Torsion angle likelihood obtained from shift and sequence similarity) predictions confirmed that, under physiological conditions, the fibrillar form of CA150.WW2 adopts a significantly different beta structure than the native WW-domain fold.

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

PubMed

Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

2014-02-25

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.

PubMed

McCaffrey, Jesse E; James, Zachary M; Thomas, David D

2015-01-01

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

Characterisation of transition state structures for protein folding using ‘high’, ‘medium’ and ‘low’ Φ-values

PubMed Central

Geierhaas, Christian D.; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-01-01

It has been suggested that Φ-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Φ-values indicate almost completely folded regions in the TS, intermediate Φ-values regions with a detectable amount of structure and low Φ-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Φ-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Φ-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Φ-values can provide sufficient information for characterising the architecture of a TS for folding of a protein. PMID:18299294

Protein folding on the ribosome studied using NMR spectroscopy

PubMed Central

Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

2013-01-01

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

A biofilm microreactor system for simultaneous electrochemical and nuclear magnetic resonance techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.

2014-03-01

In order to fully understand electrochemically active biofilms and the limitations to their scale-up in industrial biofilm reactors, a complete picture of the microenvironments inside the biofilm is needed. Nuclear magnetic resonance (NMR) techniques are ideally suited for the study of biofilms and for probing their microenvironments because these techniques allow for non-invasive interrogation and in situ monitoring with high resolution. By combining NMR with simultaneous electrochemical techniques, it is possible to sustain and study live electrochemically active biofilms. Here, we introduce a novel biofilm microreactor system that allows for simultaneous electrochemical and NMR techniques (EC-NMR) at the microscale. Microreactorsmore » were designed with custom radiofrequency resonator coils, which allowed for NMR measurements of biofilms growing on polarized gold electrodes. For an example application of this system, we grew Geobacter sulfurreducens biofilms. NMR was used to investigate growth media flow velocities, which were compared to simulated laminar flow, and electron donor concentrations inside the biofilms. We use Monte Carlo error analysis to estimate standard deviations of the electron donor concentration measurements within the biofilm. The EC-NMR biofilm microreactor system can ultimately be used to correlate extracellular electron transfer rates with metabolic reactions and explore extracellular electron transfer mechanisms.« less

A Multidisciplinary Approach to High Throughput Nuclear Magnetic Resonance Spectroscopy

PubMed Central

Pourmodheji, Hossein; Ghafar-Zadeh, Ebrahim; Magierowski, Sebastian

2016-01-01

Nuclear Magnetic Resonance (NMR) is a non-contact, powerful structure-elucidation technique for biochemical analysis. NMR spectroscopy is used extensively in a variety of life science applications including drug discovery. However, existing NMR technology is limited in that it cannot run a large number of experiments simultaneously in one unit. Recent advances in micro-fabrication technologies have attracted the attention of researchers to overcome these limitations and significantly accelerate the drug discovery process by developing the next generation of high-throughput NMR spectrometers using Complementary Metal Oxide Semiconductor (CMOS). In this paper, we examine this paradigm shift and explore new design strategies for the development of the next generation of high-throughput NMR spectrometers using CMOS technology. A CMOS NMR system consists of an array of high sensitivity micro-coils integrated with interfacing radio-frequency circuits on the same chip. Herein, we first discuss the key challenges and recent advances in the field of CMOS NMR technology, and then a new design strategy is put forward for the design and implementation of highly sensitive and high-throughput CMOS NMR spectrometers. We thereafter discuss the functionality and applicability of the proposed techniques by demonstrating the results. For microelectronic researchers starting to work in the field of CMOS NMR technology, this paper serves as a tutorial with comprehensive review of state-of-the-art technologies and their performance levels. Based on these levels, the CMOS NMR approach offers unique advantages for high resolution, time-sensitive and high-throughput bimolecular analysis required in a variety of life science applications including drug discovery. PMID:27294925

Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins.

PubMed

Ayuso-Tejedor, Sara; Angarica, Vladimir Espinosa; Bueno, Marta; Campos, Luis A; Abián, Olga; Bernadó, Pau; Sancho, Javier; Jiménez, M Angeles

2010-07-23

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Chemical shift and electric field gradient tensors for the amide and carboxyl hydrogens in the model peptide N-acetyl-D,L-valine. Single-crystal deuterium NMR study.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerald, R. E., II; Bernhard, T.; Haeberlen, U.

1993-01-01

Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper themore » authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton NMR are that it works in the presence of {sup 14}N spins which are very hard to decouple from protons and that additional information in form of the EFG tensors can be derived. The change in the CS and EFG tensors upon exchange of a deuteron for a proton (the isotope effect) is anticipated to be very small; the effect on the CS tensors is certainly smaller than the experimental errors. NAV has served as a model peptide before in a variety of NMR studies, including those concerned with developing solid-state NMR spectroscopy as a method for determining the structure of proteins. NMR experiments on peptide or protein samples which are oriented in at least one dimension can provide important information about the three-dimensional structure of the peptide or the protein. In order to interpret the NMR data in terms of the structure of the polypeptide, the relationship of the CS and EFG tensors to the local symmetry elements of an amino acide, e.g., the peptide plane, is essential. The main purpose of this work is to investigate this relationship for the amide hydrogen CS tensor. The amide hydrogen CS tensor will also provide orientational information for peptide bonds in proteins complementary to that from the nitrogen CS and EFG tensors and the nitrogen-hydrogen heteronuclear dipole-dipole coupling which have been used previously to determine protein structures by solid-state NMR spectroscopy. This information will be particularly valuable because the amide hydrogen CS tensor is not axially symmetric. In addition, the use of the amide hydrogen CS interaction in high-field solid-state NMR experiments will increase the available resolution among peptide sites.« less

Lithium Visibility in Rat Brain and Muscle in Vivoby 7Li NMR Imaging

NASA Astrophysics Data System (ADS)

Komoroski, Richard A.; Pearce, John M.; Newton, Joseph E. O.

1998-07-01

The apparent concentration of lithium (Li)in vivowas determined for several regions in the brain and muscle of rats by7Li NMR imaging at 4.7 T with inclusion of an external standard of known concentration and visibility. The average apparent concentrations were 10.1 mM for muscle, and 4.2-5.3 mM for various brain regions under the dosing conditions used. The results were compared to concentrations determinedin vitroby high-resolution7Li NMR spectroscopy of extracts of brain and muscle tissue from the same rats. The comparison provided estimates of the7Li NMR visibility of the Li cation in each tissue region. Although there was considerable scatter of the calculated visibilities among the five rats studied, the results suggested essentially full visibility (96%) for Li in muscle, and somewhat reduced visibility (74-93%) in the various brain regions.

NMR imaging of cell phone radiation absorption in brain tissue

PubMed Central

Gultekin, David H.; Moeller, Lothar

2013-01-01

A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry. PMID:23248293

Determination of Diethyl Phthalate and Polyhexamethylene Guanidine in Surrogate Alcohol from Russia

PubMed Central

Monakhova, Yulia B.; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W.

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and 1H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and 1H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. 1H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while 1H NMR is recommended for specific confirmatory analysis if required. PMID:21647285

Determination of diethyl phthalate and polyhexamethylene guanidine in surrogate alcohol from Russia.

PubMed

Monakhova, Yulia B; Kuballa, Thomas; Leitz, Jenny; Lachenmeier, Dirk W

2011-01-01

Analytical methods based on spectroscopic techniques were developed and validated for the determination of diethyl phthalate (DEP) and polyhexamethylene guanidine (PHMG), which may occur in unrecorded alcohol. Analysis for PHMG was based on UV-VIS spectrophotometry after derivatization with Eosin Y and (1)H NMR spectroscopy of the DMSO extract. Analysis of DEP was performed with direct UV-VIS and (1)H NMR methods. Multivariate curve resolution and spectra computation methods were used to confirm the presence of PHMG and DEP in the investigated beverages. Of 22 analysed alcohol samples, two contained DEP or PHMG. (1)H NMR analysis also revealed the presence of signals of hawthorn extract in three medicinal alcohols used as surrogate alcohol. The simple and cheap UV-VIS methods can be used for rapid screening of surrogate alcohol samples for impurities, while (1)H NMR is recommended for specific confirmatory analysis if required.

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy

PubMed Central

Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús

2017-01-01

Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

NMR imaging of cell phone radiation absorption in brain tissue.

PubMed

Gultekin, David H; Moeller, Lothar

2013-01-02

A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry.

Moissanite anvil cell design for giga-pascal nuclear magnetic resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, Thomas; Herzig, Tobias; Haase, Jürgen

2014-04-15

A new design of a non-magnetic high-pressure anvil cell for nuclear magnetic resonance (NMR) experiments at Giga-Pascal pressures is presented, which uses a micro-coil inside the pressurized region for high-sensitivity NMR. The comparably small cell has a length of 22 mm and a diameter of 18 mm, so it can be used with most NMR magnets. The performance of the cell is demonstrated with external-force vs. internal-pressure experiments, and the cell is shown to perform well at pressures up to 23.5 GPa using 800 μm 6H-SiC large cone Boehler-type anvils. {sup 1}H, {sup 23}Na, {sup 27}Al, {sup 69}Ga, and {supmore » 71}Ga NMR test measurements are presented, which show a resolution of better than 4.5 ppm, and an almost maximum possible signal-to-noise ratio.« less

Control of Chemical Dynamics Using Arbitrary Shaped Optical Pulses and Laser-Enhanced NMR Spectroscopy.

NASA Astrophysics Data System (ADS)

Goswami, Debabrata

A key feature of this thesis is the application of novel laser techniques to various fields of spectroscopy. The overall effort has been towards achieving either chemical control or enhanced spectroscopic resolution. The issue of chemical control forms the major bulk. Over the past decade, theoretical and technological developments have made it possible for a modern day chemist to be a more active participant in nature's chemical processes. Consequently, although the idea of manipulating chemical reactions has been a long term dream, it is only now that realization of such dreams has become realistic. One of the major contributions that is leading towards this realization is the development of pulse shaping techniques. Here, we concentrate on the important developments in this area that has come by recently, particularly emphasizing new results from our laboratory. We discuss in detail the current state-of-the-art, and present some experimental and theoretical demonstrations of chemical control by using arbitrarily shaped pulses. The major strength of our approach to pulse shaping has been in considering "robustness in the laboratory" as a primary constraint. Most of the shapes, addressed here, work under adiabatic conditions where the exact shape of the pulse is not critical as long as the basic criteria dictated by the adiabatic theorem are satisfied. A novel approach of "molecular pulse shaping"--using the molecule itself to generate its own pulse shape--is presented as an example of the ultimate form of robustness. Finally, we get into the issue of resolution enhancement by coupling laser radiation into a Nuclear Magnetic Resonance (NMR) spectrometer. Spectroscopic resolution enhancement is an everlasting effort in the field of NMR--even more for biological NMR. We present some of the recent experimental findings in our laboratory that show selective dispersion in the NMR spectrum when it is acquired under a non-resonant laser irradiation of the sample. Albeit promising, the observed effects are weak and the theoretical understanding of these experiments is not profound enough for implementing any immediate applications.

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures.

PubMed

Dass, Rupashree; Grudzia Ż, Katarzyna; Ishikawa, Takao; Nowakowski, Michał; Dȩbowska, Renata; Kazimierczuk, Krzysztof

2017-01-01

The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1 H experiments have been reported in studies of bacterial metabolism monitored in situ . However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes , an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13 C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

Novel sst2-selective somatostatin agonists. Three-dimensional consensus structure by NMR

PubMed Central

Grace, Christy Rani R.; Erchegyi, Judit; Koerber, Steven C.; Reubi, Jean Claude; Rivier, Jean; Riek, Roland

2008-01-01

The three-dimensional NMR structures of six octapeptide agonist analogues of somatostatin (SRIF) in the free form are described. These analogues, with the basic sequence H-DPhe/Phe2-c[Cys3-Xxx7-DTrp8-Lys9-Thr10-Cys14]-Thr-NH2 (the numbering refers to the position in native SRIF), with Xxx7 being Ala/Aph, exhibit potent and highly selective binding to human SRIF type 2 (sst2) receptors. The backbone of these sst2-selective analogues have the usual type-II’ β-turn reported in the literature for sst2/3/5-subtype-selective analogues. Correlating biological results and NMR studies led to the identification of the side chains of DPhe2, DTrp8 and Lys9 as the necessary components of the sst2 pharmacophore. This is the first study to show that the aromatic ring at position 7 (Phe7) is not critical for sst2 binding and that it plays an important role in sst3 and sst5 binding. This pharmacophore is therefore different from that proposed by others for sst2/3/5 analogues. PMID:16854054

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells.

PubMed

Vasile, Francesca; Panigada, Maddalena; Siccardi, Antonio; Potenza, Donatella; Tiana, Guido

2018-04-24

The development of small-molecule inhibitors of influenza virus Hemagglutinin could be relevant to the opposition of the diffusion of new pandemic viruses. In this work, we made use of Nuclear Magnetic Resonance (NMR) spectroscopy to study the interaction between two derivatives of sialic acid, Neu5Ac-α-(2,6)-Gal-β-(1⁻4)-GlcNAc and Neu5Ac-α-(2,3)-Gal-β-(1⁻4)-GlcNAc, and hemagglutinin directly expressed on the surface of recombinant human cells. We analyzed the interaction of these trisaccharides with 293T cells transfected with the H5 and H1 variants of hemagglutinin, which thus retain their native trimeric conformation in such a realistic environment. By exploiting the magnetization transfer between the protein and the ligand, we obtained evidence of the binding event, and identified the epitope. We analyzed the conformational features of the glycans with an approach combining NMR spectroscopy and data-driven molecular dynamics simulations, thus obtaining useful information for an efficient drug design.

A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 113th Congress

Sen. Cantwell, Maria [D-WA

2013-11-20

Senate - 11/20/2013 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 112th Congress

Sen. Akaka, Daniel K. [D-HI

2011-11-16

Senate - 11/16/2011 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution recognizing National Native American Heritage Month and celebrating the heritages and cultures of Native Americans and the contributions of Native Americans to the United States.

THOMAS, 113th Congress

Sen. Tester, Jon [D-MT

2014-11-20

Senate - 11/20/2014 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Quantitative analysis of sitagliptin using the (19)F-NMR method: a universal technique for fluorinated compound detection.

PubMed

Zhang, Fen-Fen; Jiang, Meng-Hong; Sun, Lin-Lin; Zheng, Feng; Dong, Lei; Shah, Vishva; Shen, Wen-Bin; Ding, Ya

2015-01-07

To expand the application scope of nuclear magnetic resonance (NMR) technology in quantitative analysis of pharmaceutical ingredients, (19)F nuclear magnetic resonance ((19)F-NMR) spectroscopy has been employed as a simple, rapid, and reproducible approach for the detection of a fluorine-containing model drug, sitagliptin phosphate monohydrate (STG). ciprofloxacin (Cipro) has been used as the internal standard (IS). Influential factors, including the relaxation delay time (d1) and pulse angle, impacting the accuracy and precision of spectral data are systematically optimized. Method validation has been carried out in terms of precision and intermediate precision, linearity, limit of detection (LOD) and limit of quantification (LOQ), robustness, and stability. To validate the reliability and feasibility of the (19)F-NMR technology in quantitative analysis of pharmaceutical analytes, the assay result has been compared with that of (1)H-NMR. The statistical F-test and student t-test at 95% confidence level indicate that there is no significant difference between these two methods. Due to the advantages of (19)F-NMR, such as higher resolution and suitability for biological samples, it can be used as a universal technology for the quantitative analysis of other fluorine-containing pharmaceuticals and analytes.

Further refinement of 17O TRAPDOR NMR methods for determining oxygen speciation in multi-component oxide glasses

NASA Astrophysics Data System (ADS)

LaComb, M.; Stebbins, J. F.

2017-12-01

Solid state nuclear magnetic resonance (NMR) spectroscopy has often been utilized to determine network speciation in oxide glasses, typically using NMR-active nuclides such as 11B, 27Al and 17O. High field strength magnets allow for visible separation between bridging (BO) and non-bridging oxygens (NBO) in 17O magic-angle spinning (MAS) NMR spectra, but many questions remain due to limited ability to directly observe NBO associated with silicon, boron or aluminum in ternary glass systems with MAS NMR techniques. Recent studies have utilized the combination of 17O{27Al} and 17O{11B} TRAnsfer of Population in DOuble-Resonance (TRAPDOR) NMR to attempt to separate out resonances for these different bridging and non-bridging oxygen species in multicomponent calcium aluminosilicate and aluminoborosilicate glasses and rare-earth aluminoborosilicates. With improved technology and better resolution of spectral components we were able to expand this study to a wider range of calcium aluminosilicate, aluminoborate and aluminoborosilicate glasses and further separate out resonances for both bridging and non-bridging oxygens coordinated with aluminum, boron and/or silicon cations in these glasses.

Feasibility of high-resolution one-dimensional relaxation imaging at low magnetic field using a single-sided NMR scanner applied to articular cartilage.

PubMed

Rössler, Erik; Mattea, Carlos; Stapf, Siegfried

2015-02-01

Low field Nuclear Magnetic Resonance increases the contrast of the longitudinal relaxation rate in many biological tissues; one prominent example is hyaline articular cartilage. In order to take advantage of this increased contrast and to profile the depth-dependent variations, high resolution parameter measurements are carried out which can be of critical importance in an early diagnosis of cartilage diseases such as osteoarthritis. However, the maximum achievable spatial resolution of parameter profiles is limited by factors such as sensor geometry, sample curvature, and diffusion limitation. In this work, we report on high-resolution single-sided NMR scanner measurements with a commercial device, and quantify these limitations. The highest achievable spatial resolution on the used profiler, and the lateral dimension of the sensitive volume were determined. Since articular cartilage samples are usually bent, we also focus on averaging effects inside the horizontally aligned sensitive volume and their impact on the relaxation profiles. Taking these critical parameters into consideration, depth-dependent relaxation time profiles with the maximum achievable vertical resolution of 20 μm are discussed, and are correlated with diffusion coefficient profiles in hyaline articular cartilage in order to reconstruct T(2) maps from the diffusion-weighted CPMG decays of apparent relaxation rates. Copyright © 2014 Elsevier Inc. All rights reserved.

Comprehensive multiphase NMR spectroscopy: Basic experimental approaches to differentiate phases in heterogeneous samples

NASA Astrophysics Data System (ADS)

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G.; Simpson, Myrna J.; Maas, Werner E.; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J.; Hume, Alan; Simpson, André J.

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate 1H and 13C spectra for the different phases. In addition, 19F performance is also addressed. To illustrate the capability of 19F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state.

Comprehensive multiphase NMR spectroscopy: basic experimental approaches to differentiate phases in heterogeneous samples.

PubMed

Courtier-Murias, Denis; Farooq, Hashim; Masoom, Hussain; Botana, Adolfo; Soong, Ronald; Longstaffe, James G; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Andrew, Brian; Struppe, Jochem; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Hume, Alan; Simpson, André J

2012-04-01

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate (1)H and (13)C spectra for the different phases. In addition, (19)F performance is also addressed. To illustrate the capability of (19)F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state. Copyright © 2012 Elsevier Inc. All rights reserved.

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

Solid state nuclear magnetic resonance studies of prion peptides and proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heller, Jonathan

1997-08-01

High-resolution structural studies using x-ray diffraction and solution nuclear magnetic resonance (NMR) are not feasible for proteins of low volubility and high tendency to aggregate. Solid state NMR (SSNMR) is in principle capable of providing structural information in such systems, however to do this efficiently and accurately, further SSNMR tools must be developed This dissertation describes the development of three new methods and their application to a biological system of interest, the priori protein (PrP).

Online monitoring of a photocatalytic reaction by real-time high resolution FlowNMR spectroscopy.

PubMed

Hall, Andrew M R; Broomfield-Tagg, Rachael; Camilleri, Matthew; Carbery, David R; Codina, Anna; Whittaker, David T E; Coombes, Steven; Lowe, John P; Hintermair, Ulrich

2017-12-19

We demonstrate how FlowNMR spectroscopy can readily be applied to investigate photochemical reactions that require sustained input of light and air to yield mechanistic insight under realistic conditions. The Eosin Y mediated photo-oxidation of N-allylbenzylamine is shown to produce imines as primary reaction products from which undesired aldehydes form after longer reaction times. Facile variation of reaction conditions during the reaction in flow allows for probe experiments that give information about the mode of action of the photocatalyst.

Assessment of a 1H high-resolution magic angle spinning NMR spectroscopy procedure for free sugars quantification in intact plant tissue.

PubMed

Delgado-Goñi, Teresa; Campo, Sonia; Martín-Sitjar, Juana; Cabañas, Miquel E; San Segundo, Blanca; Arús, Carles

2013-08-01

In most plants, sucrose is the primary product of photosynthesis, the transport form of assimilated carbon, and also one of the main factors determining sweetness in fresh fruits. Traditional methods for sugar quantification (mainly sucrose, glucose and fructose) require obtaining crude plant extracts, which sometimes involve substantial sample manipulation, making the process time-consuming and increasing the risk of sample degradation. Here, we describe and validate a fast method to determine sugar content in intact plant tissue by using high-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HR-MAS NMR). The HR-MAS NMR method was used for quantifying sucrose, glucose and fructose in mesocarp tissues from melon fruits (Cucumis melo var. reticulatus and Cucumis melo var. cantalupensis). The resulting sugar content varied among individual melons, ranging from 1.4 to 7.3 g of sucrose, 0.4-2.5 g of glucose; and 0.73-2.83 g of fructose (values per 100 g fw). These values were in agreement with those described in the literature for melon fruit tissue, and no significant differences were found when comparing them with those obtained using the traditional, enzymatic procedure, on melon tissue extracts. The HR-MAS NMR method offers a fast (usually <30 min) and sensitive method for sugar quantification in intact plant tissues, it requires a small amount of tissue (typically 50 mg fw) and avoids the interferences and risks associated with obtaining plant extracts. Furthermore, this method might also allow the quantification of additional metabolites detectable in the plant tissue NMR spectrum.

Non-destructive Ripeness Sensing by Using Proton NMR [Nuclear Magnetic Resonance

DOE R&D Accomplishments Database

Cho, Seong In; Krutz, G. W.; Stroshine, R. L.; Bellon, V.

1990-01-01

More than 80 kinds of fruits and vegetables are available in the United States. But only about 6 of them have their quality standards (Dull, 1986). In the 1990 Fresh Trends survey (Zind, 1990), consumers were asked to rate 16 characteristics important to their decision to purchase fresh produce. The four top ranking factors were ripeness/freshness, taste/flavor, appearance/condition and nutritional value. Of these surveyed, 96% rated ripeness/freshness as extremely important or very important. Therefore, the development of reliable grading or sorting techniques for fresh commodities is essential. Determination of fruit quality often involves cutting and tasting. Non-destructive quality control in fruit and vegetables is a goal of growers and distributors, as well as the food processing industry. Many nondestructive techniques have been evaluated including soft x-ray, optical transmission, near infrared radiation, and machine vision. However, there are few reports of successful non-destructive measurement of sugar content directly in fruit. Higher quality fruit could be harvested and available to consumers if a nondestructive sensor that detects ripeness level directly by measuring sugar content were available. Using proton Nuclear Magnetic Resonance (NMR) principle is the possibility. A nondestructive ripeness (or sweetness) sensor for fruit quality control can be developed with the proton NMR principle (Cho, 1989). Several feasibility studies were necessary for the ripeness sensor development. Main objectives in this paper was to investigate the feasibilities (1) to detect ripeness (or sweetness level) of raw fruit tissue with an high resolution proton NMR spectroscopy (200 MHz) and (2) to measure sugar content of intact fruit with a low resolution proton NMR spectroscopy (10 MHz).

Joint inversion of NMR and SIP data to estimate pore size distribution of geomaterials

NASA Astrophysics Data System (ADS)

Niu, Qifei; Zhang, Chi

2018-03-01

There are growing interests in using geophysical tools to characterize the microstructure of geomaterials because of the non-invasive nature and the applicability in field. In these applications, multiple types of geophysical data sets are usually processed separately, which may be inadequate to constrain the key feature of target variables. Therefore, simultaneous processing of multiple data sets could potentially improve the resolution. In this study, we propose a method to estimate pore size distribution by joint inversion of nuclear magnetic resonance (NMR) T2 relaxation and spectral induced polarization (SIP) spectra. The petrophysical relation between NMR T2 relaxation time and SIP relaxation time is incorporated in a nonlinear least squares problem formulation, which is solved using Gauss-Newton method. The joint inversion scheme is applied to a synthetic sample and a Berea sandstone sample. The jointly estimated pore size distributions are very close to the true model and results from other experimental method. Even when the knowledge of the petrophysical models of the sample is incomplete, the joint inversion can still capture the main features of the pore size distribution of the samples, including the general shape and relative peak positions of the distribution curves. It is also found from the numerical example that the surface relaxivity of the sample could be extracted with the joint inversion of NMR and SIP data if the diffusion coefficient of the ions in the electrical double layer is known. Comparing to individual inversions, the joint inversion could improve the resolution of the estimated pore size distribution because of the addition of extra data sets. The proposed approach might constitute a first step towards a comprehensive joint inversion that can extract the full pore geometry information of a geomaterial from NMR and SIP data.

High-resolution NMR spectroscopic trends and assignment rules of metal-free, metallated and substituted corroles.

PubMed

Balazs, Yael S; Saltsman, Irena; Mahammed, Atif; Tkachenko, Elena; Golubkov, Galina; Levine, Joshua; Gross, Zeev

2004-07-01

Major advances over the last few years have facilitated the synthesis of a large variety of meso-only substituted corroles that display interesting catalytic, therapeutic and photophysical properties. This work is the first to study extensively the NMR spectral characteristics of both metallated and non-metallated triarylcorroles in various organic solvents and provide guidelines for easy and reliable assignments of 1D 1H spectra from trends of J coupling constants and chemical shifts. An excellent correlation is found between C=C bond lengths derived from 3J(H,H) values and experimental lengths determined by x-ray crystallography of the same molecules. The nuclear Overhauser effect provides a robust 1D 1H NMR tool for determining the selectivity of electrophilic substitutions. Variable-temperature NMR and isotopic labelling reveal a single preferred tautomerization state and unsymmetric ring orientations at -70 degrees C. The beta-pyrrole protons demonstrate long-range heteronuclear couplings with the coordination core (15N) and with the ortho-19F nuclei of the meso-carbon aryl rings. In sum, application of multinuclear magnetic resonance to corroles and their metal complexes, through the compilation of chemical shifts and J couplings and the recognition of trends therein, provides basic information essential to reliable spectral assignments. Additionally, the conclusions drawn about the structures of corroles and the electron densities at various positions of the corrole macrocycle resulting from the application of high-resolution NMR techniques are of importance to an in-depth understanding of the molecular interactions and processes of this relatively new and rapidly expanding class of compounds. Copyright 2004 John Wiley & Sons, Ltd.

Diversity and antifungal activity of the endophytic fungi associated with the native medicinal cactus Opuntia humifusa (Cactaceae) from the United States.

PubMed

Silva-Hughes, Alice F; Wedge, David E; Cantrell, Charles L; Carvalho, Camila R; Pan, Zhiqiang; Moraes, Rita M; Madoxx, Victor L; Rosa, Luiz H

2015-06-01

The endophytic fungal community associated with the native cactus Opuntia humifusa in the United States was investigated and its potential for providing antifungal compounds. A hundred-eight endophytic fungal isolates were obtained and identified by molecular methods into 17 different taxa of the genera Alternaria, Aureobasidium, Biscogniauxia, Cladosporium, Cryptococcus, Curvularia, Diaporthe, Epicoccum, Paraconiothyrium, Pestalotiopsis and Phoma. The most frequent species associated with O. humifusa were Alternaria sp. 3, Aureobasidium pullulans and Diaporthe sp. The fungal community of O. humifusa had a high richness and diversity; additionally, the species richness obtained indicates that the sample effort was enough to recover the diversity pattern obtained. Six extracts of endophytes showed antifungal properties and (1)H NMR analyses of the extracts of Alternaria sp. 5 Ohu 8B2, Alternaria sp. 3 Ohu 30A, Cladosporium funiculosum Ohu 17C1 and Paraconiothyrium sp. Ohu 17A indicated the presence of functional groups associated with unsaturated fatty-acid olefinic protons and fatty acid methylene and methyl protons. GC-FID analysis of these extracts confirmed the presence of a mixture of different fatty acids. The (1)H NMR analyses of Biscogniauxia mediterranea Ohu 19B extracts showed the presence of aromatic compounds. From the extract of B. mediterranea we isolated the compound 5-methylmellein that displayed moderate antifungal activity against the phytopathogenic fungi Phomopsis obscurans. Our results suggest that native medicinal cacti of the United States can live symbiotically with rich and diverse endophytic communities and may be a source of bioactive molecules, including those able to inhibit or control plant disease pathogens. Copyright © 2015 Elsevier GmbH. All rights reserved.

High-resolution nuclear magnetic resonance measurements in inhomogeneous magnetic fields: A fast two-dimensional J-resolved experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yuqing; Cai, Shuhui; Yang, Yu

2016-03-14

High spectral resolution in nuclear magnetic resonance (NMR) is a prerequisite for achieving accurate information relevant to molecular structures and composition assignments. The continuous development of superconducting magnets guarantees strong and homogeneous static magnetic fields for satisfactory spectral resolution. However, there exist circumstances, such as measurements on biological tissues and heterogeneous chemical samples, where the field homogeneity is degraded and spectral line broadening seems inevitable. Here we propose an NMR method, named intermolecular zero-quantum coherence J-resolved spectroscopy (iZQC-JRES), to face the challenge of field inhomogeneity and obtain desired high-resolution two-dimensional J-resolved spectra with fast acquisition. Theoretical analyses for this methodmore » are given according to the intermolecular multiple-quantum coherence treatment. Experiments on (a) a simple chemical solution and (b) an aqueous solution of mixed metabolites under externally deshimmed fields, and on (c) a table grape sample with intrinsic field inhomogeneity from magnetic susceptibility variations demonstrate the feasibility and applicability of the iZQC-JRES method. The application of this method to inhomogeneous chemical and biological samples, maybe in vivo samples, appears promising.« less

Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides.

PubMed

Armstrong, Geoffrey S; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2005-03-01

Four-dimensional nuclear magnetic resonance spectroscopy with high resolution of signals in the indirect dimensions is reported as an implementation of the filter diagonalization method (FDM). Using an oligosaccharide derivatized with 13C-labeled acetyl isotags, a four-dimensional constant-time pulse sequence was tailored for conjoint use with the FDM. Results demonstrate that high resolution in all dimensions can be achieved using a relatively short experimental time period (19 h), even though the spectrum is highly congested in the direct and all three indirect dimensions. The combined use of isotags, constant-time pulse sequences, and FDM permits rapid isolation of sugar ring proton spin systems in multiple dimensions and enables all endocyclic J-couplings to be simply measured, the key goal to assigning sugar stereochemistry and anomeric configuration. A general method for rapid, unambiguous elucidation of spin systems in oligosaccharides has been a long-sought goal of carbohydrate NMR, and isotags combined with the FDM now enable this to be easily performed. Additional general advantages of the FDM program for generating high-resolution 2D slices in any dimension from a 4D spectrum are emphasized.

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.

Increased synthesis of a new oleanane-type saponin in hairy roots of marigold (Calendula officinalis) after treatment with jasmonic acid.

PubMed

Markowski, Michał; Długosz, Marek; Szakiel, Anna; Durli, Mathieu; Poinsignon, Sophie; Bouguet-Bonnet, Sabine; Vernex-Loset, Lionel; Krier, Gabriel; Henry, Max

2018-04-18

Native plant of marigold (Calendula officinalis L.) synthesizes oleanolic acid saponins classified as glucosides or glucuronides according to the first residue in sugar chain bound to C-3 hydroxyl group. Hairy root culture, obtained by transformation with Agrobacterium rhizogenes strain 15834, exhibit a potent ability of synthesis of oleanolic acid glycosides. The HPLC profile of saponin fraction obtained from C. officinalis hairy roots treated with plant stress hormone, jasmonic acid, showed the 10-times increase of the content of one particular compound, determined by NMR and MALDI TOF as a new bisdesmoside saponin, 3-O-β-d-glucuronopyranosyl-28-O-β-d-galactopyranosyl-oleanolic acid. Such a diglycoside does not occur in native C. officinalis plant. It is a glucuronide, whereas in the native plant glucuronides are mainly accumulated in flowers, while glucosides are the most abundant saponins in roots. Thus, our results revealed that the pathways of saponin biosynthesis, particularly reactions of glycosylation, are altered in C. officinalis hairy root culture.

Improving sensitivity and resolution of MQMAS spectra: A 45Sc-NMR case study of scandium sulphate pentahydrate

NASA Astrophysics Data System (ADS)

Chandran, C. Vinod; Cuny, Jérôme; Gautier, Régis; Pollès, Laurent Le; Pickard, Chris J.; Bräuniger, Thomas

2010-04-01

To efficiently obtain multiple-quantum magic-angle spinning (MQMAS) spectra of the nuclide 45Sc (I = 7/2), we have combined several previously suggested techniques to enhance the signal-to-noise ratio and to improve spectral resolution for the test sample, scandium sulphate pentahydrate (ScSPH). Whereas the 45Sc-3QMAS spectrum of ScSPH does not offer sufficient resolution to clearly distinguish between the 3 scandium sites present in the crystal structure, these sites are well-resolved in the 5QMAS spectrum. The loss of sensitivity incurred by using MQMAS with 5Q coherence order is partly compensated for by using fast-amplitude modulated (FAM) sequences to improve the efficiency of both 5Q coherence excitation and conversion. Also, heteronuclear decoupling is employed to minimise dephasing of the 45Sc signal during the 5Q evolution period due to dipolar couplings with the water protons in the ScSPH sample. Application of multi-pulse decoupling schemes such as TPPM and SPINAL results in improved sensitivity and resolution in the F1 (isotropic) dimension of the 5QMAS spectrum, the best results being achieved with the recently suggested SWf-TPPM sequence. By numerical fitting of the 45Sc-NMR spectra of ScSPH from 3QMAS, 5QMAS and single-quantum MAS at magnetic fields B0 = 9.4 T and 17.6 T, the isotropic chemical shift δiso, the quadrupolar coupling constant χ, and the asymmetry parameter η were obtained. Averaging over all experiments, the NMR parameters determined for the 3 scandium sites, designated (a), (b) and (c) are: δiso(a) = -15.5 ± 0.5 ppm, χ(a) = 5.60 ± 0.10 MHz, η(a) = 0.06 ± 0.05; δiso(b) = -12.9 ± 0.5 ppm, χ(b) = 4.50 ± 0.10 MHz, η(b) = 1.00 ± 0.00; and δiso(c) = -4.7 ± 0.2 ppm, χ(c) = 4.55 ± 0.05 MHz, η(c) = 0.50 ± 0.02. The NMR scandium species were assigned to the independent crystallographic sites by evaluating their experimental response to proton decoupling, and by density functional theory (DFT) calculations using the PAW and GIPAW approaches, in the following way: Sc(1) to (c), Sc(2) to (a), and Sc(3) to (b). The need to compute NMR parameters using an energy-optimised crystal structure is once again demonstrated.

Improving sensitivity and resolution of MQMAS spectra: a 45Sc-NMR case study of scandium sulphate pentahydrate.

PubMed

Chandran, C Vinod; Cuny, Jérôme; Gautier, Régis; Le Pollès, Laurent; Pickard, Chris J; Bräuniger, Thomas

2010-04-01

To efficiently obtain multiple-quantum magic-angle spinning (MQMAS) spectra of the nuclide 45Sc (I=7/2), we have combined several previously suggested techniques to enhance the signal-to-noise ratio and to improve spectral resolution for the test sample, scandium sulphate pentahydrate (ScSPH). Whereas the 45Sc-3QMAS spectrum of ScSPH does not offer sufficient resolution to clearly distinguish between the 3 scandium sites present in the crystal structure, these sites are well-resolved in the 5QMAS spectrum. The loss of sensitivity incurred by using MQMAS with 5Q coherence order is partly compensated for by using fast-amplitude modulated (FAM) sequences to improve the efficiency of both 5Q coherence excitation and conversion. Also, heteronuclear decoupling is employed to minimise dephasing of the 45Sc signal during the 5Q evolution period due to dipolar couplings with the water protons in the ScSPH sample. Application of multi-pulse decoupling schemes such as TPPM and SPINAL results in improved sensitivity and resolution in the F(1) (isotropic) dimension of the 5QMAS spectrum, the best results being achieved with the recently suggested SW(f)-TPPM sequence. By numerical fitting of the 45Sc-NMR spectra of ScSPH from 3QMAS, 5QMAS and single-quantum MAS at magnetic fields B(0)=9.4 T and 17.6 T, the isotropic chemical shift delta(iso), the quadrupolar coupling constant chi, and the asymmetry parameter eta were obtained. Averaging over all experiments, the NMR parameters determined for the 3 scandium sites, designated (a), (b) and (c) are: delta(iso)(a)=-15.5+/-0.5 ppm, chi(a)=5.60+/-0.10 MHz, eta(a)=0.06+/-0.05; delta(iso)(b)=-12.9+/-0.5 ppm, chi(b)=4.50+/-0.10 MHz, eta(b)=1.00+/-0.00; and delta(iso)(c)=-4.7+/-0.2 ppm, chi(c)=4.55+/-0.05 MHz, eta(c)=0.50+/-0.02. The NMR scandium species were assigned to the independent crystallographic sites by evaluating their experimental response to proton decoupling, and by density functional theory (DFT) calculations using the PAW and GIPAW approaches, in the following way: Sc(1) to (c), Sc(2) to (a), and Sc(3) to (b). The need to compute NMR parameters using an energy-optimised crystal structure is once again demonstrated. 2009 Elsevier Inc. All rights reserved.

A Preliminary Investigation of NSCL/P Plasma and Urine in Guizhou Province in China Using NMR-Based Metabonomics.

PubMed

Lei, Huang Guang; Hong, Luo; Kun, Song Ju; Hai, Yin Xin; Dong, Wang Ya; Ke, Zhao; Ping, Xu; Hao, Chen

2013-09-01

Objective : To assess the feasibility of metabonomics in clinical studies. This is a pilot study introducing nuclear magnetic resonance (NMR)-based metabonomics to elucidate and compare the metabolism of patients with nonsyndromic cleft lip and/or palate (NSCL/P) and children without orofacial clefts. Methods : High-resolution (1)H NMR spectroscopy was performed on plasma and urine samples obtained from NSCL/P and healthy children. The (1)H NMR spectra were further analyzed with principal component analysis. Results : Compared to the control group, the level of low-molecular-weight metabolites in plasma such as asparagine was higher in NSCL/P patients, while arginine, lysine, acetate, lactate, proline, glutamine, pyruvate, creatinine, choline, and β-glucose were lower. The carnitine, citrate, and formate excretion in urine appeared to be higher in the healthy children, while the NSCL/P group excreted higher concentrations of aspartic acid and phenylalanine in urine. Conclusion : The present study clearly demonstrated the great potential of NMR-based metabonomics in elucidating NSCL/P plasma metabolism and the possible application of this technology in clinical diagnosis and screening.

Structural study of the membrane protein MscL using cell-free expression and solid-state NMR

NASA Astrophysics Data System (ADS)

Abdine, Alaa; Verhoeven, Michiel A.; Park, Kyu-Ho; Ghazi, Alexandre; Guittet, Eric; Berrier, Catherine; Van Heijenoort, Carine; Warschawski, Dror E.

2010-05-01

High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75 kDa pentameric α-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.

Investigation of hydrogenation of toluene to methylcyclohexane in a trickle bed reactor by low-field nuclear magnetic resonance spectroscopy.

PubMed

Guthausen, Gisela; von Garnier, Agnes; Reimert, Rainer

2009-10-01

Low-field nuclear magnetic resonance (NMR) spectroscopy is applied to study the hydrogenation of toluene in a lab-scale reactor. A conventional benchtop NMR system was modified to achieve chemical shift resolution. After an off-line validity check of the approach, the reaction product is analyzed on-line during the process, applying chemometric data processing. The conversion of toluene to methylcyclohexane is compared with off-line gas chromatographic analysis. Both classic analytical and chemometric data processing was applied. As the results, which are obtained within a few tens of seconds, are equivalent within the experimental accuracy of both methods, low-field NMR spectroscopy was shown to provide an analytical tool for reaction characterization and immediate feedback.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy.

PubMed

Becker, Walter; Bhattiprolu, Krishna Chaitanya; Gubensäk, Nina; Zangger, Klaus

2018-04-17

Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Apolipoprotein AI tertiary structures determine stability and phospholipid-binding activity of discoidal high-density lipoprotein particles of different sizes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Bin; Ren, Xuefeng; Neville, Tracey

2009-05-18

Human high-density lipoprotein (HDL) plays a key role in the reverse cholesterol transport pathway that delivers excess cholesterol back to the liver for clearance. In vivo, HDL particles vary in size, shape and biological function. The discoidal HDL is a 140-240 kDa, disk-shaped intermediate of mature HDL. During mature spherical HDL formation, discoidal HDLs play a key role in loading cholesterol ester onto the HDL particles by activating the enzyme, lecithin:cholesterol acyltransferase (LCAT). One of the major problems for high-resolution structural studies of discoidal HDL is the difficulty in obtaining pure and, foremost, homogenous sample. We demonstrate here that themore » commonly used cholate dialysis method for discoidal HDL preparation usually contains 5-10% lipid-poor apoAI that significantly interferes with the high-resolution structural analysis of discoidal HDL using biophysical methods. Using an ultracentrifugation method, we quickly removed lipid-poor apoAI. We also purified discoidal reconstituted HDL (rHDL) into two pure discoidal HDL species of different sizes that are amendable for high-resolution structural studies. A small rHDL has a diameter of 7.6 nm, and a large rHDL has a diameter of 9.8 nm. We show that these two different sizes of discoidal HDL particles display different stability and phospholipid-binding activity. Interestingly, these property/functional differences are independent from the apoAI -helical secondary structure, but are determined by the tertiary structural difference of apoAI on different discoidal rHDL particles, as evidenced by two-dimensional NMR and negative stain electron microscopy data. Our result further provides the first high-resolution NMR data, demonstrating a promise of structural determination of discoidal HDL at atomic resolution using a combination of NMR and other biophysical techniques.« less

In vivo multiphoton tomography and fluorescence lifetime imaging of human brain tumor tissue.

PubMed

Kantelhardt, Sven R; Kalasauskas, Darius; König, Karsten; Kim, Ella; Weinigel, Martin; Uchugonova, Aisada; Giese, Alf

2016-05-01

High resolution multiphoton tomography and fluorescence lifetime imaging differentiates glioma from adjacent brain in native tissue samples ex vivo. Presently, multiphoton tomography is applied in clinical dermatology and experimentally. We here present the first application of multiphoton and fluorescence lifetime imaging for in vivo imaging on humans during a neurosurgical procedure. We used a MPTflex™ Multiphoton Laser Tomograph (JenLab, Germany). We examined cultured glioma cells in an orthotopic mouse tumor model and native human tissue samples. Finally the multiphoton tomograph was applied to provide optical biopsies during resection of a clinical case of glioblastoma. All tissues imaged by multiphoton tomography were sampled and processed for conventional histopathology. The multiphoton tomograph allowed fluorescence intensity- and fluorescence lifetime imaging with submicron spatial resolution and 200 picosecond temporal resolution. Morphological fluorescence intensity imaging and fluorescence lifetime imaging of tumor-bearing mouse brains and native human tissue samples clearly differentiated tumor and adjacent brain tissue. Intraoperative imaging was found to be technically feasible. Intraoperative image quality was comparable to ex vivo examinations. To our knowledge we here present the first intraoperative application of high resolution multiphoton tomography and fluorescence lifetime imaging of human brain tumors in situ. It allowed in vivo identification and determination of cell density of tumor tissue on a cellular and subcellular level within seconds. The technology shows the potential of rapid intraoperative identification of native glioma tissue without need for tissue processing or staining.

Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy

PubMed Central

2018-01-01

Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers’ structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution. PMID:29697958

Atomic-resolution 3D structure of amyloid β fibrils: The Osaka mutation

DOE PAGES

Schutz, Anne K.; Wall, Joseph; Vagt, Toni; ...

2014-11-13

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ 1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods

PubMed Central

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-01-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L2-norm regularization. However, sparse representation methods via L1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72–88, 2013. PMID:23847452

In Situ and Ex Situ Low-Field NMR Spectroscopy and MRI Endowed by SABRE Hyperpolarization**

PubMed Central

Barskiy, Danila A.; Kovtunov, Kirill V.; Koptyug, Igor V.; He, Ping; Groome, Kirsten A.; Best, Quinn A.; Shi, Fan; Goodson, Boyd M.; Shchepin, Roman V.; Truong, Milton L.; Coffey, Aaron M.; Waddell, Kevin W.; Chekmenev, Eduard Y.

2015-01-01

By using 5.75 and 47.5 mT nuclear magnetic resonance (NMR) spectroscopy, up to 105-fold sensitivity enhancement through signal amplification by reversible exchange (SABRE) was enabled, and subsecond temporal resolution was used to monitor an exchange reaction that resulted in the buildup and decay of hyperpolarized species after parahydrogen bubbling. We demonstrated the high-resolution low-field proton magnetic resonance imaging (MRI) of pyridine in a 47.5 mT magnetic field endowed by SABRE. Molecular imaging (i.e. imaging of dilute hyperpolarized substances rather than the bulk medium) was conducted in two regimes: in situ real-time MRI of the reaction mixture (in which pyridine was hyperpolarized), and ex situ MRI (in which hyperpolarization decays) of the liquid hyperpolarized product. Low-field (milli-Tesla range, e.g. 5.75 and 47.5 mT used in this study) parahydrogen-enhanced NMR and MRI, which are free from the limitations of high-field magnetic resonance (including susceptibility-induced gradients of the static magnetic field at phase interfaces), potentially enables new imaging applications as well as differentiation of hyperpolarized chemical species on demand by exploiting spin manipulations with static and alternating magnetic fields. PMID:25367202

Determination of the absolute configuration of 2-hydroxyglutaric acid and 5-oxoproline in urine samples by high-resolution NMR spectroscopy in the presence of chiral lanthanide complexes.

PubMed

Bal, Dominika; Gradowska, Wanda; Gryff-Keller, Adam

2002-06-15

Determination of the absolute configuration of some metabolites in body fluids is important for the diagnosis of some inborn errors of metabolism. Presently available methods of such determinations are tedious and usually require highly specialized instrumentation. In this work, an alternative method, based on high-resolution nuclear magnetic resonance spectroscopy in the presence of the chiral lanthanide shift reagent as an auxiliary additive, has been proposed (NMR/LSR). The method involves the lineshape analysis of a chosen multiplet of the one-dimensional 1H NMR spectrum or application of the two-dimensional 1H-13C correlation spectroscopy (HSQC). In order to confirm the resonance assignments and to boost the signal-noise ratio, the addition of an amount of racemic analyte to the urine sample is recommended. The entire procedure is simple in application and demands minimal or no preprocessing of urine samples. The effectiveness of the method has been confirmed by finding the expected forms of 2-hydroxyglutaric acid and 5-oxoproline in the urine samples of an independently diagnosed patient with 2-D-hydroxyglutaric aciduria and 5-L-oxoprolinuria, respectively.

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods.

PubMed

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-05-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L 2 -norm regularization. However, sparse representation methods via L 1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L 1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72-88, 2013.

High-resolution diffusion and relaxation-edited magic angle spinning 1H NMR spectroscopy of intact liver tissue.

PubMed

Rooney, O M; Troke, J; Nicholson, J K; Griffin, J L

2003-11-01

High-resolution magic angle spinning (HRMAS) (1)H NMR spectroscopy is ideal for monitoring the metabolic environment within tissues, particularly when spectra are weighted by physical properties such as T(1) and T(2) relaxation times and apparent diffusion coefficients (ADCs). In this study, spectral-editing using T(1) and T(2) relaxation times and ADCs at variable diffusion times was used in conjunction with HRMAS (1)H NMR spectroscopy at 14.1 T in liver tissue. To enhance the sensitivity of ADC measurements to low molecular weight metabolites a T(2) spin echo was included in a standard stimulated gradient spin-echo sequence. Fatty liver induced in rats by chronic orotic acid feeding was investigated using this modified sequence. An increase in the combined ADC for the co-resonant peaks glucose, betaine, and TMAO during fatty liver disease was detected (ADCs = 0.60 +/- 0.11 and 0.35 +/- 0.1 * 10(-9) m(2)s(-1) (n = 3) for rats fed with and without orotic acid), indicative of a reduction in glucose and betaine and an increase in TMAO. Copyright 2003 Wiley-Liss, Inc.

(3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates.

PubMed

Brodaczewska, Natalia; Košťálová, Zuzana; Uhrín, Dušan

2018-02-01

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1 H chemical shifts; larger dispersion of 13 C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1 H, 13 C HSQC-TOCSY experiment. For this methodology to work, 13 C chemical shift must be resolved. In case of 13 C chemical shifts overlap, 1 H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1 H, 13 C BIRD r,X -HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F 1 dimension. The required high-resolution in the 13 C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

NASA Astrophysics Data System (ADS)

Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

2018-02-01

The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

Can NMR solve some significant challenges in metabolomics?

PubMed Central

Gowda, G.A. Nagana; Raftery, Daniel

2015-01-01

The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact biospecimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory. PMID:26476597

Can NMR solve some significant challenges in metabolomics?

NASA Astrophysics Data System (ADS)

Nagana Gowda, G. A.; Raftery, Daniel

2015-11-01

The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

Use of earth field spin echo NMR to search for liquid minerals

DOEpatents

Stoeffl, Wolfgang

2001-01-01

An instrument for measuring the spatial, qualitative and quantitative parameters of an underground nuclear magnetic resonance (NMR) active liquid mineral deposit, including oil and water. A phased array of excitation and receiver antennas on the surface and/or in a borehole excites the NMR active nuclei in the deposit, and using known techniques from magnetic resonance imaging (MRI), the spatial and quantitative distribution of the deposit can be measured. A surface array may utilize, for example, four large (50-500 diameter) diameter wire loops laid on the ground surface, and a weak (1.5-2.5 kHz) alternating current (AC) field applied, matching the NMR frequency of hydrogen in the rather flat and uniform earth magnetic field. For a short duration (a few seconds) an additional gradient field can be generated, superimposed to the earth field, by applying direct current (DC) to the grid (wire loops), enhancing the position sensitivity of the spin-echo and also suppressing large surface water signals by shifting them to a different frequency. The surface coil excitation can be combined with downhole receivers, which are much more radio-quiet compared to surface receivers, and this combination also enhances the position resolution of the MRI significantly. A downhole receiver module, for example, may have a 5.5 inch diameter and fit in a standard six inch borehole having a one-quarter inch thick stainless steel casing. The receiver module may include more than one receiver units for improved penetration and better position resolution.

Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c.

PubMed

Kumar, Rajesh; Sharma, Deepak; Jain, Rishu; Kumar, Sandeep; Kumar, Rajesh

2015-12-01

Carbonmonoxycytochrome c refolds to a native-like compact state (NCO-state), where the non-native Fe(2+)-CO interaction persists. Structural and molecular properties extracted from CD, fluorescence and NMR experiments reveal that the NCO-state shows the generic properties of molten globules. Slow thermal-dissociation of CO transforms the NCO-state to native-state (N-state), where the native Fe(2+)-M80 bond recovers. To determine the role of crowding agents and salt ions on the structural-fluctuation of NCO, the kinetic and thermodynamic parameters for CO-dissociation from NCO (NCO→N+CO) were measured at varying concentrations of crowding agents (dextran 70, dextran 40, ficoll 70) and salt ions (anion: ClO4(-), I(-), Br(-), NO3(-), Cl(-); cation: NH4(+), K(+), Na(+)). As [crowding agent] or [ion] is increased, the rate coefficient of CO-dissociation (kdiss) decreases exponentially. Furthermore, the extent of decrease in kdiss is found to be dependent on (i) size, charge density and charge dispersion of the ion, and (ii) size, shape, and viscosity of the crowding agent. Copyright © 2015 Elsevier B.V. All rights reserved.

The NMR contribution to protein-protein networking in Fe-S protein maturation.

PubMed

Banci, Lucia; Camponeschi, Francesca; Ciofi-Baffoni, Simone; Piccioli, Mario

2018-03-22

Iron-sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe-S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe-2S], [3Fe-4S] and [4Fe-4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe-S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe-S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of "Fe-S interactomics". This contribution was particularly effective when protein-protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.

Native multimer analysis of plasma and platelet von Willebrand factor compared to denaturing separation: implication for the interpretation of satellite bands.

PubMed

Hohenstein, Kurt; Griesmacher, Andrea; Weigel, Günter; Golderer, Georg; Ott, Helmut Werner

2011-06-01

Blue native electrophoresis (BNE) was applied to analyze the von Willebrand factor (vWF) multimers in their native state and to present a methodology to perform blue native electrophoresis on human plasma proteins, which has not been done before. The major difference between this method and the commonly used SDS-agarose gel electrophoresis is the lack of satellite bands in the high-resolution native gel. To further analyze this phenomenon, a second dimension was performed under denaturing conditions. Thereby, we obtained a pattern in which each protein sub-unit from the first dimension dissociates into three distinct sub-bands. These bands confirm the triplet structure, which consists of an intermediate band and two satellite bands. By introducing the second dimension, our novel method separates the triplet structure into a higher resolution than the commonly used SDS-agarose gel electrophoresis does. This helps considerably in the classification of ambiguous von Willebrand's disease subtypes. In addition, our method has the additional advantage of being able to resolve the triplet structure of platelet vWF multimers, which has not been identified previously through conventional SDS-agarose electrophoresis multimer analysis. This potential enables us to compare the triplet structure from platelet and plasmatic vWF, and may help to find out whether structural abnormalities concern the vWF molecule in the platelet itself, or whether they are due to the physiological processing of vWF shed into circulation. Owing to its resolution and sensitivity, this native separation technique offers a promising tool for the analysis and detection of von Willebrand disorder, and for the classification of von Willebrand's disease subtypes. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cationization of kappa- and iota-carrageenan--Characterization and properties of amphoteric polysaccharides.

PubMed

Barahona, Tamara; Prado, Héctor J; Bonelli, Pablo R; Cukierman, Ana L; Fissore, Eliana L; Gerschenson, Lia N; Matulewicz, María C

2015-08-01

Commercial kappa- and iota carrageenans were cationized with 3-chloro-2-hydroxypropyltrimethylammonium chloride in aqueous sodium hydroxide solution. For kappa-carrageenan three derivatives with different degrees of substitution were obtained. Native and amphoteric kappa-carrageenans were characterized by NMR and infrared spectroscopy, scanning electron and atomic force microscopy; methanolysis products were studied by electrospray ionization mass spectrometry. Young moduli and the strain at break of films, differential scanning calorimetry, rheological and flocculation behavior were also evaluated; the native and the amphoteric derivatives showed different and interesting properties. Cationization of iota-carrageenan was more difficult, indicating as it was previously observed for agarose, that substitution starts preferentially on the 2-position of 3,6-anhydrogalactose residues; in iota-carrageenan this latter unit is sulfated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

PubMed Central

NISHIMURA, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate. PMID:28077807

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

PubMed

Nishimura, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Protein Delivery into Plant Cells: Toward In vivo Structural Biology

PubMed Central

Cedeño, Cesyen; Pauwels, Kris; Tompa, Peter

2017-01-01

Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress. PMID:28469623

A (1)H-NMR study on the effect of high pressures on beta-lactoglobulin.

PubMed

Belloque, J; López-Fandiño, R; Smith, G M

2000-09-01

1H NMR was used to study the effect of high pressure on changes in the structure of beta-lactoglobulin (beta-Lg), particularly the strongly bonded regions, the "core". beta-Lg was exposed to pressures ranging from 100 to 400 MPa at neutral pH. After depressurization and acidification to pH 2.0, (1)H NMR spectra were taken. Pressure-induced unfolding was studied by deuterium exchange. Refolding was also evaluated. Our results showed that the core was unaltered at 100 MPa but increased its conformational flexibility at >/=200 MPa. Even though the core was highly flexible at 400 MPa, its structure was found to be identical to the native structure after equilibration back to atmospheric pressure. It is suggested that pressure-induced aggregates are formed by beta-Lg molecules maintaining most of their structure, and the intermolecular -SS- bonds, formed by -SH/-SS- exchange reaction, are likely to involve C(66)-C(160) rather than C(106)-C(119). In addition, the beta-Lg variants A and B could be distinguished in a (1)H NMR spectrum from a solution made with the AB mixed variant, by the differences in chemical shifts of M(107) and C(106); structural implications are discussed. Under pressure, the core of beta-Lg A seemed to unfold faster than that of beta-LgB. The structural recovery of the core was full for both variants.

Studies of phospholipid hydration by high-resolution magic-angle spinning nuclear magnetic resonance.

PubMed Central

Zhou, Z; Sayer, B G; Hughes, D W; Stark, R E; Epand, R M

1999-01-01

A sample preparation method using spherical glass ampoules has been used to achieve 1.5-Hz resolution in 1H magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of aqueous multilamellar dispersions of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), serving to differentiate between slowly exchanging interlamellar and bulk water and to reveal new molecular-level information about hydration phenomena in these model biological membranes. The average numbers of interlamellar water molecules in multilamellar vesicles (MLVs) of DOPC and POPC were found to be 37.5 +/- 1 and 37.2 +/- 1, respectively, at a spinning speed of 3 kHz. Even at speeds as high as 9 kHz, the number of interlamellar waters remained as high as 31, arguing against dehydration effects for DOPC and POPC. Both homonuclear and heteronuclear nuclear Overhauser enhancement spectroscopy (NOESY and HOESY) were used to establish the location of water near the headgroup of a PC bilayer. 1H NMR comparisons of DOPC with a lipid that can hydrogen bond (monomethyldioleoylphosphatidylethanolamine, MeDOPE) showed the following trends: 1) the interlamellar water resonance was shifted to lower frequency for DOPC but to higher frequency for MeDOPE, 2) the chemical shift variation with temperature for interlamellar water was less than that of bulk water for MeDOPE MLVs, 3) water exchange between the two lipids was rapid on the NMR time scale if they were mixed in the same bilayer, 4) water exchange was slow if they were present in separate MLVs, and 5) exchange between bulk and interlamellar water was found by two-dimensional exchange experiments to be slow, and the exchange rate should be less than 157 Hz. These results illustrate the utility of ultra-high-resolution 1H MAS NMR for determining the nature and extent of lipid hydration as well as the arrangement of nuclei at the membrane/water interface. PMID:9876150

A resolution recognizing National American Indian and Alaska Native Heritage Month and celebrating the heritage and culture of American Indians and Alaska Natives and the contributions of American Indians and Alaska Natives to the United States.

THOMAS, 111th Congress

Sen. Dorgan, Byron L. [D-ND

2010-11-19

Senate - 11/19/2010 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

A resolution recognizing National American Indian and Alaska Native Heritage Month and celebrating the heritage and culture of American Indians and Alaska Natives and the contributions of American Indians and Alaska Natives to the United States.

THOMAS, 111th Congress

Sen. Dorgan, Byron L. [D-ND

2009-11-05

Senate - 11/05/2009 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (All Actions) Tracker: This bill has the status Agreed to in SenateHere are the steps for Status of Legislation:

Which kind of aromatic structures are produced during biomass charring? New insights provided by modern solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Knicker, Heike; Paneque-Carmona, Marina; Velasco-Molina, Marta; de la Rosa, José Maria; León-Ovelar, Laura Regina; Fernandez-Boy, Elena

2017-04-01

Intense research on biochar and charcoal of the last years has revealed that depending on the production conditions, the chemical and physical characteristics of their aromatic network can greatly vary. Since such variations are determining the behavior and stability of charred material in soils, a better understanding of the structural changes occurring during their heating and the impact of those changes on their function is needed. One method to characterize pyrogenic organic matter (PyOM) represents solid-state 13C NMR spectroscopy applying the cross polarization (CP) magic angle spinning technique (MAS). A drawback of this technique is that the quantification of NMR spectra of samples with highly condensed and proton-depleted structures is assumed to be bias. Typical samples with such attributes are charcoals produced at temperatures above 700°C under pyrolytic conditions. Commonly their high condensation degree leads to graphenic structures that are not only reducing the CP efficiency but create also a conductive lattice which acts as a shield and prevents the entering of the excitation pulse into the sample during the NMR experiments. Since the latter can damage the NMR probe and in the most cases the obtained NMR spectra show only one broad signal assignable to aromatic C, this technique is rarely applied for characterizing high temperature chars or soot. As a consequence, a more detailed knowledge of the nature of the aromatic ring systems is still missing. The latter is also true for the aromatic domains of PyOM produced at lower temperatures, since older NMR instruments operating at low magnetic fields deliver solid-state 13C NMR spectra with low resolution which turns a more detailed analysis of the aromatic chemical shift region into a challenging task. In order to overcome this disadvantages, modern NMR spectroscopy offers not only instruments with greatly improved resolution but also special pulse sequences for NMR experiments which allow a more detailed chemical shift assignment. Applying the latter to various charcoals and biochars, we intended to test their usefulness for a better characterization of PyOM and elucidation how specific aromatic features can affect their behavior in soils. We could demonstrate that furans represent the major compound class of low temperature chars produced from woody material. As indicated by 2D techniques, residual alkyl C in such chars has minor covalent binding to the aromatic network. Reducing the electrical conductivity of high-temperature chars by addition of aluminum oxide permitted the application of the cross CP technique. Determination of the relaxation and CP dynamics confirmed high rigidity of their aromatic domains which were dominated by coronene-type moieties. In contrast to common view, we could demonstrate that quantifiable CP NMR spectra can be obtained from high temperature chars with contact times of 3 to 5 ms and pulse delays > 3 s.

Improved in-cell structure determination of proteins at near-physiological concentration

PubMed Central

Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Güntert, Peter; Ito, Yutaka

2016-01-01

Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells. PMID:27910948

Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

NASA Astrophysics Data System (ADS)

Minch, Michael J.

1998-02-01

There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

PubMed

Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

2015-11-24

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

Detection of XerC and XerD recombinases in gram-negative bacteria of the family Enterobacteriaceae.

PubMed Central

Sirois, S; Szatmari, G

1995-01-01

XerC and XerD are site-specific recombinases of the lambda integrase family which resolve multimeric replicons to monomers by acting at specific sites such as cer, ckr, nmr, parB, and psi, which are found in plasmids, or at the dif site found in the Escherichia coli chromosome. By using Southern hybridizations to cloned E. coli xerC and xerD genes and a cer-nmr plasmid-based resolution assay, the presence of these genes in several species of Enterobacteriaceae is shown. PMID:7608100

A new anthraquinone and eight constituents from Hedyotis caudatifolia Merr. et Metcalf: isolation, purification and structural identification.

PubMed

Luo, Peng; Su, Jiale; Zhu, Yilin; Wei, Jianhua; Wei, Wanxing; Pan, Weigao

2016-10-01

Hedyotis caudatifolia Merr. et Metcalf. (HC), a folk medicine in Yao nationalities areas in China, was used to investigate the chemical constituents. Through silica gel and Sephadex LH-20 column chromatography, nine compounds were isolated and purified. By physical and chemical properties, IR, MS (EI-MS, high resolution EI-MS), 1D NMR ((1)H NMR, (13)C NMR) and 2D NMR (HSQC, (1)H-(1)H COSY, HMBC), their structures were identified as β-sitosterol (1), stigmasterol (2), scopolin (3), 2-hydroxy-1,7,8-trimethoxyanthracene-9,10-dione (4), oleanolic acid (5), ursolic acid (6), methyl barbinervate (7), β-daucosterol (8) and p-Hydroxybenzoic acid (9). These compounds were isolated from HC for the first time, and 4 a new anthraquinone whose biological activities are worth to be investigated in future. These compounds may contribute to the HC's pharmacological effects on treating diseases, and may be used as candidates for control index in establishing the quality control standard of HC.

High Resolution NMR Studies of Encapsulated Proteins In Liquid Ethane

PubMed Central

Peterson, Ronald W.; Lefebvre, Brian G.; Wand, A. Joshua

2005-01-01

Many of the difficulties presented by large, aggregation-prone, and membrane proteins to modern solution NMR spectroscopy can be alleviated by actively seeking to increase the effective rate of molecular reorientation. An emerging approach involves encapsulating the protein of interest within the protective shell of a reverse micelle, and dissolving the resulting particle in a low viscosity fluid, such as the short chain alkanes. Here we present the encapsulation of proteins with high structural fidelity within reverse micelles dissolved in liquid ethane. The addition of appropriate co-surfactants can significantly reduce the pressure required for successful encapsulation. At these reduced pressures, the viscosity of the ethane solution is low enough to provide sufficiently rapid molecular reorientation to significantly lengthen the spin-spin NMR relaxation times of the encapsulated protein. PMID:16028922

Satellite transitions acquired in real time by magic angle spinning (STARTMAS): ``Ultrafast'' high-resolution MAS NMR spectroscopy of spin I =3/2 nuclei

NASA Astrophysics Data System (ADS)

Thrippleton, Michael J.; Ball, Thomas J.; Wimperis, Stephen

2008-01-01

The satellite transitions acquired in real time by magic angle spinning (STARTMAS) NMR experiment combines a train of pulses with sample rotation at the magic angle to refocus the first- and second-order quadrupolar broadening of spin I =3/2 nuclei in a series of echoes, while allowing the isotropic chemical and quadrupolar shifts to evolve. The result is real-time isotropic NMR spectra at high spinning rates using conventional MAS equipment. In this paper we describe in detail how STARTMAS data can be acquired and processed with ease on commercial equipment. We also discuss the advantages and limitations of the approach and illustrate the discussion with numerical simulations and experimental data from four different powdered solids.

Low-field nuclear magnetic resonance characterization of organic content in shales

USGS Publications Warehouse

Washburn, Kathryn E.; Birdwell, Justin E.; Seymour, Joseph D.; Kirkland, Catherine; Vogt, Sarah J.

2013-01-01

Low-field nuclear magnetic resonance (LF-NMR) relaxometry is a non-invasive technique commonly used to assess hydrogen-bearing fluids in petroleum reservoir rocks. Longitudinal T1 and transverse T2 relaxation time measurements made using LF-NMR on conventional reservoir systems provides information on rock porosity, pore size distributions, and fluid types and saturations in some cases. Recent improvements in LF-SNMR instrument electronics have made it possible to apply these methods to assess highly viscous and even solid organic phases within reservoir rocks. T1 and T2 relaxation responses behave very differently in solids and liquids, therefore the relationship between these two modes of relaxation can be used to differentiate organic phases in rock samples or to characterize extracted organic materials. Using T1-T2 correlation data, organic components present in shales, such as kerogen and bitumen, can be examined in laboratory relaxometry measurements. In addition, implementation of a solid-echo pulse sequence to refocus some types of T2 relaxation during correlation measurements allows for improved resolution of solid phase photons. LF-NMR measurements of T1 and T2 relaxation time correlations were carried out on raw oil shale samples from resources around the world. These shales vary widely in mineralogy, total organic carbon (TOC) content and kerogen type. NMR results were correlcated with Leco TOC and geochemical data obtained from Rock-Eval. There is excellent correlation between NMR data and programmed pyrolysis parameters, particularly TOC and S2, and predictive capability is also good. To better understand the NMR response, the 2D NMR spectra were compared to similar NMR measurements made using high-field (HF) NMR equipment.

Comparison of native high-resolution 3D and contrast-enhanced MR angiography for assessing the thoracic aorta.

PubMed

von Knobelsdorff-Brenkenhoff, Florian; Gruettner, Henriette; Trauzeddel, Ralf F; Greiser, Andreas; Schulz-Menger, Jeanette

2014-06-01

To omit risks of contrast agent administration, native magnetic resonance angiography (MRA) is desired for assessing the thoracic aorta. The aim was to evaluate a native steady-state free precession (SSFP) three-dimensional (3D) MRA in comparison with contrast-enhanced MRA as the gold standard. Seventy-six prospective patients with known or suspicion of thoracic aortic disease underwent MRA at 1.5 T using (i) native 3D SSFP MRA with ECG and navigator gating and high isotropic spatial resolution (1.3 × 1.3 × 1.3 mm(3)) and (ii) conventional contrast-enhanced ECG-gated gradient-echo 3D MRA (1.3 × 0.8 × 1.8 mm(3)). Datasets were compared at nine aortic levels regarding image quality (score 0-3: 0 = poor, 3 = excellent) and aortic diameters, as well as observer dependency and final diagnosis. Statistical tests included paired t-test, correlation analysis, and Bland-Altman analysis. Native 3D MRA was acquired successfully in 70 of 76 subjects (mean acquisition time 8.6 ± 2.7 min), while irregular breathing excluded 6 of 76 subjects. Aortic diameters agreed close between both methods at all aortic levels (r = 0.99; bias ± SD -0.12 ± 1.2 mm) with low intra- and inter-observer dependency (intraclass correlation coefficient 0.99). Native MRA studies resulted in the same final diagnosis as the contrast-enhanced MRA. The mean image quality score was superior with native compared with contrast-enhanced MRA (2.4 ± 0.6 vs. 1.6 ± 0.5; P < 0.001). Accuracy of aortic size measurements, certainty in defining the diagnosis and benefits in image quality at the aortic root, underscore the use of the tested high-resolution native 3D SSFP MRA as an appropriate alternative to contrast-enhanced MRA to assess the thoracic aorta. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2014. For permissions please email: journals.permissions@oup.com.

High-resolution magic angle spinning 1H-NMR spectroscopy studies on the renal biochemistry in the bank vole (Clethrionomys glareolus) and the effects of arsenic (As3+) toxicity.

PubMed

Griffin, J L; Walker, L; Shore, R F; Nicholson, J K

2001-06-01

1. High-resolution magic angle spinning (MAS) 1H-NMR spectroscopy was used to study renal metabolism and the toxicity of As3+, a common environmental contaminant, in the bank vole (Clethrionomys glareolus), a wild species of rodent. 2. Following a 14-day exposure to an environmentally relevant dose of As2O3 (28 mg kg(-1) feed), voles displayed tissue damage at autopsy. MAS 1H spectra indicated abnormal lipid profiles in these samples. 3. Tissue necrosis was also evident from measurements of the apparent diffusion coefficient of water in the intact tissue using MAS 1H diffusion-weighted spectroscopy, its first application to toxicology. 4. Comparison of renal tissue from the wood mouse (Apodemus sylvaticus) exposed to identical exposure levels of As3+ suggested that the bank vole is particularly vulnerable to As3+ toxicity.

Can NMR solve some significant challenges in metabolomics?

PubMed

Nagana Gowda, G A; Raftery, Daniel

2015-11-01

The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory. Copyright © 2015 Elsevier Inc. All rights reserved.

Development of high resolution NMR spectroscopy as a structural tool

NASA Astrophysics Data System (ADS)

Feeney, James

1992-06-01

The discovery of the nuclear magnetic resonance (NMR) phenomenon and its development and exploitation as a scientific tool provide an excellent basis for a case-study for examining the factors which control the evolution of scientific techniques. Since the detection of the NMR phenomenon and the subsequent rapid discovery of all the important NMR spectral parameters in the late 1940s, the method has emerged as one of the most powerful techniques for determining structures of molecules in solution and for analysis of complex mixtures. The method has made a dramatic impact on the development of structural chemistry over the last 30 years and is now one of the key techniques in this area. Support for NMR instrumentation attracts a dominant slice of public funding in most scientifically developed countries. The technique is an excellent example of how instrumentation and technology have revolutionised structural chemistry and it is worth exploring how it has been developed so successfully. Clearly its wide range of application and the relatively direct connection between the NMR data and molecular structure has created a major market for the instrumentation. This has provided several competing manufacturers with the incentive to develop better and better instruments. Understanding the complexity of the basics of NMR spectroscopy has been an ongoing challenge attracting the attention of physicists. The well-organised specialist NMR literature and regular scientific meetings have ensured rapid exploitation of any theoretical advances that have a practical relevance. In parallel, the commercial development of the technology has allowed the fruits of such theoretical advances to be enjoyed by the wider scientific community.

Portable, low-cost NMR with laser-lathe lithography produced microcoils.

PubMed

Demas, Vasiliki; Herberg, Julie L; Malba, Vince; Bernhardt, Anthony; Evans, Lee; Harvey, Christopher; Chinn, Sarah C; Maxwell, Robert S; Reimer, Jeffrey

2007-11-01

Nuclear Magnetic Resonance (NMR) is unsurpassed in its ability to non-destructively probe chemical identity. Portable, low-cost NMR sensors would enable on-site identification of potentially hazardous substances, as well as the study of samples in a variety of industrial applications. Recent developments in RF microcoil construction (i.e. coils much smaller than the standard 5mm NMR RF coils), have dramatically increased NMR sensitivity and decreased the limits-of-detection (LOD). We are using advances in laser pantographic microfabrication techniques, unique to LLNL, to produce RF microcoils for field deployable, high sensitivity NMR-based detectors. This same fabrication technique can be used to produce imaging coils for MRI as well as for standard hardware shimming or "ex-situ" shimming of field inhomogeneities typically associated with inexpensive magnets. This paper describes a portable NMR system based on the use of a 2 kg hand-held permanent magnet, laser-fabricated microcoils, and a compact spectrometer. The main limitations for such a system are the low resolution and sensitivity associated with the low field values and quality of small permanent magnets, as well as the lack of large amounts of sample of interest in most cases. The focus of the paper is on the setting up of this system, initial results, sensitivity measurements, discussion of the limitations and future plans. The results, even though preliminary, are promising and provide the foundation for developing a portable, inexpensive NMR system for chemical analysis. Such a system will be ideal for chemical identification of trace substances on site.

NMR of α-synuclein–polyamine complexes elucidates the mechanism and kinetics of induced aggregation

PubMed Central

Fernández, Claudio O; Hoyer, Wolfgang; Zweckstetter, Markus; Jares-Erijman, Elizabeth A; Subramaniam, Vinod; Griesinger, Christian; Jovin, Thomas M

2004-01-01

The aggregation of α-synuclein is characteristic of Parkinson's disease (PD) and other neurodegenerative synucleinopathies. The 140-aa protein is natively unstructured; thus, ligands binding to the monomeric form are of therapeutic interest. Biogenic polyamines promote the aggregation of α-synuclein and may constitute endogenous agents modulating the pathogenesis of PD. We characterized the complexes of natural and synthetic polyamines with α-synuclein by NMR and assigned the binding site to C-terminal residues 109–140. Dissociation constants were derived from chemical shift perturbations. Greater polyamine charge (+2 → +5) correlated with increased affinity and enhancement of fibrillation, for which we propose a simple kinetic mechanism involving a dimeric nucleation center. According to the analysis, polyamines increase the extent of nucleation by ∼104 and the rate of monomer addition ∼40-fold. Significant secondary structure is not induced in monomeric α-synuclein by polyamines at 15°C. Instead, NMR reveals changes in a region (aa 22–93) far removed from the polyamine binding site and presumed to adopt the β-sheet conformation characteristic of fibrillar α-synuclein. We conclude that the C-terminal domain acts as a regulator of α-synuclein aggregation. PMID:15103328

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

PubMed Central

Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.

2014-01-01

The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is TΔSTotal = 1.4 kcal⋅mol−1 per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding (ΩU/ΩN). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (TΔShelix−sheet = 0.5 kcal⋅mol−1), a property not fully reflected in the amide N-H and carbonyl C=O bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. PMID:25313044

Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B.

PubMed

Hanoulle, Xavier; Badillo, Aurélie; Wieruszeski, Jean-Michel; Verdegem, Dries; Landrieu, Isabelle; Bartenschlager, Ralf; Penin, François; Lippens, Guy

2009-05-15

We report here a biochemical and structural characterization of domain 2 of the nonstructural 5A protein (NS5A) from the JFH1 Hepatitis C virus strain and its interactions with cyclophilins A and B (CypA and CypB). Gel filtration chromatography, circular dichroism spectroscopy, and finally NMR spectroscopy all indicate the natively unfolded nature of this NS5A-D2 domain. Because mutations in this domain have been linked to cyclosporin A resistance, we used NMR spectroscopy to investigate potential interactions between NS5A-D2 and cellular CypA and CypB. We observed a direct molecular interaction between NS5A-D2 and both cyclophilins. The interaction surface on the cyclophilins corresponds to their active site, whereas on NS5A-D2, it proved to be distributed over the many proline residues of the domain. NMR heteronuclear exchange spectroscopy yielded direct evidence that many proline residues in NS5A-D2 form a valid substrate for the enzymatic peptidyl-prolyl cis/trans isomerase (PPIase) activity of CypA and CypB.

Molecular understanding of mutagenicity using potential energy methods. Progress report, July 1, 1992--September 30, 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

Broyde, S.; Shapiro, R.

1993-09-01

Our objective has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by highly mutagenic aromatic amines and hydrocarbons. The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence but it may be enhanced greatly after covalent modification by a mutagenic substance. The methods that we use to elucidate structures are computational, but we keep in close contact with experimental developments, and we incorporate data from NMR studiesmore » in our calculations when they are available. X-ray and low resolution spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. Even the high resolution NMR method cannot alone yield molecular views, though it does so in combination with our computations. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations of static structures with solvent and salt can be carried out with the program AMBER; this yields mobile views in a medium that mimics aspects of the natural aqueous environment of the cell.« less

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy.

PubMed

Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

2015-12-07

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica-associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random-coil and β-strand conformations. Furthermore, biosilica-associated long-chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Composition of Different Botanical Origin Honeys Produced by Sicilian Black Honeybees (Apis mellifera ssp. sicula).

PubMed

Mannina, Luisa; Sobolev, Anatoly P; Di Lorenzo, Arianna; Vista, Silvia; Tenore, Gian Carlo; Daglia, Maria

2015-07-01

In 2008 a Slow Food Presidium was launched in Sicily (Italy) for an early warning of the risk of extinction of the Sicilian native breed of black honeybee (Apis mellifera L. ssp sicula). Today, the honey produced by these honeybees is the only Sicilian honey produced entirely by the black honeybees. In view of few available data regarding the chemical composition of A. mellifera ssp. sicula honeys, in the present investigation the chemical compositions of sulla honey (Hedysarum coronarium L.) and dill honey (Anethum graveolens L.) were studied with a multimethodological approach, which consists of HPLC-PDA-ESI-MSn and NMR spectroscopy. Moreover, three unifloral honeys (lemon honey (obtained from Citrus limon (L.) Osbeck), orange honey (Citrus arantium L.), and medlar honey (Eriobotrya japonica (Thunb.) Lindl)), with known phenol and polyphenol compositions, were studied with NMR spectroscopy to deepen the knowledge about sugar and amino acid compositions.

Matching multiple rigid domain decompositions of proteins

PubMed Central

Flynn, Emily; Streinu, Ileana

2017-01-01

We describe efficient methods for consistently coloring and visualizing collections of rigid cluster decompositions obtained from variations of a protein structure, and lay the foundation for more complex setups that may involve different computational and experimental methods. The focus here is on three biological applications: the conceptually simpler problems of visualizing results of dilution and mutation analyses, and the more complex task of matching decompositions of multiple NMR models of the same protein. Implemented into the KINARI web server application, the improved visualization techniques give useful information about protein folding cores, help examining the effect of mutations on protein flexibility and function, and provide insights into the structural motions of PDB proteins solved with solution NMR. These tools have been developed with the goal of improving and validating rigidity analysis as a credible coarse-grained model capturing essential information about a protein’s slow motions near the native state. PMID:28141528

A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

PubMed Central

Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

2008-01-01

We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

A combined computational and structural model of the full-length human prolactin receptor

PubMed Central

Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

2016-01-01

The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg. PMID:27174498

A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

NASA Astrophysics Data System (ADS)

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff-based computation is employed in the scoring function to evaluate the probability of side-chain resonance assignments to generate the observed NMR spectra. The complexity of the assignment problem is first reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is used to find a set of optimal side-chain resonance assignments that best fit the NMR data. We have tested our algorithm on NMR data for five proteins, including the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), human ubiquitin, the ubiquitin-binding zinc finger domain of the human Y-family DNA polymerase Eta (pol η UBZ), and the human Set2-Rpb1 interacting domain (hSRI). Our algorithm assigns resonances for more than 90% of the protons in the proteins, and achieves about 80% correct side-chain resonance assignments. The final structures computed using distance restraints resulting from the set of assigned side-chain resonances have backbone RMSD 0.5 - 1.4 Å and all-heavy-atom RMSD 1.0 - 2.2 Å from the reference structures that were determined by X-ray crystallography or traditional NMR approaches. These results demonstrate that our algorithm can be successfully applied to automate side-chain resonance assignment and high-quality protein structure determination. Since our algorithm does not require any specific NMR experiments for measuring the through-bond interactions with side-chain protons, it can save a significant amount of both experimental cost and spectrometer time, and hence accelerate the NMR structure determination process.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

NASA Astrophysics Data System (ADS)

Savorani, F.; Tomasi, G.; Engelsen, S. B.

2010-02-01

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

In vivo carbon-13 nuclear magnetic resonance studies of heart metabolism.

PubMed Central

Neurohr, K J; Barrett, E J; Shulman, R G

1983-01-01

Guinea pig heart metabolism was studied in vivo by 13C NMR at 20.18 MHz. High-quality proton-decoupled 13C NMR spectra with excellent signal-to-noise ratios and resolution could be obtained in 6 min. Natural-abundance spectra showed resonances that could be assigned to fatty acids, but glycogen was not seen. During intravenous infusion of D-[1-13C]glucose and insulin, the time course of myocardial glycogen synthesis was followed serially for up to 4 hr. Anoxia resulted in degradation of the labeled glycogen within 6 min and appearance of 13C label in lactic acid. Infusion of sodium [2-13C]acetate resulted in incorporation of label into the C-4, C-2, and C-3 positions of glutamate and glutamine, reflecting "scrambling" of the label expected from tricarboxylic acid cycle activity. Examination of the 31P NMR spectrum of the guinea pig heart in vivo demonstrated no change in the high-energy phosphates during the time periods of the 13C NMR experiments. Our studies indicate that 13C NMR is a unique non-destructive tool for the study of heart metabolism in vivo. PMID:6572924

UV-visible-DAD and 1H-NMR spectroscopy data fusion for studying the photodegradation process of azo-dyes using MCR-ALS.

PubMed

Fernández, Cristina; Pilar Callao, M; Larrechi, M Soledad

2013-12-15

The photodegradation process of three azo-dyes - Acid Orange 61, Acid Red 97 and Acid Brown 425 - was monitored simultaneously by ultraviolet-visible spectroscopy with diode array detector (UV-vis-DAD) and (1)H-nuclear magnetic resonance ((1)H-NMR). Multivariate curve resolution-alternating least squares (MCR-ALS) was applied to obtain the concentration and spectral profile of the chemical compounds involved in the process. The analysis of the H-NMR data suggests there are more intermediate compounds than those obtained with the UV-vis-DAD data. The fusion of UV-vis-DAD and the (1)H-NMR signal before the multivariate analysis provides better results than when only one of the two detector signals was used. It was concluded that three degradation products were present in the medium when the three azo-dyes had practically degraded. This study is the first application of UV-vis-DAD and (1)H-NMR spectroscopy data fusion in this field and illustrates its potential as a quick method for evaluating the evolution of the azo-dye photodegradation process. © 2013 Elsevier B.V. All rights reserved.

One dimensional spatial resolution optimization on a hybrid low field MRI-gamma detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agulles-Pedrós, L., E-mail: lagullesp@unal.edu.co; Abril, A., E-mail: ajabrilf@unal.edu.co

Hybrid systems like Positron Emission Tomography/Magnetic Resonance Imaging (PET/MRI) and MRI/gamma camera, offer advantages combining the resolution and contrast capability of MRI with the better contrast and functional information of nuclear medicine techniques. However, the radiation detectors are expensive and need an electronic set-up, which can interfere with the MRI acquisition process or viceversa. In order to improve these drawbacks, in this work it is presented the design of a low field NMR system made up of permanent magnets compatible with a gamma radiation detector based on gel dosimetry. The design is performed using the software FEMM for estimation ofmore » the magnetic field, and GEANT4 for the physical process involved in radiation detection and effect of magnetic field. The homogeneity in magnetic field is achieved with an array of NbFeB magnets in a linear configuration with a separation between the magnets, minimizing the effect of Compton back scattering compared with a no-spacing linear configuration. The final magnetic field in the homogeneous zone is ca. 100 mT. In this hybrid proposal, although the gel detector do not have spatial resolution per se, it is possible to obtain a dose profile (1D image) as a function of the position by using a collimator array. As a result, the gamma detector system described allows a complete integrated radiation detector within the low field NMR (lfNMR) system. Finally we present the better configuration for the hybrid system considering the collimator parameters such as height, thickness and distance.« less

Boron environments in Pyrex® glass--a high resolution, Double-Rotation NMR and thermodynamic modelling study.

PubMed

Howes, A P; Vedishcheva, N M; Samoson, A; Hanna, J V; Smith, M E; Holland, D; Dupree, R

2011-07-07

It is shown, using the important technological glass Pyrex® as an example, that 1D and 2D (11)B Double-Rotation (DOR) NMR experiments, in combination with thermodynamic modelling, are able to provide unique structural information about complex glasses. (11)B DOR NMR has been applied to Pyrex® glass in order to remove both dipolar and quadrupolar broadening of the NMR lines, leading to high resolution spectra that allow unambiguous, accurate peak fitting to be carried out, of particular importance in the case of the 3-coordinated [BO(3)] (B3) trigonal planar environments. The data obtained are of sufficient quality that they can be used to test the distributions of borate and borosilicate superstructural units predicted by the thermodynamics-based Model of Associated Solutions. The model predicts the dominant boron-containing chemical groupings in Pyrex® glass to be those associated with B(2)O(3) and sodium tetraborate (with smaller amounts of sodium triborate, sodium diborate, sodium pentaborate, danburite and reedmergnerite). Excellent agreement is found between model and experiment provided the (11)B peaks with isotropic chemical shifts of -1.4 ppm and 0.5 ppm are assigned to B4 species from borosilicate units ([B(OSi)(4)] and [B(OSi)(3)(OB)]) and borate superstructural units (mainly triborate rings with some pentaborate and diborate) respectively. The peaks with isotropic shifts of 14 ppm and 18.1 ppm are then assigned to B3 in borate superstructural units (mainly triborate and pentaborate along with connecting B3) and boroxol rings respectively. The assignments of the DOR NMR peaks, are supported by the presence of cross-peaks in (11)B spin-diffusion DOR NMR spectra which can be used to develop a structural model in which B(2)O(3)-like regions are linked, via borate and borosilicate superstructural units, to the majority silica network. Pyrex® is thus shown to have a heterogeneous structure, with distinct molecular groupings that are far removed from a random distribution of network polyhedra with only short-range order. This journal is © the Owner Societies 2011

Identification of phenanthrene derivatives in Aerides rosea (Orchidaceae) using the combined systems HPLC-ESI-HRMS/MS and HPLC-DAD-MS-SPE-UV-NMR.

PubMed

Cakova, Veronika; Urbain, Aurélie; Antheaume, Cyril; Rimlinger, Nicole; Wehrung, Patrick; Bonté, Frédéric; Lobstein, Annelise

2015-01-01

In our continued efforts to contribute to the general knowledge on the chemical diversity of orchids, we have decided to focus our investigations on the Aeridinae subtribe. Following our previous phytochemical study of Vanda coerulea, which has led to the identification of phenanthrene derivatives, a closely related species, Aerides rosea Lodd. ex Lindl. & Paxton, was chosen for investigation. To identify new secondary metabolites, and to avoid isolation of those already known, by means of the combined systems HPLC-DAD(diode-array detector) with high-resolution tandem mass spectrometry (HRMS/MS) and HPLC-DAD-MS-SPE(solid-phase extraction)-UV-NMR. A dereplication strategy was developed using a HPLC-DAD-HRMS/MS targeted method and applied to fractions from A. rosea stem extract. Characterisation of unknown minor compounds was then performed using the combined HPLC-DAD-MS-SPE-UV-NMR system. The dereplication method allowed the characterisation of four compounds (gigantol, imbricatin, methoxycoelonin and coelonin), previously isolated from Vanda coerulea stem extract. The analyses of two fractions permitted the identification of five additional minor constituents including one phenanthropyran, two phenanthrene and two dihydrophenanthrene derivatives. The full set of NMR data of each compound was obtained from microgram quantities. Nine secondary metabolites were characterised in A. rosea stems, utilising HPLC systems combined with high-resolution analytical systems. Two of them are newly described phenanthrene derivatives: aerosanthrene (5-methoxyphenanthrene-2,3,7-triol) and aerosin (3-methoxy-9,10-dihydro-2,5,7-phenanthrenetriol). Copyright © 2014 John Wiley & Sons, Ltd.

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

A portable single-sided magnet system for remote NMR measurements of pulmonary function.

PubMed

Dabaghyan, Mikayel; Muradyan, Iga; Hrovat, Alan; Butler, James; Frederick, Eric; Zhou, Feng; Kyriazis, Angelos; Hardin, Charles; Patz, Samuel; Hrovat, Mirko

2014-12-01

In this work, we report initial results from a light-weight, low field magnetic resonance device designed to make relative pulmonary density measurements at the bedside. The development of this device necessarily involves special considerations for the magnet, RF and data acquisition schemes as well as a careful analysis of what is needed to provide useful information in the ICU. A homogeneous field region is created remotely from the surface of the magnet such that when the magnet is placed against the chest, an NMR signal is measured from a small volume in the lung. In order to achieve portability, one must trade off field strength and therefore spatial resolution. We report initial measurements from a ping-pong ball size region in the lung as a function of lung volume. As expected, we measured decreased signal at larger lung volumes since lung density decreases with increasing lung volume. Using a CPMG sequence with ΔTE=3.5 ms and a 20 echo train, a signal to noise ratio ~1100 was obtained from an 8.8mT planar magnet after signal averaging for 43 s. This is the first demonstration of NMR measurements made on a human lung with a light-weight planar NMR device. We argue that very low spatial resolution measurements of different lobar lung regions will provide useful diagnostic information for clinicians treating Acute Respiratory Distress Syndrome as clinicians want to avoid ventilator pressures that cause either lung over distension (too much pressure) or lung collapse (too little pressure). Copyright © 2014 John Wiley & Sons, Ltd.

A portable single-sided magnet system for remote NMR measurements of pulmonary function

PubMed Central

Mikayel, Dabaghyan; Iga, Muradyan; James, Butler; Eric, Frederick; Feng, Zhou; Angelos, Kyriazis; Charles, Hardin; Samuel, Patz; Mirko, Hrovat

2014-01-01

In this work, we report initial results from a light-weight, low field magnetic resonance device designed to make relative pulmonary density measurements at the bedside. The development of this device necessarily involves special considerations for the magnet, RF and data acquisition schemes as well as a careful analysis of what is needed to provide useful information in the ICU. A homogeneous field region is created remotely from the surface of the magnet such that when the magnet is placed against the chest, an NMR signal is measured from a small volume in the lung. In order to achieve portability, one must trade off field strength and therefore spatial resolution. We report initial measurements from a ping-pong ball size region in the lung as a function of lung volume. As expected, we measured decreased signal at larger lung volumes since lung density decreases with increasing lung volume. Using a CPMG sequence with ΔTE=3.5 ms and a 20 echo train, a signal to noise ratio ~1100 was obtained from an 8.8mT planar magnet after signal averaging for 43 s. This is the first demonstration of NMR measurements made on a human lung with a light-weight planar NMR device. We argue that very low spatial resolution measurements of different lobar lung regions will provide useful diagnostic information for clinicians treating Acute Respiratory Distress Syndrome as clinicians want to avoid ventilator pressures that cause either lung over distension (too much pressure) or lung collapse (too little pressure). PMID:24953556

Discerning the Location and Nature of Coke Deposition from Surface to Bulk of Spent Zeolite Catalysts

NASA Astrophysics Data System (ADS)

Devaraj, Arun; Vijayakumar, Murugesan; Bao, Jie; Guo, Mond F.; Derewinski, Miroslaw A.; Xu, Zhijie; Gray, Michel J.; Prodinger, Sebastian; Ramasamy, Karthikeyan K.

2016-11-01

The formation of carbonaceous deposits (coke) in zeolite pores during catalysis leads to temporary deactivation of catalyst, necessitating regeneration steps, affecting throughput, and resulting in partial permanent loss of catalytic efficiency. Yet, even to date, the coke molecule distribution is quite challenging to study with high spatial resolution from surface to bulk of the catalyst particles at a single particle level. To address this challenge we investigated the coke molecules in HZSM-5 catalyst after ethanol conversion treatment by a combination of C K-edge X-ray absorption spectroscopy (XAS), 13C Cross polarization-magic angle spinning nuclear magnetic resonance (CP-MAS NMR) spectroscopy, and atom probe tomography (APT). XAS and NMR highlighted the aromatic character of coke molecules. APT permitted the imaging of the spatial distribution of hydrocarbon molecules located within the pores of spent HZSM-5 catalyst from surface to bulk at a single particle level. 27Al NMR results and APT results indicated association of coke molecules with Al enriched regions within the spent HZSM-5 catalyst particles. The experimental results were additionally validated by a level-set-based APT field evaporation model. These results provide a new approach to investigate catalytic deactivation due to hydrocarbon coking or poisoning of zeolites at an unprecedented spatial resolution.

In situ and ex situ low-field NMR spectroscopy and MRI endowed by SABRE hyperpolarization.

PubMed

Barskiy, Danila A; Kovtunov, Kirill V; Koptyug, Igor V; He, Ping; Groome, Kirsten A; Best, Quinn A; Shi, Fan; Goodson, Boyd M; Shchepin, Roman V; Truong, Milton L; Coffey, Aaron M; Waddell, Kevin W; Chekmenev, Eduard Y

2014-12-15

By using 5.75 and 47.5 mT nuclear magnetic resonance (NMR) spectroscopy, up to 10(5)-fold sensitivity enhancement through signal amplification by reversible exchange (SABRE) was enabled, and subsecond temporal resolution was used to monitor an exchange reaction that resulted in the buildup and decay of hyperpolarized species after parahydrogen bubbling. We demonstrated the high-resolution low-field proton magnetic resonance imaging (MRI) of pyridine in a 47.5 mT magnetic field endowed by SABRE. Molecular imaging (i.e. imaging of dilute hyperpolarized substances rather than the bulk medium) was conducted in two regimes: in situ real-time MRI of the reaction mixture (in which pyridine was hyperpolarized), and ex situ MRI (in which hyperpolarization decays) of the liquid hyperpolarized product. Low-field (milli-Tesla range, e.g. 5.75 and 47.5 mT used in this study) parahydrogen-enhanced NMR and MRI, which are free from the limitations of high-field magnetic resonance (including susceptibility-induced gradients of the static magnetic field at phase interfaces), potentially enables new imaging applications as well as differentiation of hyperpolarized chemical species on demand by exploiting spin manipulations with static and alternating magnetic fields. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy.

PubMed

Warner, Lisa; Gjersing, Erica; Follett, Shelby E; Elliott, K Wade; Dzyuba, Sergei V; Varga, Krisztina

2016-12-01

Ionic liquids have great potential in biological applications and biocatalysis, as some ionic liquids can stabilize proteins and enhance enzyme activity, while others have the opposite effect. However, on the molecular level, probing ionic liquid interactions with proteins, especially in solutions containing high concentration of ionic liquids, has been challenging. In the present work the 13 C, 15 N-enriched GB1 model protein was used to demonstrate applicability of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy to investigate ionic liquid - protein interactions. Effect of an ionic liquid (1-butyl-3-methylimidazolium bromide, [C 4 -mim]Br) on GB1was studied over a wide range of the ionic liquid concentrations (0.6 to 3.5 M, which corresponds to 10%-60% v/v). Interactions between GB1 and [C 4 -mim]Br were observed from changes in the chemical shifts of the protein backbone as well as the changes in 15 N ps-ns dynamics and rotational correlation times. Site-specific interactions between the protein and [C 4 -mim]Br were assigned using 3D methods under HR-MAS conditions. Thus, HR-MAS NMR is a viable tool that could aid in elucidation of the molecular mechanism of ionic liquid - protein interactions.

Discerning the Location and Nature of Coke Deposition from Surface to Bulk of Spent Zeolite Catalysts

PubMed Central

Devaraj, Arun; Vijayakumar, Murugesan; Bao, Jie; Guo, Mond F.; Derewinski, Miroslaw A.; Xu, Zhijie; Gray, Michel J.; Prodinger, Sebastian; Ramasamy, Karthikeyan K.

2016-01-01

The formation of carbonaceous deposits (coke) in zeolite pores during catalysis leads to temporary deactivation of catalyst, necessitating regeneration steps, affecting throughput, and resulting in partial permanent loss of catalytic efficiency. Yet, even to date, the coke molecule distribution is quite challenging to study with high spatial resolution from surface to bulk of the catalyst particles at a single particle level. To address this challenge we investigated the coke molecules in HZSM-5 catalyst after ethanol conversion treatment by a combination of C K-edge X-ray absorption spectroscopy (XAS), 13C Cross polarization-magic angle spinning nuclear magnetic resonance (CP-MAS NMR) spectroscopy, and atom probe tomography (APT). XAS and NMR highlighted the aromatic character of coke molecules. APT permitted the imaging of the spatial distribution of hydrocarbon molecules located within the pores of spent HZSM-5 catalyst from surface to bulk at a single particle level. 27Al NMR results and APT results indicated association of coke molecules with Al enriched regions within the spent HZSM-5 catalyst particles. The experimental results were additionally validated by a level-set–based APT field evaporation model. These results provide a new approach to investigate catalytic deactivation due to hydrocarbon coking or poisoning of zeolites at an unprecedented spatial resolution. PMID:27876869

Advanced slow-magic angle spinning probe for magnetic resonance imaging and spectroscopy

DOEpatents

Wind, Robert A.; Hu, Jian Zhi; Minard, Kevin R.; Rommereim, Donald N.

2006-01-24

The present invention relates to a probe and processes useful for magnetic resonance imaging and spectroscopy instruments. More particularly, the invention relates to a MR probe and processes for obtaining resolution enhancements of fluid objects, including live specimens, using an ultra-slow (magic angle) spinning (MAS) of the specimen combined with a modified phase-corrected magic angle turning (PHORMAT) pulse sequence. Proton NMR spectra were measured of the torso and the top part of the belly of a female BALBc mouse in a 2T field, while spinning the animal at a speed of 1.5 Hz. Results show that even in this relatively low field with PHORMAT, an isotropic spectrum is obtained with line widths that are a factor 4.6 smaller than those obtained in a stationary mouse. Resolution of ¹H NMR metabolite spectra are thus significantly enhanced. Results indicate that PHORMAT has the potential to significantly increase the utility of ¹H NMR spectroscopy for in vivo biochemical, biomedical and/or medical applications involving large-sized biological objects such as mice, rats and even humans within a hospital setting. For small-sized objects, including biological objects, such as excised tissues, organs, live bacterial cells, and biofilms, use of PASS at a spinning rate of 30 Hz and above is preferred.

Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

PubMed

Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

2017-09-19

In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Going, Catherine C.; Xia, Zijie; Williams, Evan R.

2016-06-01

Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling.

Flow-through lipid nanotube arrays for structure-function studies of membrane proteins by solid-state NMR spectroscopy.

PubMed

Chekmenev, Eduard Y; Gor'kov, Peter L; Cross, Timothy A; Alaouie, Ali M; Smirnov, Alex I

2006-10-15

A novel method for studying membrane proteins in a native lipid bilayer environment by solid-state NMR spectroscopy is described and tested. Anodic aluminum oxide (AAO) substrates with flow-through 175 nm wide and 60-mum-long nanopores were employed to form macroscopically aligned peptide-containing lipid bilayers that are fluid and highly hydrated. We demonstrate that the surfaces of both leaflets of such bilayers are fully accessible to aqueous solutes. Thus, high hydration levels as well as pH and desirable ion and/or drug concentrations could be easily maintained and modified as desired in a series of experiments with the same sample. The method allows for membrane protein NMR experiments in a broad pH range that could be extended to as low as 1 and as high as 12 units for a period of up to a few hours and temperatures as high as 70 degrees C without losing the lipid alignment or bilayers from the nanopores. We demonstrate the utility of this method by a solid-state 19.6 T (17)O NMR study of reversible binding effects of mono- and divalent ions on the chemical shift properties of the Leu(10) carbonyl oxygen of transmembrane pore-forming peptide gramicidin A (gA). We further compare the (17)O shifts induced by binding metal ions to the binding of protons in the pH range from 1 to 12 and find a significant difference. This unexpected result points to a difference in mechanisms for ion and proton conduction by the gA pore. We believe that a large number of solid-state NMR-based studies, including structure-function, drug screening, proton exchange, pH, and other titration experiments, will benefit significantly from the method described here.

Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

PubMed

Gupta, Sebanti; Bhattacharjya, Surajit

2014-11-01

The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen-activated protein kinase cascades. In the current study, urea-induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. © 2014 Wiley Periodicals, Inc.

Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability

NASA Astrophysics Data System (ADS)

Camilloni, Carlo; Sala, Benedetta Maria; Sormanni, Pietro; Porcari, Riccardo; Corazza, Alessandra; De Rosa, Matteo; Zanini, Stefano; Barbiroli, Alberto; Esposito, Gennaro; Bolognesi, Martino; Bellotti, Vittorio; Vendruscolo, Michele; Ricagno, Stefano

2016-05-01

A wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (β2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed β2m variants that alter the aggregation-prone exposed surface of wild-type and W60G β2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in β2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.

Advantages of Molecular Weight Identification during Native MS Screening.

PubMed

Khan, Ahad; Bresnick, Anne; Cahill, Sean; Girvin, Mark; Almo, Steve; Quinn, Ronald

2018-05-09

Native mass spectrometry detection of ligand-protein complexes allowed rapid detection of natural product binders of apo and calcium-bound S100A4 (a member of the metal binding protein S100 family), T cell/transmembrane, immunoglobulin (Ig), and mucin protein 3, and T cell immunoreceptor with Ig and ITIM (immunoreceptor tyrosine-based inhibitory motif) domains precursor protein from extracts and fractions. Based on molecular weight common hits were detected binding to all four proteins. Seven common hits were identified as apigenin 6- C - β - D -glucoside 8- C - α - L -arabinoside, sweroside, 4',5-dihydroxy-7-methoxyflavanone-6- C -rutinoside, loganin acid, 6- C -glucosylnaringenin, biochanin A 7- O -rutinoside and quercetin 3- O -rutinoside. Mass guided isolation and NMR identification of hits confirmed the mass accuracy of the ligand in the ligand-protein MS complexes. Thus, molecular weight ID from ligand-protein complexes by electrospray ionization Fourier transform mass spectrometry allowed rapid dereplication. Native mass spectrometry using electrospray ionization Fourier transform mass spectrometry is a tool for dereplication and metabolomics analysis. Georg Thieme Verlag KG Stuttgart · New York.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

PubMed

Spasic, Aleksandar; Kennedy, Scott D; Needham, Laura; Manoharan, Muthiah; Kierzek, Ryszard; Turner, Douglas H; Mathews, David H

2018-05-01

The RNA "GAGU" duplex, (5'GAC GAGU GUCA) 2 , contains the internal loop (5'-GAGU-3') 2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans -Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'- endo conformation. This differs markedly from the internal loops, (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-UAGG-3') 2 , which all have cis -Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis -Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-G AG C-3') 2 , (5'-A AG U-3') 2 , and (5'-U AG G-3') 2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3') 2 , equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3') 2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3') 2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed. © 2018 Spasic et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Rates and Mechanisms of Oil Shale Pyrolysis: A Chemical Structure Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fletcher, Thomas; Pugmire, Ronald

2015-01-01

Three pristine Utah Green River oil shale samples were obtained and used for analysis by the combined research groups at the University of Utah and Brigham Young University. Oil shale samples were first demineralized and the separated kerogen and extracted bitumen samples were then studied by a host of techniques including high resolution liquid-state carbon-13 NMR, solid-state magic angle sample spinning 13C NMR, GC/MS, FTIR, and pyrolysis. Bitumen was extracted from the shale using methanol/dichloromethane and analyzed using high resolution 13C NMR liquid state spectroscopy, showing carbon aromaticities of 7 to 11%. The three parent shales and the demineralized kerogensmore » were each analyzed with solid-state 13C NMR spectroscopy. Carbon aromaticity of the kerogen was 23-24%, with 10-12 aromatic carbons per cluster. Crushed samples of Green River oil shale and its kerogen extract were pyrolyzed at heating rates from 1 to 10 K/min at pressures of 1 and 40 bar and temperatures up to 1000°C. The transient pyrolysis data were fit with a first-order model and a Distributed Activation Energy Model (DAEM). The demineralized kerogen was pyrolyzed at 10 K/min in nitrogen at atmospheric pressure at temperatures up to 525°C, and the pyrolysis products (light gas, tar, and char) were analyzed using 13C NMR, GC/MS, and FTIR. Details of the kerogen pyrolysis have been modeled by a modified version of the chemical percolation devolatilization (CPD) model that has been widely used to model coal combustion/pyrolysis. This refined CPD model has been successful in predicting the char, tar, and gas yields of the three shale samples during pyrolysis. This set of experiments and associated modeling represents the most sophisticated and complete analysis available for a given set of oil shale samples.« less

NMR approach for monitoring post-mortem changes in Atlantic salmon fillets stored at 0 and 4°C.

PubMed

Shumilina, Elena; Ciampa, Alessandra; Capozzi, Francesco; Rustad, Turid; Dikiy, Alexander

2015-10-01

High resolution NMR technique has been used to monitor post-mortem changes in salmon (Salmo salar) fillets upon storage at 4 and 0°C. Thirty-one different fish metabolites influencing freshness and taste properties have been unequivocally assigned by NMR using either available standard compounds or ad hoc acquired 2D (1)H-(1)H TOCSY and (1)H-(13)С HSQC spectra. The monitored fish metabolites include amino acids, dipeptides, sugars, vitamins, biogenic amines, as well as different products of the ATP degradation. The detection and monitoring of biogenic amines by NMR, upon fish storage, is information of interest for consumers, since some of these compounds are toxic. The data from this study shows that NMR spectroscopy also provides the amount of all metabolites necessary for the calculation of the K-index used to express fish freshness. A good correlation was found between the K-index increase and the formation of the undesired biogenic amines. The metabolite concentrations and the K-index found in this work were compared and found coherent with literature data. The performed study reveals the strengths and the suitability of the NMR approach to monitor different biochemical processes occurring during fish storage and qualitatively and quantitatively characterise fish metabolites determining fish quality. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Natural abundance high-resolution solid state 2 H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Aliev, Abil E.; Harris, Kenneth D. M.; Apperley, David C.

1994-08-01

We report for the first time an approach for natural abundance solid state 2 H NMR spectroscopy involving magic angle sample spinning (MAS), high-power 1 H decoupling (HPPD) and 1 H- 2 H cross polarization (CP). Taking tetrakis(trimethylsilyl)silane (TTMSS), adamantane, 1-chloroadamantane, hexamethylbenzene (HMB), 2,2-dimethyl-1,3-propanediol (DMPD) and 2-hydroxymethyl-2-methyl-1,3-propanediol (HMPD) as examples, it has been shown that the combination of HPPD and MAS can be applied readily to study rotator phase solids, allowing isotropic peaks arising from chemically inequivalent 2 H nuclei to be resolved. For natural abundance samples of TTMSS and chloroadamantane, it has been shown that 2 H CP/HPPD/MAS NMR experiments, involving polarization transfer from 1 H to 2 H, may provide considerable sensitivity enhancement in comparison with single pulse experiments.

Natural abundance high-resolution solid state 2 H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Aliev, Abil E.; Harris, Kenneth D. M.; Apperley, David C.

1994-08-01

We report for the first time an approach for natural abundance solid state 2H NMR spectroscopy involving magic angle sample spinning (MAS), high-power 1H decoupling (HPPD) and 1H- 2H cross polarization (CP). Taking tetrakis(trimethylsilyl)silane (TTMSS), adamantane, 1-chloroadamantane, hexamethylbenzene (HMB), 2,2-dimethyl-1,3-propanediol (DMPD) and 2-hydroxymethyl-2-methyl-1,3-propanediol (HMPD) as examples, it has been shown that the combination of HPPD and MAS can be applied readily to study rotator phase solids, allowing isotropic peaks arising from chemically inequivalent 2H nuclei to be resolved. For natural abundance samples of TTMSS and chloroadamantane, it has been shown that 2H CP/HPPD/MAS NMR experiments, involving polarization transfer from 1H to 2H, may provide considerable sensitivity enhancement in comparison with single pulse experiments.

Structural characterization of native high-methoxylated pectin using nuclear magnetic resonance spectroscopy and ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Comparative use of 2,5-dihydroxybenzoic acid and nor-harmane as UV-MALDI matrices.

PubMed

Monge, María Eugenia; Negri, R Martín; Kolender, Adriana A; Erra-Balsells, Rosa

2007-01-01

The successful analysis by ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (UV-MALDI-TOF MS) of native and hydrolyzed high-methoxylated pectin samples is described. In order to find the optimal conditions for UV-MALDI-TOF MS analysis several experimental variables were studied such as: different UV-MALDI matrices (nor-harmane, 2,5-dihydroxybenzoic acid), sample preparation methods (mixture, sandwich), inorganic salt addition (doping salts, NaCl, KCl, NH(4)Cl), ion mode (positive, negative), linear and reflectron mode, etc. nor-Harmane has never been used as a UV-MALDI matrix for the analysis of pectins but its use avoids pre-treatment of the sample, such as an enzymatic digestion or an acid hydrolysis, and there is no need to add salts, making the analysis easier and faster. This study suggested an alternative way of analyzing native high-methoxylated pectins, with UV-MALDI-TOF MS, by using nor-harmane as the matrix in negative ion mode. The analysis by (1)H and (13)C nuclear magnetic resonance (NMR) spectroscopy of the native and hydrolyzed pectin is also briefly described. Copyright (c) 2007 John Wiley & Sons, Ltd.

Choreographing an enzyme’s dance

PubMed Central

Villali, Janice; Kern, Dorothee

2010-01-01

While ground state structures combined with chemical tools and enzyme kinetics deliver useful information on possible chemical mechanisms of enzyme catalysis, they do not unravel the finely balanced energy inventory to explain the impressive rate enhancement of enzymes. For this goal, a complete description of enzyme catalysis in the form of an energy landscape is needed. Since the rate of catalysis is determined by the climb over a sequence of energy barriers, we focus here on the critical question of transition pathways. A combination of time-resolved NMR and simulation deliver a glimpse into how proteins can so efficiently move within the ensemble of the native conformations while avoiding unfolding during that journey. The loss of energy due to breakage of native contacts is compensated by non-native transient hydrogen bonds during the transition thereby “holding on” to the energy until the new native contacts form that define the alternate functional state. The use of kinetic isotope effects (KIE) to study the chemical step show that coordinated atomic fluctuations of the protein component dictate the probability of “correct” distance and orientation, due to its extreme sensitivity to distance. The examples here stress the point that highly choreographed conformational sampling together with chemical integrity is a prerequisite for efficient enzyme catalysis. PMID:20822946

Chemical modification of citrus pectin: Structural, physical and rheologial implications.

PubMed

Fracasso, Aline Francielle; Perussello, Camila Augusto; Carpiné, Danielle; Petkowicz, Carmen Lúcia de Oliveira; Haminiuk, Charles Windson Isidoro

2018-04-01

The present study aimed to investigate the physical, structural and rheological modifications caused by the chemical modification process of citrus pectin. Therefore, three commercial citrus pectins with different degree of esterification were chemically modified by sequential alkali and acidic hydrolytic process to produce modified citrus pectins (MCP) with special properties. The molar mass (M w ), degree of esterification (DE), monosaccharide composition, 13 C NMR spectra, homogeneity, morphology (SEM) and rheological behavior of both native and modified citrus pectins (MCP) were investigated. The chemical modification reduced the acid uronic content (up to 28.3%) and molar mass (up to 29.98%), however, showed little influence on the degree of esterification of native pectins. Modified citrus pectins presented higher amounts of neutral monosaccharides, mainly galactose, arabinose and rhamnose, typical of the Ramnogalacturonana-I (RG-I) region. Rheological tests indicated that the native and modified citrus pectins presented pseudoplastic behavior, however, the MCP samples were less viscous, compared to the native ones. Modified samples presented better dissolution in water and less strong gels, with good stability during oscillatory shearing at 25°C. This study aims to better understand the implications that chemical modifications may impose on the structure of citrus pectins. Copyright © 2017 Elsevier B.V. All rights reserved.

Hierarchical folding free energy landscape of HP35 revealed by most probable path clustering.

PubMed

Jain, Abhinav; Stock, Gerhard

2014-07-17

Adopting extensive molecular dynamics simulations of villin headpiece protein (HP35) by Shaw and co-workers, a detailed theoretical analysis of the folding of HP35 is presented. The approach is based on the recently proposed most probable path algorithm which identifies the metastable states of the system, combined with dynamical coring of these states in order to obtain a consistent Markov state model. The method facilitates the construction of a dendrogram associated with the folding free-energy landscape of HP35, which reveals a hierarchical funnel structure and shows that the native state is rather a kinetic trap than a network hub. The energy landscape of HP35 consists of the entropic unfolded basin U, where the prestructuring of the protein takes place, the intermediate basin I, which is connected to U via the rate-limiting U → I transition state reflecting the formation of helix-1, and the native basin N, containing a state close to the NMR structure and a native-like state that exhibits enhanced fluctuations of helix-3. The model is in line with recent experimental observations that the intermediate and native states differ mostly in their dynamics (locked vs unlocked states). Employing dihedral angle principal component analysis, subdiffusive motion on a multidimensional free-energy surface is found.

The Resolution of Visual Noise in Word Recognition

ERIC Educational Resources Information Center

Pae, Hye K.; Lee, Yong-Won

2015-01-01

This study examined lexical processing in English by native speakers of Korean and Chinese, compared to that of native speakers of English, using normal, alternated, and inverse fonts. Sixty four adult students participated in a lexical decision task. The findings demonstrated similarities and differences in accuracy and latency among the three L1…

Remote sensing of native and invasive species in Hawaiian forests

Treesearch

Gregory P. Asner; Matthew O. Jones; Roberta E. Martin; David E. Knapp; R. Flint Hughes

2008-01-01

Detection and mapping of invasive species is an important component of conservation and management efforts in Hawai'i, but the spectral separability of native, introduced, and invasive species has not been established. We used high spatial resolution airborne imaging spectroscopy to analyze the canopy hyperspectral reflectance properties of 37 distinct species or...

Selectivity in L1 Attrition: Differential Object Marking in Spanish Near-Native Speakers of English

ERIC Educational Resources Information Center

Chamorro, Gloria; Sturt, Patrick; Sorace, Antonella

2016-01-01

Previous research has shown L1 attrition to be restricted to structures at the interfaces between syntax and pragmatics, but not to occur with syntactic properties that do not involve such interfaces ("Interface Hypothesis", Sorace and Filiaci in "Anaphora resolution in near-native speakers of Italian." "Second Lang…

SAGE III/ISS L2 Solar Event Species Profiles (Native) V5 (g3bsspb)

Atmospheric Science Data Center

2017-12-21

SAGE III/ISS L2 Solar Event Species Profiles (Native) V5 (g3bsspb)   Project ... present Temporal Resolution:  1 file per event File Format:  BINARY Tools:  Earthdata ... Radiation Longwave Radiation Shortwave Radiation Event Tag Event Type Obs Beta Angle Order Data:  ...

SAGE III/ISS L2 Lunar Event Species Profiles (Native) V5 (g3blspb)

Atmospheric Science Data Center

2018-01-08

SAGE III/ISS L2 Lunar Event Species Profiles (Native) V5 (g3blspb)   Project ... present Temporal Resolution:  1 file per event File Format:  BINARY Tools:  Earthdata ... Radiation Longwave Radiation Shortwave Radiation Event Tag Event Type Obs Beta Angle Order Data:  ...

Versatility of non-native forms of human cytochrome c: pH and micellar concentration dependence.

PubMed

Simon, Matthieu; Metzinger-Le Meuth, Valérie; Chevance, Soizic; Delalande, Olivier; Bondon, Arnaud

2013-01-01

In addition to its electron transfer activity, cytochrome c is now known to trigger apoptosis via peroxidase activity. This new function is related to a structural modification of the cytochrome upon association with anionic lipids, particularly cardiolipin present in the mitochondrial membrane. However, the exact nature of the non-native state induced by this interaction remains an active subject of debate. In this work, using human cytochromes c (native and two single-histidine mutants and the corresponding double mutant) and micelles as a hydrophobic medium, we succeeded, through UV-visible spectroscopy, circular dichroism spectroscopy and NMR spectroscopy, in fully characterizing the nature of the sixth ligand replacing the native methionine. Furthermore, careful pH titrations permitted the identification of the amino acids involved in the iron binding over a range of pH values. Replacement of the methionine by lysine was only observed at pH above 8.5, whereas histidine binding is dependent on both pH and micelle concentration. The pH variation range for histidine protonation is relatively narrow and is consistent with the mitochondrial intermembrane pH changes occurring during apoptosis. These results allow us to rule out lysine as the sixth ligand at pH values close to neutrality and reinforce the role of histidines (preferentially His33 vs. His26) as the main candidate to replace methionine in the non-native cytochrome c. Finally, on the basis of these results and molecular dynamics simulations, we propose a 3D model for non-native cytochrome c in a micellar environment.

Anion Transport in a Chemically Stable, Sterically Bulky alpha-C Modified Imidazolium Functionalized Anion Exchange Membrane

DTIC Science & Technology

2014-06-24

AEM is often inconvenient, as ambient carbon dioxide (at publication time, 400 ppm) will react with the OH− to form a mixture of CO3 2− and HCO3 − in... crystal . Spectra were obtained in the range 500−4000 cm−1, with 256 scans and a resolution of 8 cm−1. Figure 1. Structure of 1,4,5-trimethyl-2-(2,4,6...pulsed-field gradient nuclear magnetic resonance (PFG NMR) on an AVANCEIII NMR spectrometer with a 5 mm Bruker single -axis DIFF60L Z-diffusion probe. The

Monitoring of fluid motion in a micromixer by dynamic NMR microscopy.

PubMed

Ahola, Susanna; Casanova, Federico; Perlo, Juan; Münnemann, Kerstin; Blümich, Bernhard; Stapf, Siegfried

2006-01-01

The velocity distribution of liquid flowing in a commercial micromixer has been determined directly by using pulsed-field gradient NMR. Velocity maps with a spatial resolution of 29 microm x 43 microm were obtained by combining standard imaging gradient units with a homebuilt rectangular surface coil matching the mixer geometry. The technique provides access to mixers and reactors of arbitrary shape regardless of optical transparency. Local heterogeneities in the signal intensity and the velocity pattern were found and serve to investigate the quality and functionality of a micromixer, revealing clogging and inhomogeneous flow distributions.

Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR.

PubMed

Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus

2014-03-26

We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

Quantification of Propionic Acid in the Bovine Spinal Disk After Infection of the Tissue With Propionibacteria acnes Bacteria.

PubMed

Magnitsky, Sergey; Dudli, Stefan; Tang, Xinyan; Kaur, Jaskanwaljeet; Diaz, Joycelyn; Miller, Steve; Lotz, Jeffrey C

2018-06-01

Research. The goal of this study was to investigate whether Propionibacteria acnes infection of the intervertebral disc can be detected noninvasively by nuclear magnetic resonance (NMR) spectroscopy. Microbiological studies of surgical samples suggest that a significant subpopulation of back pain patients may have occult disc infection with P. acnes bacteria. This hypothesis is further supported by a double-blind clinical trial showing that back pain patients with Modic type 1 changes may respond to antibiotic treatment. Because significant side effects are associated with antibiotic treatment, there is a need for a noninvasive method to detect whether specific discs in back pain patients are infected with P acnes bacteria. P. acnes bacteria were obtained from human patients. NMR detection of a propionic acid (PA) in the bacteria extracts was conducted on 500 MHz high-resolution spectrometer, whereas in vivo NMR spectroscopy of an isolated bovine disk tissue infected with P. acnes was conducted on 7 T magnetic resonance imaging scanner. NMR spectra of P. acnes metabolites revealed a distinct NMR signal with identical chemical shits (1.05 and 2.18 ppm) as PA (a primary P. acne metabolite). The 1.05 ppm signal does not overlap with other bacteria metabolites, and its intensity increases linearly with P. acnes concentration. Bovine disks injected with P. acnes bacteria revealed a very distinct NMR signal at 1.05 ppm, which linearly increased with P. acnes concentration. The 1.05 ppm NMR signal from PA can be used as a marker of P. acnes infection of discs. This signal does not overlap with other disc metabolites and linearly depends on P. acnes concentration. Consequently, NMR spectroscopy may provide a noninvasive method to detect disc infection in the clinical setting. N/A.

Depth-Dependent Glycosaminoglycan Concentration in Articular Cartilage by Quantitative Contrast-Enhanced Micro–Computed Tomography

PubMed Central

Mittelstaedt, Daniel

2015-01-01

Objective A quantitative contrast-enhanced micro–computed tomography (qCECT) method was developed to investigate the depth dependency and heterogeneity of the glycosaminoglycan (GAG) concentration of ex vivo cartilage equilibrated with an anionic radiographic contrast agent, Hexabrix. Design Full-thickness fresh native (n = 19 in 3 subgroups) and trypsin-degraded (n = 6) articular cartilage blocks were imaged using micro–computed tomography (μCT) at high resolution (13.4 μm3) before and after equilibration with various Hexabrix bathing concentrations. The GAG concentration was calculated depth-dependently based on Gibbs-Donnan equilibrium theory. Analysis of variance with Tukey’s post hoc was used to test for statistical significance (P < 0.05) for effect of Hexabrix bathing concentration, and for differences in bulk and zonal GAG concentrations individually and compared between native and trypsin-degraded cartilage. Results The bulk GAG concentration was calculated to be 74.44 ± 6.09 and 11.99 ± 4.24 mg/mL for native and degraded cartilage, respectively. A statistical difference was demonstrated for bulk and zonal GAG between native and degraded cartilage (P < 0.032). A statistical difference was not demonstrated for bulk GAG when comparing Hexabrix bathing concentrations (P > 0.3214) for neither native nor degraded cartilage. Depth-dependent GAG analysis of native cartilage revealed a statistical difference only in the radial zone between 30% and 50% Hexabrix bathing concentrations. Conclusions This nondestructive qCECT methodology calculated the depth-dependent GAG concentration for both native and trypsin-degraded cartilage at high spatial resolution. qCECT allows for more detailed understanding of the topography and depth dependency, which could help diagnose health, degradation, and repair of native and contrived cartilage. PMID:26425259

On the influence of crystal size and wavelength on native SAD phasing.

PubMed

Liebschner, Dorothee; Yamada, Yusuke; Matsugaki, Naohiro; Senda, Miki; Senda, Toshiya

2016-06-01

Native SAD is an emerging phasing technique that uses the anomalous signal of native heavy atoms to obtain crystallographic phases. The method does not require specific sample preparation to add anomalous scatterers, as the light atoms contained in the native sample are used as marker atoms. The most abundant anomalous scatterer used for native SAD, which is present in almost all proteins, is sulfur. However, the absorption edge of sulfur is at low energy (2.472 keV = 5.016 Å), which makes it challenging to carry out native SAD phasing experiments as most synchrotron beamlines are optimized for shorter wavelength ranges where the anomalous signal of sulfur is weak; for longer wavelengths, which produce larger anomalous differences, the absorption of X-rays by the sample, solvent, loop and surrounding medium (e.g. air) increases tremendously. Therefore, a compromise has to be found between measuring strong anomalous signal and minimizing absorption. It was thus hypothesized that shorter wavelengths should be used for large crystals and longer wavelengths for small crystals, but no thorough experimental analyses have been reported to date. To study the influence of crystal size and wavelength, native SAD experiments were carried out at different wavelengths (1.9 and 2.7 Å with a helium cone; 3.0 and 3.3 Å with a helium chamber) using lysozyme and ferredoxin reductase crystals of various sizes. For the tested crystals, the results suggest that larger sample sizes do not have a detrimental effect on native SAD data and that long wavelengths give a clear advantage with small samples compared with short wavelengths. The resolution dependency of substructure determination was analyzed and showed that high-symmetry crystals with small unit cells require higher resolution for the successful placement of heavy atoms.

High-resolution proton NMR studies of intracellular metabolites in yeast using 13C decoupling

NASA Astrophysics Data System (ADS)

Sillerud, Laurel O.; Alger, Jeffry R.; Shulman, Robert G.

The resolution and specificity of 1H NMR in studies of yeast cellular metabolism were increased by feeding a 13C-labeled substrate and observing 1H difference spectra in the presence and absence of 13C decoupling fields. [2- 13C]Acetate was utilized as a respiratory substrate in an aerobic suspension of Saccharomyces cerevisiae. The broad cellular background proton resonances are removed by the technique, leaving only signals from the protons of the substrate, or its metabolites, that are coupled to 13C. Spectra of the yeast suspension after acetate feeding show the disappearance of label from the acetate pool and the subsequent appearance of 13C in glutamate C 3 and C 4 and in aspartate C 3. These results are in accord with the known fluxes of metabolites. Selective single-frequency 13C decoupling was used to provide assignments for the difference signals. The limitations on single-frequency decoupling coming from finite decoupling fields are investigated. The technique shows a potential for application in a wide variety of systems where the resolution of the 13C spectrum may be combined with the sensitivity for proton detection to observe metabolites that have been previously unobservable.

Enantiomeric separation of antimalarial drugs by capillary electrophoresis using neutral and negatively charged cyclodextrins.

PubMed

Németh, Krisztina; Tárkányi, Gábor; Varga, Erzsébet; Imre, Tímea; Mizsei, Réka; Iványi, Róbert; Visy, Júlia; Szemán, Julianna; Jicsinszky, László; Szente, Lajos; Simonyi, Miklós

2011-02-20

Capillary electrophoresis (CE) methods for chiral resolution of five antimalarial drugs (primaquine, tafenoquine, mefloquine, chloroquine and quinacrine) were developed by using a wide selection of neutral and anionic cyclodextrin (CD) derivatives. The use of sulfobutyl-β-CD and carboxymethyl-β-CD (CMBCD) resulted in good resolution of quinacrine and tafenoquine, respectively. New results are presented for resolutions of chloroquine and mefloquine. Application of carboxyalkyl- and sulfobutyl-CD derivatives provided improved resolution for primaquine. The impurity in primaquine sample detected by CE was identified as quinocide by MS and NMR. CMBCD provided not only the best separation of primaquine from quinocide but also the simultaneous complete resolution of both compounds. Copyright © 2010 Elsevier B.V. All rights reserved.

NMR Methods, Applications and Trends for Groundwater Evaluation and Management

NASA Astrophysics Data System (ADS)

Walsh, D. O.; Grunewald, E. D.

2011-12-01

Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of Energy have produced an NMR logging tool that is much smaller and less costly than comparable oilfield NMR logging tools. This system is specifically designed for near surface groundwater investigations, incorporates small diameter probes (as small as 1.67 inches diameter) and man-portable surface stations, and provides NMR data and information content on par with oilfield NMR logging tools. A direct-push variant of this logging tool has also been developed. Key challenges associated with small diameter tools include inherently lower SNR and logging speeds, the desire to extend the sensitive zone as far as possible into unconsolidated formations, and simultaneously maintaining high power and signal fidelity. Our ongoing research in groundwater NMR aims to integrating surface and borehole measurements for regional-scale permeability mapping, and to develop in-place NMR sensors for long term monitoring of contaminant and remediation processes. In addition to groundwater resource characterization, promising new applications of NMR include assessing water content in ice and permafrost, management of groundwater in mining operations, and evaluation and management of groundwater in civil engineering applications.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

PubMed

Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

2014-09-23

Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A

PubMed Central

Kitahara, Ryo; Simorellis, Alana K.; Hata, Kazumi; Maeno, Akihiro; Yokoyama, Shigeyuki; Koide, Shohei; Akasaka, Kazuyuki

2012-01-01

Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer β-sheet connecting the N- and C-terminal domains with τ << ms, which may give the two domains certain independence in mobility and thermodynamic stability. Furthermore, we found that folded, native OspA is in equilibrium (τ >> ms) with a minor conformer I, which is almost fully disordered and hydrated for the entire C-terminal part of the polypeptide chain from β8 to the C-terminus. Conformer I is characterized with ΔG0 = 32 ± 9 kJ/mol and ΔV0 = −140 ± 40 mL/mol, populating only ∼0.001% at 40°C at 0.1 MPa, pH 5.9. Because in the folded conformer the receptor binding epitope of OspA is buried in the C-terminal domain, its transition into conformer I under in vivo conditions may be critical for the infection of B. burgdorferi. The formation and stability of the peculiar conformer I are apparently supported by a large packing defect or cavity located in the C-terminal domain. PMID:22385863

Joint experimental and computational 17O solid state NMR study of Brownmillerite Ba2In2O5.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Holmes, Lesley A; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2014-02-14

Structural characterization of Brownmillerite Ba2In2O5 was achieved by an approach combining experimental solid-state NMR spectroscopy, density functional theory (DFT) energetics, and GIPAW NMR calculations. While in the previous study of Ba2In2O5 by Adler et al. (S. B. Adler, J. A. Reimer, J. Baltisberger and U. Werner, J. Am. Chem. Soc., 1994, 116, 675-681), three oxygen resonances were observed in the (17)O NMR spectra and assigned to the three crystallographically unique O sites, the present high resolution (17)O NMR measurements under magic angle spinning (MAS) find only two resonances. The resonances have been assigned using first principles (17)O GIPAW NMR calculations to the combination of the O ions connecting the InO4 tetrahedra and the O ions in equatorial sites in octahedral InO6 coordination, and to the axial O ions linking the four- and six-fold coordinated In(3+) ions. Possible structural disorder was investigated in two ways: firstly, by inclusion of the high-energy structure also previously studied by Mohn et al. (C. E. Mohn, N. L. Allan, C. L. Freeman, P. Ravindran and S. Stølen, J. Solid State Chem., 2005, 178, 346-355), where the structural O vacancies are stacked rather than staggered as in Brownmillerite and, secondly, by exploring structures derived from the ground-state structure but with randomly perturbed atomic positions. There is no noticeable NMR evidence for any substantial occupancy of the high-energy structure at room temperature.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.

PubMed

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide

NASA Astrophysics Data System (ADS)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Remotely detected high-field MRI of porous samples

NASA Astrophysics Data System (ADS)

Seeley, Juliette A.; Han, Song-I.; Pines, Alexander

2004-04-01

Remote detection of NMR is a novel technique in which an NMR-active sensor surveys an environment of interest and retains memory of that environment to be recovered at a later time in a different location. The NMR or MRI information about the sensor nucleus is encoded and stored as spin polarization at the first location and subsequently moved to a different physical location for optimized detection. A dedicated probe incorporating two separate radio frequency (RF)—circuits was built for this purpose. The encoding solenoid coil was large enough to fit around the bulky sample matrix, while the smaller detection solenoid coil had not only a higher quality factor, but also an enhanced filling factor since the coil volume comprised purely the sensor nuclei. We obtained two-dimensional (2D) void space images of two model porous samples with resolution less than 1.4 mm 2. The remotely reconstructed images demonstrate the ability to determine fine structure with image quality superior to their directly detected counterparts and show the great potential of NMR remote detection for imaging applications that suffer from low sensitivity due to low concentrations and filling factor.

A small-diameter NMR logging tool for groundwater investigations

USGS Publications Warehouse

Walsh, David; Turner, Peter; Grunewald, Elliot; Zhang, Hong; Butler, James J.; Reboulet, Ed; Knobbe, Steve; Christy, Tom; Lane, John W.; Johnson, Carole D.; Munday, Tim; Fitzpatrick, Andrew

2013-01-01

A small-diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively inexpensive, small-diameter probes that can be run in open or PVC-cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small-diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct-push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high-resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore-size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations.

Robustness of NMR-based metabolomics to generate comparable data sets for olive oil cultivar classification. An inter-laboratory study on Apulian olive oils.

PubMed

Piccinonna, Sara; Ragone, Rosa; Stocchero, Matteo; Del Coco, Laura; De Pascali, Sandra Angelica; Schena, Francesco Paolo; Fanizzi, Francesco Paolo

2016-05-15

Nuclear Magnetic Resonance (NMR) spectroscopy is emerging as a powerful technique in olive oil fingerprinting, but its analytical robustness has to be proved. Here, we report a comparative study between two laboratories on olive oil (1)H NMR fingerprinting, aiming to demonstrate the robustness of NMR-based metabolomics in generating comparable data sets for cultivar classification. Sample preparation and data acquisition were performed independently in two laboratories, equipped with different resolution spectrometers (400 and 500 MHz), using two identical sets of mono-varietal olive oils. Partial Least Squares (PLS)-based techniques were applied to compare the data sets produced by the two laboratories. Despite differences in spectrum baseline, and in intensity and shape of peaks, the amount of shared information was significant (almost 70%) and related to cultivar (same metabolites discriminated between cultivars). In conclusion, regardless of the variability due to operator and machine, the data sets from the two participating units were comparable for the purpose of classification. Copyright © 2015 Elsevier Ltd. All rights reserved.

Prospects for sub-micron solid state nuclear magnetic resonance imaging with low-temperature dynamic nuclear polarization.

PubMed

Thurber, Kent R; Tycko, Robert

2010-06-14

We evaluate the feasibility of (1)H nuclear magnetic resonance (NMR) imaging with sub-micron voxel dimensions using a combination of low temperatures and dynamic nuclear polarization (DNP). Experiments are performed on nitroxide-doped glycerol-water at 9.4 T and temperatures below 40 K, using a 30 mW tunable microwave source for DNP. With DNP at 7 K, a 0.5 microL sample yields a (1)H NMR signal-to-noise ratio of 770 in two scans with pulsed spin-lock detection and after 80 db signal attenuation. With reasonable extrapolations, we infer that (1)H NMR signals from 1 microm(3) voxel volumes should be readily detectable, and voxels as small as 0.03 microm(3) may eventually be detectable. Through homonuclear decoupling with a frequency-switched Lee-Goldburg spin echo technique, we obtain 830 Hz (1)H NMR linewidths at low temperatures, implying that pulsed field gradients equal to 0.4 G/d or less would be required during spatial encoding dimensions of an imaging sequence, where d is the resolution in each dimension.

Prospects for Sub-Micron Solid State Nuclear Magnetic Resonance Imaging with Low-Temperature Dynamic Nuclear Polarization

PubMed Central

Thurber, Kent R.; Tycko, Robert

2010-01-01

Summary We evaluate the feasibility of 1H nuclear magnetic resonance (NMR) imaging with sub-micron voxel dimensions using a combination of low temperatures and dynamic nuclear polarization (DNP). Experiments are performed on nitroxide-doped glycerol/water at 9.4 T and temperatures below 40 K, using a 30 mW tunable microwave source for DNP. With DNP at 7 K, a 0.5 µl sample yields a 1H NMR signal-to-noise ratio of 770 in two scans with pulsed spin-lock detection and after 80 db signal attenuation. With reasonable extrapolations, we infer that 1H NMR signals from 1 µm3 voxel volumes should be readily detectable, and voxels as small as 0.03 µm3 may eventually be detectable. Through homonuclear decoupling with a frequency-switched Lee-Goldburg spin echo technique, we obtain 830 Hz 1H NMR linewidths at low temperatures, implying that pulsed field gradients equal to 0.4 G/d or less would be required during spatial encoding dimensions of an imaging sequence, where d is the resolution in each dimension. PMID:20458431

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

2014-09-01

We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

Photochemical Degradation of the Anticancer Drug Bortezomib by V-UV/UV (185/254 nm) Investigated by (1)H NMR Fingerprinting: A Way to Follow Aromaticity Evolution.

PubMed

Martignac, Marion; Balayssac, Stéphane; Gilard, Véronique; Benoit-Marquié, Florence

2015-06-18

We have investigated the removal of bortezomib, an anticancer drug prescribed in multiple myeloma, using the photochemical advanced oxidation process of V-UV/UV (185/254 nm). We used two complementary analytical techniques to follow the removal rate of bortezomib. Nuclear magnetic resonance (NMR) is a nonselective method requiring no prior knowledge of the structures of the byproducts and permits us to provide a spectral signature (fingerprinting approach). This untargeted method provides clues to the molecular structure changes and information on the degradation of the parent drug during the irradiation process. This holistic NMR approach could provide information for monitoring aromaticity evolution. We use liquid chromatography, coupled with high-resolution mass spectrometry (LC-MS), to correlate results obtained by (1)H NMR and for accurate identification of the byproducts, in order to understand the mechanistic degradation pathways of bortezomib. The results show that primary byproducts come from photoassisted deboronation of bortezomib at 254 nm. A secondary byproduct of pyrazinecarboxamide was also identified. We obtained a reliable correlation between these two analytical techniques.

Challenge of representing entropy at different levels of resolution in molecular simulation.

PubMed

Huang, Wei; van Gunsteren, Wilfred F

2015-01-22

The role of entropic contributions in processes involving biomolecules is illustrated using the process of vaporization or condensation of the solvents water and methanol and the process of polypeptide folding in solution using molecular models at different levels of resolution: subatomic, atomic, supra-atomic, and supramolecular. For the folding process, a β-hexapeptide that adopts, as inferred from NMR experiments, both a right-handed 2.710/12-helical fold and a left-handed 314-helical fold in methanol, is used to illustrate the challenge of modeling thermodynamically driven processes at different levels of resolution.

High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Schmitt-Kopplin, P.

2013-03-01

High-performance, non-target, high-resolution organic structural spectroscopy was applied to solid phase extracted marine dissolved organic matter (SPE-DOM) isolated from four different depths in the open South Atlantic Ocean off the Angola coast (3° E, 18° S; Angola Basin) and provided molecular level information with extraordinary coverage and resolution. Sampling was performed at depths of 5 m (Angola Current; near-surface photic zone), 48 m (Angola Current; fluorescence maximum), 200 m (still above Antarctic Intermediate Water, AAIW; upper mesopelagic zone) and 5446 m (North Atlantic Deep Water, NADW; abyssopelagic, ~30 m above seafloor) and produced SPE-DOM with near 40% carbon yield and beneficial nuclear magnetic resonance (NMR) relaxation properties, a crucial prerequisite for the acquisition of NMR spectra with excellent resolution. 1H and 13C NMR spectra of all four marine SPE-DOM showed smooth bulk envelopes, reflecting intrinsic averaging from massive signal overlap, with a few percent of visibly resolved signatures and variable abundances for all major chemical environments. The abundance of singly oxygenated aliphatics and acetate derivatives in 1H NMR spectra declined from surface to deep marine SPE-DOM, whereas C-based aliphatics and carboxyl-rich alicyclic molecules (CRAM) increased in abundance. Surface SPE-DOM contained fewer methyl esters than all other samples, likely a consequence of direct exposure to sunlight. Integration of 13C NMR spectra revealed continual increase of carboxylic acids and ketones from surface to depth, reflecting a progressive oxygenation, with concomitant decline of carbohydrate-related substructures. Aliphatic branching increased with depth, whereas the fraction of oxygenated aliphatics declined for methine, methylene and methyl carbon. Lipids in the oldest SPE-DOM at 5446 m showed a larger share of ethyl groups and methylene carbon than observed in the other samples. Two-dimensional NMR spectra showed exceptional resolution and depicted resolved molecular signatures in excess of a certain minimum abundance. Classical methyl groups terminating aliphatic chains represented ~15% of total methyl in all samples investigated. A noticeable fraction of methyl (~2%) was bound to olefinic carbon. Methyl ethers were abundant in surface marine SPE-DOM, and the chemical diversity of carbohydrates was larger than that of freshwater and soil DOM. In all samples, we identified sp2-hybridized carbon chemical environments with discrimination of isolated and conjugated olefins and α,β-unsaturated double bonds. Olefinic proton and carbon atoms were more abundant than aromatic ones; olefinic unsaturation in marine SPE-DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation. The abundance of furan, pyrrol and thiophene derivatives was marginal, whereas benzene derivatives, phenols and six-membered nitrogen heterocycles were prominent; a yet unassigned set of six-membered N-heterocycles with likely more than one single nitrogen occurred in all samples. Various key polycyclic aromatic hydrocarbon substructures suggested the presence of thermogenic organic matter at all water depths. Progressive NMR cross-peak attenuation from surface to deep marine SPE-DOM was particularly strong in COSY NMR spectra and indicated a continual disappearance of biosignatures as well as entropy gain from an ever increased molecular diversity. Nevertheless, a specific near-seafloor SPE-DOM signature of unsaturated molecules recognized in both NMR and Fourier transform ion cyclotron mass spectrometry (FTICR/MS) possibly originated from sediment leaching. The conformity of key NMR and FTICR/MS signatures suggested the presence of a large set of identical molecules throughout the entire ocean column even though the investigated water masses belonged to different oceanic regimes and currents. FTICR/MS showed abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks and average mass from surface to bottom SPE-DOM. The proportion of CHO and CHNO negative ions increased from surface to depth, whereas CHOS and especially CHNOS molecular series markedly declined. While certain rather aliphatic CHOS and CHNOS ions were observed solely in the surface, deep marine SPE-DOM was enriched in unique unsaturated and rather oxygenated CHO and CHNO molecular series. With the exception of abyssopelagic SPE-DOM at 5446 m, which showed a peculiar CHOS chemistry of unsaturated carbon and reduced sulphur (black sulphur), CHO and CHNO molecular series contributed ~87% to total positive electrospray ionization FTICR mass peak integral, with a near constant ratio of CHNO / CHO molecular compositions near 1.13 ± 0.05. In case of all four marine SPE-DOM, remarkably disparate average elemental compositions as determined from either MS and NMR spectra were observed, caused by a pronounced ionization selectivity in electrospray ionization FTICR/MS. The study demonstrates that the exhaustive characterization of complex unknowns in marine DOM will enable a meaningful classification of individual marine biogeosignatures. Future in-depth functional biodiversity studies with a clear understanding of DOM structure and function might eventually lead to a novel, unified perception of biodiversity and biogeochemistry.

NMR high-resolution magic angle spinning rotor design for quantification of metabolic concentrations

NASA Astrophysics Data System (ADS)

Holly, R.; Damyanovich, A.; Peemoeller, H.

2006-05-01

A new high-resolution magic angle spinning nuclear magnetic resonance technique is presented to obtain absolute metabolite concentrations of solutions. The magnetic resonance spectrum of the sample under investigation and an internal reference are acquired simultaneously, ensuring both spectra are obtained under the same experimental conditions. The robustness of the technique is demonstrated using a solution of creatine, and it is shown that the technique can obtain solution concentrations to within 7% or better.

Resolution Improvements in in Vivo1H NMR Spectra with Increased Magnetic Field Strength

NASA Astrophysics Data System (ADS)

Gruetter, Rolf; Weisdorf, Sally A.; Rajanayagan, Vasantham; Terpstra, Melissa; Merkle, Hellmut; Truwit, Charles L.; Garwood, Michael; Nyberg, Scott L.; Ugurbil, Kâmil

1998-11-01

The measurement of cerebral metabolites using highly homologous localization techniques and similar shimming methods was performed in the human brain at 1.5 and 4 T as well as in the dog and rat brain at 9.4 T. In rat brain, improved resolution was achieved by shimming all first- and second-order shim coils using a fully adiabatic FASTMAP sequence. The spectra showed a clear improvement in spectral resolution for all metabolite resonances with increased field strength. Changes in cerebral glutamine content were clearly observed at 4 T compared to 1.5 T in patients with hepatic encephalopathy. At 9.4 T, glutamine H4 at 2.46 ppm was fully resolved from glutamate H4 at 2.37 ppm, as was the potential resonance from γ-amino-butyric acid at 2.30 ppm and N-acetyl-aspartyl-glutamate at 2.05 ppm. Singlet linewidths were found to be as low as 6 Hz (0.015 ppm) at 9.4 T, indicating a substantial decrease in ppm linewidth with field strength. Furthermore, the methylene peak of creatine was partially resolved from phosphocreatine, indicating a close to 1:1 relationship in gray matter. We conclude that increasing the magnetic field strength increases spectral resolution also for1H NMR, which can lead to more than linear sensitivity gains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Junjing; Vine, David J.; Chen, Si

X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. Here, by working with cells that have been rapidly frozen without the use of chemicalmore » fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.« less

High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy

NASA Astrophysics Data System (ADS)

Jaroniec, Christopher P.; Macphee, Cait E.; Bajaj, Vikram S.; McMahon, Michael T.; Dobson, Christopher M.; Griffin, Robert G.

2004-01-01

Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible spongiform encephalopathies. Despite the immense medical importance of amyloid fibrils, no atomic-resolution structures are available for these materials, because the intact fibrils are insoluble and do not form diffraction-quality 3D crystals. Here we report the high-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105-115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves not only the backbone fold but also the precise conformation of the side chains. Nearly complete 13C and 15N resonance assignments for TTR(105-115) formed the basis for the extraction of a set of distance and dihedral angle restraints. A total of 76 self-consistent experimental measurements, including 41 restraints on 19 backbone dihedral angles and 35 13C-15N distances between 3 and 6 Å were obtained from 2D and 3D NMR spectra recorded on three fibril samples uniformly 13C, 15N-labeled in consecutive stretches of four amino acids and used to calculate an ensemble of peptide structures. Our results indicate that TTR(105-115) adopts an extended -strand conformation in the amyloid fibrils such that both the main- and side-chain torsion angles are close to their optimal values. Moreover, the structure of this peptide in the fibrillar form has a degree of long-range order that is generally associated only with crystalline materials. These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly.

Field-cycling NMR with high-resolution detection under magic-angle spinning: determination of field-window for nuclear hyperpolarization in a photosynthetic reaction center.

PubMed

Gräsing, Daniel; Bielytskyi, Pavlo; Céspedes-Camacho, Isaac F; Alia, A; Marquardsen, Thorsten; Engelke, Frank; Matysik, Jörg

2017-09-21

Several parameters in NMR depend on the magnetic field strength. Field-cycling NMR is an elegant way to explore the field dependence of these properties. The technique is well developed for solution state and in relaxometry. Here, a shuttle system with magic-angle spinning (MAS) detection is presented to allow for field-dependent studies on solids. The function of this system is demonstrated by exploring the magnetic field dependence of the solid-state photochemically induced nuclear polarization (photo-CIDNP) effect. The effect allows for strong nuclear spin-hyperpolarization in light-induced spin-correlated radical pairs (SCRPs) under solid-state conditions. To this end, 13 C MAS NMR is applied to a photosynthetic reaction center (RC) of the purple bacterium Rhodobacter (R.) sphaeroides wildtype (WT). For induction of the effect in the stray field of the magnet and its subsequent observation at 9.4 T under MAS NMR conditions, the sample is shuttled by the use of an aerodynamically driven sample transfer technique. In the RC, we observe the effect down to 0.25 T allowing to determine the window for the occurrence of the effect to be between about 0.2 and 20 T.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

PubMed

Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

2005-04-01

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

Thermal heterogeneity within aqueous materials quantified by 1H NMR spectroscopy: Multiparametric validation in silico and in vitro

NASA Astrophysics Data System (ADS)

Lutz, Norbert W.; Bernard, Monique

2018-02-01

We recently suggested a new paradigm for statistical analysis of thermal heterogeneity in (semi-)aqueous materials by 1H NMR spectroscopy, using water as a temperature probe. Here, we present a comprehensive in silico and in vitro validation that demonstrates the ability of this new technique to provide accurate quantitative parameters characterizing the statistical distribution of temperature values in a volume of (semi-)aqueous matter. First, line shape parameters of numerically simulated water 1H NMR spectra are systematically varied to study a range of mathematically well-defined temperature distributions. Then, corresponding models based on measured 1H NMR spectra of agarose gel are analyzed. In addition, dedicated samples based on hydrogels or biological tissue are designed to produce temperature gradients changing over time, and dynamic NMR spectroscopy is employed to analyze the resulting temperature profiles at sub-second temporal resolution. Accuracy and consistency of the previously introduced statistical descriptors of temperature heterogeneity are determined: weighted median and mean temperature, standard deviation, temperature range, temperature mode(s), kurtosis, skewness, entropy, and relative areas under temperature curves. Potential and limitations of this method for quantitative analysis of thermal heterogeneity in (semi-)aqueous materials are discussed in view of prospective applications in materials science as well as biology and medicine.

NTP and PCr responses to hypoxia by hypothermic and normothermic respiring, superfused, neonatal rat cerebrocortical slices: an NMR spectroscopy study at 14.1 Tesla.

PubMed

Litt, L; Hirai, K; Basus, V J; James, T L

2003-01-01

Although mechanisms of hypothermic neuroprotection during oxygen deprivation have long been investigated, further characterizations of various molecular mechanisms are appropriate. Anticipating future studies of hypothermia and hypoxia/ischemia, we investigated the extent to which our ex vivo, NMR-based, superfused brain slice model might be helpful. (Slices are approximately 350 microm thick, with 18 slices per 8 mm NMR tube.) 31P NMR spectroscopic measurements were made of hypothermia-induced changes in high energy phosphates, while simultaneously monitoring and controlling tissue temperature, using 1H NMR, the high spectroscopic resolution available at 14.1 Tesla (600 MHz for protons), and a recently published protocol. NTP and PCr concentrations in healthy, well-oxygenated slices decreased to (55 +/- 15)% and (66 +/- 30)% of their respective values at 28.0 degrees C when warmed to 38.0 degrees C, in approximate agreement with earlier in vivo studies by others. During 30 min hypoxia NTP and PCr decreased to non-observable values, regardless of temperature. After reoxygenation, NTP and PCr recoveries as percentages of respective prehypoxia values were (63% +/- 16%; 70%) +/- 5%) for hypothermic slices (28.0 degrees C), and (46% +/- 13%; 41% +/- hypothermic neuroprotection during oxygen deprivation in this model, which appears suitable for use in further studies.

Testing signal enhancement mechanisms in the dissolution NMR of acetone

NASA Astrophysics Data System (ADS)

Alonso-Valdesueiro, Javier; Elliott, Stuart J.; Bengs, Christian; Meier, Benno; Levitt, Malcolm H.

2018-01-01

In cryogenic dissolution NMR experiments, a substance of interest is allowed to rest in a strong magnetic field at cryogenic temperature, before dissolving the substance in a warm solvent, transferring it to a high-resolution NMR spectrometer, and observing the solution-state NMR spectrum. In some cases, negative enhancements of the 13C NMR signals are observed, which have been attributed to quantum-rotor-induced polarization. We show that in the case of acetone (propan-2-one) the negative signal enhancements of the methyl 13C sites may be understood by invoking conventional cross-relaxation within the methyl groups. The 1H nuclei acquire a relative large net polarization through thermal equilibration in a magnetic field at low temperature, facilitated by the methyl rotation which acts as a relaxation sink; after dissolution, the 1H magnetization slowly returns to thermal equilibrium at high temperature, in part by cross-relaxation processes, which induce a transient negative polarization of nearby 13C nuclei. We provide evidence for this mechanism experimentally and theoretically by saturating the 1H magnetization using a radiofrequency field pulse sequence before dissolution and comparing the 13 C magnetization evolution after dissolution with the results obtained from a conventional 1 H-13 C cross relaxation model of the CH3 moieties in acetone.

SAGE III/ISS L1B Solar Event Transmission Data (Native) V5 (g3btb)

Atmospheric Science Data Center

2017-12-21

SAGE III/ISS L1B Solar Event Transmission Data (Native) V5 (g3btb)   Project Title:  ... present Temporal Resolution:  1 file per event File Format:  BINARY Tools:  Earthdata ... Radiation Longwave Radiation Shortwave Radiation Event Tag Event Type Obs Beta Angle Order Data:  ...

Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association.

PubMed

Lindström, Fredrick; Williamson, Philip T F; Gröbner, Gerhard

2005-05-11

Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic potential present at the surface of biological model membranes, the electrostatic charge distribution across the membrane interface, and changes that occur upon peptide association. The spectral resolution in (31)P and (14)N MAS NMR spectra is sufficient to probe directly the negatively charged phosphate and positively charged choline segment of the electrostatic P(-)-O-CH(2)-CH(2)-N(+)(CH(3))(3) headgroup dipole of zwitterionic DMPC (dimyristoylphosphatidylcholine) in mixed-lipid systems. The isotropic shifts report on the size of the potential existing at the phosphate and ammonium group within the lipid headgroup while the chemical shielding anisotropy ((31)P) and anisotropic quadrupolar interaction ((14)N) characterize changes in headgroup orientation in response to surface potential. The (31)P/(14)N isotropic chemical shifts for DMPC show opposing systematic changes in response to changing membrane potential, reflecting the size of the electrostatic potential at opposing ends of the P(-)-N(+) dipole. The orientational response of the DMPC lipid headgroup to electrostatic surface variations is visible in the anisotropic features of (14)N and (31)P NMR spectra. These features are analyzed in terms of a modified "molecular voltmeter" model, with changes in dynamic averaging reflecting the tilt of the C(beta)-N(+)(CH)(3) choline and PO(4)(-) segment. These properties have been exploited to characterize the changes in surface potential upon the binding of nociceptin to negatively charged membranes, a process assumed to proceed its agonistic binding to its opoid G-protein coupled receptor.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

USGS Publications Warehouse

Thorn, K.A.; Cox, L.G.

2009-01-01

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS 15N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by 15N NMR. Liquid state 15N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (1H-15N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.

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

NASA Astrophysics Data System (ADS)

Zhang, Guannan; Schilling, Franz; Glaser, Steffen J.; Hilty, Christian

2016-11-01

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 0.02 ppm when measured on a 400 MHz NMR spectrometer. Notably, the appearance of decoupling side-bands, which scale with peak intensity, appears to be of secondary importance.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thorn, Kevin A.; Cox, Larry G.

2009-02-28

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS ¹⁵N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprisedmore » the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by ¹⁵N NMR. Liquid state ¹⁵N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (¹H–¹⁵N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.« less

Toward an atomistic description of the urea-denatured state of proteins.

PubMed

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-04-09

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.

Toward an atomistic description of the urea-denatured state of proteins

PubMed Central

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-01-01

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea. PMID:23536295

Protein vivisection reveals elusive intermediates in folding

PubMed Central

Zheng, Zhongzhou; Sosnick, Tobin R.

2010-01-01

Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu→Glu−) to destabilize and unfold a specific region of the protein. We apply this strategy to Ubiquitin, reversibly trapping a folding intermediate in which the β5 strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high energy states. PMID:20144618

1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New Metabolite—Malylglutamate

PubMed Central

2017-01-01

Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using 1H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts. The newly detected but known metabolites 2-aminobutyrate, nicotinurate, Nδ,Nδ,Nδ-trimethylornithine, and trigonelline are reported along with a novel compound, malylglutamate, elucidated using 2D NMR and high-resolution MS/MS. We postulate that malylglutamate acts as a glutamate/malate store, chelator, and anionic osmolyte and helps to provide electrolyte balance. PMID:28753027

1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New Metabolite-Malylglutamate.

PubMed

Griffith, Corey M; Williams, Preston B; Tinoco, Luzineide W; Dinges, Meredith M; Wang, Yinsheng; Larive, Cynthia K

2017-09-01

Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using 1 H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts. The newly detected but known metabolites 2-aminobutyrate, nicotinurate, Nδ,Nδ,Nδ-trimethylornithine, and trigonelline are reported along with a novel compound, malylglutamate, elucidated using 2D NMR and high-resolution MS/MS. We postulate that malylglutamate acts as a glutamate/malate store, chelator, and anionic osmolyte and helps to provide electrolyte balance.

Études RMN haute résolution et RPE des composés Ba 3C 60 et Ba 6C 60

NASA Astrophysics Data System (ADS)

Rezzouk, Abdellah; Dafir, Driss; Errammach, Youssef; Rachdi, Férid

2003-07-01

We report the results of 13C MAS NMR and EPR measurements on Ba 3C 60 and Ba 6C 60 fullerides. Using high resolution NMR, we were able to identify an isotropic line around 156 ppm for Ba 3C 60 and a broad isotropic one with three components at 132, 134.6, 139.9 ppm for Ba 6C 60 compound. The latter line is consistent with orientationally ordered C 60 molecules leading to three unequivalent carbon sites in agreement with X-ray studies. A strong diamagnetic shift was observed for the NMR line of Ba 6C 60 that is interpreted in terms of transition moment in an indirect gap system. EPR results confirm the insulating nature of both studied compounds. To cite this article: A. Rezzouk et al., C. R. Physique 4 (2003).

Protein Dynamics from NMR and Computer Simulation

NASA Astrophysics Data System (ADS)

Wu, Qiong; Kravchenko, Olga; Kemple, Marvin; Likic, Vladimir; Klimtchuk, Elena; Prendergast, Franklyn

2002-03-01

Proteins exhibit internal motions from the millisecond to sub-nanosecond time scale. The challenge is to relate these internal motions to biological function. A strategy to address this aim is to apply a combination of several techniques including high-resolution NMR, computer simulation of molecular dynamics (MD), molecular graphics, and finally molecular biology, the latter to generate appropriate samples. Two difficulties that arise are: (1) the time scale which is most directly biologically relevant (ms to μs) is not readily accessible by these techniques and (2) the techniques focus on local and not collective motions. We will outline methods using ^13C-NMR to help alleviate the second problem, as applied to intestinal fatty acid binding protein, a relatively small intracellular protein believed to be involved in fatty acid transport and metabolism. This work is supported in part by PHS Grant GM34847 (FGP) and by a fellowship from the American Heart Association (QW).

The metabolic profile of lemon juice by proton HR-MAS NMR: the case of the PGI Interdonato Lemon of Messina.

PubMed

Cicero, Nicola; Corsaro, Carmelo; Salvo, Andrea; Vasi, Sebastiano; Giofré, Salvatore V; Ferrantelli, Vincenzo; Di Stefano, Vita; Mallamace, Domenico; Dugo, Giacomo

2015-01-01

We have studied by means of High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) the metabolic profile of the famous Sicilian lemon known as 'Interdonato Lemon of Messina PGI'. The PGI Interdonato Lemon of Messina possesses high organoleptic and healthy properties and is recognised as one of the most nutrient fruits. In particular, some of its constituents are actively studied for their chemo-preventive and therapeutic properties. In this paper, we have determined by means of HR-MAS NMR spectroscopy the molar concentration of the main metabolites constituent the juice of PGI Interdonato Lemon of Messina in comparison with that of the not-PGI Interdonato Lemon of Turkey. Our aim is to develop an analytical technique, in order to determine a metabolic fingerprint able to reveal commercial frauds in national and international markets.

Structure elucidation and chemical synthesis of stigmolone, a novel type of prokaryotic pheromone.

PubMed

Hull, W E; Berkessel, A; Plaga, W

1998-09-15

Approximately 2 micromol of a novel prokaryotic pheromone, involved in starvation-induced aggregation and formation of fruiting bodies by the myxobacterium Stigmatella aurantiaca, were isolated by a large-scale elution procedure. The pheromone was purified by HPLC, and high-resolution MS, IR, 1H-NMR, and 13C-NMR were used to identify the active substance as the hydroxy ketone 2,5, 8-trimethyl-8-hydroxy-nonan-4-one, which has been named stigmolone. The analysis was complicated by a solvent-dependent equilibrium between stigmolone and the cyclic enol-ether 3,4-dihydro-2,2, 5-trimethyl-6-(2-methylpropyl)-2H-pyran formed by intramolecular nucleophilic attack of the 8-OH group at the ketone C4 followed by loss of H2O. Both compounds were synthesized chemically, and their structures were confirmed by NMR analysis. Natural and synthetic stigmolone have the same biological activity at ca. 1 nM concentration.

Characterization of Free Surface-Bound and Entrapped Water Environments in Poly(N-Isopropyl Acrylamide) Hydrogels via 1H HRMAS PFG NMR Spectroscopy

DOE PAGES

Alam, Todd Michael; Childress, Kimberly Kay; Pastoor, Kevin; ...

2014-09-19

We found that different water environments in poly(N-isopropyl acrylamide) (PNIPAAm) hydrogels are identified and characterized using 1H high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR). Local water environments corresponding to a “free” highly mobile species, along with waters showing restricted dynamics are resolved in these swollen hydro-gels. For photo-initiated polymerized PNIPAAm gels, an additional entrapped water species is observed. Spin–spin R 2 relaxation experiments support the argument of reduced mobility in the restricted and entrapped water species. Furthermore, by combining pulse field gradient techniques with HRMAS NMR it is possible to directly measure the self-diffusion rate for thesemore » different water environments. The behavior of the heterogeneous water environments through the lower critical solution temperature transition is described.« less

High resolution magic angle spinning NMR spectroscopy reveals that pectoralis muscle dystrophy in chicken is associated with reduced muscle content of anserine and carnosine.

PubMed

Sundekilde, Ulrik K; Rasmussen, Martin K; Young, Jette F; Bertram, Hanne Christine

2017-02-15

Increased incidences of pectoralis muscle dystrophy are observed in commercial chicken products, but the muscle physiological causes for the condition remain to be identified. In the present study a high-resolution magic angle spinning (HR-MAS) proton ((1)H) NMR spectroscopic examination of intact pectoralis muscle samples (n=77) were conducted to explore metabolite perturbations associated with the muscle dystrophy condition for the very first time. Both in chicken with an age of 21 and 31days, respectively, pectoralis muscle dystrophy was associated with a significantly lower content of anserine (p=0.034), carnosine (p=0.019) and creatine (p=0.049). These findings must be considered intriguing as they corroborate that characteristic muscle di-peptides composed of β-alanine and histidine derivatives such as anserine are extremely important in homeostasis of contractile muscles as a results of their role as buffering, anti-oxidative, and anti-glycation capacities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Does aluminium bind to histidine? An NMR investigation of amyloid β12 and amyloid β16 fragments.

PubMed

Narayan, Priya; Krishnarjuna, Bankala; Vishwanathan, Vinaya; Jagadeesh Kumar, Dasappa; Babu, Sudhir; Ramanathan, Krishna Venkatachala; Easwaran, Kalpathy Ramaier Katchap; Nagendra, Holenarasipur Gundurao; Raghothama, Srinivasarao

2013-07-01

Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in Aβ (amyloid β) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal Aβ fragments, DAEFRHDSGYEV (Aβ12) and DAEFRHDSGYEVHHQK (Aβ16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with Aβ12 and Aβ16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in Aβ12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets. © 2013 John Wiley & Sons A/S.

Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth.

PubMed

Masoom, Hussain; Courtier-Murias, Denis; Farooq, Hashim; Soong, Ronald; Kelleher, Brian P; Zhang, Chao; Maas, Werner E; Fey, Michael; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, Myrna J; Simpson, André J

2016-02-16

Since the isolation of soil organic matter in 1786, tens of thousands of publications have searched for its structure. Nuclear magnetic resonance (NMR) spectroscopy has played a critical role in defining soil organic matter but traditional approaches remove key information such as the distribution of components at the soil-water interface and conformational information. Here a novel form of NMR with capabilities to study all physical phases termed Comprehensive Multiphase NMR, is applied to analyze soil in its natural swollen-state. The key structural components in soil organic matter are identified to be largely composed of macromolecular inputs from degrading biomass. Polar lipid heads and carbohydrates dominate the soil-water interface while lignin and microbes are arranged in a more hydrophobic interior. Lignin domains cannot be penetrated by aqueous solvents even at extreme pH indicating they are the most hydrophobic environment in soil and are ideal for sequestering hydrophobic contaminants. Here, for the first time, a complete range of physical states of a whole soil can be studied. This provides a more detailed understanding of soil organic matter at the molecular level itself key to develop the most efficient soil remediation and agricultural techniques, and better predict carbon sequestration and climate change.

Multinuclear NMR studies of relaxor ferroelectrics

NASA Astrophysics Data System (ADS)

Zhou, Donghua

Multinuclear NMR of 93Nb, 45Sc, and 207Pb has been carried out to study the structure, disorder, and dynamics of a series of important solid solutions: perovskite relaxor ferroelectric materials (1-x) Pb(Mg1/3Nb 2/3)O3-x Pb(Sc1/2Nb1/2)O 3 (PMN-PSN). 93Nb NMR investigations of the local structure and cation order/disorder are presented as a function of PSN concentration, x. The superb fidelity and accuracy of 3QMAS allows us to make clear and consistent assignments of spectral intensities to the 28 possible nearest B-site neighbor (nBn) configurations, (NMg, NSc, NNb), where each number ranges from 0 to 6 and their sum is 6. For most of the 28 possible nBn configurations, isotropic chemical shifts and quadrupole product constants have been extracted from the data. The seven configurations with only larger cations, Mg 2+ and Sc3+ (and no Nb5+) are assigned to the seven observed narrow peaks, whose deconvoluted intensities facilitate quantitative evaluation of, and differentiation between, different models of B-site (chemical) disorder. The "completely random" model is ruled out and the "random site" model is shown to be in qualitative agreement with the NMR experiments. To obtain quantitative agreement with observed NMR intensities, the random site model is slightly modified by including unlike-pair interaction energies. To date, 45Sc studies have not been as fruitful as 93Nb NMR because the resolution is lower in the 45Sc spectra. The lower resolution of 45Sc spectra is due to a smaller span of isotropic chemical shift (40 ppm for 45Sc vs. 82 ppm for 93Nb) and to the lack of a fortuitous mechanism that simplifies the 93Nb spectra; for 93Nb the overlap of the isotropic chemical shifts of 6-Sc and 6-Nb configurations results in the alignment of all the 28 configurations along only seven quadrupole distribution axes. Finally we present variable temperature 207Pb static, MAS, and 2D-PASS NMR studies. Strong linear correlations between isotropic and anisotropic chemical shifts show that Pb-O bonds vary from more ionic to more covalent environments. Distributions of Pb-O bond lengthes are also quantitatively described. Such distributions are used to examine two competing models of Pb displacements; the shell model and the unique direction model. Only the latter model is able to reproduce the observed Pb-O distance distribution.

27 Al MAS NMR Studies of HBEA Zeolite at Low to High Magnetic Fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian Zhi; Wan, Chuan; Vjunov, Aleksei

27Al single pulse (SP) MAS NMR spectra of HBEA zeolites with high Si/Al ratios of 71 and 75 were obtained at three magnetic field strengths of 7.05, 11.75 and 19.97 T. High field 27Al MAS NMR spectra acquired at 19.97 T show significantly improved spectral resolution, resulting in at least two well-resolved tetrahedral-Al NMR peaks. Based on the results obtained from 27Al MAS and MQMAS NMR acquired at 19.97 T, four different quadrupole peaks are used to deconvolute the 27Al SP MAS spectra acquired at vari-ous fields by using the same set of quadrupole coupling constants, asymmetric parameters and relativemore » integrated peak intensities for the tetrahedral Al peaks. The line shapes of individual peaks change from typical quadrupole line shape at low field to essentially symmetrical line shapes at high field. We demonstrate that for fully hydrated HBEA zeolites the effect of second order quadrupole interaction can be ignored and quantitative spectral analysis can be performed by directly fitting the high field spectra using mixed Gaussian/Lorentzian line shapes. Also, the analytical steps described in our work allow direct assignment of spectral intensity to individual Al tetrahedral sites (T-sites) of zeolite HBEA. Finally, the proposed concept is suggested generally applicable to other zeo-lite framework types, thus, allowing a direct probing of Al distributions by NMR spectroscopic methods in zeolites with high confi-dence.« less

1H MAS NMR (magic-angle spinning nuclear magnetic resonance) techniques for the quantitative determination of hydrogen types in solid catalysts and supports.

PubMed

Kennedy, Gordon J; Afeworki, Mobae; Calabro, David C; Chase, Clarence E; Smiley, Randolph J

2004-06-01

Distinct hydrogen species are present in important inorganic solids such as zeolites, silicoaluminophosphates (SAPOs), mesoporous materials, amorphous silicas, and aluminas. These H species include hydrogens associated with acidic sites such as Al(OH)Si, non-framework aluminum sites, silanols, and surface functionalities. Direct and quantitative methodology to identify, measure, and monitor these hydrogen species are key to monitoring catalyst activity, optimizing synthesis conditions, tracking post-synthesis structural modifications, and in the preparation of novel catalytic materials. Many workers have developed several techniques to address these issues, including 1H MAS NMR (magic-angle spinning nuclear magnetic resonance). 1H MAS NMR offers many potential advantages over other techniques, but care is needed in recognizing experimental limitations and developing sample handling and NMR methodology to obtain quantitatively reliable data. A simplified approach is described that permits vacuum dehydration of multiple samples simultaneously and directly in the MAS rotor without the need for epoxy, flame sealing, or extensive glovebox use. We have found that careful optimization of important NMR conditions, such as magnetic field homogeneity and magic angle setting are necessary to acquire quantitative, high-resolution spectra that accurately measure the concentrations of the different hydrogen species present. Details of this 1H MAS NMR methodology with representative applications to zeolites, SAPOs, M41S, and silicas as a function of synthesis conditions and post-synthesis treatments (i.e., steaming, thermal dehydroxylation, and functionalization) are presented.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Heat Management Strategies for Solid-state NMR of Functional Proteins

PubMed Central

Fowler, Daniel J.; Harris, Michael J.; Thompson, Lynmarie K.

2012-01-01

Modern solid-state NMR methods can acquire high-resolution protein spectra for structure determination. However, these methods use rapid sample spinning and intense decoupling fields that can heat and denature the protein being studied. Here we present a strategy to avoid destroying valuable samples. We advocate first creating a sacrificial sample, which contains unlabeled protein (or no protein) in buffer conditions similar to the intended sample. This sample is then doped with the chemical shift thermometer Sm2Sn2O7. We introduce a pulse scheme called TCUP (for Temperature Calibration Under Pulseload) that can characterize the heating of this sacrificial sample rapidly, under a variety of experimental conditions, and with high temporal resolution. Sample heating is discussed with respect to different instrumental variables such as spinning speed, decoupling strength and duration, and cooling gas flow rate. The effects of different sample preparation variables are also discussed, including ionic strength, the inclusion of cryoprotectants, and the physical state of the sample (i.e. liquid, solid, or slurry). Lastly, we discuss probe detuning as a measure of sample thawing that does not require retuning the probe or using chemical shift thermometer compounds. Use of detuning tests and chemical shift thermometers with representative sample conditions makes it possible to maximize the efficiency of the NMR experiment while retaining a functional sample. PMID:22868258

The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warner, Lisa; Gjersing, Erica; Follett, Shelby E.

Ionic liquids have great potential in biological applications and biocatalysis, as some ionic liquids can stabilize proteins and enhance enzyme activity, while others have the opposite effect. However, on the molecular level, probing ionic liquid interactions with proteins, especially in solutions containing high concentrations of ionic liquids, has been challenging. In the present work the 13C, 15N-enriched GB1 model protein was used to demonstrate applicability of high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy to investigate ionic liquid-protein interactions. Effect of an ionic liquid (1-butyl-3-methylimidazolium bromide, [C 4-mim]Br) on GB1was studied over a wide range of the ionic liquid concentrations (0.6-3.5 M, whichmore » corresponds to 10-60% v/v). Interactions between GB1 and [C 4-mim]Br were observed from changes in the chemical shifts of the protein backbone as well as the changes in 15N ps-ns dynamics and rotational correlation times. Site-specific interactions between the protein and [C 4-mim]Br were assigned using 3D methods under HR-MAS conditions. Furthermore, HR-MAS NMR is a viable tool that could aid in elucidation of molecular mechanisms of ionic liquid-protein interactions.« less

[Bacterial synthesis, purification, and solubilization of transmembrane segments of ErbB family members].

PubMed

Goncharuk, M V; Shul'ga, A A; Ermoliuk, Ia S; Tkach, E N; Goncharuk, S A; Pustovalova, Iu E; Mineev, K S; Bocharov, É V; Maslennikov, I V; Arsen'ev, A S; Kirpichnikov, M P

2011-01-01

A family of epidermal growth factor receptors, ErbB, represents an important class of receptor tyrosine kinases, playing a leading role in cellular growth, development and differentiation. Transmembrane domains of these receptors transduce biochemical signals across plasma membrane via lateral homo- and heterodimerization. Relatively small size of complexes of ErbB transmembrane domains with detergents or lipids allows one to study their detailed spatial structure using three-dimensional heteronuclear high-resolution NMR spectroscopy. Here, we describe the effective expression system and purification procedure for preparative-scale production of transmembrane peptides from four representatives of ErbB family, ErbB1, ErbB2, ErbB3, ErbB4, for structural studies. The recombinant peptides were produced in Escherichia coli BL21(DE3)pLysS as C-terminal extensions of thioredoxin A. The fusion protein cleavage was accomplished with the light subunit of human enterokinase. Several (10-30) milligrams of purified isotope-labeled transmembrane peptides were isolated with the use of a simple and convenient procedure, which consists of consecutive steps of immobilized metal affinity chromatography and cation-exchange chromatography. The purified peptides were reconstituted in lipid/detergent environment (micelles or bicelles) and characterized using dynamic light scattering, CD and NMR spectroscopy. The data obtained indicate that the purified ErbB transmembrane peptides are suitable for structural and dynamic studies of their homo- and heterodimer complexes using high resolution NMR spectroscopy.