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Sample records for solution nmr caracterizacao

  1. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  2. Solution NMR Spectroscopy in Target-Based Drug Discovery.

    Science.gov (United States)

    Li, Yan; Kang, Congbao

    2017-08-23

    Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

  3. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  4. Dynamics of solutions and fluid mixtures by NMR

    International Nuclear Information System (INIS)

    Delpuech, J.J.

    1994-01-01

    After a short introduction to NMR spectroscopy, with a special emphasis on dynamical aspects, an overview on two fundamental aspects of molecular dynamics, NMR relaxation and its relationship with molecular reorientation, and magnetization transfer phenomena induced by molecular rate processes (dynamic NMR) is presented, followed by specific mechanisms of relaxation encountered in paramagnetic systems or with quadrupolar nuclei. Application fields are then reviewed: solvent exchange on metal ions with a variable pressure NMR approach, applications of field gradients in NMR, aggregation phenomena and micro-heterogeneity in surfactant solutions, polymers and biopolymers in the liquid state, liquid-like molecules in rigid matrices and in soft matter (swollen polymers and gels, fluids in and on inorganic materials, food)

  5. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  6. Molecular motion of micellar solutes: a 13C NMR relaxation study

    International Nuclear Information System (INIS)

    Stark, R.E.; Kasakevich, M.L.; Granger, J.W.

    1982-01-01

    A series of simple NMR relaxation experiments have been performed on nitrobenzene and aniline dissolved in the ionic detergents sodium dodecyl sulfate (SDS) and hexadecyltrimethylammonium bromide (CTAB). Using 13 C relaxation rates at various molecular sites, and comparing data obtained in organic media with those for micellar solutions, the viscosity at the solubilization site was estimated and a detailed picture of motional restrictions imposed by the micellar enviroment was derived. Viscosities of 8 to 17 cp indicate a rather fluid environment for solubilized nitrobenzene; both additives exhibit altered motional preferences in CTAB solutions only. As an aid in interpretation of the NMR data, quasi-elastic light scattering and other physical techniques have been used to evaluate the influence of organic solutes on micellar size and shape. The NMR methods are examined critically in terms of their general usefulness for studies of solubilization in detergent micelles. 48 references

  7. NMR studies of phase behaviour in polyacrylonitrile solutions

    International Nuclear Information System (INIS)

    Golightly, J.A.

    1998-10-01

    The aim of the thesis was to study the phase behaviour of aqueous polyacrylonitrile/NaSCN solutions using a variety of nuclear magnetic resonance techniques. Polyacrylonitrile (PAN) is the basis of the acrylic fibre industry, as such fibres contain at least 85% PAN. Despite this industrial importance, the available literature describing the phase behaviour of PAN in solution is far from comprehensive. Bulk 1 H NMR relaxation measurements were carried out over a wide range of concentrations and temperatures to probe the molecular dynamics of the PAN and water molecules. The relaxation data was found to be biexponential decay for all samples, the relative amplitudes of which were shown to be equal to the ratio of PAN protons to water protons. Both species were found to be in the regime of rapid molecular motion. Bulk 1 H NMR self diffusion measurements, using the PFGSTE technique, exhibited a bi-exponential decay of the echo amplitudes. By careful selection of the observation time, Δ, it was possible to independently probe the water and PAN translational diffusion. A background gradient, resulting from inhomogeneities of the magnetic field, complicated the analysis of the data and a novel polynomial least squares fitting procedure was devised to overcome this effect. The measured attenuation of the water diffusion coefficients (D∼10 -6 -10 -5 cm 2 s -1 ) with increasing PAN volume fraction was modelled according to various theories, including free volume and scaling laws. The study of the PAN diffusion coefficient (D∼10 -7 -10 -6 cm 2 s -1 ) was limited by the experimental constraints of the NMR spectrometer. A 1 H NMR one-dimensional imaging technique was used to study the non-solvent induced phase separation (coagulation) of a PAN solution. The time dependence of the measured profiles allowed observation of the coagulation process. A diffusion model was developed to fit the experimental data using a semi-infinite diffusion framework. The fitting parameters

  8. Probing Spin Crossover in a Solution by Paramagnetic NMR Spectroscopy.

    Science.gov (United States)

    Pavlov, Alexander A; Denisov, Gleb L; Kiskin, Mikhail A; Nelyubina, Yulia V; Novikov, Valentin V

    2017-12-18

    Spin transitions in spin-crossover compounds are now routinely studied in the solid state by magnetometry; however, only a few methods exist for studies in solution. The currently used Evans method, which relies on NMR spectroscopy to measure the magnetic susceptibility, requires the availability of a very pure sample of the paramagnetic compound and its exact concentration. To overcome these limitations, we propose an alternative NMR-based technique for evaluating spin-state populations by only using the chemical shifts of a spin-crossover compound; those can be routinely obtained for a solution that contains unknown impurities and paramagnetic admixtures or is contaminated otherwise.

  9. NMR and rotational angles in solution conformation of polypeptides

    Science.gov (United States)

    Bystrov, V. F.

    1985-01-01

    Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

  10. High resolution NMR study of cellulose in solid state and in solution

    International Nuclear Information System (INIS)

    Saint-Germain, Jean

    1983-01-01

    This research thesis reports the study of native cellulose (cotton) and wood by nuclear magnetic resonance (NMR). As far as the cotton spectrum is concerned, the author assigned resonances which more specifically corresponded to amorphous or crystalline areas. Wood was studied in its bulk condition, and resonances have been determined for the different wood components. The behaviour of cellulose in solution in a solvent has been studied by liquid high resolution NMR. The solvation mechanism has been determined and a study of model components of the macromolecule allowed a conformational study of cellulose in this solvent to be performed. Bi-dimensional NMR and longitudinal relaxation time measurements highlighted the existence of an intramolecular hydrogen bond in the cellulose in solution [fr

  11. NMR study of thermoresponsive block copolymer in aqueous solution

    Czech Academy of Sciences Publication Activity Database

    Spěváček, Jiří; Konefal, Rafal; Čadová, Eva

    2016-01-01

    Roč. 217, č. 12 (2016), s. 1370-1375 ISSN 1022-1352 R&D Projects: GA ČR(CZ) GA15-13853S Institutional support: RVO:61389013 Keywords : aqueous solutions * NMR * NOESY Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.500, year: 2016

  12. Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, Alexander N., E-mail: ovolkov@vub.ac.be; Nuland, Nico A. J. van [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)

    2013-07-15

    Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.

  13. Solution structures of α-conotoxin G1 determined by two-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    Pardi, A.; Galdes, A.; Florance, J.; Maniconte, D.

    1989-01-01

    Two-dimensional NMR data have been used to generate solution structures of α-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro 5 and Arg 9 . The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins

  14. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology.

    Science.gov (United States)

    Horst, Reto; Wüthrich, Kurt

    2015-07-20

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [ 2 H, 15 N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al ., 2013). 2D [ 15 N, 1 H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

  15. Characterization of natural bentonite by NMR; Caracterizacao de bentonitas naturais por ressonancia magnetica nuclear

    Energy Technology Data Exchange (ETDEWEB)

    Leite, Sidnei Q.M.; Dieguez, Lidia C [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia; Menezes, Sonia M.C. [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas; San Gil, Rosane A.S. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Quimica

    1994-12-31

    Solid state NMR as well as several other instrumental chemical analysis techniques were used in order to characterize two natural occurring bentonite. The methodology is described. The NMR spectra, together with the other used techniques suggest that the observed differences are due to iron inclusions in tetrahedral and octahedral sites 5 refs., 3 figs., 5 tabs.

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

    Science.gov (United States)

    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/...

  17. Gravity-driven pH adjustment for site-specific protein pKa measurement by solution-state NMR

    Science.gov (United States)

    Li, Wei

    2017-12-01

    To automate pH adjustment in site-specific protein pKa measurement by solution-state NMR, I present a funnel with two caps for the standard 5 mm NMR tube. The novelty of this simple-to-build and inexpensive apparatus is that it allows automatic gravity-driven pH adjustment within the magnet, and consequently results in a fully automated NMR-monitored pH titration without any hardware modification on the NMR spectrometer.

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

    Science.gov (United States)

    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...

  19. Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR Methodology

    Directory of Open Access Journals (Sweden)

    Run-Cang Sun

    2013-01-01

    Full Text Available The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA, nitrobenzene oxidation (NBO, and derivatization followed by reductive cleavage (DFRC. Recent advances in nuclear magnetic resonance (NMR technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ, as well as their applications are reviewed.

  20. Characterization of polyurethane/organophilic montmorillonite nanocomposites by low field NMR; Caracterizacao de nanocompositos de poliuretano/montmorilonita organofilica por RMN de baixo campo

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Marcos Anacleto da [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Laboratorio de Nanocompositos Polimericos; Tavares, Maria I.B.; Nascimento, Suelen A.M.; Rodrigues, Elton J. da R [Universidade Federal do Rio de Janeiro (NUCAT/PEQ/COPPE/UFRJ), RJ (Brazil). Laboratorio de Nanocompositos Polimericos

    2012-07-01

    Polyurethanes are important and versatile materials, mainly due to some of their properties, such as high resistance to abrasion and tearing, excellent absorption of mechanical shocks and good flexibility and elasticity. However, they have some drawbacks as well, such as low thermal stability and barrier properties. To overcome these disadvantages, various studies have been conducted involving organophilic polyurethane/montmorillonite nanocomposites. The investigation of the structure of polyurethane/clay nanocomposites has mainly been done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). In this work, PU/clay nanocomposite films obtained by solution intercalation were studied. The nanocomposites were characterized by XRD and low-field nuclear magnetic resonance (LF-NMR). The LF-NMR measurements, with determination of the spin-lattice relaxation time of the hydrogen nucleus, supplied important information about the molecular dynamics of these nanocomposites. The X-ray diffraction measurements validated the results found by NMR. The thermal stability of the material was also determined by thermogravimetric analysis (TGA) under an inert atmosphere. A slight improvement in this stability was observed in the nanocomposite in comparison with polyurethane (author)

  1. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

  2. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution

    DEFF Research Database (Denmark)

    Eriksen, Janus J.; Olsen, Jógvan Magnus H.; Aidas, Kestutis

    2011-01-01

    to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations......In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...

  3. NMR 11B, 19F of hydroxofluoroborate solutions in acetic and peracetic acids

    International Nuclear Information System (INIS)

    Shchetinina, G.P.; Brovkina, O.V.; Chernyshov, B.N.

    1985-01-01

    Hydroxofluoroborate solutions in acetic and peracetic acids are studied by the 11 B, 19 F NMR method. The reactions of substitutions of acetate- and peracetate ions for nucleophilic hydroxogroups with the formation of the respective complexes are shown to occur in these solutions, with monodentate coordination of BF 3 CH 3 COO - - and BF 3 CH 3 COOO - - groups being accomplished in this case

  4. Optimized bacterial expression and purification of the c-Src catalytic domain for solution NMR studies

    International Nuclear Information System (INIS)

    Piserchio, Andrea; Ghose, Ranajeet; Cowburn, David

    2009-01-01

    Progression of a host of human cancers is associated with elevated levels of expression and catalytic activity of the Src family of tyrosine kinases (SFKs), making them key therapeutic targets. Even with the availability of multiple crystal structures of active and inactive forms of the SFK catalytic domain (CD), a complete understanding of its catalytic regulation is unavailable. Also unavailable are atomic or near-atomic resolution information about their interactions, often weak or transient, with regulating phosphatases and downstream targets. Solution NMR, the biophysical method best suited to tackle this problem, was previously hindered by difficulties in bacterial expression and purification of sufficient quantities of soluble, properly folded protein for economically viable labeling with NMR-active isotopes. Through a choice of optimal constructs, co-expression with chaperones and optimization of the purification protocol, we have achieved the ability to bacterially produce large quantities of the isotopically-labeled CD of c-Src, the prototypical SFK, and of its activating Tyr-phosphorylated form. All constructs produce excellent spectra allowing solution NMR studies of this family in an efficient manner

  5. NMR spectrometric assay for determining enzymatic hydrolysis of β-lactam antibiotics with bacteria in aqueous solution

    International Nuclear Information System (INIS)

    O'hara, K.; Shiomi, Y.; Kono, M.

    1984-01-01

    An application of a nuclear magnetic resonance (NMR) spectrometer for the measurement of β-lactamase activity in clinical material containing bacteria is presented. By means of proton ( 1 H)-NMR, it was easy to measure quantitatively β-lactamase activity in human bacteriuria, without performing any such pretreatment as isolation of bacteria or extraction of crude enzymes and without preparing special reagents for the detection. This is the first report on the application of 1 H-NMR analysis of structural changes for determining hydrolysis of β-lactam antibiotics with β-lactamase-producing bacteria in aqueous solution. (Auth.)

  6. Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins

    International Nuclear Information System (INIS)

    Kucharska, Iga; Edrington, Thomas C.; Liang, Binyong; Tamm, Lukas K.

    2015-01-01

    Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore, there is a need to explore alternative more bilayer-like media to mimic the natural environment of membrane proteins. Lipid bicelles and lipid nanodiscs have emerged as two alternative membrane mimetics that are compatible with solution NMR spectroscopy. Here, we have conducted a comprehensive comparison of the physical and spectroscopic behavior of two outer membrane proteins from Pseudomonas aeruginosa, OprG and OprH, in lipid micelles, bicelles, and nanodiscs of five different sizes. Bicelles stabilized with a fraction of negatively charged lipids yielded spectra of almost comparable quality as in the best micellar solutions and the secondary structures were found to be almost indistinguishable in the two environments. Of the five nanodiscs tested, nanodiscs assembled from MSP1D1ΔH5 performed the best with both proteins in terms of sample stability and spectral resolution. Even in these optimal nanodiscs some broad signals from the membrane embedded barrel were severely overlapped with sharp signals from the flexible loops making their assignments difficult. A mutant OprH that had two of the flexible loops truncated yielded very promising spectra for further structural and dynamical analysis in MSP1D1ΔH5 nanodiscs

  7. Solution NMR characterization of Sgf73(1-104) indicates that Zn ion is required to stabilize zinc finger motif

    International Nuclear Information System (INIS)

    Lai, Chaohua; Wu, Minhao; Li, Pan; Shi, Chaowei; Tian, Changlin; Zang, Jianye

    2010-01-01

    Zinc finger motif contains a zinc ion coordinated by several conserved amino acid residues. Yeast Sgf73 protein was identified as a component of SAGA (Spt/Ada/Gcn5 acetyltransferase) multi-subunit complex and Sgf73 protein was known to contain two zinc finger motifs. Sgf73(1-104), containing the first zinc finger motif, was necessary to modulate the deubiquitinase activity of SAGA complex. Here, Sgf73(1-104) was over-expressed using bacterial expression system and purified for solution NMR (nuclear magnetic resonance) structural studies. Secondary structure and site-specific relaxation analysis of Sgf73(1-104) were achieved after solution NMR backbone assignment. Solution NMR and circular dichroism analysis of Sgf73(1-104) after zinc ion removal using chelation reagent EDTA (ethylene-diamine-tetraacetic acid) demonstrated that zinc ion was required to maintain stable conformation of the zinc finger motif.

  8. 13C and 17O NMR binding constant studies of uranyl carbonate complexes in near-neutral aqueous solution. Yucca Mountain Project Milestone Report 3351

    International Nuclear Information System (INIS)

    Clark, D.L.; Newton, T.W.; Palmer, P.D.; Zwick, B.D.

    1995-01-01

    Valuable structural information, much of it unavailable by other methods, can be obtained about complexes in solution through NMR spectroscopy. From chemical shift and intensity measurements of complexed species, NMR can serve as a species-specific structural probe for molecules in solution and can be used to validate thermodynamic constants used in geochemical modeling. Fourier-transform nuclear magnetic resonance (FT-NMR) spectroscopy has been employed to study the speciation of uranium(VI) ions in aqueous carbonate solutions as a function of pH, ionic strength, carbonate concentration, uranium concentration, and temperature. Carbon-13 and oxygen-17 NMR spectroscopy were used to monitor the fractions, and hence thermodynamic binding constants of two different uranyl species U0 2 (CO 3 ) 3 4- and (UO 2 ) 3 (CO 3 ) 6 6- in aqueous solution. Synthetic buffer solutions were prepared under the ionic strength conditions used in the NMR studies in order to obtain an accurate measure of the hydrogen ion concentration, and a discussion of pH = -log(a H + ) versus p[H] = -log[H+] is provided. It is shown that for quantitative studies, the quantity p[H] needs to be used. Fourteen uranium(VI) binding constants recommended by the OECD NEA literature review were corrected to the ionic strengths employed in the NMR study using specific ion interaction theory (SIT), and the predicted species distributions were compared with the actual species observed by multinuclear NMR. Agreement between observed and predicted stability fields is excellent. This establishes the utility of multinuclear NMR as a species-specific tool for the study of the actinide carbonate complexation constants, and serves as a means for validating the recommendations provided by the OECD NEA

  9. Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.; Myler, Peter J.

    2018-01-02

    Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.

  10. NMR and molecular dynamics of small solutes in liquid crystals

    International Nuclear Information System (INIS)

    Luyten, P.R.

    1984-01-01

    NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

  11. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy); Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Luchinat, Claudio, E-mail: garib@mrc-lmb.cam.ac.uk [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy)

    2014-04-01

    Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

  12. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

    International Nuclear Information System (INIS)

    Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N.; Luchinat, Claudio

    2014-01-01

    Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state

  13. Investigation of Sc(3) state in nonaqueous solutions by the 45Sc NMR method of high permission

    International Nuclear Information System (INIS)

    Buslaev, Yu.A.; Kirakosyan, G.A.; Tarasov, V.P.

    1980-01-01

    The ScCl 3 + CH 3 CN and ScCl 3 + KNCS + CH 3 CN solutions have been studied by a high-resolution NMR 45 Sc method. It has been estimated that in acetonitrile solutions, with competing ligands of Cl - and NCS - being available, hexacoordination Sc(3) complexes of various compositions are formed, and solvent molecules also take part in formation of the coordination sphere of scandium. Chemical shifts in NMR 45 Sc signals depend linearly on the number of chlor- or NCS - ions bound to scandium(3). This made it possible to determine the value of chemical shifts in signals of all 28 potential complexes formed in a system with three competing ligands

  14. Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

    Science.gov (United States)

    Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

    2014-04-21

    Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

  15. Investigation into state of phosphomolybdovanadic heteropolyacids in aqueous solutions by the NMR method

    International Nuclear Information System (INIS)

    Maksimovskaya, R.I.; Fedotov, M.A.; Mastikhin, V.M.; Kuznetsova, L.I.; Matveev, K.I.

    1978-01-01

    The methods of 31 P, 51 V, and 17 O NMR have been used for studying the solutions of phospho-molybdenum-vanadium heteropolyacids (HPA) with x=0,1,2,3 (HPA-x) and their mixture with changing concentration, acidity, temperature, and upon partial reduction for separating the lines corresponding to HPA with a certain x. It has been found that in aqueous solutions HPA is present as a mixture of HPA of different compositions; the relationship has been observed between chemical shifts of the lines and the solution acidity which is of a different character for HPA with different x. This allows to make a conclusion about the mechanism of HPA protonation

  16. NMR determination of chemically related metals in solution as a new method of inorganic analysis

    International Nuclear Information System (INIS)

    Fedorov, L.A.

    1989-01-01

    An NMR spectroscopic method for the determination of chemically related metals in solution is suggested. The metals are determined in complexes with specially selected polydentate ligands. Structural requirements to ligands, analytical properties and general limits of the application of the method are discussed. (orig.)

  17. Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin

    Science.gov (United States)

    De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.

    2017-05-01

    In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

  18. Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.

    Science.gov (United States)

    Takeda, Mitsuhiro; Chang, Chung-ke; Ikeya, Teppei; Güntert, Peter; Chang, Yuan-hsiang; Hsu, Yen-lan; Huang, Tai-huang; Kainosho, Masatsune

    2008-07-18

    The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.

  19. 33S NMR cryogenic probe for taurine detection

    Science.gov (United States)

    Hobo, Fumio; Takahashi, Masato; Maeda, Hideaki

    2009-03-01

    With the goal of a S33 nuclear magnetic resonance (NMR) probe applicable to in vivo NMR on taurine-biological samples, we have developed the S33 NMR cryogenic probe, which is applicable to taurine solutions. The NMR sensitivity gain relative to a conventional broadband probe is as large as 3.5. This work suggests that improvements in the preamplifier could allow NMR measurements on 100 μM taurine solutions, which is the level of sensitivity necessary for biological samples.

  20. 1H NMR investigation of self-association of vanillin in aqueous solution

    International Nuclear Information System (INIS)

    Bogdan, Mircea; Floare, Calin G; PIrnau, Adrian

    2009-01-01

    A self-association of vanillin have been studied by 1 H NMR spectroscopy using the analysis of proton chemical shifts changes in aqueous solution as a function of concentration. The experimental results have been analysed using indefinite non-cooperative and cooperative models of molecular self-association, enabling the determination of equilibrium constants, parameters of cooperativity and the limiting values of vanillin proton chemical shifts in the complex. It was found that the dimer formation creates energetically favourable conditions for subsequent molecular association.

  1. Direct NMR Monitoring of Phase Separation Behavior of Highly Supersaturated Nifedipine Solution Stabilized with Hypromellose Derivatives.

    Science.gov (United States)

    Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu

    2017-07-03

    We investigated the phase separation behavior and maintenance mechanism of the supersaturated state of poorly water-soluble nifedipine (NIF) in hypromellose (HPMC) derivative solutions. Highly supersaturated NIF formed NIF-rich nanodroplets through phase separation from aqueous solution containing HPMC derivative. Dissolvable NIF concentration in the bulk water phase was limited by the phase separation of NIF from the aqueous solution. HPMC derivatives stabilized the NIF-rich nanodroplets and maintained the NIF supersaturation with phase-separated NIF for several hours. The size of the NIF-rich phase was different depending on the HPMC derivatives dissolved in aqueous solution, although the droplet size had no correlation with the time for which NIF supersaturation was maintained without NIF crystallization. HPMC acetate and HPMC acetate succinate (HPMC-AS) effectively maintained the NIF supersaturation containing phase-separated NIF compared with HPMC. Furthermore, HPMC-AS stabilized NIF supersaturation more effectively in acidic conditions. Solution 1 H NMR measurements of NIF-supersaturated solution revealed that HPMC derivatives distributed into the NIF-rich phase during the phase separation of NIF from the aqueous solution. The hydrophobicity of HPMC derivative strongly affected its distribution into the NIF-rich phase. Moreover, the distribution of HPMC-AS into the NIF-rich phase was promoted at lower pH due to the lower aqueous solubility of HPMC-AS. The distribution of a large amount of HPMC derivatives into NIF-rich phase induced the strong inhibition of NIF crystallization from the NIF-rich phase. Polymer distribution into the drug-rich phase directly monitored by solution NMR technique can be a useful index for the stabilization efficiency of drug-supersaturated solution containing a drug-rich phase.

  2. A solution-state NMR approach to elucidating pMDI-wood bonding mechanisms in loblolly pine

    Science.gov (United States)

    Daniel Joseph Yelle

    2009-01-01

    Solution-state NMR spectroscopy is a powerful tool for unambiguously determining the existence or absence of covalent chemical bonds between wood components and adhesives. Finely ground wood cell wall material dissolves in a solvent system containing DMSO-d6 and NMI-d6, keeping wood component polymers intact and in a near-...

  3. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach

    Energy Technology Data Exchange (ETDEWEB)

    Sinnige, Tessa; Houben, Klaartje [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Pritisanac, Iva [Physical and Theoretical Chemistry Laboratory (United Kingdom); Renault, Marie [Institute of Pharmacology and Structural Biology (France); Boelens, Rolf; Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-04-15

    The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a “divide and conquer” approach in which we first obtained resonance assignments for BamA’s periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.

  4. 1H NMR visibility of mammalian glycogen in solution

    International Nuclear Information System (INIS)

    Zang, L.H.; Rothman, D.L.; Shulman, R.G.

    1990-01-01

    High-resolution 1 H NMR spectra of rabbit liver glycogen in 2 H 2 O were obtained at 500 MHz, and several resonances were assigned by comparison with the chemical shifts of α-linked diglucose molecules. The NMR relaxation times T 1 and T 2 of glycogen in 2 H 2 O were determined to be 1.1 and 0.029 s, respectively. The measured natural linewidth of the carbon-1 proton is in excellent agreement with that calculated from T 2 . The visibility measurements made by digesting glycogen and comparing glucose and glycogen signal intensities demonstrate that in spite of the very high molecular weight, all of the proton nuclei in glycogen contribute to the NMR spectrum. The result is not unexpected, since 100% NMR visibility was previously observed from the carbon nuclei of glycogen, due to the rapid intramolecular motions

  5. Assessment of preparation methods for organic phosphorus analysis in phosphorus-polluted Fe/Al-rich Haihe river sediments using solution 31P-NMR.

    Directory of Open Access Journals (Sweden)

    Wenqiang Zhang

    Full Text Available Fe/Al-rich river sediments that were highly polluted with phosphorus (P were used in tests to determine the optimum preparation techniques for measuring organic P (Po using solution (31P nuclear magnetic resonance spectroscopy ((31P-NMR. The optimum pre-treatment, extraction time, sediment to solution ratio and sodium hydroxide-ethylenediaminetetraacetic acid (NaOH-EDTA extractant solution composition were determined. The total P and Po recovery rates were higher from freeze- and air-dried samples than from fresh samples. An extraction time of 16 h was adequate for extracting Po, and a shorter or longer extraction time led to lower recoveries of total P and Po, or led to the degradation of Po. An ideal P recovery rate and good-quality NMR spectra were obtained at a sediment:solution ratio of 1:10, showing that this ratio is ideal for extracting Po. An extractant solution of 0.25 M NaOH and 50 mM EDTA was found to be more appropriate than either NaOH on its own, or a more concentrated NaOH-EDTA mixture for (31P-NMR analysis, as this combination minimized interference from paramagnetic ions and was appropriate for the detected range of Po concentrations. The most appropriate preparation method for Po analysis, therefore, was to extract the freeze-dried and ground sediment sample with a 0.25 M NaOH and 50 mM EDTA solution at a sediment:solution ratio of 1:10, for 16 h, by shaking. As lyophilization of the NaOH-EDTA extracts proved to be an optimal pre-concentration method for Po analysis in the river sediment, the extract was lyophilized as soon as possible, and analyzed by (31P-NMR.

  6. Characterization of functional polymers by NMR; Caracterizacao de polimeros funcionalizados por ressonancia magnetica nuclear

    Energy Technology Data Exchange (ETDEWEB)

    Neto, Oscar H.S. A.S.; San Gil, Rosane A.S.; Nakayama, T; Costa Neto, Claudio [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Quimica

    1994-12-31

    Several synthetic polymers are used in the chemical analysis of complexes mixtures aiming to extract certain specific functional groups for further identification. This work describes the utilization of NMR in the characterization of one of the above mentioned compounds which will be used as reagent for the synthesis of another compound of the same type, which will be further used in the chemical analysis of alcohols and phenols. The methodology is described. The results are described and discussed 4 refs., 2 figs.

  7. Structural characterization of alkyl-benzene fractions by carbon-13, hydrogen-1, NMR; Caracterizacao estrutural de fracoes de alquilbenzenos por RMN de {sup 13} C e de {sup 1} H

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz, Jorge F. de; San Gil, Rosane A.S. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Quimica; Marques, Rosana G.G. [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas

    1994-12-31

    This work presents studies concerning the utilization of carbon-13, hydrogen-1, NMR as chemical analytical technique to evaluate molecular characteristics of alkyl-benzene fractions. The methodology is described, including standards solutions and their preparations, as well as the experimental techniques used. The results are presented and discussed 2 refs., 4 tabs.

  8. 1H NMR analysis of the heteroassociation of antitumor antibiotics novotrone and actinomycin D in aqueous solution

    International Nuclear Information System (INIS)

    Evstigneev, M.P.; Rozvadovskaya, A.O.; Kisurkin, D.V.; Dehvis, D.B.; Veselkov, A.N.

    2004-01-01

    The heteroassociation of antitumor antibiotics novotrone (NOV) and actinomycin D (AMD) in aqueous solution has been studied by one- and two-dimensional 1 H-NMR spectroscopy (500 MHz) in order to elucidate the molecular mechanism of the action of antibiotics in combination. It has been shown that heterocomplexes become predominant in the mixed solution at r > 12. It is concluded that aromatic antibiotics (e. g. novotrone and actinomycin D) may form energetically stable heteroassociation complexes in aqueous solution and hence affect their medical-biological activity

  9. NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia.

    Science.gov (United States)

    Moberg, Per; Nilsson, Stefan; Ståhl, Annelie; Eriksson, Anna-Carin; Glaser, Elzbieta; Mäler, Lena

    2004-03-05

    We have isolated, characterized and determined the three-dimensional NMR solution structure of the presequence of ATPsynthase F1beta subunit from Nicotiana plumbaginifolia. A general method for purification of presequences is presented. The method is based on overexpression of a mutant precursor containing a methionine residue introduced at the processing site, followed by CNBr-cleavage and purification of the presequence on a cation-exchange column. The F1beta presequence, 53 amino acid residues long, retained its native properties as evidenced by inhibition of in vitro mitochondrial import and processing at micromolar concentrations. CD spectroscopy revealed that the F1beta presequence formed an alpha-helical structure in membrane mimetic environments such as SDS and DPC micelles (approximately 50% alpha-helix), and in acidic phospholipid bicelles (approximately 60% alpha-helix). The NMR solution structure of the F1beta presequence in SDS micelles was determined on the basis of 518 distance and 21 torsion angle constraints. The structure was found to contain two helices, an N-terminal amphipathic alpha-helix (residues 4-15) and a C-terminal alpha-helix (residues 43-53), separated by a largely unstructured 27 residue long internal domain. The N-terminal amphipathic alpha-helix forms the putative Tom20 receptor binding site, whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site.

  10. Two dimensional solid state NMR

    International Nuclear Information System (INIS)

    Kentgens, A.P.M.

    1987-01-01

    This thesis illustrates, by discussing some existing and newly developed 2D solid state experiments, that two-dimensional NMR of solids is a useful and important extension of NMR techniques. Chapter 1 gives an overview of spin interactions and averaging techniques important in solid state NMR. As 2D NMR is already an established technique in solutions, only the basics of two dimensional NMR are presented in chapter 2, with an emphasis on the aspects important for solid spectra. The following chapters discuss the theoretical background and applications of specific 2D solid state experiments. An application of 2D-J resolved NMR, analogous to J-resolved spectroscopy in solutions, to natural rubber is given in chapter 3. In chapter 4 the anisotropic chemical shift is mapped out against the heteronuclear dipolar interaction to obtain information about the orientation of the shielding tensor in poly-(oxymethylene). Chapter 5 concentrates on the study of super-slow molecular motions in polymers using a variant of the 2D exchange experiment developed by us. Finally chapter 6 discusses a new experiment, 2D nutation NMR, which makes it possible to study the quadrupole interaction of half-integer spins. 230 refs.; 48 figs.; 8 tabs

  11. {sup 1}H NMR investigation of self-association of vanillin in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Bogdan, Mircea; Floare, Calin G; PIrnau, Adrian, E-mail: mircea.bogdan@itim-cj.r [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania)

    2009-08-01

    A self-association of vanillin have been studied by {sup 1}H NMR spectroscopy using the analysis of proton chemical shifts changes in aqueous solution as a function of concentration. The experimental results have been analysed using indefinite non-cooperative and cooperative models of molecular self-association, enabling the determination of equilibrium constants, parameters of cooperativity and the limiting values of vanillin proton chemical shifts in the complex. It was found that the dimer formation creates energetically favourable conditions for subsequent molecular association.

  12. Acid-base equilibrium in aqueous solutions of 1,3-dimethylbarbituric acid as studied by 13C NMR spectroscopy

    Science.gov (United States)

    Gryff-Keller, A.; Kraska-Dziadecka, A.

    2011-12-01

    13C NMR spectra of 1,3-dimethylbarbituric acid in aqueous solutions of various acidities and for various solute concentrations have been recorded and interpreted. The spectra recorded at pH = 2 and below contain the signals of the neutral solute molecule exclusively, while the ones recorded at pH = 7 and above only the signals of the appropriate anion, which has been confirmed by theoretical GIAO-DFT calculations. The signals in the spectra recorded for solutions of pH pH variation have been observed for the parent barbituric acid.

  13. NMR and superfluidity of 3He in 3He-4He solutions

    International Nuclear Information System (INIS)

    Ivanova, K.D.; Mejerovich, A.Eh.

    1986-01-01

    Two possibilities of determining the superfluid transition temperature for 3 He in a 3 He- 4 He solution by the NMR technique are discussed. One of the methods consists in measuring the spin diffusion coefficient in weak magnetic fields at ultralow temperatures, and the other in measuring the ratio of the spin diffusion coefficient to the spin wave absorption coefficient at not very low temperatures. The transition temperature is estimated on the basis of the available experimental data. The effect of the superfluid transition in a system of 3 He quasiparticles on the propagation of transverse spin waves and longitudinal spin-sound oscillations in 3 He- 4 He solutions is studied. It is shown that there is a range of weak magnetic field intensities restricted from both sides in which the propagation of weakly damped spin-sound waves is possible

  14. From proton nuclear magnetic resonance spectra to pH. Assessment of {sup 1}H NMR pH indicator compound set for deuterium oxide solutions

    Energy Technology Data Exchange (ETDEWEB)

    Tynkkynen, Tuulia, E-mail: tuulia.tynkkynen@uku.fi [Laboratory of Chemistry, Department of Biosciences, University of Kuopio, PO Box 1627, 70211 Kuopio (Finland); Tiainen, Mika; Soininen, Pasi; Laatikainen, Reino [Laboratory of Chemistry, Department of Biosciences, University of Kuopio, PO Box 1627, 70211 Kuopio (Finland)

    2009-08-19

    In this study, a protocol for pH determination from D{sub 2}O samples using {sup 1}H NMR pH indicator compounds was developed and assessed by exploring the pH-dependency of 13 compounds giving pH-dependent {sup 1}H NMR signals. The indicators cover the pH range from pH* 0 to 7.2. Equations to transform the indicator chemical shifts to pH estimates are given here for acetic acid, formic acid, chloroacetic acid, dichloroacetic acid, creatine, creatinine, glycine, histidine, 1,2,4-triazole, and TSP (2,2,3,3-tetradeutero-3-(trimethylsilyl)-propionic acid). To characterize the method in presence of typical solutes, the effects of common metabolites, albumin and ionic strength were also evaluated. For the ionic strengths, the effects were also modelled. The experiments showed that the use of pH sensitive {sup 1}H NMR chemical shifts allows the pH determination of typical metabolite solutions with accuracy of 0.01-0.05 pH units. Also, when the ionic strength is known with accuracy better than 0.1 mol dm{sup -3} and the solute concentrations are low, pH{sub nmr}{sup *} (the NMR estimate of pH) can be assumed to be within 0.05 pH units from potentiometrically determined pH.

  15. IR and NMR studies of hierarchical material obtained by the treatment of zeolite Y by ammonia solution

    Science.gov (United States)

    Gackowski, Mariusz; Kuterasiński, Łukasz; Podobiński, Jerzy; Sulikowski, Bogdan; Datka, Jerzy

    2018-03-01

    Ammonia treatment of ultrastable zeolite Y has a great impact on its features. XRD showed a partial loss of crystallinity coupled with a loss of long-distance zeolite ordering. However, a typical short-range zeolite ordering, in the light of 29Si NMR studies, was largely preserved. 27Al MAS NMR spectra evidenced that most of Al was located in zeolitic tetrahedral positions, but some of them adopted a distorted configuration. Evolution of zeolites acidity was followed quantitatively by using IR. In particular, such studies revealed the presence of strongly acidic Sisbnd OHsbnd Al groups. IR studies suggest also heterogeneity of these OH groups. The heterogeneity of Sisbnd OHsbnd Al groups was a consequence of the less ordered structure of zeolites treated with ammonia solutions. It was also found that the treatment with ammonia solutions yields hierarchical material. The samples revealed promising catalytic properties in the liquid phase isomerization of α-pinene. Zeolites desilicated with ammonia may constitute an inexpensive route yielding viable hierarchical catalysts.

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

    Science.gov (United States)

    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...

  17. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state 13C NMR and solution 31P NMR spectroscopy

    International Nuclear Information System (INIS)

    Liu, Shasha; Zhu, Yuanrong; Meng, Wei; He, Zhongqi; Feng, Weiying; Zhang, Chen; Giesy, John P.

    2016-01-01

    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state 13 C NMR and solution 31 P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O–C–O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH 3 and COO/N–C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH 3 and COO/N–C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes. - Highlights: • WEOM derived from aquatic macrophytes was characterized. • C and P in WEOM were characterized by solid 13 C NMR and solution 31 P NMR. • Degradation and transformation of macrophyte-derived C and P were investigated. • Macrophyte-derived WEOM are important source for bioavailable nutrients in lakes.

  18. Characterization of derivates of carbo-anhydride by NMR; Caracterizacao de derivados do anidrido carbico por RMN

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Marcos Pery Amaral [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil); Bergter, Lothar [Cia. Souza Cruz, Rio de Janeiro, RJ (Brazil); Seidl, Peter Rudolf [Centro de Tecnologia Mineral, Rio de Janeiro, RJ (Brazil)

    1994-12-31

    The term molecular recognition may be applied to several phenomena of different complexities. The compounds which work as blockers or acceptors in this process are generally complexes with functional groups positioned in specific positions. This work presents the NMR characterization of carbo-anhydride derivates which are important in the preparation of synthetic acceptors 2 figs.

  19. Analytical solution to the coupled evolution of multidimensional NMR data

    International Nuclear Information System (INIS)

    Mueller, Geoffrey A.

    2009-01-01

    A substantial time savings in the collection of multidimensional NMR data can be achieved by coupling the evolution of nuclei in the indirect dimensions. In order to save time, the sampling of the indirect dimensions is inherently incomplete. Therefore, many algorithms and samplings schemes have been developed aimed at separating the coevolved frequencies into analyzable data with limited artifacts. This paper extends the use of circulant matrices to describe coupled evolution with convolutions. By understanding the data in terms of convolutions, there is an exact solution to the inversion problem of extracting the orthogonal vectors from the coupled dimensions. Previously, this inversion problem has been solved using peak coordinates extracted from spectra. In contrast, the method described here uses spectra directly. This solution suggests a simple sampling scheme of collecting N orthogonal spectra, and N + 1 projections at specific projection angles, however, the theory developed can be extended generally to arbitrary projection angles. The circulant matrix methodology is demonstrated for simulated and real data. Further, an algorithm for separating overlapped signals in the detected dimension is presented. The algorithm involves the forward calculation of the coupled spectra from the orthogonal spectra, followed by back calculation of the orthogonal spectra from the coupled spectra, thus permitting rigorous cross-validation. This algorithm is shown to be robust in that erroneous solutions give rise to large artifacts

  20. NMR study of Albemoschus esculentus characterization

    International Nuclear Information System (INIS)

    Bathista, A.L.B.S; Silva, E.O.; Nogueira, Jose de S.; Tavares, M.I.B.

    2001-01-01

    The investigation of the main compounds presented in the Albemoschus esculentus has been carried out employing nuclear magnetic resonance spectroscopy (NMR), using solution and solid state NMR when it one was necessary. The evaluation of NMR data allowed us to characterize the main type of components presented in this kind of sample. It was necessary to use a total information from solid state NMR and also the solution response. From these information we could get that four main components were presented in this sample. One in the shell, that is cellulose, another one between the shell and seeds that is a polysaccharide and in the seed two components were found one is a starch and the second one is an oil, a triacylglycerol. These components are responsible by its physical chemistry properties. (author)

  1. NMR studies of the solution conformation and dynamics of the tyrocidine peptide antibiotics

    International Nuclear Information System (INIS)

    Zhou, N.

    1985-01-01

    The tyrocidine B and tyrocidine C 1 H NMR spectra in DMSO-d 6 were assigned by using 2D 1 H- 1 H correlation spectroscopy and 1D double resonance experiments. Based on the proton chemical shifts, 3 J/sub NH-Nα/ coupling constants, the chemical shift temperature dependence, and 1D and 2D 1 H- 1 H NOE values, a backbone conformation consisting of an anti-parallel β-pleated sheet, a type I β-turn and a type II' β-turn was suggested for both tyrocidines B and C. Seven out of ten side chains were determined to exist predominantly in one classical Chi 1 rotamer; while the residues Val 1 and Leu 3 had two Chi 1 rotamers which were significantly populated. Chi 2 angles were determined for residues Phe 4 , Trp 6 , DPhe 7 (D Trp 7 ) and Asn 8 . The natural abundance 13 C spectra of tyrocidine B and tyrocidine C were assigned by using 1 H- 13 C correlation spectroscopy. A study of the effect of soluble paramagnetic nitroxide compounds on tyrocidine A proton T 1 values were performed which confirmed the proposed tyrocidine A conformation. It also proved that these nitroxide compounds are very useful in studying proton solvent exposure, and therefore in delineating hydrogen bonding. A proton NMR study of the opioid peptide dynorphin-(1-13) in aqueous solution was reported which was consistent with a non-ordered molecule in the solution

  2. Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

    Science.gov (United States)

    Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

    2010-06-15

    Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution.

  3. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

    International Nuclear Information System (INIS)

    Oktaviani, Nur Alia; Risør, Michael W.; Lee, Young-Ho; Megens, Rik P.; Jong, Djurre H. de; Otten, Renee; Scheek, Ruud M.; Enghild, Jan J.; Nielsen, Niels Chr.; Ikegami, Takahisa; Mulder, Frans A. A.

    2015-01-01

    Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in ‘proton-less’ NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α 1 -antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h

  4. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

    Energy Technology Data Exchange (ETDEWEB)

    Oktaviani, Nur Alia [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Risør, Michael W. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Lee, Young-Ho [Osaka University, Institute for Protein Research (Japan); Megens, Rik P. [University of Groningen, Stratingh Institute for Chemistry (Netherlands); Jong, Djurre H. de; Otten, Renee; Scheek, Ruud M. [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Enghild, Jan J. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics (Denmark); Nielsen, Niels Chr. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Ikegami, Takahisa [Yokohama City University, Graduate School of Medical Life Science (Japan); Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands)

    2015-06-15

    Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T{sub 1} relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T{sub 1} values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in ‘proton-less’ NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α{sub 1}-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

  5. Complexation of rhodium(II) tetracarboxylates with aliphatic diamines in solution: 1H and 13C NMR and DFT investigations.

    Science.gov (United States)

    Jaźwiński, Jarosław; Sadlej, Agnieszka

    2013-10-01

    The complexation of rhodium(II) tetraacetate, tetrakistrifluoroaceate and tetrakisoctanoate with a set of diamines (ethane-1,diamine, propane-1,3-diamine and nonane-1,9-diamine) and their N,N'-dimethyl and N,N,N',N'-tetramethyl derivatives in chloroform solution has been investigated by (1) H and (13) C NMR spectroscopy and density functional theory (DFT) modelling. A combination of two bifunctional reagents, diamines and rhodium(II) tetracarboxylates, yielded insoluble coordination polymers as main products of complexation and various adducts in the solution, being in equilibrium with insoluble material. All diamines initially formed the 2 : 1 (blue), (1 : 1)n oligomeric (red) and 1 : 2 (red) axial adducts in solution, depending on the reagents' molar ratio. Adducts of primary and secondary diamines decomposed in the presence of ligand excess, the former via unstable equatorial complexes. The complexation of secondary diamines slowed down the inversion at nitrogen atoms in NH(CH3 ) functional groups and resulted in the formation of nitrogenous stereogenic centres, detectable by NMR. Axial adducts of tertiary diamines appeared to be relatively stable. The presence of long aliphatic chains in molecules (adducts of nonane-1,9-diamines or rhodium(II) tetrakisoctanoate) increased adduct solubility. Hypothetical structures of the equatorial adduct of rhodium(II) tetraacetate with ethane-1,2-diamine and their NMR parameters were explored by means of DFT calculations. Copyright © 2013 John Wiley & Sons, Ltd.

  6. 1D and 2D NMR Spectroscopy of Bonding Interactions within Stable and Phase-Separating Organic Electrolyte-Cellulose Solutions.

    Science.gov (United States)

    Clough, Matthew T; Farès, Christophe; Rinaldi, Roberto

    2017-09-11

    Organic electrolyte solutions (i.e. mixtures containing an ionic liquid and a polar, molecular co-solvent) are highly versatile solvents for cellulose. However, the underlying solvent-solvent and solvent-solute interactions are not yet fully understood. Herein, mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate, the co-solvent 1,3-dimethyl-2-imidazolidinone, and cellulose are investigated using 1D and 2D NMR spectroscopy. The use of a triply- 13 C-labelled ionic liquid enhances the signal-to-noise ratio for 13 C NMR spectroscopy, enabling changes in bonding interactions to be accurately pinpointed. Current observations reveal an additional degree of complexity regarding the distinct roles of cation, anion, and co-solvent toward maintaining cellulose solubility and phase stability. Unexpectedly, the interactions between the dialkylimidazolium ring C 2 -H substituent and cellulose become more pronounced at high temperatures, counteracted by a net weakening of acetate-cellulose interactions. Moreover, for mixtures that exhibit critical solution behavior, phase separation is accompanied by the apparent recombination of cation-anion pairs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Combined solid state and solution NMR studies of α,ε-15N labeled bovine rhodopsin

    International Nuclear Information System (INIS)

    Werner, Karla; Lehner, Ines; Dhiman, Harpreet Kaur; Richter, Christian; Glaubitz, Clemens; Schwalbe, Harald; Klein-Seetharaman, Judith; Khorana, H. Gobind

    2007-01-01

    Rhodopsin is the visual pigment of the vertebrate rod photoreceptor cell and is the only member of the G protein coupled receptor family for which a crystal structure is available. Towards the study of dynamics in rhodopsin, we report NMR-spectroscopic investigations of α,ε- 15 N-tryptophan labeled rhodopsin in detergent micelles and reconstituted in phospholipids. Using a combination of solid state 13 C, 15 N-REDOR and HETCOR experiments of all possible 13 C' i-1 carbonyl/ 15 N i -tryptophan isotope labeled amide pairs, and H/D exchange 1 H, 15 N-HSQC experiments conducted in solution, we assigned chemical shifts to all five rhodopsin tryptophan backbone 15 N nuclei and partially to their bound protons. 1 H, 15 N chemical shift assignment was achieved for indole side chains of Trp35 1.30 and Trp175 4.65 . 15 N chemical shifts were found to be similar when comparing those obtained in the native like reconstituted lipid environment and those obtained in detergent micelles for all tryptophans except Trp175 4.65 at the membrane interface. The results suggest that the integrated solution and solid state NMR approach presented provides highly complementary information in the study of structure and dynamics of large membrane proteins like rhodopsin

  8. (S)Pinning down protein interactions by NMR

    DEFF Research Database (Denmark)

    Teilum, Kaare; Kunze, Micha Ben Achim; Erlendsson, Simon

    2017-01-01

    Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions...... all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative...... descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background...

  9. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state {sup 13}C NMR and solution {sup 31}P NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Shasha [College of Water Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Zhu, Yuanrong, E-mail: zhuyuanrong07@mails.ucas.ac.cn [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Meng, Wei, E-mail: mengwei@craes.org.cn [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); He, Zhongqi [USDA-ARS Southern Regional Research Center, 1100 Robert E Lee Blvd, New Orleans, LA 70124 (United States); Feng, Weiying [College of Water Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Zhang, Chen [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Giesy, John P. [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Department of Biomedical and Veterinary Biosciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan (Canada)

    2016-02-01

    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state {sup 13}C NMR and solution {sup 31}P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O–C–O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH{sub 3} and COO/N–C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH{sub 3} and COO/N–C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes. - Highlights: • WEOM derived from aquatic macrophytes was characterized. • C and P in WEOM were characterized by solid {sup 13}C NMR and solution {sup 31}P NMR. • Degradation and transformation of macrophyte-derived C and P were investigated. • Macrophyte-derived WEOM are important source for bioavailable nutrients in lakes.

  10. 1H NMR quantification in very dilute toxin solutions: application to anatoxin-a analysis.

    Science.gov (United States)

    Dagnino, Denise; Schripsema, Jan

    2005-08-01

    A complete procedure is described for the extraction, detection and quantification of anatoxin-a in biological samples. Anatoxin-a is extracted from biomass by a routine acid base extraction. The extract is analysed by GC-MS, without the need of derivatization, with a detection limit of 0.5 ng. A method was developed for the accurate quantification of anatoxin-a in the standard solution to be used for the calibration of the GC analysis. 1H NMR allowed the accurate quantification of microgram quantities of anatoxin-a. The accurate quantification of compounds in standard solutions is rarely discussed, but for compounds like anatoxin-a (toxins with prices in the range of a million dollar a gram), of which generally only milligram quantities or less are available, this factor in the quantitative analysis is certainly not trivial. The method that was developed can easily be adapted for the accurate quantification of other toxins in very dilute solutions.

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

    Science.gov (United States)

    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...

  12. Identification of aquatically available carbon from algae through solution-state NMR of whole (13)C-labelled cells.

    Science.gov (United States)

    Akhter, Mohammad; Dutta Majumdar, Rudraksha; Fortier-McGill, Blythe; Soong, Ronald; Liaghati-Mobarhan, Yalda; Simpson, Myrna; Arhonditsis, George; Schmidt, Sebastian; Heumann, Hermann; Simpson, André J

    2016-06-01

    Green algae and cyanobacteria are primary producers with profound impact on food web functioning. Both represent key carbon sources and sinks in the aquatic environment, helping modulate the dissolved organic matter balance and representing a potential biofuel source. Underlying the impact of algae and cyanobacteria on an ecosystem level is their molecular composition. Herein, intact (13)C-labelled whole cell suspensions of Chlamydomonas reinhardtii, Chlorella vulgaris and Synechocystis were studied using a variety of 1D and 2D (1)H/(13)C solution-state nuclear magnetic resonance (NMR) spectroscopic experiments. Solution-state NMR spectroscopy of whole cell suspensions is particularly relevant as it identifies species that are mobile (dissolved or dynamic gels), 'aquatically available' and directly contribute to the aquatic carbon pool upon lysis, death or become a readily available food source on consumption. In this study, a wide range of metabolites and structural components were identified within the whole cell suspensions. In addition, significant differences in the lipid/triacylglyceride (TAG) content of green algae and cyanobacteria were confirmed. Mobile species in algae are quite different from those in abundance in 'classic' dissolved organic matter (DOM) indicating that if algae are major contributors to DOM, considerable selective preservation of minor components (e.g. sterols) or biotransformation would have to occur. Identifying the metabolites and dissolved components within algal cells by NMR permits future studies of carbon transfer between species and through the food chain, whilst providing a foundation to better understand the role of algae in the formation of DOM and the sequestration/transformation of carbon in aquatic environments.

  13. Solution and solid state NMR studies of the structure and dynamics of C60 and C70

    International Nuclear Information System (INIS)

    Johnson, R.D.; Yannoni, C.S.; Salem, J.; Meijer, G.; Bethune, D.S.

    1991-01-01

    This paper investigates the structure and dynamics of C 60 and C 70 with 13 C NMR spectroscopy. In solution, high-resolution spectra reveal that C 60 has a single resonance at 143 ppm, indicating a strained, aromatic system with high symmetry. This is strong evidence for a C 60 soccer ball geometry. A 2D NMR INADEQUATE experiment on 13 C-enriched C 70 reveals the bonding connectivity to be a linear string, in firm support of the proposed rugby ball structure with D 5h symmetry, and furnishes resonance assignments. Solid state NMR spectra of C 60 at ambient temperatures yield a narrow resonance, indicative of rapid molecular reorientation. Variable temperature T 1 measurements show that the rotational correlation time is ∼ 10 - 9 s at 230 K. At 77 K, this time increases to more than 1 ms, and the 13 C NMR spectrum of C 60 is a powder pattern due to chemical shift anisotropy (tensor components 220, 186, 40 ppm). At intermediate temperatures a narrow peak is superimposed on the powder pattern, suggesting a distribution of barriers to molecular motion in the sample, or the presence of an additional phase in the solid state. A Carr-Purcell dipolar experiment on C 60 in the solid state allows the first precise determination of the C 60 bond lengths: 1.45 and 1.40 Angstrom

  14. Annual reports on NMR spectroscopy

    CERN Document Server

    Webb, Graham A; McCarthy, M J

    1995-01-01

    Over recent years, no other technique has grown to such importance as that of NMR spectroscopy. It is used in all branches of science where precise structural determination is required and where the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a means for the specialist and non-specialist alike to become familiar with new applications of the technique in all branches of chemistry, including biochemistry, and pharmaceutics. This volume focuses on theoretical aspects of NMR nuclear shielding and on applications of

  15. Experimental solid state NMR of gas hydrates : problems and solutions

    Energy Technology Data Exchange (ETDEWEB)

    Moudrakovski, I.; Lu, H.; Ripmeester, J. [National Research Council of Canada, Ottawa, ON (Canada). Steacie Inst. for Molecular Sciences; Kumar, R.; Susilo, R. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemical and Biological Engineering; Luzi, M. [GeoForschungsZentrum Potsdam, Potsdam (Germany)

    2008-07-01

    Solid State NMR is a suitable spectroscopic technique for hydrate research for several reasons, including its capability to distinguish between different structural types of hydrates, its quantitative nature and potential for both in-situ and time resolved experiments. This study illustrated the applications of solid state NMR for compositional and structural studies of clathrate hydrates, with particular emphasis on experimental techniques and potential ways to overcome technical difficulties. In order to use the method to its full capacity, some instrumental developments are needed to adapt it to the specific experimental requirements of hydrate studies, such as very low temperatures and high pressures. This presentation discussed the quantification of the Carbon-13 spectra with examples from natural and synthetic hydrates prepared from multi-component mixtures of hydrocarbons. The main approach used for the first two examples was Carbon-13 NMR with Magic Angle Spinning (MAS) at -100 degrees C. The detailed characterization of mixed hydrogen hydrates required low temperature hydrogen MAS. The quantification problems encountered during these experiments were also discussed. The purpose of these recent experimental developments was to prompt wider application of Solid State NMR in hydrate research. NMR proved to be a viable method for analyzing the composition and structure of multi-component mixed gas hydrates; characterizing natural gas hydrates; and, evaluating the formation conditions and properties of mixed hydrogen hydrates. The limitations of the method were highlighted and sensible choices of experimental conditions and techniques that ensure accurate results were discussed. 34 refs., 10 figs.

  16. Phosphole complexes of Gold(I) halides: Comparison of solution and solid-state structures by a combination of solution and CP/MAS 31P NMR spectroscopy and x-ray crystallography

    International Nuclear Information System (INIS)

    Attar, S.; Nelson, J.H.; Bearden, W.H.; Alcock, N.W.; Alyea, E.C.

    1990-01-01

    A series of complexes of 1-phenyldibenzophosphole (DBP), 1-phenyl-3,4,-dimethylphosphole (DMPP), and triphenylphosphine of the type L n AuX (n = 1, L = DBP, DMPP, Ph 3 P, X = Cl, Br, I; n = 3, L = DBP, X = Cl, Br, I; n = 3, L = Ph 3 P, X = Cl; n = 4, L = DBP, DMPP, X = PF 6 ) have been prepared and characterized. The structures of (DBP)AuCl (1), (DBP) 3 AuCl (2), and (DMPP)AuCl (3) have been determined from three-dimensional x-ray data collected by counter methods. Crystal structure of the complexes is reported. The CP/MAS 31 P( 1 H) NMR spectrum of complex 1 shows two resonances in a 1:1 intensity ratio, and the CP/MAS 31 P( 1 H) NMR spectrum of complex 3 shows three resonances in a 1:1:1 intensity ratio for reasons that are not yet understood. Though the three phospholes are crystallographically inequivalent (d(AuP) = 2.359 (1), 2.382 (1), and 2.374 (2) angstrom) the molecule has effective C s symmetry as evidenced by the observation of two 31 P resonances in a 2:1 intensity ratio in its CP/MAS 31 P( 1 H) NMR spectrum. Variable-temperature 31 P( 1 H) NMR spectra obtained on solutions of LAuCl + L in various ratios were analyzed to determine the nature of the species present in solution and to gain information regarding their relative stabilities as a function of the nature of the phosphine. 79 refs., 8 figs., 9 tabs

  17. Study of micellar solutions of the 'sodium lauryl sulphate-heavy water' system by using pulsed NMR

    International Nuclear Information System (INIS)

    Fouchet, C.

    1972-01-01

    This research thesis reports the study of the nuclear magnetic resonance of protons contained by micellar solutions of sodium lauryl sulphate and heavy water. Relaxation times have been measured with respect to various parameters: concentration, temperature, frequency. The author presents the main properties of micellar solutions and indicate the various possible movements. Then, he addresses the implemented technique, and shows that NMR is sensitive to short range interactions, and allows micellar movements to be studied over an extended rate range. Experimental results are then presented and interpreted [fr

  18. 2D NMR studies of biomolecules

    International Nuclear Information System (INIS)

    Lamerichs, R.M.J.N.

    1989-01-01

    The work described in this thesis comprises two related subjects. The first part describes methods to derive high-resolution structures of proteins in solution using two-dimensional (2-D) NMR. The second part describes 2-D NMR studies on the interaction between proteins and DNA. (author). 261 refs.; 52 figs.; 23 tabs

  19. Forms and lability of phosphorus in algae and aquatic macrophytes characterized by solution 31P NMR coupled with enzymatic hydrolysis

    Science.gov (United States)

    Increased information on forms and lability of phosphorus (P) in aquatic macrophytes and algae is crucial for better understanding of P biogeochemical cycling in eutrophic lakes. In this work, solution 31P nuclear magnetic resonance (NMR) spectroscopy coupled with enzymatic hydrolysis (EH) was used ...

  20. H and C NMR investigations of Pb(Zr,Ti)O3 thin-film precursor solutions

    International Nuclear Information System (INIS)

    Assink, R.A.; Schwartz, R.W.

    1993-01-01

    Solvent reactions, ligand substitutions, and the oligomer/polymer backbone structure are important factors in the solution preparation of ceramic films. In this study the authors have used H and C NMR spectroscopy to characterize solvent and ligand effects in precursor solutions used for the deposition of ferroelectric PZT (lead zirconate titanate) thin films. Solutions were prepared by a sequential precursor addition method from carboxylate and alkoxide precursors of the three cations, and the solvent, acetic acid, methanol, and water. The results indicate that acetic acid was a key component in the solution preparation process. As observed previously for single metallic component systems, its presence resulted in esterification reactions, leading in the present case to the formation of methyl, isopropyl, and n-butyl acetates. Second, acetic acid functioned as a chemical modifier, or chelating agent, replacing essentially all of the alkoxy ligands of the original precursors. Since alkoxy replacement appeared to be complete, we may describe the PZT species formed in solution as oxo acetate in nature. Finally, the solvent and ligand behavior of a solution prepared by an inverted mixing order was compared to the behavior of the solution prepared by a sequential precursor addition. The spectra for the two solutions were similar, and only differences in the relative intensities of the ester and alcoholic resonances were observed. 29 refs., 5 figs., 3 tabs

  1. Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

    Science.gov (United States)

    Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

    2009-08-06

    The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

  2. Stochastic models (cooperative and non-cooperative) for NMR analysis of the hetero-association of aromatic molecules in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Evstigneev, Maxim P. [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine)], E-mail: max_evstigneev@mail.ru; Davies, David B. [School of Biological and Chemical Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX (United Kingdom); Veselkov, Alexei N. [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine)

    2006-01-25

    Stochastic cooperative (STOCH-C) and non-cooperative (STOCH-NC) models have been developed for NMR analysis of the hetero-association of aromatic compounds in solution, in order to take into account all physically meaningful association reactions of molecules in which there are no limitations on the lengths of the aggregates and complexes. These algorithmical approaches are compared with previously published basic (BASE) and generalized (GEN) analytical statistical thermodynamical models of hetero-association of biologically active aromatic molecules using the same sets of published NMR data measured under the same solution conditions (0.1 M phosphate buffer, pD = 7.1, T = 298 K). It is shown that, within experimental errors, the BASE analytical model may be used to describe molecular systems characterized by relatively small contributions of hetero-association reactions, whereas the GEN model may be applied to hetero-association reactions of any aromatic compound with different self-association properties. The STOCH-C computational algorithm enabled the effect on hetero-association of the interactions of molecules with different cooperativity parameters of self-association to be estimated for the first time and it is proposed that the algorithm for the stochastic models has great potential for detailed investigation and understanding of the interactions of aromatic molecules in solution.

  3. Stochastic models (cooperative and non-cooperative) for NMR analysis of the hetero-association of aromatic molecules in aqueous solution

    International Nuclear Information System (INIS)

    Evstigneev, Maxim P.; Davies, David B.; Veselkov, Alexei N.

    2006-01-01

    Stochastic cooperative (STOCH-C) and non-cooperative (STOCH-NC) models have been developed for NMR analysis of the hetero-association of aromatic compounds in solution, in order to take into account all physically meaningful association reactions of molecules in which there are no limitations on the lengths of the aggregates and complexes. These algorithmical approaches are compared with previously published basic (BASE) and generalized (GEN) analytical statistical thermodynamical models of hetero-association of biologically active aromatic molecules using the same sets of published NMR data measured under the same solution conditions (0.1 M phosphate buffer, pD = 7.1, T = 298 K). It is shown that, within experimental errors, the BASE analytical model may be used to describe molecular systems characterized by relatively small contributions of hetero-association reactions, whereas the GEN model may be applied to hetero-association reactions of any aromatic compound with different self-association properties. The STOCH-C computational algorithm enabled the effect on hetero-association of the interactions of molecules with different cooperativity parameters of self-association to be estimated for the first time and it is proposed that the algorithm for the stochastic models has great potential for detailed investigation and understanding of the interactions of aromatic molecules in solution

  4. Combined solid state and solution NMR studies of {alpha},{epsilon}-{sup 15}N labeled bovine rhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Werner, Karla; Lehner, Ines [Johann Wolfgang Goethe-Universitaet Frankfurt, Center for Biomolecular Magnetic Resonance (Germany); Dhiman, Harpreet Kaur [University of Pittsburgh School of Medicine, Department of Structural Biology (United States); Richter, Christian; Glaubitz, Clemens; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de; Klein-Seetharaman, Judith [Johann Wolfgang Goethe-Universitaet Frankfurt, Center for Biomolecular Magnetic Resonance (Germany); Khorana, H. Gobind [Massachusetts Institute of Technology, Departments of Biology and Chemistry (United States)], E-mail: khorana@mit.edu

    2007-04-15

    Rhodopsin is the visual pigment of the vertebrate rod photoreceptor cell and is the only member of the G protein coupled receptor family for which a crystal structure is available. Towards the study of dynamics in rhodopsin, we report NMR-spectroscopic investigations of {alpha},{epsilon}-{sup 15}N-tryptophan labeled rhodopsin in detergent micelles and reconstituted in phospholipids. Using a combination of solid state {sup 13}C,{sup 15}N-REDOR and HETCOR experiments of all possible {sup 13}C'{sub i-1} carbonyl/{sup 15}N{sub i}-tryptophan isotope labeled amide pairs, and H/D exchange {sup 1}H,{sup 15}N-HSQC experiments conducted in solution, we assigned chemical shifts to all five rhodopsin tryptophan backbone {sup 15}N nuclei and partially to their bound protons. {sup 1}H,{sup 15}N chemical shift assignment was achieved for indole side chains of Trp35{sup 1.30} and Trp175{sup 4.65}. {sup 15}N chemical shifts were found to be similar when comparing those obtained in the native like reconstituted lipid environment and those obtained in detergent micelles for all tryptophans except Trp175{sup 4.65} at the membrane interface. The results suggest that the integrated solution and solid state NMR approach presented provides highly complementary information in the study of structure and dynamics of large membrane proteins like rhodopsin.

  5. Solid-state NMR on complex biomolecules: novel methods and applications

    NARCIS (Netherlands)

    Nand, D.

    2011-01-01

    Solid-state NMR (ssNMR) represents a versatile technique in providing atomic-resolution information without the need for crystals or fast molecular motion required for X-ray crystallography and solution-state NMR, respectively. Recent past has witnessed the ability of this technique in providing

  6. Proton NMR studies of functionalized nanoparticles in aqueous environments

    Science.gov (United States)

    Tataurova, Yulia Nikolaevna

    Nanoscience is an emerging field that can provide potential routes towards addressing critical issues such as clean and sustainable energy, environmental remediation and human health. Specifically, porous nanomaterials, such as zeolites and mesoporous silica, are found in a wide range of applications including catalysis, drug delivery, imaging, environmental protection, and sensing. The characterization of the physical and chemical properties of nanocrystalline materials is essential to the realization of these innovative applications. The great advantage of porous nanocrystals is their increased external surface area that can control their biological, chemical and catalytic activities. Specific functional groups synthesized on the surface of nanoparticles are able to absorb heavy metals from the solution or target disease cells, such as cancer cells. In these studies, three main issues related to functionalized nanomaterials will be addressed through the application of nuclear magnetic resonance (NMR) techniques including: 1) surface composition and structure of functionalized nanocrystalline particles; 2) chemical properties of the guest molecules on the surface of nanomaterials, and 3) adsorption and reactivity of surface bound functional groups. Nuclear magnetic resonance (NMR) is one of the major spectroscopic techniques available for the characterization of molecular structure and conformational dynamics with atomic level detail. This thesis deals with the application of 1H solution state NMR to porous nanomaterial in an aqueous environment. Understanding the aqueous phase behavior of functionalized nanomaterials is a key factor in the design and development of safe nanomaterials because their interactions with living systems are always mediated through the aqueous phase. This is often due to a lack of fundamental knowledge in interfacial chemical and physical phenomena that occur on the surface of nanoparticles. The use of solution NMR spectroscopy results

  7. 15N NMR spectroscopic investigation of nitrous and nitric acids in sulfuric acid solutions of varying acidities

    International Nuclear Information System (INIS)

    Prakash, G.K.S.; Heiliger, L.; Olah, G.A.

    1990-01-01

    Both nitrous and nitric acids were studied in sulfuric acid solutions of varying acid strengths by 15 N NMR spectroscopy. The study gives new insights into the nature of intermediates present at different acid strengths. Furthermore, we have also discovered a novel redox reaction between NO 2 + and NO + ions involving the intermediacy of their respective acids. A mechanism is proposed to explain the observed results. 13 refs., 2 figs., 1 tab

  8. Preparation of polyurethane/montmorillonite nanocomposites by solution: characterization using low-field NMR and study of thermal stability

    International Nuclear Information System (INIS)

    Silva, Marcos Anacleto da; Tavares, Maria Ines B.

    2009-01-01

    Polyurethanes (PU) are important and versatile class of polymer materials, especially because of their desirable properties, such as high abrasion resistance, tear strength, excellent shock absorption, flexibility and elasticity. However, there also exist some disadvantages, for example, low thermal stability and barrier properties. To overcome the disadvantages, research on novel polyurethane/clay nanocomposites has been carried out. The investigation of the structure of polyurethane/clay nanocomposites has been mostly done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). In this work, PU/clay films were prepared by solution, and the obtained nanocomposites were characterized by XRD and low-field nuclear magnetic resonance (NMR). Low field NMR measurements were able to provide important information on molecular dynamics of the polymeric nanocomposites PU/OMMT. In addition, they also confirmed the results obtained by XRD. The thermal stability was determined by thermogravimetric analysis (TGA). (author)

  9. Investigating the Mechanisms of Amylolysis of Starch Granules by Solution-State NMR

    Science.gov (United States)

    2015-01-01

    Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch. PMID:25815624

  10. Forms and Lability of Phosphorus in Algae and Aquatic Macrophytes Characterized by Solution 31P NMR Coupled with Enzymatic Hydrolysis

    Science.gov (United States)

    Feng, Weiying; Zhu, Yuanrong; Wu, Fengchang; He, Zhongqi; Zhang, Chen; Giesy, John P.

    2016-11-01

    Solution Phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy coupled with enzymatic hydrolysis (EH) with commercially available phosphatases was used to characterize phosphorus (P) compounds in extracts of the dominant aquatic macrophytes and algae in a eutrophic lake. Total extractable organic P (Po) concentrations ranged from 504 to 1643 mg kg-1 and 2318 to 8395 mg kg-1 for aquatic macrophytes and algae, respectively. Using 31P NMR spectroscopy, 11 Po species were detected in the mono- and diester region. Additionally, orthophosphate, pyrophosphate and phosphonates were also detected. Using EH, phytate-like P was identified as the prevalent class of enzyme-labile Po, followed by labile monoester- and diester-P. Comparison of the NMR and EH data indicated that the distribution pattern of major P forms in the samples determined by the two methods was similar (r = 0.712, p < 0.05). Additional 31P NMR spectroscopic analysis of extracts following EH showed significant decreases in the monoester and pyrophosphate regions, with a corresponding increase in the orthophosphate signal, as compared to unhydrolyzed extracts. Based on these quantity and hydrolysis data, we proposed that recycling of Po in vegetative biomass residues is an important mechanism for long-term self-regulation of available P for algal blooming in eutrophic lakes.

  11. Chemical shifts of oxygen-17 NMR in polyoxotungstates

    International Nuclear Information System (INIS)

    Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

    1977-01-01

    17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

  12. Novel solution conformation of DNA observed in d(GAATTCGAATTC) by two-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    Chary, K.V.R.; Hosur, R.V.; Govil, G.; Zu-kun, T.; Miles, H.T.

    1987-01-01

    Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d(GAATTCGAATTC) have been obtained by using the two-dimensional Fourier transform NMR methods correlated spectroscopy and nuclear Overhauser effect spectroscopy. Conformational details about the sugar pucker, the glycosidic dihedral angle, and the overall secondary structure of the molecule has been derived from the relative intensities of cross peaks in the two-dimensional NMR spectra in aqueous solution. It is observed that d(GAATTCGAATTC) assumes a novel double-helical structure. The solution conformations of the two complementary strands are identical, unlike those observed in a related sequence in the solid state. Most of the five-membered sugar rings adopt an unusual O1'-endo geometry. All the glycosidic dihedral angles are in the anti domain. The AATT segments A2-T5 and A8-T11 show better stacking compared to the rest of the molecule. These features fit into a right-handed DNA model for the above two segments, with the sugar geometries different from the conventional ones. There are important structural variations in the central TCG portion, which is known to show preferences for DNase I activity, and between G1-A2 and G7-A8, which are cleavage points in the EcoRI recognition sequence. The sugar puckers for G1 and G7 are significantly different from the rest of the molecule. Further, in the three segments mentioned above, the sugar phosphate geometry is such that the distances between protons on adjacent nucleotides are much larger than those expected for a right-handed DNA. The authors suggest that such crevices in the DNA structure may act as hot points in initiation of protein recognition

  13. Integrative NMR for biomolecular research

    International Nuclear Information System (INIS)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L.

    2016-01-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  14. Integrative NMR for biomolecular research

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-04-15

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  15. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    International Nuclear Information System (INIS)

    Dolenc, Jozica; Missimer, John H.; Steinmetz, Michel O.; Gunsteren, Wilfred F. van

    2010-01-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 φ torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular α-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured 3 J(H N -H Cα )-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and 3 J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and 3 J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  16. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

    Science.gov (United States)

    Dolenc, Jozica; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-07-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 phi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and (3)J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and (3)J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  17. NMR investigation of coal extracts

    Energy Technology Data Exchange (ETDEWEB)

    Lang, I; Sebor, G [Ceskoslovenska Akademie Ved, Prague. Hornicky Ustav; Sebor, G Jr; Hajek, M; Mostecky, J [Vysoka Skola Chemicko-Technologicka, Prague (Czechoslovakia)

    1978-07-01

    Proton NMR spectroscopy was used for the evaluation of 10% coal extract solutions in deuterated pyridine. Four types of Czechoslovak coal were analyzed. Agreement was found between the aromaticity of coal extracts calculated from /sup 1/H NMR data using Brown's method and Ladner's and Williams' method and the characterization of an average molecule of the coal extract by the number of non-bridge carbon atoms of aromatic rings, by the overall number of aromatic ring carbon atoms and the number of aromatic rings, determined by the Williams and Ferris methods. The methods for calculating carbon distribution from /sup 1/H NMR data, however, contain some constants theoretically estimated or experimentally found using the method which still remain to be verified.

  18. Solution structure of the 45-residue ATP-binding peptide of adenylate kinase as determined by 2-D NMR, FTIR, and CD spectroscopy

    International Nuclear Information System (INIS)

    Fry, D.C.; Byler, D.M.; Susi, H.; Brown, E.M.; Kuby, S.A.; Mildyan, A.S.

    1986-01-01

    In the X-ray structure of adenylate kinase residues 1-45 exist as 47% α-helix, 29% β-structure (strands and turns) and 24% coil. The solution structure of a synthetic peptide corresponding to residues 1-45, which constitutes the MgATP binding site was studied by 3 independent spectroscopic methods. Globularity of the peptide was shown by its broad NMR resonances which narrow upon denaturation, and by its ability to bind MgATP with similar affinity and conformation as the intact enzyme does. COSY and NOESY NMR methods at 250 and 500 MHz reveal proximities among NH, Cα, and Cβ protons indicative of >20% α-helix, and >20% β-structure. Correlation of regions of secondary structure with the primary sequence by 2D NMR indicates at least one α-helix (res. 23 to 29) and two β-strands (res. 12 to 15 and 34 to 38). The broad amide I band in the deconvoluted FTIR spectrum could be fit as the sum of 4 peaks due to specific secondary structures, yielding ≤=45% α-helix, ≤=40% β-structure and ≥=15% coil. The CD spectrum, from 185-250 nm, interpreted with a 3-parameter basis set, yielded 20 +/- 5% α=helix, and ≤=20% β-structure. The solution structure of peptide 1-45 thus approximates that of residues 1-45 in the crystal

  19. NMR study of structure of lanthanide complexes in solution

    International Nuclear Information System (INIS)

    Choppin, G.R.

    1976-01-01

    The diagnostic value PMR studies of diamagnetic lanthanide complexes to define the nature of the species in the lanthanide-pyruvate system is discussed. The use of NMR spectra of both diamagnetic and paramagnetic lanthanide complexes to obtain detailed structural information is reviewed

  20. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

  1. Carbon-13 NMR characterization of actinyl(VI) carbonate complexes in aqueous solution

    International Nuclear Information System (INIS)

    Clark, D.L.; Hobart, D.E.; Palmer, P.D.; Sullivan, J.C.; Stout, B.E.

    1992-01-01

    The uranyl(VI) carbonate system has been re-examined using 13 C NMR of 99.9% 13 C-enriched U VI O 2 ( 13 CO 3 ) 3 4- in millimolar concentrations. By careful control of carbonate ion concentration, we have confirmed the existence of the trimer, and observed dynamic equilibrium between the monomer and the timer. In addition, the ligand exchange reaction between free and coordinated carbonate on Pu VI O 2 ( 13 CO 3 ) 3 4- and Am VI O 2 ( 13 CO 3 ) 3 4- systems has been examined by variable temperature 13 C NMR line-broadening techniques 13 C NMR line-broadening techniques. A modified Carr-Purcell-Meiboom-Gill NMR pulse sequence was written to allow for experimental determination of ligand exchange parameters for paramagnetic actinide complexes. Preliminary Eyring analysis has provided activation parameters of ΔG double-dagger 295 = 56 kJ/M, ΔH double-dagger = 38 kJ/M, and ΔS double-dagger = -60 J/M-K for the plutonyl triscarbonate system, suggesting an associative transition state for the plutonyl (VI) carbonate complex self-exchange reaction. Experiments for determination of the activation parameters for the americium (VI) carbonate system are in progress

  2. 1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

    Science.gov (United States)

    Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

    2004-07-01

    NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

  3. Viscosity of concentrated solutions and of human erythrocyte cytoplasm determined from NMR measurement of molecular correlation times

    International Nuclear Information System (INIS)

    Endre, Z.H.; Kuchel, P.W.

    1986-01-01

    Metabolically active human erythrocytes were incubated with [α- 13 C]glycine which led to the specific enrichment of intracellular glutathione. The cells were then studied using 13 C-NMR in which the longitudinal relaxation times (T 1 ) and nuclear Overhauser enhancements of the free glycine and glutathione were measured. Bulk viscosities of the erythrocyte cytoplasm were measured using Ostwald capillary viscometry. Large differences existed between the latter viscosity estimates and those based upon NMR-T 1 measurements. The authors derived an equation from the theory of the viscosity of concentrated solutions which contains two phenomenological interaction parameters, a 'shape' factor and a 'volume' factor; it was fitted to data relating to the concentration dependence of viscosity measured by both methods. Under various conditions of extracellular osmotic pressure, erythrocytes change volume and thus the viscosity of the intracellular milieu is altered. The volume changes resulted in changes in the T 1 of [α- 13 C]glycine. Conversely, the authors showed that alterations in T 1 , when appropriately calibrated, could be used for monitoring changes in volume of metabolically active cells. (Auth.)

  4. Aluminium-27 n.m.r. studies of aluminium fluoro complexes in dichloromethane solution: evidence for tetrafluoroaluminate anion

    International Nuclear Information System (INIS)

    Colton, R.; Eller, P.G.

    1989-01-01

    Mixed aluminium chloro/fluoro anions are formed in dichloromethane solution by the interaction of AlCl 3 and [Ph 3 PhCH 2 P] [H 2 F 3 ]. Aluminium-27 n.m.r. studies are restricted to the stoichiometric ranges F/Al from 1:1 to 3:1 and F/Al>8:1. Between these limits rapid precipitation reactions occur. In the fluoride-rich stoichiometric range there is rapid exchange on the n.m.r. time scale between the aluminium fluoro anion and free fluoride, so that a direct identification of the species by the multiplicity of the resonance is not possible. Indirect evidence strongly suggests that the aluminium species is [AlF 4 ] - . In the F/Al stoichiometry range from 1:1 to 3:1 aluminium-27 resonances were observed for all the other possible [AlCl χ F 4-χ ] - species. Studies on the aluminium iodo/fluoro system support the identification of [AlF 4 ] - , but the system is labile and the mixed iodo/fluoro species undergo rapid disproportionation. 12 refs., 1 fig

  5. Solution NMR structure and functional analysis of the integral membrane protein YgaP from Escherichia coli.

    Science.gov (United States)

    Eichmann, Cédric; Tzitzilonis, Christos; Bordignon, Enrica; Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

    2014-08-22

    The solution NMR structure of the α-helical integral membrane protein YgaP from Escherichia coli in mixed 1,2-diheptanoyl-sn-glycerol-3-phosphocholine/1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles is presented. In these micelles, YgaP forms a homodimer with the two transmembrane helices being the dimer interface, whereas the N-terminal cytoplasmic domain includes a rhodanese-fold in accordance to its sequence homology to the rhodanese family of sulfurtransferases. The enzymatic sulfur transfer activity of full-length YgaP as well as of the N-terminal rhodanese domain only was investigated performing a series of titrations with sodium thiosulfate and potassium cyanide monitored by NMR and EPR. The data indicate the thiosulfate concentration-dependent addition of several sulfur atoms to the catalytic Cys-63, which process can be reversed by the addition of potassium cyanide. The catalytic reaction induces thereby conformational changes within the rhodanese domain, as well as on the transmembrane α-helices of YgaP. These results provide insights into a potential mechanism of YgaP during the catalytic thiosulfate activity in vivo. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Pre-physical treatment: an important procedure to improve spectral resolution in polymers microstructure studies using 13C solution NMR

    International Nuclear Information System (INIS)

    Pedroza, Oscar J.O.; Tavares, Maria I.B.

    2004-01-01

    Changes in physical properties of polymeric materials can be evaluated from their microstructures, which can be investigated using solution carbon-13 nuclear magnetic resonance (NMR). In this type of study spectral resolution is very important, which obviously depend on the sample and solvent. A pre physical treatment allows for an improvement in the spectral resolution. Consequently, more information on chain linking can be obtained, thus facilitating the determination of the stereo sequences. (author)

  7. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    Energy Technology Data Exchange (ETDEWEB)

    Dolenc, Jozica [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland); Missimer, John H.; Steinmetz, Michel O. [Paul Scherrer Institut, Biomolecular Research (Switzerland); Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.c [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)

    2010-07-15

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 {phi} torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular {alpha}-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured {sup 3}J(H{sub N}-H{sub C{alpha}})-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and {sup 3}J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and {sup 3}J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  8. NMR studies of macroscopic and microscopic properties of liquid crystals

    International Nuclear Information System (INIS)

    Hughes, J.R.

    1998-03-01

    The work presented is concerned with studies of orientational order in liquid crystals and the behaviour of certain mesophases. The experimental technique used in common with all the work is deuterium NMR spectroscopy. Much of the work involves studies of the orientational order of deuteriated solute molecules dissolved in liquid crystal solvents. Chapter 1 gives an introduction to liquid crystals followed by a quantitative description of orientational order. Deuterium NMR in liquid crystals is described and an outline of the molecular field theory behind the orientational order of a rigid, biaxial solute in a uniaxial mesophase is given. In Chapter 2 a novel type of mesophase induction is studied using NMR, where a solute induces up to two extra phases in a discotic mesogen depending on its concentration. The purpose of this work is to try to gain an understanding into the mechanism of the phase induction involved. Chapter 3 is concerned primarily with the macroscopic behaviour of the nematic phase formed by a semi-rigid main-chain polymer in solution. Of particular interest is the study of the reorientation of the monodomain, once the director has been rotated with respect to the magnetic field of the NMR spectrometer. A mesogen which has been claimed to exhibit a biaxial nematic phase is studied in Chapter 4, in order to determine the symmetry of the phase using NMR. Finally, Chapter 5 deals with the differing behaviour of a liquid crystal monomer and its dimer dissolved in common nematic solvents in order to determine whether this agrees with molecular field theory. (author)

  9. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  10. Comparison of NMR and crystal structures for the proteins TM1112 and TM1367

    International Nuclear Information System (INIS)

    Mohanty, Biswaranjan; Serrano, Pedro; Pedrini, Bill; Jaudzems, Kristaps; Geralt, Michael; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

    2010-01-01

    NMR structures of the proteins TM1112 and TM1367 solved by the JCSG in solution at 298 K could be superimposed with the corresponding crystal structures at 100 K with r.m.s.d. values of <1.0 Å for the backbone heavy atoms. For both proteins the structural differences between multiple molecules in the asymmetric unit of the crystals correlated with structural variations within the bundles of conformers used to represent the NMR solution structures. A recently introduced JCSG NMR structure-determination protocol, which makes use of the software package UNIO for extensive automation, was further evaluated by comparison of the TM1112 structure obtained using these automated methods with another NMR structure that was independently solved in another PSI center, where a largely interactive approach was applied. The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper-limit distance constraints derived from the molecular models that represent the results of structure

  11. De novo protein structure determination using sparse NMR data

    International Nuclear Information System (INIS)

    Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

    2000-01-01

    We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

  12. Proliferating cell nuclear antigen (PCNA interactions in solution studied by NMR.

    Directory of Open Access Journals (Sweden)

    Alfredo De Biasio

    Full Text Available PCNA is an essential factor for DNA replication and repair. It forms a ring shaped structure of 86 kDa by the symmetric association of three identical protomers. The ring encircles the DNA and acts as a docking platform for other proteins, most of them containing the PCNA Interaction Protein sequence (PIP-box. We have used NMR to characterize the interactions of PCNA with several other proteins and fragments in solution. The binding of the PIP-box peptide of the cell cycle inhibitor p21 to PCNA is consistent with the crystal structure of the complex. A shorter p21 peptide binds with reduced affinity but retains most of the molecular recognition determinants. However the binding of the corresponding peptide of the tumor suppressor ING1 is extremely weak, indicating that slight deviations from the consensus PIP-box sequence dramatically reduce the affinity for PCNA, in contrast with a proposed less stringent PIP-box sequence requirement. We could not detect any binding between PCNA and the MCL-1 or the CDK2 protein, reported to interact with PCNA in biochemical assays. This suggests that they do not bind directly to PCNA, or they do but very weakly, with additional unidentified factors stabilizing the interactions in the cell. Backbone dynamics measurements show three PCNA regions with high relative flexibility, including the interdomain connector loop (IDCL and the C-terminus, both of them involved in the interaction with the PIP-box. Our work provides the basis for high resolution studies of direct ligand binding to PCNA in solution.

  13. The characterisation of polymers using pulsed NMR

    International Nuclear Information System (INIS)

    Charlesby, A.

    1983-01-01

    Broad line pulsed NMR is applied to obtain information on radiation-induced polymer changes and other aspects of polymer science based on the interpretation of spin-spin relaxation curves. Calculations are made to determine the molecular weight, the crosslink density of simple, low molecular weight, flexible polymers. For higher molecular weight polymers, a conclusion can be drawn on the concentrations of entangled and crosslinked units by means of pulsed NMR. Some typical applications of the technique are illustrated by the examples of polyethylenes, rubbers, filled polymeric systems and aqueous polyethylene oxide solutions. The morphology of polymers can be followed by pulsed NMR. (V.N.)

  14. Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

    Energy Technology Data Exchange (ETDEWEB)

    Alsanousi, Nesreen [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Sugiki, Toshihiko, E-mail: sugiki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kojima, Chojiro, E-mail: kojima-chojiro-xk@ynu.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)

    2016-09-02

    Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and

  15. The Solid Solution Sr(1-x)Ba(x)Ga2: Substitutional Disorder and Chemical Bonding Visited by NMR Spectroscopy and Quantum Mechanical Calculations.

    Science.gov (United States)

    Pecher, Oliver; Mausolf, Bernhard; Lamberts, Kevin; Oligschläger, Dirk; Niewieszol, Carina; Englert, Ulli; Haarmann, Frank

    2015-09-28

    Complete miscibility of the intermetallic phases (IPs) SrGa2 and BaGa2 forming the solid solution Sr(1-x)Ba(x)Ga2 is shown by means of X-ray diffraction, thermoanalytical and metallographic studies. Regarding the distances of Sr/Ba sites versus substitution degree, a model of isolated substitution centres (ISC) for up to 10% cation substitution is explored to study the influence on the Ga bonding situation. A combined application of NMR spectroscopy and quantum mechanical (QM) calculations proves the electric field gradient (EFG) to be a sensitive measure of different bonding situations. The experimental resolution is boosted by orientation-dependent NMR on magnetically aligned powder samples, revealing in first approximation two different Ga species in the ISC regimes. EFG calculations using superlattice structures within periodic boundary conditions are in fair agreement with the NMR spectroscopy data and are discussed in detail regarding their application on disordered IPs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Lithium salt of N,N-dimethylsalicylamide in pyridine and pyridine-water solutions. NMR study on the internal rotation about the C-N bond

    Energy Technology Data Exchange (ETDEWEB)

    Gryff-Keller, A; Szczecinski, P [Politechnika Warszawska (Poland)

    1981-01-01

    NMR spectra of the title compound in pyridine and pyridine-water mixtures have been measured at various temperatures. The dependence of internal rotation rate and of chemical shift difference between N-CH/sub 3/ signals on the solvent composition has been discussed with reference to structure of the solution investigated.

  17. Structural biology by NMR: structure, dynamics, and interactions.

    Directory of Open Access Journals (Sweden)

    Phineus R L Markwick

    2008-09-01

    Full Text Available The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data.

  18. Structure and dynamics of alpha-tocopherol in model membranes and in solution: a broad-line and high-resolution NMR study

    International Nuclear Information System (INIS)

    Ekiel, I.H.; Hughes, L.; Burton, G.W.; Jovall, P.A.; Ingold, K.U.; Smith, I.C.

    1988-01-01

    Nuclear magnetic resonance has been applied to study the conformational dynamics of alpha-tocopherol (vitamin E) in solution and in model membranes. In nonviscous solution, 1 H nuclear magnetic resonance (NMR) showed that alpha-tocopherol is in rapid equilibrium between two or more puckered conformers of its heterocyclic ring. The most likely conformers to be so involved are the two half-chair forms. Deuterium NMR spectra of specifically deuteriated alpha-tocopherol in multilamellar dispersions of egg phosphatidylcholine, measured in the liquid-crystalline state, were characteristic of axially symmetric motional averaging. The orientation of the rotational axis within the molecular framework was determined. Studies on oriented multilamellar membranes revealed that this axis is perpendicular to the surface of the membrane. The profile of quadrupolar splittings along the hydrophobic tail does not have a plateau, in contrast to that of the fatty acyl chains of the membrane lipids. Longitudinal relaxation times (T1) were short. The presence of a minimum in their temperature dependence shows that molecular motion with an effective correlation time tau eff approximately equal to 3 X 10(-9)s is responsible for relaxation. However, the temperatures and absolute values of the minima depend on the position of the deuterium in the molecule, demonstrating that tau eff represents a complex blend of motions

  19. New strategy for stable-isotope-aided, multidimensional NMR spectroscopy of DNA oligomers

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Okira; Tate, Shin-Ichi; Kainosho, Masatsune [Tokyo Metropolitan Univ., Tokyo (Japan)

    1994-12-01

    Nuclear Magnetic Resonance (NMR) is the most efficient method for determining the solution structures of biomolecules. By applying multidimensional heteronuclear NMR techniques to {sup 13}C/{sup 15}N-labeled proteins, we can determine the solution structures of proteins with molecular mass of 20 to 30kDa at an accuracy similar to that of x-ray crystallography. Improvements in NMR instrumentation and techniques as well as the development of protein engineering methods for labeling proteins have rapidly advanced multidimensional heteronuclear NMR of proteins. In contrast, multidimensional heteronuclear NMR studies of nucleic acids is less advanced because there were no efficient methods for preparing large amounts of labeled DNA/RNA oligomers. In this report, we focused on the chemical synthesis of DNA oligomers labeled at specific residue(s). RNA oligomers with specific labels, which are difficult to synthesize by the enzyme method, can be synthesized by the chemical method. The specific labels are useful for conformational analysis of larger molecules such as protein-nucleic acid complexes.

  20. Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 1, Catalyzed reactions with wood models and wood polymers

    Science.gov (United States)

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

    2011-01-01

    To better understand adhesive interactions with wood, reactions between model compounds of wood and a model compound of polymeric methylene diphenyl diisocyanate (pMDI) were characterized by solution-state NMR spectroscopy. For comparison, finely ground loblolly pine sapwood, milled-wood lignin and holocellulose from the same wood were isolated and derivatized with...

  1. Effect of alkali-earth ions on local structure of the LaAlO3-La0.67A0.33MnO3 (A = Ca, Sr, Ba) diluted solid solutions: 27Al NMR studies

    International Nuclear Information System (INIS)

    Charnaya, E.V.; Cheng Tien; Lee, M.K.; Sun, S.Y.; Chejina, N.V.

    2007-01-01

    27 Al Magic Angle Spinning (MAS) NMR studies are carried out for diluted alkali-earth metal doped lanthanum manganite solid solutions in the lanthanum aluminate (1-y)LaAlO 3 -yLa 0.67 A 0.33 MnO 3 (A = Ca, Sr, Ba) with y = 0, 2, 3, and 5 mol %. The spectra depend on the dopant species and show higher substitutional ordering for the Ba containing mixed crystals. Magnetically shifted lines are observed in all solid solutions and attributed to Al in the octahedral oxygen environment near manganese trivalent ions. Nonlinear dependences of their intensity are referred to the manganese-rich cluster formation. An additional MAS NMR line corresponding to aluminium at sites different from the octahedral site in pure LaAlO 3 is observed only in solutions doped with Ba. 3Q MAS NMR revealed that the broadening of this line is governed mainly by quadrupole coupling and allowed calculating the isotropic chemical shift [ru

  2. Development and applications of quantitative NMR spectroscopy

    International Nuclear Information System (INIS)

    Yamazaki, Taichi

    2016-01-01

    Recently, quantitative NMR spectroscopy has attracted attention as an analytical method which can easily secure traceability to SI unit system, and discussions about its accuracy and inaccuracy are also started. This paper focuses on the literatures on the advancement of quantitative NMR spectroscopy reported between 2009 and 2016, and introduces both NMR measurement conditions and actual analysis cases in quantitative NMR. The quantitative NMR spectroscopy using an internal reference method enables accurate quantitative analysis with a quick and versatile way in general, and it is possible to obtain the precision sufficiently applicable to the evaluation of pure substances and standard solutions. Since the external reference method can easily prevent contamination to samples and the collection of samples, there are many reported cases related to the quantitative analysis of biologically related samples and highly scarce natural products in which NMR spectra are complicated. In the precision of quantitative NMR spectroscopy, the internal reference method is superior. As the quantitative NMR spectroscopy widely spreads, discussions are also progressing on how to utilize this analytical method as the official methods in various countries around the world. In Japan, this method is listed in the Pharmacopoeia and Japanese Standard of Food Additives, and it is also used as the official method for purity evaluation. In the future, this method will be expected to spread as the general-purpose analysis method that can ensure traceability to SI unit system. (A.O.)

  3. NMR study of temperature-induced phase separation and polymer-solvent interactions in poly(vinyl methyl ether)/D.sub.2./sub.O/ethanol solutions

    Czech Academy of Sciences Publication Activity Database

    Hanyková, L.; Labuta, J.; Spěváček, Jiří

    2006-01-01

    Roč. 47, č. 17 (2006), s. 6107-6116 ISSN 0032-3861 Grant - others:GA UK 294/2004/B Institutional research plan: CEZ:AV0Z40500505 Keywords : poly(vinyl methyl ether)/D2O/ ethanol solutions * temperature-induced phase separation * 1H and 13C NMR spectroscopy Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.773, year: 2006

  4. NMR structure of the protein NP-247299.1: comparison with the crystal structure

    International Nuclear Information System (INIS)

    Jaudzems, Kristaps; Geralt, Michael; Serrano, Pedro; Mohanty, Biswaranjan; Horst, Reto; Pedrini, Bill; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

    2010-01-01

    Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution. The NMR structure of the protein NP-247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves

  5. Surface characterization of hydrophobic core-shell QDs using NMR techniques

    Science.gov (United States)

    Zhang, Chengqi; Zeng, Birong; Palui, Goutam; Mattoussi, Hedi

    2018-02-01

    Using a few solution phase NMR spectroscopy techniques, including 1H NMR and 31P NMR, we have characterized the organic shell on CdSe-ZnS core-shell quantum dots and tracked changes in its composition when the QD dispersions are subjected to varying degrees of purification. Combining solution phase NMR with diffusion ordered spectroscopy (DOSY), we were able to distinguish between freely diffusing ligands in the sample from those bound on the surfaces. Additionally, matrix assisted laser desorption ionization (MALDI) and FTIR measurements were used to provide complementary and supporting information on the organic ligand coating for these nanocrystals. We found that the organic shell is dominated by monomeric or oligomeric n-hexylphosphonic acid (HPA), along with small portion of 1-hexadecyl amine (HDA). The presence of TOP/TOPO (tri-n-octylphosphine / tri-noctylphosphine oxide) molecules is much smaller, even though large excess of TOP/TOPO were used during the QD growth. These results indicate that HPA (alkyl phosphonate) exhibits the strongest coordination affinity to ZnS-rich QD surfaces grown using the high temperature injection route.

  6. NMR study of the dynamics of cationic gemini surfactant 14-2-14 in mixed solutions with conventional surfactants.

    Science.gov (United States)

    Jiang, Yan; Lu, Xing-Yu; Chen, Hong; Mao, Shi-Zhen; Liu, Mai-Li; Luo, Ping-Ya; Du, You-Ru

    2009-06-18

    Three kinds of conventional surfactants, namely, two nonionic surfactants [polyethylene glycol (23) lauryl ether (Brij-35) and Triton X-100 (TX-100)], one cationic surfactant [n-tetradecyltrimethyl ammonium bromide (TTAB)], and an anionic surfactant [sodium n-dodecyl sulfate (SDS)}, were mixed into the quaternary ammonium gemini surfactant [C(14)H(29)N(+)(CH(3))(2)](2)(CH(2))(2).2Br(-) (14-2-14) in aqueous solution. The exchange rate constants between 14-2-14 molecules in the mixed micelles and those in the bulk solution were detected using two nuclear magnetic resonance (NMR) methods: one-dimensional (1D) line shape analysis and two-dimensional (2D) exchange spectroscopy (EXSY). The results obtained from these two methods were consistent. Both showed that mixing a nonionic conventional surfactant, either Brij-35 or TX-100, enhanced the exchange process between the 14-2-14 molecules in the mixed micelles and those in the bulk solution. In contrast, the anionic surfactant SDS and the cationic surfactant TTAB slowed the process slightly.

  7. 35Cl/37Cl isotope effects in 103Rh NMR of [RhCln(H2O)6−n]3−n complex anions in hydrochloric acid solution as a unique ‘NMR finger-print’ for unambiguous speciation

    International Nuclear Information System (INIS)

    Geswindt, Theodor E.; Gerber, Wilhelmus J.; Brand, D. Jacobus; Koch, Klaus R.

    2012-01-01

    Graphical abstract: 35 Cl/ 37 Cl isotope effects in 103 Rh NMR as a unique ‘NMR-fingerprints’ leading to the unambiguous assignment of [RhCl n (H 2 O) 6−n ] 3−n (n = 3–6) complexes without reliance on accurate δ( 103 Rh) chemical shifts. Highlights: ► Direct 103 Rh NMR (19.11 MHz) spectroscopic method of speciation of [RhCl n (H 2 O) 6−n ] 3−n in HCl. ► 35 Cl/ 37 Cl isotope effects in 103 Rh NMR of [RhCl n (H 2 O) 6−n ] 3−n anions isotopologue and isotopomer induced 103 Rh NMR ‘finger-print’ for unambiguous identification. ► 103 Rh NMR identification of stereoisomers without a need for accurate chemical shifts. - Abstract: A detailed analysis of the 35 Cl/ 37 Cl isotope effects observed in the 19.11 MHz 103 Rh NMR resonances of [RhCl n (H 2 O) 6−n ] 3−n complexes (n = 3–6) in acidic solution at 292.1 K, shows that the ‘fine structure’ of each 103 Rh resonance can be understood in terms of the unique isotopologue and in certain instances the isotopomer distribution in each complex. These 35 Cl/ 37 Cl isotope effects in the 103 Rh NMR resonance of the [Rh 35/37 Cl 6 ] 3− species manifest only as a result of the statistically expected 35 Cl/ 37 Cl isotopologues, whereas for the aquated species such as for example [Rh 35/37 Cl 5 (H 2 O)] 2− , cis-[Rh 35/37 Cl 4 (H 2 O) 2 ] − as well as the mer-[Rh 35/37 Cl 3 (H 2 O) 3 ] complexes, additional fine-structure due to the various possible isotopomers within each class of isotopologues, is visible. Of interest is the possibility of the direct identification of stereoisomers cis-[RhCl 4 (H 2 O) 2 ] − , trans-[RhCl 4 (H 2 O) 2 ] − , fac-[RhCl 3 (H 2 O) 3 ] and mer-[RhCl 3 (H 2 O) 3 ] based on the 103 Rh NMR line shape, other than on the basis of their very similar δ( 103 Rh) chemical shift. The 103 Rh NMR resonance structure thus serves as a novel and unique ‘NMR-fingerprint’ leading to the unambiguous assignment of [RhCl n (H 2 O) 6−n ] 3−n complexes (n = 3–6

  8. Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

    Science.gov (United States)

    Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

    2012-10-09

    NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.

  9. A microscale protein NMR sample screening pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Rossi, Paolo; Swapna, G. V. T.; Huang, Yuanpeng J.; Aramini, James M. [State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers (United States); Anklin, Clemens [Bruker Biospin Corporation (United States); Conover, Kenith; Hamilton, Keith; Xiao, Rong; Acton, Thomas B.; Ertekin, Asli; Everett, John K.; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.ed [State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers (United States)

    2010-01-15

    As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale NMR screening of proteins using a micro-cryoprobe. The process is feasible because the newest generation probe requires only small amounts of protein, typically 30-200 {mu}g in 8-35 {mu}l volume. Extensive automation has been made possible by the combination of database tools, mechanization of key process steps, and the use of a micro-cryoprobe that gives excellent data while requiring little optimization and manual setup. In this perspective, we describe the overall process used by the NESG for screening NMR samples as part of a sample optimization process, assessing optimal construct design and solution conditions, as well as for determining protein rotational correlation times in order to assess protein oligomerization states. Database infrastructure has been developed to allow for flexible implementation of new screening protocols and harvesting of the resulting output. The NESG micro NMR screening pipeline has also been used for detergent screening of membrane proteins. Descriptions of the individual steps in the NESG NMR sample design, production, and screening pipeline are presented in the format of a standard operating procedure.

  10. Behaviour of 29Si NMR and infrared spectra of aqueous sodium and potassium silica solutions as a function of (SiO2/M2+O) ratio

    International Nuclear Information System (INIS)

    Couty, R.; Fernandez, L.

    1996-01-01

    Sodium and potassium solutions of silica with silica concentration of 1,4 mo/kg and R ms = SiO 2 /M + 2 O ratios of 4.56 to 1.6 were obtained by depolymerization of amorphous silica gel in sodium and potassium hydroxide. Solutions have been characterized by 29 Si NMR and infrared spectroscopy. The results indicated that Na + and K + exhibit the same behaviour during the depolymerization of silica. (authors). 11 refs., 4 figs., 2 tabs

  11. NMR

    International Nuclear Information System (INIS)

    Kneeland, J.B.; Lee, B.C.P.; Whalen, J.P.; Knowles, R.J.R.; Cahill, P.T.

    1984-01-01

    Although still quite new, NMR imaging has already emerged as a safe, noninvasive, painless, and effective diagnostic modality requiring no ionizing radiation. Also, NMR appears already to have established itself as the method of choice for the examination of the brain spinal cord (excluding herniated disks). Another area in which NMR excels is in the examination of the pelvis. The use of surface coils offers the promise of visualizing structures with resolution unobtainable by any other means. In addition, NMR, with its superb visualization of vascular structures and potential ability to measure flow, may soon revolutionize the diagnosis of cardiovascular disease. Finally, NMR, through biochemically and physiologically based T/sub 1/ and T/sub 2/ indices or through spectroscopy, may provide a means of monitoring therapeutic response so as to permit tailoring of treatment to the individual patient. In short, NMR is today probably at the same stage as the x-ray was in Roentgen's day

  12. 1H NMR, 13C NMR and Computational Daft Study of the Solution Structure of 2-Formylcyclohexane-1,3-Dione and its Alkali Metal Salts

    International Nuclear Information System (INIS)

    Szczecinski, P.; Gryff-Keller, A.; Molchanov, S.

    2005-01-01

    Triketones have been known for many years to be efficient inhibitors of (4-hydroxyphenyl)pyruvate dioxygenase (HPPD), an enzyme very important for plants and animals, which catalyzes the tyrosine catabolism. Inhibition of this process has been used for both herbicidal and medical purposes. The mechanism of inhibition of HPPD by triketones is still under investigation. Recently, an almost complete mechanistic model of interaction between the mentioned enzyme and its inhibitor has been proposed. However, some arguments used by the authors to rationalize the proposed mechanism cannot be accepted. Therefore further developing of the investigation in this field is justified. In the present work the solution structure of 2-formylcyclohexane-1,3-dione, a simple molecular model of HPPD inhibitors, has been investigated using 1 H and 13 C NMR spectroscopic methods and theoretical DFT-based calculations. (author)

  13. Peakr: simulating solid-state NMR spectra of proteins

    International Nuclear Information System (INIS)

    Schneider, Robert; Odronitz, Florian; Hammesfahr, Bjorn; Hellkamp, Marcel; Kollmar, Martin

    2013-01-01

    When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly. (authors)

  14. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state 13C NMR and solution 31P NMR spectroscopy

    Science.gov (United States)

    LIU, S. S.; Zhu, Y.; Meng, W.; Wu, F.

    2016-12-01

    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state 13C NMR and solution 31P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O-C-O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH3 and COO/N-C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH3 and COO/N-C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes.

  15. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    International Nuclear Information System (INIS)

    Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

    2012-01-01

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  16. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    Energy Technology Data Exchange (ETDEWEB)

    Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

    2012-03-15

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  17. Chevrel-phase solid solution Mo 6Se 8- xTe x. Study of its superconducting, magnetic and NMR properties

    Science.gov (United States)

    Hamard1a, C.; Auffret, V.; Peña, O.; Le Floch, M.; Nowak, B.; Wojakowski, A.

    2000-09-01

    The Chevrel-phase solid solution Mo 6Se 8-Mo 6Te 8 was studied by X-ray diffraction, AC and DC magnetic susceptibility and 77Se and 125Te NMR spectroscopy. From the smooth evolution of the lattice parameters and superconducting critical temperatures, a progressive substitution of selenium atoms by tellurium is shown, on the whole range of composition 0⩽ x⩽8, in the formulation Mo 6Se 8- xTe x: the unit-cell volume increases linearly because of the larger ionic size of tellurium, while Tc decreases rapidly (from 6.45 down to 0 K) because of the different formal oxidation states of the anions and a probable evolution of the Fermi level in the density of states. Results of magnetic susceptibility support this model and suggest the inhibition of the intrinsic metallic behavior with increasing x. The NMR spectra of the binaries Mo 6Se 8 and Mo 6Te 8 reveal two significant features, attributed to two different chalcogen positions in the R 3¯ symmetry. At low Se contents in Mo 6Se 8- xTe x ( x=7.5, 7 and 6), selenium first fills the two X(2) sites along the three-fold axis (2c positions), and then it becomes statistically distributed over the general 6f positions, leading to broad 77Se NMR lines. On the other hand, substitution of Te atoms in Mo 6Se 8 seems to occur in a random way, creating large perturbations on the 125Te NMR spectra, over the whole range of x. Theoretical analysis based on the presence of two anisotropic lines (of axial and non-axial symmetries, respectively) allowed us to estimate their anisotropy factors and to perfectly simulate the frequency response of both Mo 6Se 8 and Mo 6Te 8 binaries. Analysis of the Knight shift anisotropy leads us to conclude about the importance of the molybdenum z 2 molecular orbital contribution which controls the Mo-X dipolar interactions.

  18. Temperature-induced phase separation and hydration in aqueous polymer solutions studied by NMR and IR spectroscopy: comparison of poly(N-vinylcaprolactam) and acrylamide-based polymers

    Czech Academy of Sciences Publication Activity Database

    Spěváček, Jiří; Dybal, Jiří

    2014-01-01

    Roč. 336, č. 1 (2014), s. 39-46 ISSN 1022-1360. [International IUPAC Conference on Polymer-Solvent Complexes and Intercalates /9./ - POLYSOLVAT-9. Kiev, 11.09.2012-14.09.2012] R&D Projects: GA ČR GA202/09/1281 Institutional support: RVO:61389013 Keywords : aqueous polymer solutions * FT-IR * NMR Subject RIV: CD - Macromolecular Chemistry

  19. Determination of stability constants for thallium(III) cyanide complexes in aqueous solution by means of 13C and 205Ti NMR

    International Nuclear Information System (INIS)

    Blixt, J.; Gyori, B.; Glaser, J.

    1989-01-01

    In contrast to what is usually assumed, we have found and proved that thallium(III) forms very strong cyanide complexes in aqueous solution. The authors have investigated this system using 205 Tl, 13 C, and 14 N NMR and potentiometry and established the existence of four thallium(III)-cyanide complexes of the composition Tl(CN) n 3-n , n = 1-4. We have measured their chemical shifts and spin-spin coupling constants and determined their formation constants at 25 degree C in dilute (0.05 M) aqueous solution in the ionic medium ([Na + ] = 1 M, [Li + ] + [H + ] = 3 M, [ClO 4 - ] = 4 M). We have also determined the stability constant for HCN in the same ionic medium, log K a = 10.11 (5)

  20. A software framework for analysing solid-state MAS NMR data

    International Nuclear Information System (INIS)

    Stevens, Tim J.; Fogh, Rasmus H.; Boucher, Wayne; Higman, Victoria A.; Eisenmenger, Frank; Bardiaux, Benjamin; Rossum, Barth-Jan van; Oschkinat, Hartmut; Laue, Ernest D.

    2011-01-01

    Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of protein structure, function and dynamics. Software development, however, has not kept pace with these advances and data analysis is mostly performed using tools developed for solution NMR which do not directly address solid-state specific issues. Here we present additions to the CcpNmr Analysis software package which enable easier identification of spinning side bands, straightforward analysis of double quantum spectra, automatic consideration of non-uniform labelling schemes, as well as extension of other existing features to the needs of solid-state MAS data. To underpin this, we have updated and extended the CCPN data model and experiment descriptions to include transfer types and nomenclature appropriate for solid-state NMR experiments, as well as a set of experiment prototypes covering the experiments commonly employed by solid-sate MAS protein NMR spectroscopists. This work not only improves solid-state MAS NMR data analysis but provides a platform for anyone who uses the CCPN data model for programming, data transfer, or data archival involving solid-state MAS NMR data.

  1. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Zhou Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  2. Structure and Dynamic Properties of Membrane Proteins using NMR

    DEFF Research Database (Denmark)

    Rösner, Heike; Kragelund, Birthe

    2012-01-01

    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  3. NMR spectrometers. Current status and assessment of demand for high-resolution NMR spectrometers and for high-performance, solid NMR spectrometers at the scientific colleges and other research institutes in the Federal Republic of Germany. Pt. 1

    International Nuclear Information System (INIS)

    Schmidt, K.

    1989-01-01

    The survey includes high-resolution NMR spectrometers for liquids and solutions with magnetic field intensities of 11.7 Tesla and more (proton frequencies from 500 to 600 MHz) as well as high-performance solid-state NMR spectrometers with field intensities of, at least, 6.3 Tesla (proton frequencies of 270 MHz and more). The given results which had been obtained from documents of the manufacturers try to meet the manufacturers' need for safety. Market shares and sites are not listed. (DG) [de

  4. NMR Characterization of Flavanone Naringenin 7-O-Glycoside Diastereomer

    Directory of Open Access Journals (Sweden)

    SUN Li-juan

    2017-12-01

    Full Text Available To discriminate R and S flavanone glycoside using NMR, the mixture of R and S naringenin 7-O-glycoside was first isolated from Gleditsia sinensis. 1H and 13C NMR data of the mixture were recorded with 1H NMR, 13C NMR, 1H-1H COSY, 1H-13C HSQC and 1H-13C HMBC in DMSO-d6 solution. The two diastereomers were then separated with chiral chromatographic isolation, with their absolute configurations determined by circular dichroism. To avoid the disturbance of protons from glucose residues to dihydroflavonoid, 1H NMR spectra were acquired for pure R and S naringenin 7-O-glycoside and their mixture in CD3CN. The two diastereomers showed the largest proton chemical shift differences at the end group of glucose residue (H-1" with a chemical shift difference of 9.4 Hz. The OH-5 proton showed a chemical shift difference of 5.8 Hz. The chemical shift of the three protons on ring C were all influenced by configuration.

  5. NMR-based approach to the analysis of radiopharmaceuticals: radiochemical purity, specific activity, and radioactive concentration values by proton and tritium NMR spectroscopy.

    Science.gov (United States)

    Schenk, David J; Dormer, Peter G; Hesk, David; Pollack, Scott R; Lavey, Carolee Flader

    2015-06-15

    Compounds containing tritium are widely used across the drug discovery and development landscape. These materials are widely utilized because they can be efficiently synthesized and produced at high specific activity. Results from internally calibrated (3)H and (1)H nuclear magnetic resonance (NMR) spectroscopy suggests that at least in some cases, this calibrated approach could supplement or potentially replace radio-high-performance liquid chromatography for radiochemical purity, dilution and scintillation counting for the measurement of radioactivity per volume, and liquid chromatography/mass spectrometry analysis for the determination of specific activity. In summary, the NMR-derived values agreed with those from the standard approaches to within 1% to 9% for solution count and specific activity. Additionally, the NMR-derived values for radiochemical purity deviated by less than 5%. A benefit of this method is that these values may be calculated at the same time that (3)H NMR analysis provides the location and distribution of tritium atoms within the molecule. Presented and discussed here is the application of this method, advantages and disadvantages of the approach, and a rationale for utilizing internally calibrated (1)H and (3)H NMR spectroscopy for specific activity, radioactive concentration, and radiochemical purity whenever acquiring (3)H NMR for tritium location. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

    Science.gov (United States)

    Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

    2017-07-19

    Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

  7. Rapid NMR method for the quantification of organic compounds in thin stillage.

    Science.gov (United States)

    Ratanapariyanuch, Kornsulee; Shen, Jianheng; Jia, Yunhua; Tyler, Robert T; Shim, Youn Young; Reaney, Martin J T

    2011-10-12

    Thin stillage contains organic and inorganic compounds, some of which may be valuable fermentation coproducts. This study describes a thorough analysis of the major solutes present in thin stillage as revealed by NMR and HPLC. The concentration of charged and neutral organic compounds in thin stillage was determined by excitation sculpting NMR methods (double pulse field gradient spin echo). Compounds identified by NMR included isopropanol, ethanol, lactic acid, 1,3-propanediol, acetic acid, succinic acid, glycerophosphorylcholine, betaine, glycerol, and 2-phenylethanol. The concentrations of lactic and acetic acid determined with NMR were comparable to those determined using HPLC. HPLC and NMR were complementary, as more compounds were identified using both methods. NMR analysis revealed that stillage contained the nitrogenous organic compounds betaine and glycerophosphorylcholine, which contributed as much as 24% of the nitrogen present in the stillage. These compounds were not observed by HPLC analysis.

  8. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state (13)C NMR and solution (31)P NMR spectroscopy.

    Science.gov (United States)

    Liu, Shasha; Zhu, Yuanrong; Meng, Wei; He, Zhongqi; Feng, Weiying; Zhang, Chen; Giesy, John P

    2016-02-01

    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state (13)C NMR and solution (31)P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O-C-O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH3 and COO/N-C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH3 and COO/N-C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. NMR studies of electrophoretic mobility in surfactant systems

    International Nuclear Information System (INIS)

    Conveney, F.M.; Strange, J.H.; Smith, A.L.; Smith, E.G.

    1989-01-01

    An experimental technique is described in which the flow of electrically charged micelles is measured in the presence of an applied electric field using an NMR technique. The method is used to determine the electrophoretic mobility at ambient temperature of a 5% aqueous solution of sodium dodecyl sulphate and is shown to provide a new technique for the study of electrophoresis in surfactant solutions. (author). 8 refs.; 4 figs

  10. Creatinine and creatininium cation in water solution. Tautomerism and quantitative interpretation of the solution acidity effect on 1H, 13C and 1:4N NMR chemical shifts

    International Nuclear Information System (INIS)

    Kotsyubynskyy, D.; Molchanov, S.; Gryff-Keller, A.

    2004-01-01

    1 H, 13 C and 1 :4N NMR chemical shifts for creatinine in water solution of various acidity have been measured. Analysis of these data enabled determination of the acidity constant of creatininium cation and the chemical shifts of the neutral and protonated forms of creatinine. Molecular energies and carbon and nitrogen magnetic shielding constants for various tautomeric structures of the investigated species have been calculated using the quantum chemistry method GIAO DFT B3LYP/6-311++G(2d,p). Compilation of the available experimental and theoretical results has provided additional information on the problem of tautomerism of this important biological molecule. (author)

  11. In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes

    International Nuclear Information System (INIS)

    Sakai, Tomomi; Tochio, Hidehito; Tenno, Takeshi; Ito, Yutaka; Kokubo, Tetsuro; Hiroaki, Hidekazu; Shirakawa, Masahiro

    2006-01-01

    In-cell NMR is an application of solution NMR that enables the investigation of protein conformations inside living cells. We have measured in-cell NMR spectra in oocytes from the African clawed frog Xenopus laevis. 15 N-labeled ubiquitin, its derivatives and calmodulin were injected into Xenopus oocytes and two-dimensional 1 H- 15 N correlation spectra of the proteins were obtained. While the spectrum of wild-type ubiquitin in oocytes had rather fewer cross-peaks compared to its in vitro spectrum, ubiquitin derivatives that are presumably unable to bind to ubiquitin-interacting proteins gave a markedly larger number of cross-peaks. This observation suggests that protein-protein interactions between ubiquitin and ubiquitin-interacting proteins may cause NMR signal broadening, and hence spoil the quality of the in-cell HSQC spectra. In addition, we observed the maturation of ubiquitin precursor derivative in living oocytes using the in-cell NMR technique. This process was partly inhibited by pre-addition of ubiquitin aldehyde, a specific inhibitor for ubiquitin C-terminal hydrolase (UCH). Our work demonstrates the potential usefulness of in-cell NMR with Xenopus oocytes for the investigation of protein conformations and functions under intracellular environmental conditions

  12. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Richard [Huazhong University of Science and Technology, School of Software Engineering (China); Wang, Yan [Huazhong University of Science and Technology, School of Life Science and Technology (China); Xue, Zhidong, E-mail: zdxue@hust.edu.cn [Huazhong University of Science and Technology, School of Software Engineering (China); Zhang, Yang, E-mail: zhng@umich.edu [University of Michigan, Department of Computational Medicine and Bioinformatics (United States)

    2015-08-15

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.

  13. Principles of high resolution NMR in solids

    CERN Document Server

    Mehring, Michael

    1983-01-01

    The field of Nuclear Magnetic Resonance (NMR) has developed at a fascinating pace during the last decade. It always has been an extremely valuable tool to the organic chemist by supplying molecular "finger print" spectra at the atomic level. Unfortunately the high resolution achievable in liquid solutions could not be obtained in solids and physicists and physical chemists had to live with unresolved lines open to a wealth of curve fitting procedures and a vast amount of speculations. High resolution NMR in solids seemed to be a paradoxon. Broad structure­ less lines are usually encountered when dealing with NMR in solids. Only with the recent advent of mUltiple pulse, magic angle, cross-polarization, two-dimen­ sional and multiple-quantum spectroscopy and other techniques during the last decade it became possible to resolve finer details of nuclear spin interactions in solids. I have felt that graduate students, researchers and others beginning to get involved with these techniques needed a book which trea...

  14. Stereochemistry of 16a-Hydroxyfriedelin and 3-Oxo-16-methylfriedel-16-ene Established by 2D NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Vagner Fernandes Knupp

    2009-02-01

    Full Text Available Friedelin (1, 3b-friedelinol (2, 28-hydroxyfriedelin (3, 16a-hydroxyfriedelin (4, 30-hydroxyfriedelin (5 and 16a,28-dihydroxyfriedelin (6 were isolated through fractionation of the hexane extract obtained from branches of Salacia elliptica. After a week in CDCl3 solution, 16a-hydroxyfriedelin (4 reacted turning into 3-oxo-16-methylfriedel-16-ene (7. This is the first report of a dehydration followed by a Nametkin rearrangement of a pentacyclic triterpene in CDCl3 solution occurring in the NMR tube. These seven pentacyclic triterpenes was identified through NMR spectroscopy and the stereochemistry of compound 4 and 7 was established by 2D NMR (NOESY spectroscopy and mass spectrometry (GC-MS. It is also the first time that all the 13C-NMR and 2D NMR spectral data are reported for compounds 4 and 7.

  15. Dynamic nuclear-polarization studies of paramagnetic species in solution

    International Nuclear Information System (INIS)

    Glad, W.E.

    1982-07-01

    Dynamic Nuclear Polarization (DNP) was used to measure the electron spin lattice relaxation times, T 1 , of transition metal ions in aqueous solution. Saturation which is induced in the electron spin system is transferred to the solvent proton spins by dipole-dipole interactions. The change in the polarization of the proton spins is much larger than it is in the electron spins. The change in proton polarization is easily measured by proton Nuclear Magnetic Resonance (NMR). In one experimental arrangement the sample solution was continuously flowed through a microwave cavity to the NMR coil. The NMR was observed with a continuous wave NMR spectrometer. In a second arrangement the whole sample tube was moved from within the microwave cavity to the NMR coil in less than 40 ms by a blast of compressed air. The NMR was then observed with a pulse-Fourier-transform spectrometer. With the second arrangement a mean-square microwave magnetic field at the sample of more than 10 G 2 is obtainable with 14 W of microwave power. Measurements of DNP at 9 GHz were made on aqueous solutions of VO 2+ , Mn 2+ , Cr(CN) 6 3- , Cu 2+ and Cu(ethylenediamine) 2 (H 2 0) 2 2+ ions from 3 to 60 0 C. It was also possible to observe DNP on resolved proton resonances from mixed water-acetonitrile solutions of VO 2+ and Cr(CN) 6 3- ions

  16. Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    LeMaster, D.M. [Northwestern Univ., Evanston, IL (United States)

    1994-12-01

    Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

  17. Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy

    International Nuclear Information System (INIS)

    Fry, D.C.; Byler, D.M.; Susi, H.; Brown, M.; Kuby, S.A.; Mildvan, A.S.

    1988-01-01

    The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme, appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase, with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of β-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% α-helix, 38% β-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possible due to disorder, it can be fit by using methods developed on well-characterized globular proteins. The CD spectrum is best fit by assuming the presence of at most 13% α-helix in the peptide, 24 +/- 2% β-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformation changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assess by CD

  18. Proton NMR study of α-MnH 0.06

    Science.gov (United States)

    Soloninin, A. V.; Skripov, A. V.; Buzlukov, A. L.; Antonov, V. E.; Antonova, T. E.

    2004-07-01

    Proton nuclear magnetic resonance (NMR) spectra and spin-lattice relaxation rates for the solid solution α-MnH 0.06 have been measured over the temperature range 11-297 K and the resonance frequency range 20-90 MHz. A considerable shift and broadening of the proton NMR line and a sharp peak of the spin-lattice relaxation rate are observed near 130 K. These effects are attributed to the onset of antiferromagnetic ordering below the Néel temperature TN≈130 K. The proton NMR line does not disappear in the antiferromagnetic phase; this suggests a small magnitude of the local magnetic fields at H-sites in α-MnH 0.06. The spin-lattice relaxation rate in the paramagnetic phase is dominated by the effects of spin fluctuations.

  19. Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers.

    Science.gov (United States)

    Jayanthi, S; Chatterjee, Bhaswati; Raghothama, S

    2009-10-01

    Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro-(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro-(L)Pro-(L)Phe-OMe (2), and Piv-(D)Pro-(L)Pro-(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The (13)C spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C(beta) and C(gamma) carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all trans form across the di-Proline segment. The results are in agreement with the X-ray analysis. Solid state (15)N resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. (1)H chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between (1)H--(13)C. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009.

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

    Science.gov (United States)

    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.

  1. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation

    International Nuclear Information System (INIS)

    Ding, Yi; Fujimoto, L. Miya; Yao, Yong; Marassi, Francesca M.

    2015-01-01

    Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396–10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure–activity correlation experiments across a wide range of timescales

  2. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Yi; Fujimoto, L. Miya; Yao, Yong; Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham Medical Research Institute (United States)

    2015-04-15

    Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396–10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure–activity correlation experiments across a wide range of timescales.

  3. Protein folding on the ribosome studied using NMR spectroscopy

    Science.gov (United States)

    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

  4. Chemical behavior of methylpyranomalvidin-3-O-glucoside in aqueous solution studied by NMR and UV-visible spectroscopy.

    Science.gov (United States)

    Oliveira, Joana; Petrov, Vesselin; Parola, A Jorge; Pina, Fernando; Azevedo, Joana; Teixeira, Natércia; Brás, Natércia F; Fernandes, Pedro A; Mateus, Nuno; Ramos, Maria João; de Freitas, Victor

    2011-02-17

    In the present work, the proton-transfer reactions of the methylpyranomalvidin-3-O-glucoside pigment in water with different pH values was studied by NMR and UV-visible spectroscopies. The results showed four equilibrium forms: the methylpyranomalvidin-3-O-glucoside cation, the neutral quinoidal base, the respective anionic quinoidal base, and a dianionic base unprotonated at the methyl group. According to the NMR data, it seems that for methylpyranomalvidin-3-O-glucoside besides the acid-base equilibrium between the pyranoflavylium cation and the neutral quinoidal base, a new species is formed at pD 4.88-6.10. This is corroborated by the appearance of a new set of signals in the NMR spectrum that may be assigned to the formation of hemiketal/cis-chalcone species to a small extent. The two ionization constants (pK(a1) and pK(a2)) obtained by both methods (NMR and UV-visible) for methylpyranomalvidin-3-O-glucoside are in agreement (pK(a1) = 5.17 ± 0.03; pK(a2) = 8.85 ± 0.08; and pK(a1) = 4.57 ± 0.07; pK(a2) = 8.23 ± 0.04 obtained by NMR and UV-visible spectroscopies, respectively). Moreover, the fully dianionic unprotonated form (at the methyl group) of the methylpyranomalvidin-3-O-glucoside is converted slowly into a new structure that displays a yellow color at basic pH. On the basis of the results obtained through LC-MS and NMR, the proposed structure was found to correspond to the flavonol syringetin-3-glucoside.

  5. 99 Tc NMR determination of the oxygen isotope content in 18 O-enriched water.

    Science.gov (United States)

    Tarasov, Valerii P; Kirakosyan, Gayana А; German, Konstantin E

    2018-03-01

    99 Tc NMR has been suggested as an original method of evaluating the content of oxygen isotopes in oxygen-18-enriched water, a precursor for the production of radioisotope fluorine-18 used in positron emission tomography. To this end, solutions of NH 4 TcO 4 or NaTcO 4 (up to 0.28 mol/L) with natural abundance of oxygen isotopes in virgin or recycled 18 O-enriched water have been studied by 99 Tc NMR. The method is based on 16 O/ 17 O/ 18 O intrinsic isotope effects in the 99 Tc NMR chemical shifts, and the statistical distribution of oxygen isotopes in the coordination sphere of TcO 4 - and makes it possible to quantify the composition of enriched water by measuring the relative intensities of the 99 Tc NMR signals of the Tc 16 O 4-n 18 O n - isotopologues. Because the oxygen exchange between TcO 4 - and enriched water in neutral and alkaline solutions is characterized by slow kinetics, gaseous HCl was bubbled through a solution for a few seconds to achieve the equilibrium distribution of oxygen isotopes in the Tc coordination sphere without distortion of the oxygen composition of the water. Pertechnetate ion was selected as a probe due to its high stability in solutions and the significant 99 Tc NMR shift induced by a single 16 O→ 18 O substitution (-0.43 ± 0.01 ppm) in TcO 4 - and spin coupling constant 1 J( 99 Tc- 17 O) (131.46 Hz) favourable for the observation of individual signals of Tc 16 O 4-n 18 O n - isotopologues. Copyright © 2017 John Wiley & Sons, Ltd.

  6. 13C and 29Si NMR as a probe to investigate polysiloxanes used in dental applications

    International Nuclear Information System (INIS)

    Silva, Naira Machado da; Tavares, Maria Ines B.

    2001-01-01

    The properties of dental mould polymeric materials are strongly influenced by the chemical structure of both the polymer and the catalyst used in the crosslink reaction between them. In order to characterize and suggest some modifications on the materials interfacial interactions, mixtures of Polymer-catalyst were prepared. The polymer and the catalyst chemical structures were obtained by 13 C, 1 H and 129 Si NMR analysis in solution state. From the solution NMR results it was obtained the structure of the polymer and the catalyst and also the kind of the crosslink reaction taken. The CPMAS 1 '3C NMR analysis in the solid state were used to identify chemical structure of the polymeric dental moulded sample. (author)

  7. Mono terpenes characterization by {sup 1} H and {sup 13} C-1 NMR; Caracterizacao de monoterpenos por RMN - {sup 1} H e de {sup 13} C-1

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Martha T. de [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Fisico-Quimica; Silveira, Carmen L.P. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Quimica Organica; Mcchesney, James D [Mississippi Univ., University, MS (United States). Research Inst. of Pharmaceutical Sciences

    1992-12-31

    Artemisinine, a new lactone sesquiterpene containing one peroxide binding, is the main anti malarial agent obtained from the Artemisia annua L. Viewing to obtain a simple synthetic route for artemisinic acid preparation, which is the key intermediary for total synthesis of this type of anti malarial agent, R-carvone has been chosen as starting material. The S-carvone was used as model for reaction optimization and preparation of derivatives to be used for NMR studies. The main objective of this work is the signalling of the {sup 13} C and {sup 1} H NMR spectra, using the 2 D-COSY and 2 D-Hector spectra 4 refs., 3 figs., 1 tab

  8. High Resolution NMR Studies of Encapsulated Proteins In Liquid Ethane

    Science.gov (United States)

    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

  9. Dissolution of lignin in green urea aqueous solution

    Science.gov (United States)

    Wang, Jingyu; Li, Ying; Qiu, Xueqing; Liu, Di; Yang, Dongjie; Liu, Weifeng; Qian, Yong

    2017-12-01

    The dissolution problem is the main obstacle for the value-added modification and depolymerization of industrial lignin. Here, a green urea aqueous solution for complete dissolution of various lignin is presented and the dissolution mechanism is analyzed by AFM, DLS and NMR. The results show that the molecular interaction of lignin decreases from 32.3 mN/m in pure water to 11.3 mN/m in urea aqueous solution. The immobility of 1H NMR spectra and the shift of 17O NMR spectra of urea in different lignin/urea solutions indicate that the oxygen of carbonyl in urea and the hydrogen of hydroxyl in lignin form new hydrogen bonds and break the original hydrogen bonds among lignin molecules. The shift of 1H NMR spectra of lignin and the decrease of interactions in model compound polystyrene indicate that urea also breaks the π-π interactions between aromatic rings of lignin. Lignin dissolved in urea aqueous has good antioxidant activity and it can scavenge at least 63% free radicals in 16 min.

  10. Covariance NMR Processing and Analysis for Protein Assignment.

    Science.gov (United States)

    Harden, Bradley J; Frueh, Dominique P

    2018-01-01

    During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

  11. Photochemical generation and 1H NMR detection of alkyl allene oxides in solution

    International Nuclear Information System (INIS)

    Breen, L.E.; Schepp, N.P.; Tan, C.-H.E.

    2005-01-01

    Irradiation of substituted 5-alkyl-4,5-epoxyvalerophenones leads to the formation of alkyl allene oxides that, in some cases, are sufficiently long-lived to be detected at room temperature by 1 H NMR spectroscopy. Absolute lifetime measurements show that the size of the alkyl group has a significant influence on the reactivity of the allene oxide, with tert-butyl allene oxide having a lifetime of 24 h in CD 3 CN at room temperature that is considerably longer than the 1.5 h lifetime of the ethyl allene oxide. The allene oxides react rapidly with water to give α-hydroxyketones. The mechanism involves nucleophilic attack to the epoxide carbon to give an enol, which can also be detected as an intermediate by 1 H NMR spectroscopy. (author)

  12. Biomolecular solid state NMR with magic-angle spinning at 25K.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2008-12-01

    A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

  13. NMR investigation of boron impurities in refined metallurgical grade silicon

    Energy Technology Data Exchange (ETDEWEB)

    Grafe, Hans-Joachim; Loeser, Wolfgang; Schmitz, Steffen; Sakaliyska, Miroslava [Leibniz Institute for Solid State and Materials Research (IFW), Dresden (Germany); Wurmehl, Sabine [Leibniz Institute for Solid State and Materials Research (IFW), Dresden (Germany); Institute for Solid State Physics, Technische Universitaet Dresden (Germany); Eisert, Stefan; Reichenbach, Birk; Mueller, Tim [Adensis GmbH, Dresden (Germany); Acker, Joerg; Rietig, Anja; Ducke, Jana [Department of Chemistry, Faculty for Natural Sciences, Brandenburg Technical University Cottbus-Senftenberg, Senftenberg (Germany)

    2015-09-15

    The nuclear magnetic resonance (NMR) method was applied for tracking boron impurities in the refining process of metallurgical grade (MG) silicon. From the NMR signal of the {sup 11}B isotope at an operating temperature 4.2 K, the boron concentration can be estimated down to the order of 1-10 wppm B. After melting and resolidification of MG-Si alloyed with Ca and Ti, a major fraction of B impurities remains in the Si solid solution as inferred from the characteristic NMR frequency. The alloying element Ti does not form substantial fractions of TiB{sub 2}. Acid leaching of crushed powders of MG-Si alloyed with Ca and Ti can diminish the initial impurity content of B suggesting its accumulation in the grain boundary phases. NMR signals of TiB{sub 2} at 4.2 K and room temperature (RT), and of poly-Si with different B doping at 4.2 K. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Deciphering ligands' interaction with Cu and Cu2O nanocrystal surfaces by NMR solution tools.

    Science.gov (United States)

    Glaria, Arnaud; Cure, Jérémy; Piettre, Kilian; Coppel, Yannick; Turrin, Cédric-Olivier; Chaudret, Bruno; Fau, Pierre

    2015-01-12

    The hydrogenolysis of [Cu2{(iPrN)2(CCH3)}2] in the presence of hexadecylamine (HDA) or tetradecylphosphonic acid (TDPA) in toluene leads to 6-9 nm copper nanocrystals. Solution NMR spectroscopy has been used to describe the nanoparticle surface chemistry during the dynamic phenomenon of air oxidation. The ligands are organized as multilayered shells around the nanoparticles. The shell of ligands is controlled by both their intermolecular interactions and their bonding strength on the nanocrystals. Under ambient atmosphere, the oxidation rate of colloidal copper nanocrystals closely relies on the chemical nature of the employed ligands (base or acid). Primary amine molecules behave as soft ligands for Cu atoms, but are even more strongly coordinated on surface Cu(I) sites, thus allowing a very efficient corrosion protection of the copper core. On the contrary, the TDPA ligands lead to a rapid oxidation rate of Cu nanoparticles and eventually to the re-dissolution of Cu(II) species at the expense of the nanocrystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. NMR in a crystallography-based high-throughput protein structure-determination environment

    International Nuclear Information System (INIS)

    Wüthrich, Kurt

    2010-01-01

    As an introduction to three papers on comparisons of corresponding crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG), an outline is provided of the JCSG strategy for combined use of the two techniques. A special commentary addresses the potentialities of the concept of ‘reference crystal structures’, which is introduced in the following three papers. An introduction is provided to three papers which compare corresponding protein crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG). Special mention is made of the JCSG strategy for combined use of the two techniques, and of potential applications of the concept of ‘reference crystal structures’, which is introduced in the following three papers

  16. Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel

    Energy Technology Data Exchange (ETDEWEB)

    Pielak, Rafal M. [Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (United States); Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115 (United States); Chou, James J., E-mail: chou@cmcd.hms.harvard.edu [Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (United States)

    2010-10-08

    Research highlights: {yields} This paper reports the structure of the V27A drug resistant mutant of the M2 channel of influenza A virus. {yields} High quality NMR data allowed a better-defined structure for the C-terminal region of the M2 channel. {yields} Using the structure, we propose a proton transfer pathway during M2 proton conduction. {yields} Structural comparison between the wildtype, V27A and S31N variants allowed an in-depth analysis of possible modes of drug resistance. {yields} Distinct feature of the V27A channel pore also provides an explanation for its faster rate of proton conduction. -- Abstract: The M2 protein of influenza A virus forms a proton-selective channel that is required for viral replication. It is the target of the anti-influenza drugs, amantadine and rimantadine. Widespread drug resistant mutants, however, has greatly compromised the effectiveness of these drugs. Here, we report the solution NMR structure of the highly pathogenic, drug resistant mutant V27A. The structure reveals subtle structural differences from wildtype that maybe linked to drug resistance. The V27A mutation significantly decreases hydrophobic packing between the N-terminal ends of the transmembrane helices, which explains the looser, more dynamic tetrameric assembly. The weakened channel assembly can resist drug binding either by destabilizing the rimantadine-binding pocket at Asp44, in the case of the allosteric inhibition model, or by reducing hydrophobic contacts with amantadine in the pore, in the case of the pore-blocking model. Moreover, the V27A structure shows a substantially increased channel opening at the N-terminal end, which may explain the faster proton conduction observed for this mutant. Furthermore, due to the high quality NMR data recorded for the V27A mutant, we were able to determine the structured region connecting the channel domain to the C-terminal amphipathic helices that was not determined in the wildtype structure. The new structural

  17. Chemical characterization of a chelator-treated soil humate by solution-state multinuclear two-dimensional NMR and FTIR and pyrolysis-GCMS

    Energy Technology Data Exchange (ETDEWEB)

    Fan, T.W.M.; Higashi, R.M.; Lane, A.N.

    2000-05-01

    A California forest soil used for contaminant bioavailability studies was extracted for humic substances (HS) and then treated with 4,5-dihydroxy-1,3-benzene disulfonate (Tiron) to remove exchangeable metal ions. This yielded HS that was readily water-soluble at neutral pH without residual Tiron contamination, and the gel electrophoretic pattern was very similar to an international reference HS. The improved solubility facilitated analysis of HS by solution-state 1-D and 2-D {sup 1}H, {sup 13}C, {sup 31}P, and {sup 13}C-{sup 1}H NMR. The amino acids Gly, Ala, Leu, lle, Val, Asp, Ser, Thr, Glu, and Pro were identified in intact HS as peptidic from scalar coupling in TOCSY and dipolar interactions in NOESY and then confirmed by acid digestion of HS with 2-D {sup 1}H NMR and GCMS analysis. The presence of peptides was also corroborated by FT-IR and pyrolysis-GCMS results. Carbohydrates containing {alpha}- and {beta}-pyranoses, methoxy-phenylpropanyl structures, phosphate mono/diesters, polyphosphates, plus phosphatidic acid esters were also evident. Furthermore, the {sup 1}H NOESY, TOCSY, and HSQC together indicated that the peptidic side chains were mobile, whereas aromatic groups were relatively rigid. Thus the peptidic moieties may be more readily accessible to aqueous contaminants than aromatic groups.

  18. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

    Science.gov (United States)

    Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

    2010-09-03

    Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR - X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.

  19. Structure determination of helical filaments by solid-state NMR spectroscopy

    Science.gov (United States)

    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

  20. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

    International Nuclear Information System (INIS)

    Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

    2010-01-01

    Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques was explored for the initial steps in the challenge of searching proteins of unknown functions for putative active sites. The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the

  1. Virtual and solution conformations of oligosaccharides

    International Nuclear Information System (INIS)

    Cumming, D.A.; Carver, J.P.

    1987-01-01

    The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

  2. NMR spectroscopy study of agar-based polymers electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Mattos, R.I.; Tambelli, C.E. [Universidade de Sao Paulo (USP), Pirassununga, SP (Brazil). Fac. de Zootecnia e Engenharia de Alimentos; Raphael, E. [Universidade Federal de Sao Joao del-Rey (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Silva, I.D.A.; Magon, C.J.; Donoso, J.P. [Universidade de Sao Paulo (IFSC/USP), Sao Carlos, SP (Brazil). Inst. de Fisica

    2012-07-01

    Full text: This communication presents the results of preparation and characterization of transparent films obtained from agar and acetic acid. The films were characterized by electrochemical impedance spectroscopy (EIS) and nuclear magnetic resonance (NMR). The film formed by agar (Sigma Aldrich) was dispersed in water and kept under stirring and heating at 100 deg C. Next, glycerol, formaldehyde and different quantities of acetic acid (25 and 50 wt%) were added to this solution. The obtained solution was placed on a glass plate and left to dry for 48 hours in oven at 50 deg C to obtain the films, which were kept under vacuum before characterization. The ionic conductivity of the films display an Arrhenius behavior with activation energy E{sub a} = 78 (25 wt% of acetic acid) and E{sub a} = 87 kJ/mol (50 wt% of acetic acid). The conductivity values were 3:0 X 10{sup -6} and 1:2 X 10{sup -4} S/cm at room temperature and 4:4 X 10{sup -4} and 1:5 X 10{sup -3}S/cm at 70 deg C, for the 25 and 50 wt% of acetic acid respectively. To investigate the mechanism of protonic conduction in the polymer proton conductor proton NMR measurements were performed in the temperature range 200-370 K. The {sup 1}H-NMR results exhibit the qualitative feature associated with the proton mobility, namely the presence of well defined {sup 1}H spin-lattice relaxation maxima at 300 K. Activation energy of the order of 40 kJ/mol was obtained from the {sup 1}H-NMR line narrowing data. The ionic conductivity of the film combined with their transparency, flexibility, homogeneity and good adhesion to the glasses or metals indicate that agar-based SPEs are promising materials for used on optoelectronic applications. (author)

  3. Solution conformation and dynamics of a tetrasaccharide related to the LewisX antigen deduced by NMR relaxation measurements

    International Nuclear Information System (INIS)

    Poveda, Ana; Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus

    1997-01-01

    1 H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-α-N-acetyl-galactosaminyl-β-galactopyranosyl-(1 → 4)[3-O-α-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, 13 C-NMR relaxation data have also been recorded at both fields. The 1 H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The 13 C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the 1 H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS 2 . Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data

  4. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum

    Directory of Open Access Journals (Sweden)

    Yunhuang Yang

    2012-06-01

    Full Text Available CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07 corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.

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

    Science.gov (United States)

    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.

  6. Purification and Characterization of Recombinant N-Terminally Pyroglutamate-Modified Amyloid-β Variants and Structural Analysis by Solution NMR Spectroscopy.

    Directory of Open Access Journals (Sweden)

    Christina Dammers

    Full Text Available Alzheimer's disease (AD is the leading cause of dementia in the elderly and is characterized by memory loss and cognitive decline. Pathological hallmark of AD brains are intracellular neurofibrillary tangles and extracellular amyloid plaques. The major component of these plaques is the highly heterogeneous amyloid-β (Aβ peptide, varying in length and modification. In recent years pyroglutamate-modified amyloid-β (pEAβ peptides have increasingly moved into the focus since they have been described to be the predominant species of all N-terminally truncated Aβ. Compared to unmodified Aβ, pEAβ is known to show increased hydrophobicity, higher toxicity, faster aggregation and β-sheet stabilization and is more resistant to degradation. Nuclear magnetic resonance (NMR spectroscopy is a particularly powerful method to investigate the conformations of pEAβ isoforms in solution and to study peptide/ligand interactions for drug development. However, biophysical characterization of pEAβ and comparison to its non-modified variant has so far been seriously hampered by the lack of highly pure recombinant and isotope-enriched protein. Here we present, to our knowledge, for the first time a reproducible protocol for the production of pEAβ from a recombinant precursor expressed in E. coli in natural isotope abundance as well as in uniformly [U-15N]- or [U-13C, 15N]-labeled form, with yields of up to 15 mg/l E. coli culture broth. The chemical state of the purified protein was evaluated by RP-HPLC and formation of pyroglutamate was verified by mass spectroscopy. The recombinant pyroglutamate-modified Aβ peptides showed characteristic sigmoidal aggregation kinetics as monitored by thioflavin-T assays. The quality and quantity of produced pEAβ40 and pEAβ42 allowed us to perform heteronuclear multidimensional NMR spectroscopy in solution and to sequence-specifically assign the backbone resonances under near-physiological conditions. Our results suggest

  7. NMR 1D-imaging of water infiltration into mesoporous matrices.

    Science.gov (United States)

    Le Feunteun, Steven; Diat, Olivier; Guillermo, Armel; Poulesquen, Arnaud; Podor, Renaud

    2011-04-01

    It is shown that coupling nuclear magnetic resonance (NMR) 1D-imaging with the measure of NMR relaxation times and self-diffusion coefficients can be a very powerful approach to investigate fluid infiltration into porous media. Such an experimental design was used to study the very slow seeping of pure water into hydrophobic materials. We consider here three model samples of nuclear waste conditioning matrices which consist in a dispersion of NaNO(3) (highly soluble) and/or BaSO(4) (poorly soluble) salt grains embedded in a bitumen matrix. Beyond studying the moisture progression according to the sample depth, we analyze the water NMR relaxation times and self-diffusion coefficients along its 1D-concentration profile to obtain spatially resolved information on the solution properties and on the porous structure at different scales. It is also shown that, when the relaxation or self-diffusion properties are multimodal, the 1D-profile of each water population is recovered. Three main levels of information were disclosed along the depth-profiles. They concern (i) the water uptake kinetics, (ii) the salinity and the molecular dynamics of the infiltrated solutions and (iii) the microstructure of the water-filled porosities: open networks coexisting with closed pores. All these findings were fully validated and enriched by NMR cryoporometry experiments and by performing environmental scanning electronic microscopy observations. Surprisingly, results clearly show that insoluble salts enhance the water progression and thereby increase the capability of the material to uptake water. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Determining pH at elevated pressure and temperature using in situ ¹³C NMR.

    Science.gov (United States)

    Surface, J Andrew; Wang, Fei; Zhu, Yanzhe; Hayes, Sophia E; Giammar, Daniel E; Conradi, Mark S

    2015-02-03

    We have developed an approach for determining pH at elevated pressures and temperatures by using (13)C NMR measurements of inorganic carbon species together with a geochemical equilibrium model. The approach can determine in situ pH with precision better than 0.1 pH units at pressures, temperatures, and ionic strengths typical of geologic carbon sequestration systems. A custom-built high pressure NMR probe was used to collect (13)C NMR spectra of (13)C-labeled CO2 reactions with NaOH solutions and Mg(OH)2 suspensions at pressures up to 107 bar and temperatures of 80 °C. The quantitative nature of NMR spectroscopy allows the concentration ratio [CO2]/[HCO3(-)] to be experimentally determined. This ratio is then used with equilibrium constants calculated for the specific pressure and temperature conditions and appropriate activity coefficients for the solutes to calculate the in situ pH. The experimentally determined [CO2]/[HCO3(-)] ratios agree well with the predicted values for experiments performed with three different concentrations of NaOH and equilibration with multiple pressures of CO2. The approach was then applied to experiments with Mg(OH)2 slurries in which the change in pH could track the dissolution of CO2 into solution, rapid initial Mg(OH)2 dissolution, and onset of magnesium carbonate precipitation.

  9. NMR imaging

    International Nuclear Information System (INIS)

    Andrew, E.R.

    1983-01-01

    Since hydrogen is the most abundant element in all living organisms, proton NMR lends itself well as a method of investigation in biology and medicine. NMR imaging has some special advantages as a diagnostic tool: no ionizing radiation is used, it is noninvasive; it provides a safer means of imaging than the use of x-rays, gamma rays, positrons, or heavy ions. In contrast with ultrasound, the radiation penetrates the bony structures without attenuation. In additional to morphological information, NMR imaging provides additional diagnostic insights through relaxation parameters, which are not available from other imaging methods. In the decade since the first primitive NMR images were obtained, the quality of images now obtained approaches those from CT x-ray scanners. Prototype instruments are being constructed for clinical evaluation and the first whole-body scanners are beginning to appear on the market at costs comparable to CT scanners. Primary differences in equipment for conventional NMR and NMR imaging are the much larger aperture magnets that are required for the examination of human subjects and the addition of coils to generate field gradients and facilities for manipulating the gradients. Early results from clinical trials in many parts of the world are encouraging, and in a few years, the usefuleness of this modality of medical imaging to the medical profession in diagnosis and treatment of disease will be defined. 10 figures

  10. pH control and rapid mixing in spinning NMR samples

    Science.gov (United States)

    Yesinowski, James P.; Sunberg, Richard J.; Benedict, James J.

    An apparatus is described which permits the acquisition of NMR spectra from spinning 20-mm sample tubes while: (1) constantly monitoring the pH; (2) adding reagents to maintain constant pH (pH-statting); (3) efficiently mixing the added reagent. The apparatus was built to study the spontaneous precipitation of calcium phosphates from supersaturated solutions using 31P NMR. Other applications include the rapid determination of NMR titration curves, and the minimization of temperature gradients in large sample tubes. The apparatus was used to measure the 31P chemical shift titration of dilute phosphoric acid, which yielded accurate shifts for the three species of protonated orthophosphate ion. The bulk magnetic susceptibility of 85% H 3PO 4 relative to a dilute aqueous sample was also measured, and is shown to contribute significantly to chemical shift measurements.

  11. NMR 1D-imaging of water infiltration into meso-porous matrices

    International Nuclear Information System (INIS)

    Le Feunteun, St.; Diat, O.; Podor, R.; Le Feunteun, St.; Poulesquen, A.; Poulesquen, A.

    2011-01-01

    It is shown that coupling nuclear magnetic resonance (NMR) 1D-imaging with the measure of NMR relaxation times and self-diffusion coefficients can be a very powerful approach to investigate fluid infiltration into porous media. Such an experimental design was used to study the very slow seeping of pure water into hydrophobic materials. We consider here three model samples of nuclear waste conditioning matrices which consist in a dispersion of NaNO 3 (highly soluble) and/or BaSO 4 (poorly soluble) salt grains embedded in a bitumen matrix. Beyond studying the moisture progression according to the sample depth, we analyze the water NMR relaxation times and self-diffusion coefficients along its 1D-concentration profile to obtain spatially resolved information on the solution properties and on the porous structure at different scales. It is also shown that, when the relaxation or self-diffusion properties are multimodal, the 1D-profile of each water population is recovered. Three main levels of information were disclosed along the depth-profiles. They concern (i) the water uptake kinetics, (ii) the salinity and the molecular dynamics of the infiltrated solutions and (iii) the microstructure of the water-filled porosities: open networks coexisting with closed pores. All these findings were fully validated and enriched by NMR cryo-poro-metry experiments and by performing environmental scanning electronic microscopy observations. Surprisingly, results clearly show that insoluble salts enhance the water progression and thereby increase the capability of the material to uptake water. (authors)

  12. Study of relaxation times of nanocomposites of starch/montmorillonite employing low field NMR

    International Nuclear Information System (INIS)

    Brito, Luciana M.; Tavares, Maria Ines B.

    2011-01-01

    Due to its various applications and features, especially in therapies for controlled release of pharmaceuticals, polymers are among the most widely used excipients in pharmaceutical technology. One of the most promising nanocomposites is formed from organic polymer and inorganic clay minerals. Nanocomposites of starch/montmorillonite were prepared employing solution intercalation and characterized by proton spin-lattice relaxation time, through NMR relaxometry. The characterization of nanocomposites was done by X-ray diffraction and by nuclear magnetic resonance. The results showed that nanostructured films were obtained by intercalation from solution. Furthermore, the use of low field NMR, T1H, provided more precise information about the movement of materials, being complementary to the results obtained by X-ray diffraction. (author)

  13. NMR-CT scanner

    International Nuclear Information System (INIS)

    Kose, Katsumi; Sato, Kozo; Sugimoto, Hiroshi; Sato, Masataka.

    1983-01-01

    A brief explanation is made on the imaging methods for a practical diagnostic NMR-CT scanner : A whole-body NMR-CT scanner utilizing a resistive magnet has been developed by Toshiba in cooperation with the Institute for Solid State Physics, the University of Tokyo. Typical NMR-CT images of volunteers and patients obtained in the clinical experiments using this device are presented. Detailed specifications are also shown about the practical NMR-CTs which are to be put on the market after obtaining the government approval. (author)

  14. Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR

    International Nuclear Information System (INIS)

    Lane, A.N.; Jenkins, T.C.; Neidle, S.; Brown, T.

    1991-01-01

    The conformation of the EcoRI dodecamer d(CGCGAATTCGCG) 2 has been examined in solution by 1 H and 31 P NMR. Spin-spin coupling constants and nuclear Overhauser (NOE) enhancement spectroscopy show that all deoxyriboses lie in the south domain, with a small admixture of the north conformation (0-20%). The time dependence of the nuclear Overhauser enhancements also reveals a relatively uniform conformation at the glycosidic bonds. The average helical twist is 36.5. Tilt angles are small, and roll angles are poorly determined. Both the NOE intensities and 31 P relaxation data imply conformational anomalies at the C3-G4/C9-G10 and the A5-A6/T7-T8 steps. Berenil binds in 1:1 stoichiometry to the dodecamer with high affinity and causes substantial changes in chemical shifts of the sugar protons of nucleotides Ado 5-Cyt 9 and of the H2 resonances of the two Ado residues. NOEs are observed between the aromatic protons of berenil and the H1' of both Thy 7 and Thy 8, as well as to Ado 5 and Ado 6 H2. These results firmly establish that berenil binds via the minor groove and closely approaches the nucleotides Ado 6, Thy 7, and Thy 8. Using the observed NOEs between the ligand and the DNA together with the derived glycosidic torsion angles, the authors have built models that satisfy all of the available solution data

  15. NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome

    International Nuclear Information System (INIS)

    Monleon, Daniel; Esteve, Vicent; Celda, Bernardo

    2003-01-01

    Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG) 2 has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG) 2 at high salt concentration includes a central alternating tetramer in Z-DNA conformation, while the initial cytosine swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. In solution, NMR data for sugar ring puckering combined with restrained molecular dynamics simulations starting from a Z-DNA form show that terminal furanose residues could adopt the conformation required for aromatic bases swinging out. Therefore, tetramer formation could be considered possible once the hexanucleotide had previously adopted the Z-DNA form. This work gives some insight into correlations between anomalous crystal structures and their accessibility in the solution state

  16. Assigning uncertainties in the inversion of NMR relaxation data.

    Science.gov (United States)

    Parker, Robert L; Song, Yi-Qaio

    2005-06-01

    Recovering the relaxation-time density function (or distribution) from NMR decay records requires inverting a Laplace transform based on noisy data, an ill-posed inverse problem. An important objective in the face of the consequent ambiguity in the solutions is to establish what reliable information is contained in the measurements. To this end we describe how upper and lower bounds on linear functionals of the density function, and ratios of linear functionals, can be calculated using optimization theory. Those bounded quantities cover most of those commonly used in the geophysical NMR, such as porosity, T(2) log-mean, and bound fluid volume fraction, and include averages over any finite interval of the density function itself. In the theory presented statistical considerations enter to account for the presence of significant noise in the signal, but not in a prior characterization of density models. Our characterization of the uncertainties is conservative and informative; it will have wide application in geophysical NMR and elsewhere.

  17. Conformational dynamics of Escherichia coli flavodoxins in apo- and holo-states by solution NMR spectroscopy.

    Directory of Open Access Journals (Sweden)

    Qian Ye

    Full Text Available Flavodoxins are a family of small FMN-binding proteins that commonly exist in prokaryotes. They utilize a non-covalently bound FMN molecule to act as the redox center during the electron transfer processes in various important biological pathways. Although extensive investigations were performed, detailed molecular mechanisms of cofactor binding and electron transfer remain elusive. Herein we report the solution NMR studies on Escherichia coli flavodoxins FldA and YqcA, belonging to the long-chain and short-chain flavodoxin subfamilies respectively. Our structural studies demonstrate that both proteins show the typical flavodoxin fold, with extensive conformational exchanges observed near the FMN binding pocket in their apo-forms. Cofactor binding significantly stabilizes both proteins as revealed by the extension of secondary structures in the holo-forms, and the overall rigidity shown by the backbone dynamics data. However, the 50 s loops of both proteins in the holo-form still show conformational exchanges on the µs-ms timescales, which appears to be a common feature in the flavodoxin family, and might play an important role in structural fine-tuning during the electron transfer reactions.

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

    Science.gov (United States)

    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.

  19. Structure and reactivity of thiazolium azo dyes: UV-visible, resonance Raman, NMR, and computational studies of the reaction mechanism in alkaline solution.

    Science.gov (United States)

    Abbott, Laurence C; Batchelor, Stephen N; Moore, John N

    2013-03-07

    UV-visible absorption, resonance Raman, and (1)H NMR spectroscopy, allied with density functional theory (DFT) calculations, have been used to study the structure, bonding, and alkaline hydrolysis mechanism of the cationic thiazloium azo dye, 2-[2-[4-(diethylamino)phenyl]diazenyl]-3-methyl-thiazolium (1a), along with a series of six related dyes with different 4-dialkylamino groups and/or other phenyl ring substituents (2a-c, 3a-c) and the related isothiazolium azo dye, 5-[2-[4-(dimethylamino)phenyl]diazenyl]-2-methyl-isothiazolium (4). These diazahemicyanine dyes are calculated to have a similar low-energy structure that is cis, trans at the (iso)thiazolium-azo group, and for which the calculated Raman spectra provide a good match with the experimental data; the calculations on these structures are used to assign and discuss the transitions giving rise to the experimental spectra, and to consider the bonding and its variation between the dyes. UV-visible, Raman, and NMR spectra recorded from minutes to several weeks after raising the pH of an aqueous solution of 1a to ca. 11.5 show that the dominant initial step in the reaction is loss of diethylamine to produce a quinonimine (ca. hours), with subsequent reactions occurring on longer time scales (ca. days to weeks); kinetic analyses give a rate constant of 2.6 × 10(-2) dm(3) mol(-1) s(-1) for reaction of 1a with OH(-). UV-visible spectra recorded on raising the pH of the other dyes in solution show similar changes that are attributed to the same general reaction mechanism, but with different rate constants for which the dependence on structure is discussed.

  20. Mobility of drugs in lipid membranes by NMR

    International Nuclear Information System (INIS)

    Yoshii, Noriyuki; Okamura, Emiko

    2011-01-01

    Mobility of drugs and biomembrane constituents is a key to elucidate the membrane transport mechanism in the cell. Lipid bilayer membrane is a dynamic structure where molecules are always fluctuating under physiological conditions. The mechanism of drug transport is related to the molecular dynamics in such soft, fluid membrane interface. To gain insight into molecular movements in membranes, we develop a noninvasive method to monitor dynamics properties of drugs and lipid components in membranes by applying multinuclear high-resolution solution NMR in combination with the pulsed-field-gradient (PFG) technique. We have quantified the diffusivity, the kinetics of membrane binding, and the bound fraction of the drug in situ by using large unilamellar vesicles of egg phosphatidylcholine as model cell membranes. The combination of 1D and PFG NMR serves to quantify the kinetics of membrane binding where the bound and the free components are unable to distinguish because of the rapid exchange on the NMR timescale. A small-sized 5-fluorouracil and fluorinated bisphenol A are used as model drug. (author)

  1. NMR of lignins

    Science.gov (United States)

    John Ralph; Larry L. Landucci

    2010-01-01

    This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

  2. The radiation induced chemistry of uranyl cation in aqueous carbonate –bicarbonate solutions as followed by NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    McNamara, Bruce K.; Snow, Lanee A.; Soderquist, Chuck Z.; Sinkov, Sergei I.; Cho, Herman M.; Friese, Judah I.

    2006-05-01

    Alpha radiation induced formation of hydrogen peroxide in carbonate ?bicarbonate media was followed by 13C NMR using dissolved [233UO2(13CO3)3]4- as the alpha source (Dalpha= 12.1 Gy/hr). Between the pH region between 5.9 and 11.6 hydrogen peroxide causes a varied speciation of the uranyl carbonates that is a function of the uranium, carbonate and the hydrogen peroxide concentrations. It is shown that the speciation of the peroxy carbonates (or other species) formed in solution by titration with hydrogen peroxide are common to those formed by hydrogen peroxide generated by radiolysis. The radiolysis experiment was carried out above pH = 9.96 to minimize the loss of 13CO2 over a 2800 hr period. Radiolytic generation of hydrogen peroxide was followed by formation of a uranyl peroxy carbonate complex and complex formation accelerated for about 1200 hours. Complex formation was observed to terminate at a concentration between 1x10-4 and 5x10-4 M. It is assumed that either a steady state H2O2 production rate was established in solution or that some limiting feature of the experiment was responsible for slowing the yield of product.

  3. Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Liu, J; Prakash, O; Cai, M; Gong, Y; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

    1996-02-06

    The solution structure of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V), whose N-terminal is unacetylated and carries an extra glycine residue, was determined by means of two-dimensional (2D) homo and 3D hetero NMR experiments in combination with a distance geometry and simulated annealing algorithm. A total of 927 interproton distances and 123 torsion angle constraints were utilized to generate 18 structures. The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain atoms and 0.95 A for all the non-hydrogen atoms of residues 3-40 and 49-67. The average structure of rCMTI-V is found to be almost the same as that of the native protein [Cai, M., Gong, Y., Kao, J.-L., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The backbone dynamics of uniformly 15N-labeled rCMTI-V were characterized by 2D 1H-15N NMR methods. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and [1H]-15N steady-state heteronuclear Overhauser effect enhancements were measured for the peptide NH units and, using the model-free formalism [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570], the following parameters were determined: overall tumbling correlation time for the protein molecule (tau m), generalized order parameters for the individual N-H vectors (S2), effective correlation times for their internal motions (tau e), and terms to account for motions on a slower time scale (second) due to chemical exchange and/or conformational averaging (R(ex)). Most of the backbone NH groups of rCMTI-V are found to be highly constrained ((S2) = 0.83) with the exception of those in the binding loop (residues 41-48, (S2) = 0.71) and the N-terminal region ((S2) = 0.73). Main-chain atoms in these regions show large RMSD values in the average NMR structure. Residues involved in turns also appear to have more mobility ((S2) = 0.80). Dynamical properties of rCMTI-V were compared with those of two other

  4. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    International Nuclear Information System (INIS)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs

  5. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    Energy Technology Data Exchange (ETDEWEB)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

  6. Solution conformation and dynamics of a tetrasaccharide related to the Lewis{sup X} antigen deduced by NMR relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Poveda, Ana [Universidad Autonoma de Madrid, Servicio Interdepartamental de Investigacion (Spain); Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus [Instituto de Quimica Organica, CSIC, Grupo de Carbohidratos (Spain)

    1997-07-15

    {sup 1}H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-{alpha}-N-acetyl-galactosaminyl-{beta}-galactopyranosyl-(1{sup {yields}}4)[3-O-{alpha}-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, {sup 13}C-NMR relaxation data have also been recorded at both fields. The {sup 1}H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The{sup 13}C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the{sup 1}H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS{sup 2}. Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data.

  7. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, Alexander N.; Vanwetswinkel, Sophie; Van de Water, Karen; Nuland, Nico A. J. van, E-mail: nvnuland@vub.ac.be [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)

    2012-03-15

    Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, {Delta}{chi}. For most nuclei, the PCSs back-calculated from the {Delta}{chi} tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches-clustered around G41, N52, and A81-exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.

  8. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy

    International Nuclear Information System (INIS)

    Volkov, Alexander N.; Vanwetswinkel, Sophie; Van de Water, Karen; Nuland, Nico A. J. van

    2012-01-01

    Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, Δχ. For most nuclei, the PCSs back-calculated from the Δχ tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches—clustered around G41, N52, and A81—exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.

  9. Billion-Fold Enhancement in Sensitivity of Nuclear Magnetic Resonance Spectroscopy for Magnesium Ions in Solution

    CERN Document Server

    Gottberg, Alexander; Kowalska, Magdalena; Bissell, Mark L; Arcisauskaite, Vaida; Blaum, Klaus; Helmke, Alexander; Johnston, Karl; Kreim, Kim; Larsen, Flemming H; Neugart, Rainer; Neyens, Gerda; Garcia Ruiz, Ronald F; Szunyogh, Daniel; Thulstrup, Peter W; Yordanov, Deyan T; Hemmingsen, Lars

    2014-01-01

    β-nuclear magnetic resonance (NMR) spectroscopy is highly sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. β-NMR has previously been successfully applied in the fields of nuclear and solid-state physics. In this work, β-NMR is applied, for the first time, to record an NMR spectrum for a species in solution. 31Mg β-NMR spectra are measured for as few as 107 magnesium ions in ionic liquid (EMIM-Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that β-NMR is applicable for the analysis of species in solution, and thus represents a novel spectroscopic technique for use in general chemistry and potentially in biochemistry.

  10. DNA nanotubes for NMR structure determination of membrane proteins.

    Science.gov (United States)

    Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

    2013-04-01

    Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

  11. Authenticity study of Phyllanthus species by NMR and FT-IR techniques coupled with chemometric methods

    International Nuclear Information System (INIS)

    Santos, Maiara S.; Pereira-Filho, Edenir R.; Ferreira, Antonio G.; Boffo, Elisangela F.; Figueira, Glyn M.

    2012-01-01

    The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as 'quebra-pedras' in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, 1 H HR-MAS NMR and 1 H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques. (author)

  12. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    LeMaster, D.M.

    1990-01-01

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  13. Additivity, redundancy, and complementarity between structural information from NMR and SAXS data

    International Nuclear Information System (INIS)

    Kojima, Masaki; Nonaka, Takamasa; Morimoto, Yasumasa; Nakagawa, Takashi; Yanagi, Shigeru; Kihara, Hiroshi

    2009-01-01

    At present protein structure in solution is determined by restrained molecular dynamics with distance restraints mainly derived from NMR. Although the small-angle X-ray scattering (SAXS) method also confers the structural information, its content is too small to determine the structure by itself. We previously developed a new algorithm that refines the protein structure by restrained molecular dynamics with SAXS constrains. In the present study we performed the protein structure calculation by restrained molecular dynamics with both NMR and SAXS constraints, in order to elucidate the essential structural information that defines the protein architecture. We used RNase T1 as a model protein, which has already been determined by NMR alone. At first we added SAXS constraints (h -1 ) into the original NMR-derived restraints for the calculation. The quality of the structure ensemble was significantly increased. Next we removed the original NMR restraints randomly in order to estimate the redundancy among the NMR-derived information. The essential topology of the resultant structures was hardly changed until the restraints were reduced below the half. Then we added the SAXS constraints into the remaining NMR restraints to expect they could complement the lost structural information. However, the structure was not recovered properly. By removing various types of structural information exclusively from the original NMR data set, we investigated whether the SAXS constraints could complement some kinds of structural information. The results showed that the SAXS could complement the tertiary structure to some extent while it could not secondary structure. (author)

  14. NMR and Solvent Effect Study on the Thymine-Adenine-Thymine ...

    African Journals Online (AJOL)

    ... discussed about the plotted graphs of relative energies versus dielectric constants of our considered solvents. Thus, we can drastically conclude that the dielectric permittivity of the solvent is a key factor that determines the chemical behavior of DNA in solution. Keywords: TAT sequence; solvent effect; NMR parameters; ...

  15. NMR imaging and pharmaceutical sciences

    International Nuclear Information System (INIS)

    Beall, P.T.; Good, W.R.

    1986-01-01

    Described is the technique of NMR-imaging in diagnostic medicine. Proton and phosphorus NMR in diagnosis of abnormal tissue pathology. Discussed is the value of NMR to the pharmaceutical sciences. NMR may play an important role in monitoring the response of tissues to drugs, determining the localization of drugs, performing real time pharmacokinetics and testing the use of NMR contrast pharmaceuticals

  16. Synergistic Applications of MD and NMR for the Study of Biological Systems

    Directory of Open Access Journals (Sweden)

    Olivier Fisette

    2012-01-01

    same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.

  17. QENS and NMR studies of 3-picoline-water solutions

    CERN Document Server

    Almasy, L; Bokor, M; Cser, L; Tompa, K; Zanotti, J M; Jancso, G

    2002-01-01

    Quasi-elastic neutron scattering measurements were performed on aqueous solutions of 3-picoline (3-methylpyridine) at room temperature. H-D substitution on both the solute and the water was used to separate the dynamics of the two species. The analysis of the translational diffusive motion at different concentrations shows that at high picoline content the diffusion coefficient of water decreases strongly and becomes similar to that of the solute, indicating strong coupling between the motions of the solute and the solvent. Activation energies characteristic of the dynamic behavior of the methyl group were determined from sup 1 H spin-lattice relaxation rate measurements for H sub 2 O and D sub 2 O solutions of 3-picoline above 310 K. (orig.)

  18. Studies on Photodarkening Effect in Glassy As2S3 Using High Field NMR

    Science.gov (United States)

    Hari, Parameswar; Su, Tining; Taylor, Craig; Reyes, Arneil; Kuhns, Phil; Moulton, William; Sullivan, N. S.

    2001-03-01

    Photodarkening, or the shift of the optical absorption edge to smaller energies after excitation with light whose energy is near that of the optical band edge, has been studied in many chalcogenide glasses for many years. Recently we have conducted nuclear magnetic resonance (NMR) studies of 75As in glassy As2S3 at 17T . We compared the 75As NMR lineshape in glassy As2S3 before and after irradiation at 77K. After irradiation at 514.5 nm for 230 hours with 170 mW/cm2 there is a subtle change in the NMR lineshape. This change is reversible on annealing at 200 C for 1.75 hours. We will discuss the implications of this result based on NMR lineshape analysis using an exact solution of the spin 3/2 Hamiltonian

  19. NMR studies of structures of lanthanide dicarboxylate complexes in solution

    International Nuclear Information System (INIS)

    Choppin, G.R.; Kullberg, L.

    PMR pand 13 C shift data were measured for complexes of Pr(III), Eu(III) and Yb(III) with ethylene 1,2-dioxydiacetate (EDODA), ethylene 1,2-dithiodiacetate (EDSDA), and ethylene, 1,2-diaminodiacetate (EDDA). Solubility problems limited analysis of the EDSDA and EDDA data to qualitative evaluation. In the EDSDA complexes, the data indicate that the sulfur atoms do not participate in bonding to the lanthanide cations. Moreover, both carboxylate groups seem to bind Pr and Eu while Yb interacts with only a single carboxylate group. The EDDA complexes are tetradentate with long lived (NMR scale) Ln-N bonds. Shift theory allowed more quantitative analysis of the EDODA complexes. They are tetradentate with a puckered chelate ring and Ln-O(ether) distances of 2.3 A

  20. A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers

    Science.gov (United States)

    Dubroca, Thierry; Smith, Adam N.; Pike, Kevin J.; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R.; Frydman, Lucio; Hill, Stephen

    2018-04-01

    Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T (1H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T (1H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 μL, i.e. 3 mm diameter NMR tubes).

  1. Determination of Molecular Self-Diffusion Coefficients Using Pulsed-Field-Gradient NMR: An Experiment for Undergraduate Physical Chemistry Laboratory

    Science.gov (United States)

    Harmon, Jennifer; Coffman, Cierra; Villarrial, Spring; Chabolla, Steven; Heisel, Kurt A.; Krishnan, Viswanathan V.

    2012-01-01

    NMR spectroscopy has become one of the primary tools that chemists utilize to characterize a range of chemical species in the solution phase, from small organic molecules to medium-sized proteins. A discussion of NMR spectroscopy is an essential component of physical and biophysical chemistry lecture courses, and a number of instructional…

  2. Development and Application of a Low-Volume Flow System for Solution-State in Vivo NMR.

    Science.gov (United States)

    Tabatabaei Anaraki, Maryam; Dutta Majumdar, Rudraksha; Wagner, Nicole; Soong, Ronald; Kovacevic, Vera; Reiner, Eric J; Bhavsar, Satyendra P; Ortiz Almirall, Xavier; Lane, Daniel; Simpson, Myrna J; Heumann, Hermann; Schmidt, Sebastian; Simpson, André J

    2018-06-18

    In vivo nuclear magnetic resonance (NMR) spectroscopy is a particularly powerful technique, since it allows samples to be analyzed in their natural, unaltered state, criteria paramount for living organisms. In this study, a novel continuous low-volume flow system, suitable for in vivo NMR metabolomics studies, is demonstrated. The system allows improved locking, shimming, and water suppression, as well as allowing the use of trace amounts of expensive toxic contaminants or low volumes of precious natural environmental samples as stressors. The use of a double pump design with a sump slurry pump return allows algal food suspensions to be continually supplied without the need for filters, eliminating the possibility of clogging and leaks. Using the flow system, the living organism can be kept alive without stress indefinitely. To evaluate the feasibility and applicability of the flow system, changes in the metabolite profile of 13 C enriched Daphnia magna over a 24-h period are compared when feeding laboratory food vs exposing them to a natural algal bloom sample. Clear metabolic changes are observed over a range of metabolites including carbohydrates, lipids, amino acids, and a nucleotide demonstrating in vivo NMR as a powerful tool to monitor environmental stress. The particular bloom used here was low in microcystins, and the metabolic stress impacts are consistent with the bloom being a poor food source forcing the Daphnia to utilize their own energy reserves.

  3. Solution structure of d-GAATTCGAATTC by 2D NMR

    International Nuclear Information System (INIS)

    Hosur, R.V.; Ravikumar, M.; Chary, K.V.R.; Sheth, A.; Govil, G.

    1986-01-01

    A new approach based on the correlated spectroscopy (COSY) in 2D NMR has been described for determination of sugar geometries in oligonucleotides. Under the usual low resolution conditions employed in COSY, the intensities of cross peaks depend on the magnitudes of coupling constants. There are five vicinal coupling constants in a deoxyribose ring which are sensitive to the sugar geometry. The presence, absence and rough comparison of relative intensities of COSY cross peaks arising from such coupling constants enable one to fix the sugar conformation to a fair degree of precision. The methodology has been applied to d-GAATTCGAATTC. It is observed that ten out of the twelve nucleotide units in this sequence exhibit a rare O1'-endo geometry. The EcoRI cleavage sites in the dodecanucleotide show an interesting variation in the conformation with the two sugars attached to the Gs acquiring a geometry between C2'-endo and C4'-endo. (Auth.)

  4. Theory of NMR probe design

    International Nuclear Information System (INIS)

    Schnall, M.D.

    1988-01-01

    The NMR probe is the intrinsic part of the NMR system which allows transmission of a stimulus to a sample and the reception of a resulting signal from a sample. NMR probes are used in both imaging and spectroscopy. Optimal probe design is important to the production of adequate signal/moise. It is important for anyone using NMR techniques to understand how NMR probes work and how to optimize probe design

  5. NMR study on the network structure of a mixed gel of kappa and iota carrageenans.

    Science.gov (United States)

    Hu, Bingjie; Du, Lei; Matsukawa, Shingo

    2016-10-05

    The temperature dependencies of the (1)H T2 and diffusion coefficient (D) of a mixed solution of kappa-carrageenan and iota-carrageenan were measured by NMR. Rheological and NMR measurements suggested an exponential formation of rigid aggregates of kappa-carrageenan and a gradual formation of fine aggregates of iota-carrageenan during two step increases of G'. The results also suggested that longer carrageenan chains are preferentially involved in aggregation, thus resulting in a decrease in the average Mw of solute carrageenans. The results of diffusion measurements for poly(ethylene oxide) (PEO) suggested that kappa-carrageenan formed thick aggregates that decreased hindrance to PEO diffusion by decreasing the solute kappa-carrageenan concentration in the voids of the aggregated chains, and that iota-carrageenan formed fine aggregates that decreased the solute iota-carrageenan concentration less. DPEO in a mixed solution of kappa-carrageenan and iota-carrageenan suggested two possibilities for the microscopic network structure: an interpenetrating network structure, or micro-phase separation. Copyright © 2016. Published by Elsevier Ltd.

  6. Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

    Science.gov (United States)

    Kupka, Teobald; Wieczorek, Piotr P.

    2016-01-01

    In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

  7. The pH behavior of a 2-aminoethyl dihydrogen phosphate zwitterion studied with NMR-titrations

    Science.gov (United States)

    Myller, A. T.; Karhe, J. J.; Haukka, M.; Pakkanen, T. T.

    2013-02-01

    In this study a bifunctional 2-aminoethyl dihydrogen phosphate (AEPH2) was 1H and 31P NMR characterized in a pH range of 1-12 in order to determine the zwitterion properties in different pH regions in H2O and D2O solutions. NMR was also used to determine the pH range where AEPH2 exists as a zwitterion. The phosphate group has two deprotonation points, around pH 1 and 6, while the amino group deprotonates at pH 11. The zwitterion form of AEPH2 (NH3+sbnd CHsbnd CHsbnd OPOH) exists as the main ion between pH 1 and 6 in water solutions and also in the solid state.

  8. Authenticity study of Phyllanthus species by NMR and FT-IR techniques coupled with chemometric methods

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Maiara S.; Pereira-Filho, Edenir R.; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSCAR), SP (Brazil). Dept. de Quimica; Boffo, Elisangela F. [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Inst. de Quimica; Figueira, Glyn M., E-mail: maiarassantos@yahoo.com.br [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Centro Pluridisciplinar de Pesquisas Quimicas, Biologicas e Agricolas

    2012-07-01

    The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as 'quebra-pedras' in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, {sup 1}H HR-MAS NMR and {sup 1}H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques. (author)

  9. Authenticity study of Phyllanthus species by NMR and FT-IR Techniques coupled with chemometric methods

    Directory of Open Access Journals (Sweden)

    Maiara S. Santos

    2012-01-01

    Full Text Available The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as "quebra-pedras" in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, ¹H HR-MAS NMR and ¹H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques.

  10. Authenticity study of Phyllanthus species by NMR and FT-IR techniques coupled with chemometric methods

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Maiara S.; Pereira-Filho, Edenir R.; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSCAR), SP (Brazil). Dept. de Quimica; Boffo, Elisangela F. [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Inst. de Quimica; Figueira, Glyn M., E-mail: maiarassantos@yahoo.com.br [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Centro Pluridisciplinar de Pesquisas Quimicas, Biologicas e Agricolas

    2012-07-01

    The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as 'quebra-pedras' in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, {sup 1}H HR-MAS NMR and {sup 1}H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques. (author)

  11. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

    Science.gov (United States)

    Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

    2018-01-02

    NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

  12. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

    Science.gov (United States)

    van der Schot, Gijs; Bonvin, Alexandre M J J

    2015-08-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  13. Rheo-NMR - how nuclear magnetic resonance is providing new insight regarding complex fluid rheology

    International Nuclear Information System (INIS)

    Callaghan, P.T.

    2000-01-01

    Over the past five decades, NMR has revolutionised chemistry, and has found widespread application in condensed matter physics, in molecular biology, in medicine and in food technology. Most recently NMR has made a significant impact in chemical engineering, where it is being extensively used for the non-invasive study of dispersion and flow in porous media. One of the most recent applications of NMR in materials science concerns its use in the study of the mechanical properties of complex fluids. This particular aspect of NMR has been extensively developed in research carried out at Massey University in New Zealand. In this short article, some of the ideas behind this work and the applications which have resulted, will be described. These examples provide a glimpse of possible applications of Nuclear Magnetic Resonance to the study of complex fluid rheology. While this is a very new field of research in which only a handful of groups presently participate, the potential exists for a substantial increase in Rheo-NMR research activity. Systems studied to date include polymer melts and semi-dilute solutions, thermotropic and lyotropic liquid crystals and liquid crystalline polymers, micellar solutions, food materials and colloidal suspensions. Rheo-NMR suffers in a number of respects by comparison with optical methods. It is expensive, it is difficult to use, it suffers from poor signal-to-noise ratios and the effective interpretation of spectra often depends on familiarity with the nuclear spin Hamiltonian and the associated effects of spin dynamics. Nonetheless NMR offers some unique advantages, including the ability to work with opaque materials, the ability to combine velocimetry with localised spectroscopy, and the ability to access a wide range of molecular properties relating to organisation, orientation and dynamics. Rheo-NMR has been able to provide a direct window on a variety of behaviours, including slip, shear-thinning, shear banding, yield stress

  14. Hydroxy protons as structural probes to reveal hydrogen bonding properties of polyols in aqueous solution by NMR spectroscopy

    Science.gov (United States)

    Oruc, Gizem; Varnali, Tereza; Bekiroglu, Somer

    2018-05-01

    The solution properties of ethylene glycol (ethane-1,2-diol), glycerol (propane-1,2,3-triol), erythritol ((2R,3S)-butane-1,2,3,4-tetraol), D-xylitol ((2R,3r,4S)-pentane-1,2,3,4,5-pentaol), D-mannitol ((2R,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), and D-sorbitol ((2S,3R,4R,5R)-hexane-1,2,3,4,5,6-hexaol), constituting a subgroup of polyalcohols/polyols of maximum six carbon atoms have been investigated using 1H NMR chemical shifts, coupling constants, temperature coefficients, and chemical exchange rates of hydroxy protons in aqueous medium. Relative within a molecule, minimum two-fold difference in rate of exchange values and higher temperature dependence of chemical shifts of the hydroxy protons on terminal carbon atoms confirm that sustainable hydrogen bonding interactions is accentuated for the hydroxyl groups on secondary carbons. Compared to the primary carbons i.e. terminal ones, the hydroxy protons on second and third carbon atoms exhibit much lower rate of exchange and smaller temperature coefficients, indicating that they are further involved in transient hydrogen bonding interactions. Scalar 3JOH,CH-couplings ranging between 3.9 and 7.2 Hz imply that the hydroxyl groups are practically in free rotation regime. Examination of the chemical shift differences with respect to the shift of glycol hydroxy proton reveals that the disparity between terminal and inner hydroxyl groups disclosed by the exchange rates and temperature coefficients is sustained with the exception of 0.003 and 0.053 ppm for O(3)H of mannitol and O(5)H of sorbitol respectively. The experimental findings have been augmented by quantum chemical calculations targeting theoretical NMR chemical shifts, as well as the conformational analysis of the structures.

  15. Applications of /sup 43/Ca, /sup 25/Mg, and /sup 67/Zn NMR spectroscopies to biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, Tohru; Hatano, Masahiro [Tohoku Univ., Sendai (Japan). Chemical Research Inst. of Non-Aqueous Solutions

    1983-12-01

    /sup 43/Ca, /sup 25/Mg and /sup 67/Zn NMR spectroscopies applied to biologically important systems are summarized mainly on the basis of our findings. It was found from our studies that (1) /sup 25/Mg NMR can be utilized for studying the dynamic and/or static behavior of Mg/sup 2 +/ in the Mg/sup 2 +/ -ATP (ADP)-kinase ternary complexes and (2) /sup 67/Zn NMR bands of diluted Zn/sup 2 +/ are much narrower than predicted and thus can be applicable for studying the dynamic and/or static behavior of Zn/sup 2 +/ in Zn/sup 2 +/ -enzyme solutions. In addition, /sup 43/Ca NMR spectra were successfully applied to some Ca/sup 2 +/ -binding proteins. In concluding remarks, we discussed possibilities of applications of those metal NMR spectroscopies to medical purposes.

  16. Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Monica Ferro

    2017-01-01

    Full Text Available Two different formulations of cyclodextrin nanosponges (CDNS, obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn, were treated with aqueous solutions of ibuprofen sodium salt (IbuNa affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1H fast MAS NMR and 13C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH after freeze-drying. 13C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13C NMR spectra collected under variable contact time cross-polarization (VCT-CP conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles.

  17. Characterization of new materials in chromatography and fuel cell development by modern NMR techniques; Charakterisierung neuer Materialien in der Chromatographie und Brennstoffzellen-Forschung mit Hilfe moderner NMR-Techniken

    Energy Technology Data Exchange (ETDEWEB)

    Schauff, S.

    2007-12-28

    New materials, suitable for the application in reversed phase liquid chromatography and fuel cell membranes, were characterized regarding their structure and dynamic properties using solid-state and suspended-state NMR spectroscopy. Both methods were found to be suitable to study the dynamic behaviour, the first to observe intrinsic mobilities of phosphonic acids, the second to monitor interaction processes taking place in a chromatography-like system. Several phosphonic acids, which are promising materials for high temperature fuel cell membranes, were investigated with respect to proton mobility and transport applying various solid-state NMR methods. In addition, water uptake and its effects on anhydride formation were studied on samples that were equilibrated with saturated salt solutions. For PVPA substantial, reversible anhydride formation was found, while MePA did not show condensation. These results show that the relation between hydrogen bond strength and proton mobility is complex. In particular, this work demonstrates that the application of simple 1D 1H and 2H NMR experiments provides easy access to information about proton/deuteron mobility on short time scales, needed for an identification of materials with high intrinsic proton conductivities. Stationary phases for reversed phase liquid chomatography were characterized by solid-state NMR spectroscopy, and their influence on different analytes was studied using suspendedstate HR-MAS NMR spectroscopy. Suspended-state HR-MAS NMR spectroscopy showed to be suitable to model the separation process of analytes on chromatographic sorbents. For this, the stationary phase was suspended in a solution of analyte dissolved in mobile phase. MePhSucc showed a peak doubling of the CH2 group in presence of monomeric C18 phase, leading to the coexistence of a narrow and a broadened peak. Thus, the dynamic interactions of MePhSucc towards the stationary phase, and under the influence of the mobile phase, could be

  18. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    NARCIS (Netherlands)

    Van Der Schot, Gijs; Bonvin, Alexandre M J J

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on

  19. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

    Science.gov (United States)

    2014-01-01

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

  20. Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis

    Science.gov (United States)

    Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby

    2012-01-01

    Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

  1. NMR studies of DNA structures in solution

    International Nuclear Information System (INIS)

    Rinkel, L.J.

    1987-01-01

    This thesis describes the conformational analysis of some polynucleotides in aqueous solution. A new graphical method is presented as an aid in the pseudorotational analysis of the sugar rings in DNA by means of sums of proton-proton coupling constants. (Auth.)

  2. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Uppsala University, Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology (Sweden); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Faculty of Science – Chemistry, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-08-15

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  3. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    International Nuclear Information System (INIS)

    Schot, Gijs van der; Bonvin, Alexandre M. J. J.

    2015-01-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution

  4. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2016-01-01

    Full Text Available Quantitative nuclear magnetic resonance (qNMR is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR and only a few fluorine qNMR (19F qNMR were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes.

  5. Osmotic dehydration of organic kiwifruit pre-treated by pulsed electric fields and monitored by NMR.

    Science.gov (United States)

    Traffano-Schiffo, Maria Victoria; Laghi, Luca; Castro-Giraldez, Marta; Tylewicz, Urszula; Rocculi, Pietro; Ragni, Luigi; Dalla Rosa, Marco; Fito, Pedro J

    2017-12-01

    Osmotic dehydration (OD) is a widely used preservation technique that consists in the reduction in food water activity by the immersion of the biological tissue in hypertonic solutions. The aim of this work was to analyze the effect of pulsed electric fields (PEF) in mass transfer as a pre-treatment of the OD using NMR. In this sense, PEF pre-treatments were done using three different voltages (100, 250 and 400V/cm) and 60 number of pulse. The OD of kiwifruit was carried out in 61.5% of sucrose solution at 25°C, for a contact period from 0 to 120min. The water distribution into the cellular tissue was studied by NMR relaxometry. In conclusion, NMR is an excellent technique for quantifying water molecules according to their interactions in the fruit tissue, obtaining the adsorbed water and opening the possibility to apply the BET model to fit the adsorbed isotherm over the whole range of water activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Dynamic pulsed-field-gradient NMR

    CERN Document Server

    Sørland, Geir Humborstad

    2014-01-01

    Dealing with the basics, theory and applications of dynamic pulsed-field-gradient NMR NMR (PFG NMR), this book describes the essential theory behind diffusion in heterogeneous media that can be combined with NMR measurements to extract important information of the system being investigated. This information could be the surface to volume ratio, droplet size distribution in emulsions, brine profiles, fat content in food stuff, permeability/connectivity in porous materials and medical applications currently being developed. Besides theory and applications it will provide the readers with background knowledge on the experimental set-ups, and most important, deal with the pitfalls that are numerously present in work with PFG-NMR. How to analyze the NMR data and some important basic knowledge on the hardware will be explained, too.

  7. Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

    Science.gov (United States)

    Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

    2016-01-04

    Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

  8. Comparison of multiple crystal structures with NMR data for engrailed homeodomain

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

    2008-03-15

    Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

  9. Determination of unreacted monomers in restorative dental resins based on dimethacrylate by NMR hydrogen

    International Nuclear Information System (INIS)

    Correa, Ivo Carlos; Miranda Junior, Walter G.; Tavares, Maria Ines B.

    2001-01-01

    The presence of unreacted monomers after photo-activation of dental composites causes mechanical and biological properties to decrease and could be detected by NMR analysis. The aim of this study was to evaluate the percentage of leachable monomers of light-cured composites under the effect of variations of exposure time of photo activation by nuclear magnetic resonance of hydrogen in solution (NMR 1 H). The composite resins tested Z250 and Fill Magic obtained similar values of unreacted monomers (%) at photo curing time suggested by the manufacturer and values were also lower than Durafill and A110 concentrations. From the NMR results, one day extractable time was efficient to quantify the amount of residual monomers in the dental composites tested, unless for Durafill composite. (author)

  10. Phosphorus NMR of isolated perfused morris hepatomas

    International Nuclear Information System (INIS)

    Graham, R.A.; Meyer, R.A.; Brown, T.R.; Sauer, L.A.

    1986-01-01

    The authors are developing techniques for the study of perfused solid tumors by NMR. Tissue-isolated solid hepatomas were grown to 1-2 cm diameter as described previously. The arterial supply was isolated and the tumors perfused (0.5 - 1.0 ml/min) in vitro at 25 C with a 15% suspension of red blood cells in Krebs-Henseliet solution. 31 P-NMR spectra were acquired at 162 MHz in a specially-designed NMR probe using a solenoidal coil. Intracellular pH (monitored from the chemical shift of inorganic phosphate) and ATP levels were stable for up to 6 hrs during perfusion. During 30 min of global ischemia, ATP decreased by 75% and pH fell from 7.0 to 6.7. These changes were reversed by 1 hr reperfusion. In addition to ATP and phosphate, the spectra included a large resonance due to phosphomonoesters, as well as peaks consistent with glycerylphosphocholine, glyceryl-phosphoethanolamine, phosphocreatine, NAD, and UDPG. However, the most novel feature of the spectra was the presence of an unidentified peak in the phosphonate region (+ 16.9 ppm). The peak was not present in spectra of muscle, liver, brain, kidney, or fat tissues excised from the same animals. They are presently attempting to identify the compound that gives rise to this peak and to establish its metabolic origin

  11. 1H NMR studies of human lysozyme: Spectral assignment and comparison with hen lysozyme

    International Nuclear Information System (INIS)

    Redfield, C.; Dobson, C.M.

    1990-01-01

    Complete main-chain (NH and αCH) 1 H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are essentially identical with those found previously in a similar study of hen lysozyme and are in close accord with the structure of the protein reported previously from x-ray diffraction studies in the crystalline state. Comparison of the chemical shifts, spin-spin coupling constants, and hydrogen exchange behavior are also consistent with closely similar structures for the two proteins in solution. In a number of cases specific differences in the NMR parameters between hen and human lysozymes can be correlated with specific differences observed in the crystal structures

  12. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

    International Nuclear Information System (INIS)

    Skinner, Simon P.; Fogh, Rasmus H.; Boucher, Wayne; Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W.

    2016-01-01

    NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

  13. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

    Energy Technology Data Exchange (ETDEWEB)

    Skinner, Simon P.; Fogh, Rasmus H. [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom); Boucher, Wayne [University of Cambridge, Department of Biochemistry (United Kingdom); Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom)

    2016-10-15

    NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

  14. Inverse problem for in vivo NMR spatial localization

    International Nuclear Information System (INIS)

    Hasenfeld, A.C.

    1985-11-01

    The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs

  15. Inverse problem for in vivo NMR spatial localization

    Energy Technology Data Exchange (ETDEWEB)

    Hasenfeld, A.C.

    1985-11-01

    The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs.

  16. Characterization of polyurethane/organophilic montmorillonite nanocomposites by low field NMR

    International Nuclear Information System (INIS)

    Silva, Marcos Anacleto da; Tavares, Maria I.B.; Nascimento, Suelen A.M.; Rodrigues, Elton J. da R

    2012-01-01

    Polyurethanes are important and versatile materials, mainly due to some of their properties, such as high resistance to abrasion and tearing, excellent absorption of mechanical shocks and good flexibility and elasticity. However, they have some drawbacks as well, such as low thermal stability and barrier properties. To overcome these disadvantages, various studies have been conducted involving organophilic polyurethane/montmorillonite nanocomposites. The investigation of the structure of polyurethane/clay nanocomposites has mainly been done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). In this work, PU/clay nanocomposite films obtained by solution intercalation were studied. The nanocomposites were characterized by XRD and low-field nuclear magnetic resonance (LF-NMR). The LF-NMR measurements, with determination of the spin-lattice relaxation time of the hydrogen nucleus, supplied important information about the molecular dynamics of these nanocomposites. The X-ray diffraction measurements validated the results found by NMR. The thermal stability of the material was also determined by thermogravimetric analysis (TGA) under an inert atmosphere. A slight improvement in this stability was observed in the nanocomposite in comparison with polyurethane (author)

  17. Complete sequence-specific 1H NMR assignments for human insulin

    International Nuclear Information System (INIS)

    Kline, A.D.; Justice, R.M. Jr.

    1990-01-01

    Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

  18. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  19. A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers.

    Science.gov (United States)

    Dubroca, Thierry; Smith, Adam N; Pike, Kevin J; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R; Frydman, Lucio; Hill, Stephen

    2018-04-01

    Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T ( 1 H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13 C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31 P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T ( 1 H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 µL, i.e. 3 mm diameter NMR tubes). Copyright © 2018 Elsevier Inc. All rights reserved.

  20. Observation of Radiolytic Field Alteration of the Uranyl Cation in Bicarbonate Solution

    Energy Technology Data Exchange (ETDEWEB)

    Snow, Lanee A.; McNamara, Bruce K.; Sinkov, Sergey I.; Cho, Herman M.; Friese, Judah I.

    2006-12-01

    In previous work we demonstrated that radiolysis of uranyl tris carbonate in near neutral pH to alkaline carbonate solutions, could be followed by 13C NMR. Radiolysis of the complex produced novel uranyl peroxo carbonate solution state species, whose structures depended on the pH and radiolytic dose rate. In this work, we investigate speciation of the uranyl carbonate trimer which is predominant in bicarbonate solution near pH 5.9. We observe radiolytically derived speciation to different mixed peroxy carbonate species than seen in the higher pH solutions. Auto radiolysis of uranium (VI) carbonate solutions between pH 5.9 and 7.2 is shown to alter the uranium speciation over relatively short periods of time and was followed by 13C NMR and visible spectrophotometry, using dissolved 233(UO2)3(CO3)6 6- both as the radiolysis source (D= 14.9 Gy/hr) and as a trap for the newly formed hydrogen peroxide. Direct addition of hydrogen peroxide to solutions of the uranyl-carbonate trimer is shown to reproduce the 13 C NMR signatures of the complexe(s) formed by radiolysis, but additionally a variety of new complexes are revealed. Ratios of H2O2/trimer < 1.5 produced a uranyl peroxo carbonate adduct, that is shown to be common to the radiolytically produced species. Ratios of H2O2/ trimer >1 resulted in formation of stable higher order peroxo carbonate complexes. The 13C NMR signatures and visible spectra of these complexes are described here. Rigorous characterization of the species is an ongoing effort.

  1. Hyperpolarized 129Xe as an NMR probe for functional studies

    International Nuclear Information System (INIS)

    Wolber, J.

    2000-01-01

    The nuclear spin polarization of 129 Xe can be enhanced by several orders of magnitude using optical pumping techniques, resulting in a dramatic enhancement of the 129 Xe Nuclear Magnetic Resonance (NMR) signal. The 'hyperpolarized' gas can be used for Magnetic Resonance Imaging (MRI) of the void spaces of the lungs after introduction of the gas into the respiratory system. Furthermore, the high solubility of xenon in blood and lipids suggests the use of 129 Xe NMR for studying blood flow, permeability, perfusion and blood volume. Hyperpolarized 129 Xe MRI has the potential of combining the high sensitivity and functional information of radioactive tracer studies with the high spatial and temporal resolution of MRI. The spin-lattice relaxation time T 1 of 129 Xe in blood determines the loss of polarization during transit from the lungs to the tissue of interest. A difference in the relaxation times of xenon in oxygenated and deoxygenated blood could be used as a contrast mechanism in functional Magnetic Resonance Imaging (fMRI). In this thesis, the hyperpolarized 129 Xe T 1 in human blood is measured in vitro as a function of blood oxygenation, and the relevant relaxation mechanisms are discussed. A new and unexpected finding is that the hyperpolarized 129 Xe NMR spectrum in blood is highly sensitive to blood oxygenation. Therefore, hyperpolarized 129 Xe NMR provides a powerful means of measuring blood oxygenation quantitatively and non-invasively. The interaction of xenon with hemoglobin is responsible for an oxygen-dependent shift of the 129 Xe NMR resonance of xenon in red blood cells. Injection delivery of hyperpolarized 129 Xe in solution could be a more efficient method of administrating the gas for functional NMR studies. For this purpose, suitable biocompatible carrier media have been studied. In particular, the use of perfluorocarbon emulsions, which are already in use as blood substitutes, as delivery media for hyperpolarized 129 Xe has been investigates

  2. Pulsed zero field NMR of solids and liquid crystals

    International Nuclear Information System (INIS)

    Thayer, A.M.

    1987-02-01

    This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs

  3. HPLC-NMR revisited: Using time-slice HPLC-SPE-NMR with database assisted dereplication

    DEFF Research Database (Denmark)

    Johansen, Kenneth; Wubshet, Sileshi Gizachew; Nyberg, Nils

    2013-01-01

    Time based trapping of chromatographically separated compounds on to solid-phase extraction cartridges (SPE) and subsequent elution to NMR-tubes was done to emulate the function of HPLC–NMR for dereplication purposes. Sufficient mass sensitivity was obtained by the use of a state-of-the-art HPLC......–SPE–NMR-system with a cryogenically cooled probe head, designed for 1.7 mm NMR-tubes. The resulting 1H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts......, is described and the code included as Supplementary Information. Two mixtures of natural products was used to test the approach; one extract of Carthamus oxyacantha (wild safflower) containing an array of spiro compounds and one extract of the endophytic fungus Penicillum namyslowski containing griseofulvin...

  4. NMR for chemists and biologists

    CERN Document Server

    Carbajo, Rodrigo J

    2013-01-01

    This book offers a concise introduction to the field of nuclear magnetic resonance or NMR. It presents the basic foundations of NMR in a non-mathematical way and provides an overview of both recent and important biological applications of NMR.

  5. Micro-coil NMR to monitor optimization of the reconstitution conditions for the integral membrane protein OmpW in detergent micelles

    International Nuclear Information System (INIS)

    Stanczak, Pawel; Zhang Qinghai; Horst, Reto; Serrano, Pedro; Wüthrich, Kurt

    2012-01-01

    Optimization of aqueous solutions of the integral membrane protein (IMP) OmpW for NMR structure determination has been monitored with micro-coil NMR, which enables the acquisition of NMR spectra using only micrograms of protein and detergent. The detergent 30-Fos (2-undecylphosphocholine) was found to yield the best 2D [ 15 N, 1 H]-TROSY correlation NMR spectra of [ 2 H, 15 N]-labeled OmpW. For the OmpW structure determination we then optimized the 30-Fos concentration, the sample temperature and long-time stability, and the deuteration level of the protein. Some emerging guidelines for reconstitution of β-barrel integral membrane proteins in structural biology are discussed.

  6. Pectins from apple pomace - characterization by 13C and 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Marcon, M.V.; Carneiro, P.I.B.; Wosiacki, G.; Beleski-Carneiro, E.; Petkowicz, C.L.O.

    2005-01-01

    Pectins were extracted from apple pomace flour with 5% (w/v) aqueous citric acid solutions under different time and temperature according to an experimental design (factorial 2 2 with triplicate of central point). Monosaccharide composition of fractions was determined by colorimetric analysis and gas chromatography. The structure of pectins was studied by NMR spectroscopy. The degree of esterification (DE=30.5-55.9), determined by FT-IR spectroscopy, was indirectly correlated with increasing temperature and time of extraction, showing that drastic conditions for extraction promote hydrolysis of esterified units. High content of galacturonic acid is consistent with the smooth region of the polysaccharide. 13 C and 1 H NMR spectroscopy confirmed the presence of uronic acids in the free and methyl ester forms. NMR data also showed the presence of arabinan and galactan as side chains. (author)

  7. Two-dimensional 1H NMR experiments show that the 23-residue magain in antibiotic peptide is an α-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution

    International Nuclear Information System (INIS)

    Gesell, Jennifer; Zasloff, Michael; Opella, Stanley J.

    1997-01-01

    Magainin2 is a 23-residue antibiotic peptide that disrupts the ionic gradient across certain cell membranes. Two-dimensional 1H NMR spectroscopy was used to investigate the structure of the peptide in three of the membrane environments most commonly employed in biophysical studies. Sequence-specific resonance assignments were determined for the peptide in perdeuterated dodecylphosphocholine (DPC) and sodium dodecylsulfate micelles and confirmed for the peptide in 2,2,2-trifluoroethanol solution. The secondary structure is shown to be helical in all of the solvent systems. The NMR data were used as a set of restraints for a simulated annealing protocol that generated a family of three-dimensional structures of the peptide in DPC micelles, which superimposed best between residues 4 and 20. For these residues, the mean pairwise rms difference for the backbone atoms is 0.47 ± 0.10A from the average structure. The calculated peptide structures appear to be curved,with the bend centered at residues Phe12 and Gly13

  8. Compact NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bluemich, Bernhard; Haber-Pohlmeier, Sabina; Zia, Wasif [RWTH Aachen Univ. (Germany). Inst. fuer Technische und Makromolekulare Chemie (ITMC)

    2014-06-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is the most popular method for chemists to analyze molecular structures, while Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic tool for medical doctors that provides high-contrast images of biological tissue. In both applications, the sample (or patient) is positioned inside a large, superconducting magnet to magnetize the atomic nuclei. Interrogating radio-frequency pulses result in frequency spectra that provide the chemist with molecular information, the medical doctor with anatomic images, and materials scientist with NMR relaxation parameters. Recent advances in magnet technology have led to a variety of small permanent magnets to allow compact and low-cost instruments. The goal of this book is to provide an introduction to the practical use of compact NMR at a level nearly as basic as the operation of a smart phone.

  9. Seed prepare for oil content determination by NMR method in six cotton varieties

    International Nuclear Information System (INIS)

    Gondim-Tomaz, Rose Marry Araujo; Erismann, Norma de Magalhaes; Sabino, Nelson Paulieri; Kondo, Julio Isao; Cia, Edivaldo; Azzini, Anisio; Soave, Daise

    1998-01-01

    Three comparative methods (chemical seed-delinting with sulphuric acid solution, flaming and seed with linter) to prepare cotton seeds for oil determination by the Nuclear Magnetic Resonance (NMR) technique were considered. The chemical treatment with sulphuric acid was the best as long the linter interference was eliminated. The seed oil contents were determined by the NMR method in six cotton varieties from the national variety test. The IAPAR (Instituto Agronomico do Parana) 71 PR3 and IAC (Instituto Agronomico de Campinas) 20 varieties presented the highest oil content followed by the CNPA 7H, CS 50, IAC 22 and CNPA Precoce 2. (author)

  10. Solid-state NMR of inorganic semiconductors.

    Science.gov (United States)

    Yesinowski, James P

    2012-01-01

    Studies of inorganic semiconductors by solid-state NMR vary widely in terms of the nature of the samples investigated, the techniques employed to observe the NMR signal, and the types of information obtained. Compared with the NMR of diamagnetic non-semiconducting substances, important differences often result from the presence of electron or hole carriers that are the hallmark of semiconductors, and whose theoretical interpretation can be involved. This review aims to provide a broad perspective on the topic for the non-expert by providing: (1) a basic introduction to semiconductor physical concepts relevant to NMR, including common crystal structures and the various methods of making samples; (2) discussions of the NMR spin Hamiltonian, details of some of the NMR techniques and strategies used to make measurements and theoretically predict NMR parameters, and examples of how each of the terms in the Hamiltonian has provided useful information in bulk semiconductors; (3) a discussion of the additional considerations needed to interpret the NMR of nanoscale semiconductors, with selected examples. The area of semiconductor NMR is being revitalized by this interest in nanoscale semiconductors, the great improvements in NMR detection sensitivity and resolution that have occurred, and the current interest in optical pumping and spintronics-related studies. Promising directions for future research will be noted throughout.

  11. Imidazole as a pH Probe: An NMR Experiment for the General Chemistry Laboratory

    Science.gov (United States)

    Hagan, William J., Jr.; Edie, Dennis L.; Cooley, Linda B.

    2007-01-01

    The analysis describes an NMR experiment for the general chemistry laboratory, which employs an unknown imidazole solution to measure the pH values. The described mechanism can also be used for measuring the acidity within the isolated cells.

  12. Transformation of meta-stable calcium silicate hydrates to tobermorite: reaction kinetics and molecular structure from XRD and NMR spectroscopy

    Science.gov (United States)

    2009-01-01

    Understanding the integrity of well-bore systems that are lined with Portland-based cements is critical to the successful storage of sequestered CO2 in gas and oil reservoirs. As a first step, we investigate reaction rates and mechanistic pathways for cement mineral growth in the absence of CO2 by coupling water chemistry with XRD and NMR spectroscopic data. We find that semi-crystalline calcium (alumino-)silicate hydrate (Al-CSH) forms as a precursor solid to the cement mineral tobermorite. Rate constants for tobermorite growth were found to be k = 0.6 (± 0.1) × 10-5 s-1 for a solution:solid of 10:1 and 1.6 (± 0.8) × 10-4 s-1 for a solution:solid of 5:1 (batch mode; T = 150°C). This data indicates that reaction rates for tobermorite growth are faster when the solution volume is reduced by half, suggesting that rates are dependent on solution saturation and that the Gibbs free energy is the reaction driver. However, calculated solution saturation indexes for Al-CSH and tobermorite differ by less than one log unit, which is within the measured uncertainty. Based on this data, we consider both heterogeneous nucleation as the thermodynamic driver and internal restructuring as possible mechanistic pathways for growth. We also use NMR spectroscopy to characterize the site symmetry and bonding environment of Al and Si in a reacted tobermorite sample. We find two [4]Al coordination structures at δiso = 59.9 ppm and 66.3 ppm with quadrupolar product parameters (PQ) of 0.21 MHz and 0.10 MHz (± 0.08) from 27Al 3Q-MAS NMR and speculate on the Al occupancy of framework sites by probing the protonation environment of Al metal centers using 27Al{1H}CP-MAS NMR. PMID:19144195

  13. Heteronuclear three-dimensional NMR spectroscopy. Natural abundance 13C chemical shift editing of 1H-1H COSY spectra

    International Nuclear Information System (INIS)

    Fesik, S.W.; Gampe, R.T. Jr.; Zuiderweg, E.R.P.

    1989-01-01

    It has been demonstrated that heteronuclear 3D NMR spectroscopy can be effectively applied to small molecules with 13 C at natural abundance. A 78mM solution of the aminoglycoside, kanamycin A was used for this experiment. The heteronuclear 3D NMR spectroscopy is shown to be a useful method for resolving spectral overlap in all frequency domains. 10 refs., 2 figs

  14. Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins

    International Nuclear Information System (INIS)

    Korzhnev, Dmitry M.; Neculai, Dante; Dhe-Paganon, Sirano; Arrowsmith, Cheryl H.; Bezsonova, Irina

    2016-01-01

    HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped replication forks into X-shaped Holliday junction structures that allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 3′-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organisms from bacteria (as a stand-alone domain) to plants, fungi and metazoan (in combination with SWI2/SNF2 helicase-like domain). The obtained structure of free HLTF HIRAN is similar to recently reported structures of its DNA bound form, while the NMR analysis also reveals that the DNA binding site of the free domain exhibits conformational heterogeneity. Sequence comparison of N-terminal regions of HLTF, SHPRH and Rad5 aided by knowledge of the HLTF HIRAN structure suggests that the SHPRH N-terminus also includes an uncharacterized structured module, exhibiting weak sequence similarity with HIRAN regions of HLTF and Rad5, and potentially playing a similar functional role.

  15. Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins

    Energy Technology Data Exchange (ETDEWEB)

    Korzhnev, Dmitry M. [University of Connecticut Health, Department of Molecular Biology and Biophysics (United States); Neculai, Dante [Zhejiang University, School of Medicine (China); Dhe-Paganon, Sirano [Dana-Farber Cancer Institute, Department of Cancer Biology (United States); Arrowsmith, Cheryl H. [University of Toronto, Structural Genomics Consortium (Canada); Bezsonova, Irina, E-mail: bezsonova@uchc.edu [University of Connecticut Health, Department of Molecular Biology and Biophysics (United States)

    2016-11-15

    HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped replication forks into X-shaped Holliday junction structures that allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 3′-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organisms from bacteria (as a stand-alone domain) to plants, fungi and metazoan (in combination with SWI2/SNF2 helicase-like domain). The obtained structure of free HLTF HIRAN is similar to recently reported structures of its DNA bound form, while the NMR analysis also reveals that the DNA binding site of the free domain exhibits conformational heterogeneity. Sequence comparison of N-terminal regions of HLTF, SHPRH and Rad5 aided by knowledge of the HLTF HIRAN structure suggests that the SHPRH N-terminus also includes an uncharacterized structured module, exhibiting weak sequence similarity with HIRAN regions of HLTF and Rad5, and potentially playing a similar functional role.

  16. Experimental Determination of pK[subscript a] Values and Metal Binding for Biomolecular Compounds Using [superscript 31]P NMR Spectroscopy

    Science.gov (United States)

    Swartz, Mason A.; Tubergen, Philip J.; Tatko, Chad D.; Baker, Rachael A.

    2018-01-01

    This lab experiment uses [superscript 31]P NMR spectroscopy of biomolecules to determine pK[subscript a] values and the binding energies of metal/biomolecule complexes. Solutions of adenosine nucleotides are prepared, and a series of [superscript 31]P NMR spectra are collected as a function of pH and in the absence and presence of magnesium or…

  17. Correlations between the 1H NMR chemical shieldings and the pKa values of organic acids and amines.

    Science.gov (United States)

    Lu, Juanfeng; Lu, Tingting; Zhao, Xinyun; Chen, Xi; Zhan, Chang-Guo

    2018-06-01

    The acid dissociation constants and 1 H NMR chemical shieldings of organic compounds are important properties that have attracted much research interest. However, few studies have explored the relationship between these two properties. In this work, we theoretically studied the NMR chemical shifts of a series of carboxylic acids and amines in the gas phase and in aqueous solution. It was found that the negative logarithms of the experimental acid dissociation constants (i.e., the pK a values) of the organic acids and amines in aqueous solution correlate almost linearly with the corresponding calculated NMR chemical shieldings. Key factors that affect the theoretically predicted pK a values are discussed in this paper. The present work provides a new way to predict the pK a values of organic/biochemical compounds. Graphical abstract The chemical shielding values of organic acids and amines correlate near linearly with their corresponding pK a values.

  18. Structure and Dynamics Studies of Cytolytic Peptides in Lipid Bilayers using NMR Spectroscopy

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh

    2015-01-01

    different and cytolytic peptides were investigated in this work. The peptides were SPF-5506-A4 from Trichoderma sp, Conolysin-Mt1 from Conus mustelinus, and Alamethicin from Trichoderma viride. The studies employed solution and solid-state NMR spectroscopy in combination with different biophysical methods...

  19. Symmetry Breaking in NMR Spectroscopy: The Elucidation of Hidden Molecular Rearrangement Processes

    Directory of Open Access Journals (Sweden)

    Michael J. McGlinchey

    2014-08-01

    Full Text Available Variable-temperature NMR spectroscopy is probably the most convenient and sensitive technique to monitor changes in molecular structure in solution. Rearrangements that are rapid on the NMR time-scale exhibit simplified spectra, whereby non-equivalent nuclear environments yield time-averaged resonances. At lower temperatures, when the rate of exchange is sufficiently reduced, these degeneracies are split and the underlying “static” molecular symmetry, as seen by X-ray crystallography, becomes apparent. Frequently, however, such rearrangement processes are hidden, even when they become slow on the NMR time-scale, because the molecular point group remains unchanged. Judicious symmetry breaking, such as by substitution of a molecular fragment by a similar, but not identical moiety, or by the incorporation of potentially diastereotopic (chemically non-equivalent nuclei, allows the elucidation of the kinetics and energetics of such processes. Examples are chosen that include a wide range of rotations, migrations and other rearrangements in organic, inorganic and organometallic chemistry.

  20. Evaluation of PHB nanocomposite by low field NMR

    International Nuclear Information System (INIS)

    Silva, Mariana Bruno Rocha e; Tavares, Maria Ines Bruno

    2009-01-01

    Poly(3-hydroxybutyrate) (PHB) based on nanocomposites containing different amounts of a commercial organically modified clay (viscogel B8) were prepared employing solution intercalation method. The relationship among the processing conditions; molecular structure and intermolecular interaction, between both nanocomposite components, were investigated using a nuclear magnetic resonance (NMR), as a part of characterization methodology, which has been used by Tavares et al. It involves the proton spin-lattice relaxation time, T1 H, by solid state nuclear magnetic resonance, employing low field NMR. X-ray diffraction was also employed because it is a conventional technique, generally used to obtain the first information on nanocomposite formation. Changes in PHB crystallinity were observed after the organophilic nanoclay had been incorporated in the polymer matrix. These changes, in the microstructure, were detected by the variation of proton nuclear relaxation time values and by X-ray, which showed an increase in the clay interlamellar space due to the intercalation of the polymer in the clay between lamellae. (author)

  1. Solution structure of the 3'-5' cyclic dinucleotide d. A combined NMR, UV melting, and molecular mechanics study

    International Nuclear Information System (INIS)

    Blommers, M.J.J.; Haasnoot, C.A.G.; Walters, J.A.L.I.; van der Marel, G.A.; van Boom, J.H.; Hilbers, C.W.

    1988-01-01

    The 3'-5' cyclic dinucleotide d 1 H and 13 C NMR experiments, UV-melting experiments, and molecular mechanics calculations. The 1 H and 13 C NMR spectra were analyzed by means of 2-dimensional NMR experiments. J-Coupling analysis of the 1D and 2D 1 H and 13 C spectra was used to determine the conformation of the ring systems in the molecule. It appeared that at low temperature (283 K) the deoxyribose sugars adopt a N-type conformation. The geometry is best described by an intermediate between the 3 2 T and 3 E forms. In addition, the authors were able to derive all other torsion angles in the phosphate backbone ring system, i.e., α + , β/sup t/, γ + , δ (=89/degrees/), ε/sup t/ and /zeta/ + . When the molecule is subjected to an energy minimization procedure (using the program AMBER), the sugar ring system retains, practically speaking, the torsion angles found from the NMR experiments, while the torsion angles around the glycosidic bond adopt a value of 175/degrees/ in the minimum energy conformation. UV-melting experiments indicate that two molecules can form a dimer in which the adenine bases are intercalated. The feasibility of this structure is indicated by molecular mechanics calculations. At higher temperatures the dimer is converted into separate monomers. In the monomer form the sugars exhibit S-pucker 20% of the time. Concomitantly with the conversion of the N- to the S-conformation, the torsion angles α and γ change

  2. NMR structure of the HIV-1 reverse transcriptase thumb subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Sharaf, Naima G. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Brereton, Andrew E. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Byeon, In-Ja L. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Andrew Karplus, P. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Gronenborn, Angela M., E-mail: amg100@pitt.edu [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States)

    2016-12-15

    The solution NMR structure of the isolated thumb subdomain of HIV-1 reverse transcriptase (RT) has been determined. A detailed comparison of the current structure with dozens of the highest resolution crystal structures of this domain in the context of the full-length enzyme reveals that the overall structures are very similar, with only two regions exhibiting local conformational differences. The C-terminal capping pattern of the αH helix is subtly different, and the loop connecting the αI and αJ helices in the p51 chain of the full-length p51/p66 heterodimeric RT differs from our NMR structure due to unique packing interactions in mature RT. Overall, our data show that the thumb subdomain folds independently and essentially the same in isolation as in its natural structural context.

  3. Solution Structure of an Antifreeze Protein CfAFP-501 from Choristoneura fumiferana

    International Nuclear Information System (INIS)

    Li Congmin; Guo Xianrong; Jia Zongchao; Xia Bin; Jin Changwen

    2005-01-01

    Antifreeze proteins (AFPs) are widely employed by various organisms as part of their overwintering survival strategy. AFPs have the unique ability to suppress the freezing point of aqueous solution and inhibit ice recrystallization through binding to the ice seed crystals and restricting their growth. The solution structure of CfAFP-501 from spruce budworm has been determined by NMR spectroscopy. Our result demonstrates that CfAFP-501 retains its rigid and highly regular structure in solution. Overall, the solution structure is similar to the crystal structure except the N- and C-terminal regions. NMR spin-relaxation experiments further indicate the overall rigidity of the protein and identify a collection of residues with greater flexibilities. Furthermore, Pro91 shows a cis conformation in solution instead of the trans conformation determined in the crystal structure

  4. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

    This textbook begins with an overview of NMR development and applications in biological systems. It describes recent developments in instrument hardware and methodology. Chapters highlight the scope and limitation of NMR methods. While detailed math and quantum mechanics dealing with NMR theory have been addressed in several well-known NMR volumes, chapter two of this volume illustrates the fundamental principles and concepts of NMR spectroscopy in a more descriptive manner. Topics such as instrument setup, data acquisition, and data processing using a variety of offline software are discussed. Chapters further discuss several routine stategies for preparing samples, especially for macromolecules and complexes. The target market for such a volume includes researchers in the field of biochemistry, chemistry, structural biology and biophysics.

  5. Preparation of EVA/silica nano composites characterized with solid state nuclear magnetic resonance; Obtencao de nanocomposito de EVA/SILICA e caracterizacao por ressonancia magnetica nuclear no estado solido

    Energy Technology Data Exchange (ETDEWEB)

    Passos, Adriano A; Tavares, Maria I.B.; Neto, Roberto C.P.; Moreira, Leonardo A; Ferreira, Antonio G., E-mail: mibt@ima.ufrj.br [Centro de Tecnologia, Instituto de Macromoleculas Professora Eloisa Mano, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil)

    2011-07-01

    Nano composites of poly(ethylene-co-vinyl acetate)/silica (SiO{sub 2}) with dimensions of ca. 40 nm were prepared via solution intercalation employing chloroform as a solvent. They were mainly characterized with nuclear magnetic resonance spectroscopy (NMR) employing carbon-13 (polymeric matrix), silicon-29 (nanoparticles) and through the determination of the proton spin-lattice relaxation time in the rotating frame (T{sub 1{rho}H}) (polymer matrix). From the NMR results it was inferred that up to 5% of silica in mass a well dispersed nano composite was obtained, owing to a strong interaction between silica and the EVA matrix. (author)

  6. Speciation of platinum(IV) in nitric acid solutions.

    Science.gov (United States)

    Vasilchenko, Danila; Tkachev, Sergey; Baidina, Iraida; Korenev, Sergey

    2013-09-16

    The speciation of platinum(IV) ions in nitric acid (6-15.8 M) solutions of H2[Pt(OH)6] has been studied by (195)Pt NMR and Raman spectroscopy. Series of aqua-hydroxo-nitrato complexes [Pt(L)(x)(NO3)(6-x)] (L = H2O or OH(-); x = 0, ..., 6) were found to exist in such solutions. The pair additivity model of chemical shifts and statistical theory were used to assign signals in NMR spectra to particular [Pt(L)(x)(NO3)(6-x)] species. Mononuclear hexanitratoplatinates(IV) have been isolated in solid state in substantial yield as pyridinium salt (PyH)2[Pt(NO3)6] and characterized by single-crystal X-ray diffraction. Aging of the platinum nitric acid solutions for more than 5-6 h results in oligomerization of [Pt(L)(x)(NO3)(6-x)] species and the formation of oligonuclear aqua-hydroxo-nitrato complexes with OH(-) and NO3(-) bridging ligands. Oligomeric platinum(IV) complexes with two and four nuclei were unambiguously detected by NMR on (195)Pt -enriched samples. Oligomers with even higher nuclearity were also detected. Dimeric anions [Pt2(μ-OH)2(NO3)8](2-) have been isolated as single crystals of tetramethylammonium salt and characterized by X-ray diffraction.

  7. A global analysis of NMR distance constraints from the PDB

    International Nuclear Information System (INIS)

    Vranken, Wim

    2007-01-01

    Information obtained from Nuclear Magnetic Resonance (NMR) experiments is encoded as a set of constraint lists when calculating three-dimensional structures for a protein. With the amount of constraint data from the world wide Protein Data Bank (wwPDB) that is now available, it is possible to do a global, large-scale analysis using only information from the constraints, without taking the coordinate information into account. This article describes such an analysis of distance constraints from NOE data based on a set of 1834 NMR PDB entries containing 1909 protein chains. In order to best represent the quality and extent of the data that is currently deposited at the wwPDB, only the original data as deposited by the authors was used, and no attempt was made to 'clean up' and further interpret this information. Because the constraint lists provide a single set of data, and not an ensemble of structural solutions, they are easier to analyse and provide a reduced form of structural information that is relevant for NMR analysis only. The online resource resulting from this analysis makes it possible to check, for example, how often a particular contact occurs when assigning NOESY spectra, or to find out whether a particular sequence fragment is likely to be difficult to assign. In this respect it formalises information that scientists with experience in spectrum analysis are aware of but cannot necessarily quantify. The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community

  8. Ligand-receptor Interactions by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Novak. P.

    2008-04-01

    Full Text Available Today NMR spectroscopy is a method of choice for elucidation of interactions between biomolecules and the potential ligands. Knowledge on these interactions is an essential prerequisite for the rational drug design. The most important contribution of NMR to drug design a few years ago was the 3D structure determination of proteins. Besides delivering the 3D structures of the free proteins as a raw material for the modeling studies on ligand binding, NMR can directly yield valuable experimental data on the biologically important protein-ligand complexes. In addition to X-ray diffraction, NMR spectroscopy can provide information on the internal protein dynamics ordynamics of intermolecular interactions. Changes in NMR parameters allow us to detect ("SAR by NMR" and quantitatively determine binding affinities (titration, diffusion NMR experiments, etc. of potential ligands. Also, it is possible to determine the binding site and conformations of ligands, receptors and receptor-ligand complexes with the help of NMR methods such as tr-NOESY. Epitopes or functional groups responsible for binding of ligands to the receptor can be identified by employing STD or WaterLOGSY experiments. In this review are described some of the most frequent NMR methods for the characterization of the interactions between biomolecules and ligands, together with their advantages and disadvantages.

  9. Advanced NMR technology for bioscience and biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Hammel, P.C.; Hernandez, G.; Trewhella, J.; Unkefer, C.J. [Los Alamos National Lab., NM (US); Boumenthal, D.K. [Univ. of Utah, Salt Lake City, UT (US); Kennedy, M.A. [Pacific Northwest National Lab., Richland, WA (US); Moore, G.J. [Wayne State Univ., Detroit, MI (US)

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). NMR plays critical roles in bioscience and biotechnology in both imaging and structure determination. NMR is limited, however, by the inherent low sensitivity of the NMR experiment and the demands for spectral resolution required to study biomolecules. The authors addressed both of these issues by working on the development of NMR force microscopy for molecular imaging, and high field NMR with isotope labeling to overcome limitations in the size of biomolecules that can be studied using NMR. A novel rf coil design for NMR force microscopy was developed that increases the limits of sensitivity in magnetic resonance detection for imaging, and the authors demonstrated sub-surface spatial imaging capabilities. The authors also made advances in the miniaturization of two critical NMR force microscope components. They completed high field NMR and isotope labeling studies of a muscle protein complex which is responsible for regulating muscle contraction and is too large for study using conventional NMR approaches.

  10. Reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor-V: function, thermodynamic stability, and NMR solution structure.

    Science.gov (United States)

    Cai, M; Gong, Y; Prakash, O; Krishnamoorthi, R

    1995-09-26

    Reactive-site (Lys44-Asp45 peptide bond) hydrolyzed Cucurbita maxima trypsin inhibitor-V (CMTI-V*) was prepared and characterized: In comparison to the intact form, CMTI-V* exhibited markedly reduced inhibitory properties and binding affinities toward trypsin and human blood coagulation factor XIIa. The equilibrium constant of trypsin-catalyzed hydrolysis, Khyd, defined as [CMTI-V*]/[CMTI-V], was measured to be approximately 9.4 at 25 degrees C (delta G degrees = -1.3 kcal.mol-1). From the temperature dependence of delta G degrees, the following thermodynamic parameters were estimated: delta H degrees = 1.6 kcal.mol-1 and delta S degrees = 9.8 eu. In order to understand the functional and thermodynamic differences between the two forms, the three-dimensional solution structure of CMTI-V* was determined by a combined approach of NMR, distance geometry, and simulated annealing methods. Thus, following sequence-specific and stereospecific resonance assignments, including those of beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens, 809 interhydrogen distances and 123 dihedral angle constraints were determined, resulting in the computation and energy-minimization of 20 structures for CMTI-V*. The average root mean squared deviation in position for equivalent atoms between the 20 individual structures and the mean structure obtained by averaging their coordinates is 0.67 +/- 0.15 A for the main chain atoms and 1.19 +/- 0.23 A for all the non-hydrogen atoms of residues 5-40 and residues 48-67.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.O.; Sutton; Ell, P.

    1986-01-01

    The object of this book is to discuss and evaluate an area of Nuclear Magnetic Resonance which to date has been less emphasized than it might be, namely the use of NMR for functional studies. The book commences with a discussion of the areas in which the NMR techniques might be needed due to deficiencies in other techniques. The physics of NMR especially relating to functional measurement are then explained. Technical factors in producing functional images are discussed and the use of paramagnetic substances for carrying out flow studies are detailed. Particular attention is paid to specific studies in the various organs. The book ends with a survey of imaging in each organ and the relation of NMR images to other techniques such as ultrasound, nuclear medicine and X-rays

  12. Solid NMR study of lithium ions accommodated in various transition metal oxides

    International Nuclear Information System (INIS)

    Kanzaki, Yasushi; Suzuki, Noriko

    2008-01-01

    Solid NMR was used to elucidate the lithium accommodation/extraction reaction in various transition metal oxides. The first study was the lithium ion exchange reaction of titanium antimonic acid (TiSbA). The effect of hydration on the selectivity of lithium ion in the solid phase was examined using 7 Li NMR. The second study was the irreversible ion exchange behavior of HNbO 3 . The selectivity for the lithium ion and the irreversible behavior were examined using 1 H and 7 Li NMR. The third study was the isotope separation between 6 Li and 7 Li in various inorganic ion exchangers. The high isotope separation coefficient was ascribed to the degree of dehydration during the ion exchange reaction. The degree of dehydration was examined by 1 H and 7 Li NMR studies. The last study was determining the mechanism of the lithium accommodation/extraction reaction of λ-MnO 2 in an aqueous solution. The different paths between the accommodation and extraction and the formation of MnO 4- during the accommodation were determined by chemical analysis. The Knight shift in the 7 Li MAS-NMR spectra of Li 0.5 MnO 2 suggested the localization of the electron density on the lithium nuclei. An XPS study also suggested the presence of an electron density on the lithium nuclei. A pH-independent redox couple was assumed to account for the accommodation/extraction reaction of lithium ions, such as Li(I)/Li(0). (author)

  13. Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Kerem

    2018-04-18

    Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome manual absolute quantitation step of metabolites in 1D 1H NMR spectra. This provides more consistency between inter-laboratory comparisons. Integration of 2D NMR metabolomics databases under a unified web server allowed very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry. These hybrid NMR/MS approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing to profile ever larger number of metabolites in application studies.

  14. Magic Angle Spinning NMR Metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhi Hu, Jian

    2016-01-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a non-destructive, quantitative, reproducible, untargeted and unbiased method that requires no or minimal sample preparation, and is one of the leading analytical tools for metabonomics research [1-3]. The easy quantification and the no need of prior knowledge about compounds present in a sample associated with NMR are advantageous over other techniques [1,4]. 1H NMR is especially attractive because protons are present in virtually all metabolites and its NMR sensitivity is high, enabling the simultaneous identification and monitoring of a wide range of low molecular weight metabolites.

  15. Rheo-NMR: nuclear magnetic resonance and the rheology of complex fluids

    International Nuclear Information System (INIS)

    Callaghan, Paul T.

    1999-01-01

    The application of nuclear magnetic resonance methods to the study of complex fluids under shearing and extensional flows is reviewed. Both NMR velocimetry and spectroscopy approaches are discussed while specific systems studied include polymer melts, rigid rod and random coil polymers in solution, lyotropic and thermotropic liquid crystals and liquid crystalline polymers, and wormlike micelles. Reference is made to food systems. (author)

  16. On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

    Energy Technology Data Exchange (ETDEWEB)

    Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr [Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris (France); Charpentier, Thibault [CEA, IRAMIS, NIMBE, LSDRM, UMR CEA-CNRS 3685, F-91191 Gif-sur-Yvette Cedex (France)

    2015-11-21

    Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFG tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.

  17. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

  18. Discovery of Intermediates of lacZ β-Galactosidase Catalyzed Hydrolysis Using dDNP NMR

    DEFF Research Database (Denmark)

    Kjeldsen, Christian; Ardenkjær-Larsen, Jan Henrik; Duus, Jens Ø.

    2018-01-01

    Using dissolution dynamic nuclear polarization, the sensitivity of single scan solution state 13C NMR can be improved up to 4 orders of magnitude. In this study, the enzyme lacZ β-galactosidase from Escherichia coli was subjected to hyperpolarized substrate, and previously unknown reaction...

  19. Discovery of Intermediates of lacZ beta-Galactosidase Catalyzed Hydrolysis Using dDNP NMR

    DEFF Research Database (Denmark)

    Kjeldsen, Christian; Ardenkjær-Larsen, Jan Henrik; Duus, Jens Øllgaard

    2018-01-01

    Using dissolution dynamic nuclear polarization, the sensitivity of single scan solution state C-13 NMR can be improved up to 4 orders of magnitude. In this study, the enzyme lacZ beta-galactosidase from Escherichia coli was subjected to hyperpolarized substrate, and previously unknown reaction...

  20. NMR studies of sodium cholate-lecithin mixed micelles

    International Nuclear Information System (INIS)

    Eriksson, P.-O.; Lindblom, G.; Arvidson, G.

    1983-01-01

    T 1 and T 2 2 H-NMR relaxation times have been measured for 2 H-labelled phosphatidylcholine in the aqueous solution phase of the ternary system lecithin-sodium cholate-water. In this phase aggregates are formed by a mixture of cholate and lecithin. Information about the dimension of these miscellar aggregates has been obtained from a simple model of the relaxation times in which two modes of molecular motion are considered. The results obtained accord well with recent investigations using laser-light scattering techniques

  1. NMR imaging of cerebral infarction

    International Nuclear Information System (INIS)

    Takusagawa, Yoshihiko; Yamaoka, Naoki; Doi, Kazuaki; Okada, Keisei

    1987-01-01

    One hundred and five patients with cerebral infarction were studied by nuclear magnetic resonance (NMR) CT (resistive type of magnet with strength of 0.1 tesla) and X-ray CT. Pulse sequences used saturation recovery (Tr = 600 mSec), Inversion recovery (Tr = 500 mSec, Td = 300 mSec) and spin echo (Tr = 1500 mSec, Te = 40, 80, 120, 160 mSec). Fifteen cases were examined by NMR-CT within 24 hours from onset. Proton NMR imaging could not detect cerebral ischemia as early as 2 hours after onset, but except could detect the lesions in Se image the area of cerebral infarct 3 hours after onset. After 5 hours from onset image changes in SE were evident and corresponded to the area of cerebral infarct, but image changes in IR could not fully delineate the infarcted area. NMR images of 41 year-old woman with cerebral embolism by MCA trunck occlusion associated with mitral stenosis were presented, and NMR-CT was examined 10 hours, 9th and 43th days after episode of MCA occlusion. Sixty patents (64 times) with lacunar infarction were studied by NMR-CT and X-ray CT. The inversion recovery images were used mainly for detection of lesions and comparison with X-ray CT. In 160 lesions which were detected by NMR-CT or X-ray CT, could 156 lesions be detected by NMR-CT and 78 lesions by X-ray CT. Inversion recovery images were more useful for detection of lacunes than X-ray CT. Calculated T1 and T2 values prolonged with time course from onset. (author)

  2. Study of xenon binding in cryptophane-A using laser-induced NMR polarization enhancement

    International Nuclear Information System (INIS)

    Luhmer, M.; Goodson, B.M.; Song, Y.Q.; Laws, D.D.; Kaiser, L.; Pines, A.; Lawrence Berkeley National Lab., CA

    1999-01-01

    Xenon is chemically inert, yet exhibits NMR parameters that are highly sensitive to its chemical environment. Considerable work has therefore capitalized on the utility of 129 Xe (I = 1/2) as a magnetic resonance probe of molecules, materials, and biological systems. In solution, spin-polarization transfer between laser-polarized xenon and the hydrogen nuclei of nearby molecules leads to signal enhancements in the resolved 1 H NMR spectrum, offering new opportunities for probing the chemical environment of xenon atoms. Following binding of laser-polarized xenon to molecules of cryptophane-A, selective enhancements of the 1 H NMR signals were observed. A theoretical framework for the interpretation of such experimental results is provided, and the spin polarization-induced nuclear Overhauser effects are shown to yield information about the molecular environment of xenon. The observed selective 1 H enhancements allowed xenon-proton internuclear distances to be estimated. These distances reveal structural characteristics of the complex, including the preferred molecular conformations adopted by cryptophane-A upon binding of xenon

  3. Discrimination of sugarcane according to cultivar by 1H NMR and chemometric analyses

    Energy Technology Data Exchange (ETDEWEB)

    Alves Filho, Elenilson G.; Silva, Lorena M.A.; Choze, Rafael; Liao, Luciano M. [Laboratorio de Ressonancia Magnetica Nuclear, Instituto de Quimica, Universidade Federal de Goias (UFG), Goiania, GO (Brazil); Honda, Neli K.; Alcantara, Glaucia B. [Departamento de Quimica, Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil)

    2012-07-01

    Several technologies for the development of new sugarcane cultivars have mainly focused on the increase in productivity and greater disease resistance. Sugarcane cultivars are usually identified by the organography of the leaves and stems, the analysis of peroxidase and esterase isoenzyme activities and the total soluble protein as well as soluble solid content. Nuclear magnetic resonance (NMR) associated with chemometric analysis has proven to be a valuable tool for cultivar assessment. Thus, this article describes the potential of chemometric analysis applied to 1H high resolution magic angle spinning (HRMAS) and NMR in solution for the investigation of sugarcane cultivars. For this purpose, leaves from eight different cultivars of sugarcane were investigated by {sup 1}H NMR spectroscopy in combination with chemometric analysis. The approach shows to be a useful tool for the distinction and classification of different sugarcane cultivars as well as to access the differences on its chemical composition. (author)

  4. Preparation, spectroscopic and high field NMR relaxometry studies of gadolinium(III) complexes with the asymmetric tetraamine 1,4,7,11-tetraazaundecane

    Science.gov (United States)

    Hatzipanayioti, Despina; Veneris, Antonis

    2009-10-01

    The reaction of Gd(III) with asymmetric tetramine 1,4,7,11-tetraazaundecane (2,2,3-tet, L1) ligand has been studied via NMR spectroscopy. The ligand proton longitudinal relaxation rates ( R1) have been used to estimate the distances of these protons from the Gd(III) center, in Gd(III)- L1 reaction solutions, in H 2O/D 2O 5/1 mixtures. Two Gd(III) complexes [Gd(III)( L1)(NH 3)(H 2O) 4](CH 3COO) 3·2H 2O ( 1) and [Gd(III)( L1)(NH 3)(H 2O) 2]Cl 3·EtOH ( 2) have been isolated and characterized by elemental analyses, TGA, IR, NMR and relaxometry measurements. The NMR relaxation measurements of 2 in aqueous solutions have been performed, under various temperature or concentration conditions, and compared with those of the commercial contrast agents Gd(III)-DTPA and Gd(III)-DTPA-BMA. It has also been studied the influence of (i) the Gd(III) inner-sphere water molecule number ( q) alteration and (ii) the steric constraint enhancement on the metal site, over the relaxation rate values of the parent aqueous solution of Gd(III)-2,2,3-tet, and of the aqueous solutions of 2.

  5. Improving the efficiency of quantitative (1)H NMR: an innovative external standard-internal reference approach.

    Science.gov (United States)

    Huang, Yande; Su, Bao-Ning; Ye, Qingmei; Palaniswamy, Venkatapuram A; Bolgar, Mark S; Raglione, Thomas V

    2014-01-01

    The classical internal standard quantitative NMR (qNMR) method determines the purity of an analyte by the determination of a solution containing the analyte and a standard. Therefore, the standard must meet the requirements of chemical compatibility and lack of resonance interference with the analyte as well as a known purity. The identification of such a standard can be time consuming and must be repeated for each analyte. In contrast, the external standard qNMR method utilizes a standard with a known purity to calibrate the NMR instrument. The external standard and the analyte are measured separately, thereby eliminating the matter of chemical compatibility and resonance interference between the standard and the analyte. However, the instrumental factors, including the quality of NMR tubes, must be kept the same. Any deviations will compromise the accuracy of the results. An innovative qNMR method reported herein utilizes an internal reference substance along with an external standard to assume the role of the standard used in the traditional internal standard qNMR method. In this new method, the internal reference substance must only be chemically compatible and be free of resonance-interference with the analyte or external standard whereas the external standard must only be of a known purity. The exact purity or concentration of the internal reference substance is not required as long as the same quantity is added to the external standard and the analyte. The new method reduces the burden of searching for an appropriate standard for each analyte significantly. Therefore the efficiency of the qNMR purity assay increases while the precision of the internal standard method is retained. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. The Three-Dimensional Solution Structure of the Src Homology Domain-2 of the Growth Factor Receptor-Bound Protein-2

    International Nuclear Information System (INIS)

    Senior, Mary M.; Frederick, Anne F.; Black, Stuart; Murgolo, Nicholas J.; Perkins, Louise M.; Wilson, Oswald; Snow, Mark E.; Wang Yusen

    1998-01-01

    A set of high-resolution three-dimensional solution structures of the Src homology region-2 (SH2) domain of the growth factor receptor-bound protein-2 was determined using heteronuclear NMR spectroscopy. The NMR data used in this study were collected on a stable monomeric protein solution that was free of protein aggregates and proteolysis. The solution structure was determined based upon a total of 1439 constraints, which included 1326 nuclear Overhauser effect distance constraints, 70 hydrogen bond constraints, and 43 dihedral angle constraints. Distance geometry-simulated annealing calculations followed by energy minimization yielded a family of 18 structures that converged to a root-mean-square deviation of 1.09 A for all backbone atoms and 0.40 A for the backbone atoms of the central β-sheet. The core structure of the SH2 domain contains an antiparallel β-sheet flanked by two parallel α-helices displaying an overall architecture that is similar to other known SH2 domain structures. This family of NMR structures is compared to the X-ray structure and to another family of NMR solution structures determined under different solution conditions

  7. NMR spectroscopic characterization of β-cyclodextrin inclusion complex with vanillin

    International Nuclear Information System (INIS)

    Pirnau, Adrian; Bogdan, Mircea; Floare, Calin G

    2009-01-01

    The inclusion of vanillin by β-cyclodextrin was investigated by 1 H NMR. The continuous variation technique was used to evidence the formation of soluble 1:1 complex in aqueous solution. The association constant of vanillin with β-cyclodextrin has been obtained at 298 K by fitting the experimental chemical shifts differences, Δδ obs δ free - δ obs of the observed guest and host protons, with a non-linear regression method. Besides the effective association constant, the fitting procedure allows a precise determination of all chemical shift parameters characterizing the pure complex. They can by used for an analysis of the geometry of the molecular complex in solution.

  8. β-NMR sample optimization

    CERN Document Server

    Zakoucka, Eva

    2013-01-01

    During my summer student programme I was working on sample optimization for a new β-NMR project at the ISOLDE facility. The β-NMR technique is well-established in solid-state physics and just recently it is being introduced for applications in biochemistry and life sciences. The β-NMR collaboration will be applying for beam time to the INTC committee in September for three nuclei: Cu, Zn and Mg. Sample optimization for Mg was already performed last year during the summer student programme. Therefore sample optimization for Cu and Zn had to be completed as well for the project proposal. My part in the project was to perform thorough literature research on techniques studying Cu and Zn complexes in native conditions, search for relevant binding candidates for Cu and Zn applicable for ß-NMR and eventually evaluate selected binding candidates using UV-VIS spectrometry.

  9. Solution structure of leptospiral LigA4 Big domain

    Energy Technology Data Exchange (ETDEWEB)

    Mei, Song; Zhang, Jiahai [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zhang, Xuecheng [School of Life Sciences, Anhui University, Hefei, Anhui 230039 (China); Tu, Xiaoming, E-mail: xmtu@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.

  10. Solution structure of leptospiral LigA4 Big domain

    International Nuclear Information System (INIS)

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-01-01

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca"2"+ binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca"2"+-binding site was identified by strains-all and NMR chemical shift perturbation.

  11. Microprocessorized NMR measurement

    International Nuclear Information System (INIS)

    Rijllart, A.

    1984-01-01

    An MC68000 CAMAC microprocessor system for fast and accurate NMR signal measurement will be presented. A stand-alone CAMAC microprocessor system (MC68000 STAC) with a special purpose interface sweeps a digital frequency synthesizer and digitizes the NMR signal with a 16-bit ADC of 17 μs conversion time. It averages the NMR signal data over many sweeps and then transfers it through CAMAC to a computer for calculation of the signal parameters. The computer has full software control over the timing and sweep settings of this signal averager, and thus allows optimization of noise suppression. Several of these processor systems can be installed in the same crate for parallel processing, and the flexibility of the STAC also allows easy adaptation to other applications such as transient recording or phase-sensitive detection. (orig.)

  12. Determination of the intracellular pH of intact erythrocytes by 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Rabenstein, D.L.; Isab, A.A.

    1982-01-01

    A method is described for determining the intracellular pH of intact erythrocytes by 1 H NMR. The determination is based on the pH dependence of the chemical shifts of resonances for carbon-bounded protons of an indicator molecule (imidazole) in intact cells. The imidazole is introduced into the erythrocytes by incubation in an isotonic saline solution of the indicator. The pH dependence of the chemical shifts of the imidazole resonances is calibrated from 1 H NMR spectra of the imidazole-containing red cell lysates whose pH is varied by the addition of acid or base and measured directly with a pH electrode. To reduce in intensity or eliminate the much more intense envelope of resonances from the hemoglobin, the 1 H NMR measurements are made by either the spin-echo Fourier transform technique or by the transfer-or-saturation by cross-relaxation method

  13. Fourier transform n.m.r. spectroscopy

    International Nuclear Information System (INIS)

    Shaw, D.

    1976-01-01

    This book is orientated to techniques rather than applications. The basic theory of n.m.r. is dealt with in a unified approach to the Fourier theory. The middle section of the book concentrates on the practical aspects of Fourier n.m.r., both instrumental and experimental. The final chapters briefly cover general application of n.m.r., but concentrate strongly on those areas where Fourier n.m.r. can give information which is not available by conventional techniques

  14. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S

    2006-01-01

    NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

  15. An introduction to biological NMR spectroscopy

    International Nuclear Information System (INIS)

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). (authors)

  16. Optical pumping and xenon NMR

    International Nuclear Information System (INIS)

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping 129 Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the 131 Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen

  17. Carbonaceous species (coke) characterization in zeolites by solid state {sup 13} C NMR; Caracterizacao de especies carbonaceas (coque) em zeolitos por RMN de {sup 13} C estado solido (CP/MAS)

    Energy Technology Data Exchange (ETDEWEB)

    Mota, Claudio J.A.; Menezes, Sonia C [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas

    1992-12-31

    This work applies solid state {sup 13} C NMR for characterization of carbonaceous species (coke) deposited on zeolites after contact with n-hexane at 370 deg C. The results have shown two types of carbon: saturated (sp{sup 3}) and unsaturated (sp{sup 2}) 4 refs., 4 tabs.

  18. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.; Ell, P.J.

    1987-01-01

    This volume is based on a series of lectures delivered at a one-day teaching symposium on functional and metabolic aspects of NMR measurements held at the Middlesex Hospital Medical School on 1st September 1985 as a part of the European Nuclear Medicine Society Congress. Currently the major emphasis in medical NMR in vivo is on its potential to image and display abnormalities in conventional radiological images, providing increased contrast between normal and abnormal tissue, improved definition of vasculature, and possibly an increased potential for differential diagnosis. Although these areas are undeniably of major importance, it is probable that NMR will continue to complement conventional measurement methods. The major potential benefits to be derived from in vivo NMR measurements are likely to arise from its use as an instrument for functional and metabolic studies in both clinical research and in the everyday management of patients. It is to this area that this volume is directed

  19. Untangle soil-water-mucilage interactions: 1H NMR Relaxometry is lifting the veil

    Science.gov (United States)

    Brax, Mathilde; Buchmann, Christian; Schaumann, Gabriele Ellen

    2017-04-01

    Mucilage is mainly produced at the root tips and has a high water holding capacity derived from highly hydrophilic gel-forming substances. The objective of the MUCILAGE project is to understand the mechanistic role of mucilage for the regulation of water supply for plants. Our subproject investigates the chemical and physical properties of mucilage as pure gel and mixed with soil. 1H-NMR Relaxometry and PFG NMR represent non-intrusive powerful methods for soil scientific research by allowing quantification of the water distribution as well as monitoring of the water mobility in soil pores and gel phases.Relaxation of gel water differs from the one of pure water due to additional interactions with the gel matrix. Mucilage in soil leads to a hierarchical pore structure, consisting of the polymeric biohydrogel network surrounded by the surface of soil particles. The two types of relaxation rates 1/T1 and 1/T2 measured with 1H-NMR relaxometry refer to different relaxation mechanisms of water, while PFG-NMR measures the water self-diffusion coefficient. The objective of our study is to distinguish in situ water in gel from pore water in a simplified soil system, and to determine how the "gel effect" affects both relaxation rates and the water self-diffusion coefficient in porous systems. We demonstrate how the mucilage concentration and the soil solution alter the properties of water in the respective gel phases and pore systems in model soils. To distinguish gel-inherent processes from classical processes, we investigated the variations of the water mobility in pure chia mucilage under different conditions by using 1H-NMR relaxometry and PFG NMR. Using model soils, the signals coming from pore water and gel water were differentiated. We combined the equations describing 1H-NMR relaxation in porous systems and our experimental results, to explain how the presence of gel in soil affects 1H-NMR relaxation. Out of this knowledge we propose a method, which determines in

  20. NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes.

    Science.gov (United States)

    Dias, David M; Ciulli, Alessio

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. PIC microcontroller based external fast analog to digital converter to acquire wide-lined solid NMR spectra by BRUKER DRX and Avance-I spectrometers.

    Science.gov (United States)

    Koczor, Bálint; Rohonczy, János

    2015-01-01

    Concerning many former liquid or hybrid liquid/solid NMR consoles, the built in Analog-to-Digital Converters (ADCs) are incapable of digitizing the fids at sampling rates in the MHz range. Regarding both strong anisotropic interactions in the solid state and wide chemical shift dispersion nuclei in solution phase such as (195)Pt, (119)Sn, (207)Pb etc., the spectrum range of interest might be in the MHz range. As determining the informative tensor components of anisotropic NMR interactions requires nonlinear fitting over the whole spectrum including the asymptotic baseline, it is prohibited by low sampling rates of the ADCs. Wide spectrum width is also useful in solution NMR, since windowing of wide chemical shift ranges is avoidable. We built an external analog to digital converter with 10 MHz maximal sampling rate, which can work simultaneously with the built in ADC of the spectrometer. The ADC was tested on both Bruker DRX and Avance-I NMR consoles. In addition to the analog channels it only requires three external digital lines of the NMR console. The ADC sends data to PC via USB. The whole process is controlled by software written in JAVA which is implemented under TopSpin. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. PINE-SPARKY.2 for automated NMR-based protein structure research.

    Science.gov (United States)

    Lee, Woonghee; Markley, John L

    2018-05-01

    Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm. whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu. Supplementary data are available at Bioinformatics online.

  3. NMR in structure-based drug design.

    Science.gov (United States)

    Carneiro, Marta G; Ab, Eiso; Theisgen, Stephan; Siegal, Gregg

    2017-11-08

    NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  4. Structural studies of bacterial transcriptional regulatory proteins by multidimensional heteronuclear NMR

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, Brian Finley [Univ. of California, Berkeley, CA (United States)

    1995-02-01

    Nuclear magnetic resonance spectroscopy was used to elucidate detailed structural information for peptide and protein molecules. A small peptide was designed and synthesized, and its three-dimensional structure was calculated using distance information derived from two-dimensional NMR measurements. The peptide was used to induce antibodies in mice, and the cross-reactivity of the antibodies with a related protein was analyzed with enzyme-linked immunosorbent assays. Two proteins which are involved in regulation of transcription in bacteria were also studied. The ferric uptake regulation (Fur) protein is a metal-dependent repressor which controls iron uptake in bacteria. Two- and three-dimensional NMR techniques, coupled with uniform and selective isotope labeling allowed the nearly complete assignment of the resonances of the metal-binding domain of the Fur protein. NTRC is a transcriptional enhancer binding protein whose N-terminal domain is a "receiver domain" in the family of "two-component" regulatory systems. Phosphorylation of the N-terminal domain of NTRC activates the initiation of transcription of aeries encoding proteins involved in nitrogen regulation. Three- and four-dimensional NMR spectroscopy methods have been used to complete the resonance assignments and determine the solution structure of the N-terminal receiver domain of the NTRC protein. Comparison of the solution structure of the NTRC receiver domain with the crystal structures of the homologous protein CheY reveals a very similar fold, with the only significant difference being the position of helix 4 relative to the rest of the protein. The determination of the structure of the NTRC receiver domain is the first step toward understanding a mechanism of signal transduction which is common to many bacterial regulatory systems.

  5. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping

    2013-06-05

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  6. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

    2013-01-01

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  7. Lectures on pulsed NMR

    International Nuclear Information System (INIS)

    Pines, A.

    1986-09-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 55 figs

  8. Measurement of solute proton spin-lattice relaxation times in water using the 1,3,3,1 sequence

    International Nuclear Information System (INIS)

    Sankar, S.S.; Mole, P.A.; Coulson, R.L.

    1986-01-01

    1 H NMR spin-lattice relaxation times (T1) of the N-CH3 proton resonances of phosphocreatine (PCr) and creatine (Cr) in water solutions were obtained using the 1,3,3,1 pulse sequence. These T1 values were equivalent to those obtained in D 2 O and water using either the conventional inversion-recovery experiment or the 1,3,3,1 pulse sequence. Thus, the 1,3,3,1 sequence of proton NMR can provide an independent means along with phosphorous NMR for assess PCr and for the study of the creatine kinase reaction (PCr + ADP in equilibrium ATP + Cr) in aqueous solutions and perhaps in biological preparations

  9. From Cellulosic Based Liquid Crystalline Sheared Solutions to 1D and 2D Soft Materials

    Directory of Open Access Journals (Sweden)

    Maria Helena Godinho

    2014-06-01

    Full Text Available Liquid crystalline cellulosic-based solutions described by distinctive properties are at the origin of different kinds of multifunctional materials with unique characteristics. These solutions can form chiral nematic phases at rest, with tuneable photonic behavior, and exhibit a complex behavior associated with the onset of a network of director field defects under shear. Techniques, such as Nuclear Magnetic Resonance (NMR, Rheology coupled with NMR (Rheo-NMR, rheology, optical methods, Magnetic Resonance Imaging (MRI, Wide Angle X-rays Scattering (WAXS, were extensively used to enlighten the liquid crystalline characteristics of these cellulosic solutions. Cellulosic films produced by shear casting and fibers by electrospinning, from these liquid crystalline solutions, have regained wider attention due to recognition of their innovative properties associated to their biocompatibility. Electrospun membranes composed by helical and spiral shape fibers allow the achievement of large surface areas, leading to the improvement of the performance of this kind of systems. The moisture response, light modulated, wettability and the capability of orienting protein and cellulose crystals, opened a wide range of new applications to the shear casted films. Characterization by NMR, X-rays, tensile tests, AFM, and optical methods allowed detailed characterization of those soft cellulosic materials. In this work, special attention will be given to recent developments, including, among others, a moisture driven cellulosic motor and electro-optical devices.

  10. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW

    2013-01-01

    NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

  11. NMR studies of isotopically labeled RNA

    Energy Technology Data Exchange (ETDEWEB)

    Pardi, A. [Univ. of Colorado, Boulder, CO (United States)

    1994-12-01

    In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

  12. 1H-NMR, 1H-NMR T2-edited, and 2D-NMR in bipolar disorder metabolic profiling.

    Science.gov (United States)

    Sethi, Sumit; Pedrini, Mariana; Rizzo, Lucas B; Zeni-Graiff, Maiara; Mas, Caroline Dal; Cassinelli, Ana Cláudia; Noto, Mariane N; Asevedo, Elson; Cordeiro, Quirino; Pontes, João G M; Brasil, Antonio J M; Lacerda, Acioly; Hayashi, Mirian A F; Poppi, Ronei; Tasic, Ljubica; Brietzke, Elisa

    2017-12-01

    The objective of this study was to identify molecular alterations in the human blood serum related to bipolar disorder, using nuclear magnetic resonance (NMR) spectroscopy and chemometrics. Metabolomic profiling, employing 1 H-NMR, 1 H-NMR T 2 -edited, and 2D-NMR spectroscopy and chemometrics of human blood serum samples from patients with bipolar disorder (n = 26) compared with healthy volunteers (n = 50) was performed. The investigated groups presented distinct metabolic profiles, in which the main differential metabolites found in the serum sample of bipolar disorder patients compared with those from controls were lipids, lipid metabolism-related molecules (choline, myo-inositol), and some amino acids (N-acetyl-L-phenyl alanine, N-acetyl-L-aspartyl-L-glutamic acid, L-glutamine). In addition, amygdalin, α-ketoglutaric acid, and lipoamide, among other compounds, were also present or were significantly altered in the serum of bipolar disorder patients. The data presented herein suggest that some of these metabolites differentially distributed between the groups studied may be directly related to the bipolar disorder pathophysiology. The strategy employed here showed significant potential for exploring pathophysiological features and molecular pathways involved in bipolar disorder. Thus, our findings may contribute to pave the way for future studies aiming at identifying important potential biomarkers for bipolar disorder diagnosis or progression follow-up.

  13. Lectures on pulsed NMR

    International Nuclear Information System (INIS)

    Pines, A.

    1988-08-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 32 refs., 56 figs

  14. Solid-state NMR basic principles and practice

    CERN Document Server

    Apperley, David C; Hodgkinson, Paul

    2014-01-01

    Nuclear Magnetic Resonance (NMR) has proved to be a uniquely powerful and versatile tool for analyzing and characterizing chemicals and materials of all kinds. This book focuses on the latest developments and applications for "solid-state" NMR, which has found new uses from archaeology to crystallography to biomaterials and pharmaceutical science research. The book will provide materials engineers, analytical chemists, and physicists, in and out of lab, a survey of the techniques and the essential tools of solid-state NMR, together with a practical guide on applications. In this concise introduction to the growing field of solid-state nuclear magnetic resonance spectroscopy The reader will find: * Basic NMR concepts for solids, including guidance on the spin-1/2 nuclei concept * Coverage of the quantum mechanics aspects of solid state NMR and an introduction to the concept of quadrupolar nuclei * An understanding relaxation, exchange and quantitation in NMR * An analysis and interpretation of NMR data, with e...

  15. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1999-01-01

    High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

  16. Interaction Between Cyanine Dye IR-783 and Polystyrene Nanoparticles in Solution.

    Science.gov (United States)

    Zhang, Yunzhi; Xu, Hui; Casabianca, Leah B

    2018-05-17

    The interactions between small molecule drugs or dyes and nanoparticles are important to the use of nanoparticles in medicine. Noncovalent adsorption of dyes on nanoparticle surfaces is also important to the development of nanoparticle dual-use imaging contrast agents. In the present work, solution-state NMR is used to examine the noncovalent interaction between a near-infrared cyanine dye and the surface of polystyrene nanoparticles in solution. Using 1D proton NMR, we can approximate the number of dye molecules that associate with each nanoparticle for different sized nanoparticles. Saturation-Transfer Difference (STD)-NMR was also used to show that protons near the positively-charged nitrogen in the dye are more strongly associated with the negatively-charged nanoparticle surface than protons near the negatively-charged sulfate groups of the dye. The methods described here can be used to study similar drug or dye molecules interacting with the surface of organic nanoparticles. This article is protected by copyright. All rights reserved.

  17. High resolution NMR spectroscopy of synthetic polymers in bulk

    International Nuclear Information System (INIS)

    Komorski, R.A.

    1986-01-01

    The contents of this book are: Overview of high-resolution NMR of solid polymers; High-resolution NMR of glassy amorphous polymers; Carbon-13 solid-state NMR of semicrystalline polymers; Conformational analysis of polymers of solid-state NMR; High-resolution NMR studies of oriented polymers; High-resolution solid-state NMR of protons in polymers; and Deuterium NMR of solid polymers. This work brings together the various approaches for high-resolution NMR studies of bulk polymers into one volume. Heavy emphasis is, of course, given to 13C NMR studies both above and below Tg. Standard high-power pulse and wide-line techniques are not covered

  18. Structural characterization of supramolecular assemblies by {sup 13}C spin dilution and 3D solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam, E-mail: adla@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)

    2013-01-15

    {sup 13}C spin diluted protein samples can be produced using [1-{sup 13}C] and [2-{sup 13}C]-glucose (Glc) carbon sources in the bacterial growth medium. The {sup 13}C spin dilution results in favorable {sup 13}C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-{sup 13}C]- and [2-{sup 13}C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-{sup 13}C]-glycerol ({sup 13}C labeled C{alpha} sites on a {sup 12}C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17-26, 2011 ). Inspired by this approach and our own recent results using [2-{sup 13}C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of {sup 13}C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.

  19. NMR spectroscopic characterization of {beta}-cyclodextrin inclusion complex with vanillin

    Energy Technology Data Exchange (ETDEWEB)

    Pirnau, Adrian; Bogdan, Mircea; Floare, Calin G, E-mail: adrian.pirnau@itim-cj.r [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania)

    2009-08-01

    The inclusion of vanillin by {beta}-cyclodextrin was investigated by {sup 1}H NMR. The continuous variation technique was used to evidence the formation of soluble 1:1 complex in aqueous solution. The association constant of vanillin with {beta}-cyclodextrin has been obtained at 298 K by fitting the experimental chemical shifts differences, {Delta}{delta}{sub obs} {delta}{sub free} - {delta}{sub obs} of the observed guest and host protons, with a non-linear regression method. Besides the effective association constant, the fitting procedure allows a precise determination of all chemical shift parameters characterizing the pure complex. They can by used for an analysis of the geometry of the molecular complex in solution.

  20. International symposium on NMR spectroscopy

    International Nuclear Information System (INIS)

    The publication consists of 32 papers and presentations from the field of NMR spectroscopy applications submitted to the International Symposium on NMR Spectroscopy held at Smolenice between 29 Sep and 3 Oct, 1980. (B.S.)

  1. Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

    Science.gov (United States)

    Missimer, John H; Dolenc, Jožica; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-01-01

    Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and 3J(HN,HCα)-coupling constants, and a set of 20 model structures was proposed. Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured 3J(HN-HCα)-coupling constant values, indicating that the α-helical propensity is not uniform along the GCN4 trigger sequence. A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation 3J-coupling restraints could satisfy the entire set of the experimental data. In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures. Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures. PMID:20954244

  2. Oriented solid-state NMR spectrosocpy

    DEFF Research Database (Denmark)

    Bertelsen, Kresten

    This thesis is concerned with driving forward oriented solid-state NMR spectroscopy as a viable technique for studying peptides in membrane bilayers. I will show that structural heterogeneity is an intrinsic part of the peptide/lipid system and that NMR can be used to characterize static...... and dynamic structural features of the peptides and its local surroundings. In fact one need to take into account the dynamical features of the system in order to correctly predict the structure from oriented solid-state NMR spectra.      ...

  3. Continuous Flow 1H and 13C NMR Spectroscopy in Microfluidic Stripline NMR Chips

    NARCIS (Netherlands)

    Oosthoek-de Vries, Anna Jo; Bart, Jacob; Tiggelaar, Roald M.; Janssen, Johannes W.G.; van Bentum, Jan (P.J.M.); Gardeniers, Han J.G.E.; Kentgens, Arno P.M.

    2017-01-01

    Microfluidic stripline NMR technology not only allows for NMR experiments to be performed on small sample volumes in the submicroliter range, but also experiments can easily be performed in continuous flow because of the stripline's favorable geometry. In this study we demonstrate the possibility of

  4. Binuclear Pt-Tl bonded complex with square pyramidal coordination around Pt: a combined multinuclear NMR, EXAFS, UV-Vis, and DFT/TDDFT study in dimethylsulfoxide solution.

    Science.gov (United States)

    Purgel, Mihály; Maliarik, Mikhail; Glaser, Julius; Platas-Iglesias, Carlos; Persson, Ingmar; Tóth, Imre

    2011-07-04

    The structure and bonding of a new Pt-Tl bonded complex formed in dimethylsulfoxide (dmso), (CN)(4)Pt-Tl(dmso)(5)(+), have been studied by multinuclear NMR and UV-vis spectroscopies, and EXAFS measurements in combination with density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations. This complex is formed following the equilibrium reaction Pt(CN)(4)(2-) + Tl(dmso)(6)(3+) ⇆ (CN)(4)Pt-Tl(dmso)(5)(+) + dmso. The stability constant of the Pt-Tl bonded species, as determined using (13)C NMR spectroscopy, amounts to log K = 2.9 ± 0.2. The (NC)(4)Pt-Tl(dmso)(5)(+) species constitutes the first example of a Pt-Tl bonded cyanide complex in which the sixth coordination position around Pt (in trans with respect to the Tl atom) is not occupied. The spectral parameters confirm the formation of the metal-metal bond, but differ substantially from those measured earlier in aqueous solution for complexes (CN)(5)Pt-Tl(CN)(n)(H(2)O)(x)(n-) (n = 0-3). The (205) Tl NMR chemical shift, δ = 75 ppm, is at extraordinary high field, while spin-spin coupling constant, (1)J(Pt-Tl) = 93 kHz, is the largest measured to date for a Pt-Tl bond in the absence of supporting bridging ligands. The absorption spectrum is dominated by two strong absorption bands in the UV region that are assigned to MMCT (Pt → Tl) and LMCT (dmso → Tl) bands, respectively, on the basis of MO and TDDFT calculations. The solution of the complex has a bright yellow color as a result of a shoulder present on the low energy side of the band at 355 nm. The geometry of the (CN)(4)Pt-Tl core can be elucidated from NMR data, but the particular stoichiometry and structure involving the dmso ligands are established by using Tl and Pt L(III)-edge EXAFS measurements. The Pt-Tl bond distance is 2.67(1) Å, the Tl-O bond distance is 2.282(6) Å, and the Pt-C-N entity is linear with Pt-C and Pt···N distances amounting to 1.969(6) and 3.096(6) Å, respectively. Geometry optimizations on

  5. SIMPSON: A general simulation program for solid-state NMR spectroscopy

    Science.gov (United States)

    Bak, Mads; Rasmussen, Jimmy T.; Nielsen, Niels Chr.

    2011-12-01

    A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tel scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basicly, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple ID experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at http://nmr.imsb.au.dk. The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments.

  6. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR.

    Science.gov (United States)

    Schreckenbach, Georg

    2002-12-16

    In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors.

  7. Solid-state NMR spectroscopy on complex biomolecules

    NARCIS (Netherlands)

    Renault, M.A.M.; Cukkemane, A.A.; Baldus, M.

    2010-01-01

    Biomolecular applications of NMR spectroscopy are often merely associated with soluble molecules or magnetic resonance imaging. However, since the late 1970s, solid-state NMR (ssNMR) spectroscopy has demonstrated its ability to provide atomic-level insight into complex biomolecular systems ranging

  8. NMR experiments on ion permeation in irradiated model membranes

    International Nuclear Information System (INIS)

    Sprinz, H.; Winkler, E.; Schaefer, H.

    1981-01-01

    In aqueous solutions of egg-lecithin vesicles treated with ultrasonics the 1 H NMR parameters line width, area, and chemical shift of the signal of the (CH 3 ) 3 N + group were determined as a function of the gamma dose (0 ... 12 kGy). Using europium and the line shape analysis, it has been possible to calculate these parameters for the inside as well as for the outside lipid layer. Increasing 60 Co radiation dose leads to linear increases of the line widths, which are significantly more rapid for the outer than for the inner layer. From that it can be concluded that the outside lipid layer has been more damaged by irradiation. The asymmetry may be the consequence of a radiation effect induced by the radicals of water radiolysis. From the temporal changes of the NMR parameters information can be obtained about the radiation effect on transport processes in the vesicles. Beginning at a threshold (approx. 5 kGy) the permeation of Eu +++ ions to the (CH 3 ) 3 N + head groups, previously not accessible, increases significantly. (author)

  9. NMR-MPar: A Fault-Tolerance Approach for Multi-Core and Many-Core Processors

    Directory of Open Access Journals (Sweden)

    Vanessa Vargas

    2018-03-01

    Full Text Available Multi-core and many-core processors are a promising solution to achieve high performance by maintaining a lower power consumption. However, the degree of miniaturization makes them more sensitive to soft-errors. To improve the system reliability, this work proposes a fault-tolerance approach based on redundancy and partitioning principles called N-Modular Redundancy and M-Partitions (NMR-MPar. By combining both principles, this approach allows multi-/many-core processors to perform critical functions in mixed-criticality systems. Benefiting from the capabilities of these devices, NMR-MPar creates different partitions that perform independent functions. For critical functions, it is proposed that N partitions with the same configuration participate of an N-modular redundancy system. In order to validate the approach, a case study is implemented on the KALRAY Multi-Purpose Processing Array (MPPA-256 many-core processor running two parallel benchmark applications. The traveling salesman problem and matrix multiplication applications were selected to test different device’s resources. The effectiveness of NMR-MPar is assessed by software-implemented fault-injection. For evaluation purposes, it is considered that the system is intended to be used in avionics. Results show the improvement of the application reliability by two orders of magnitude when implementing NMR-MPar on the system. Finally, this work opens the possibility to use massive parallelism for dependable applications in embedded systems.

  10. Quartz Crystal Temperature Sensor for MAS NMR

    Science.gov (United States)

    Simon, Gerald

    1997-10-01

    Quartz crystal temperature sensors (QCTS) were tested for the first time as wireless thermometers in NMR MAS rotors utilizing the NMR RF technique itself for exiting and receiving electro-mechanical quartz resonances. This new tool in MAS NMR has a high sensitivity, linearity, and precision. When compared to the frequently used calibration of the variable temperature in the NMR system by a solid state NMR chemical shift thermometer (CST), such as lead nitrate, QCTS shows a number of advantages. It is an inert thermometer in close contact with solid samples operating parallel to the NMR experiment. QCTS can be manufactured for any frequency to be near a NMR frequency of interest (typically 1 to 2 MHz below or above). Due to the strong response of the crystal, signal detection is possible without changing the tuning of the MAS probe. The NMR signal is not influenced due to the relative sharp crystal resonance, restricted excitation by finite pulses, high probeQvalues, and commonly used audio filters. The quadratic dependence of the temperature increase on spinning speed is the same for the QCTS and for the CST lead nitrate and is discussed in terms of frictional heat in accordance with the literature about lead nitrate and with the results of a simple rotor speed jump experiment with differently radial located lead nitrate in the rotor.

  11. Exploring translocation of proteins on DNA by NMR

    International Nuclear Information System (INIS)

    Marius Clore, G.

    2011-01-01

    While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the species and molecular mechanisms involved in the target search process, including the detection of highly transient sparsely-populated states. The main tool in these studies involves the application of paramagnetic relaxation enhancement, supplemented by z-exchange spectroscopy, lineshape analysis and residual dipolar couplings. These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution.

  12. Basics of spectroscopic instruments. Hardware of NMR spectrometer

    International Nuclear Information System (INIS)

    Sato, Hajime

    2009-01-01

    NMR is a powerful tool for structure analysis of small molecules, natural products, biological macromolecules, synthesized polymers, samples from material science and so on. Magnetic Resonance Imaging (MRI) is applicable to plants and animals Because most of NMR experiments can be done by an automation mode, one can forget hardware of NMR spectrometers. It would be good to understand features and performance of NMR spectrometers. Here I present hardware of a modern NMR spectrometer which is fully equipped with digital technology. (author)

  13. Total synthesis of (-)-basiliskamide A and NMR studies on the conversion of basiliskamide A to basiliskamide B

    International Nuclear Information System (INIS)

    Dias, Luiz C.; Goncalves, Caroline C.S.

    2010-01-01

    We describe herein our approach to the total synthesis of the antifungal polyketide (-)-basiliskamide A, as well as 1 H NMR studies on the migration of the cinnamoyl side chain of basiliskamide A to form basiliskamide B in CDCl 3 solution. (author)

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

    DEFF Research Database (Denmark)

    Meier, Sebastian; Petersen, Bent O.; Duus, Jens Øllgaard

    2009-01-01

    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.......The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of 13C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the 1H spins...

  15. Scaling exponent and dispersity of polymers in solution by diffusion NMR.

    Science.gov (United States)

    Williamson, Nathan H; Röding, Magnus; Miklavcic, Stanley J; Nydén, Magnus

    2017-05-01

    Molecular mass distribution measurements by pulsed gradient spin echo nuclear magnetic resonance (PGSE NMR) spectroscopy currently require prior knowledge of scaling parameters to convert from polymer self-diffusion coefficient to molecular mass. Reversing the problem, we utilize the scaling relation as prior knowledge to uncover the scaling exponent from within the PGSE data. Thus, the scaling exponent-a measure of polymer conformation and solvent quality-and the dispersity (M w /M n ) are obtainable from one simple PGSE experiment. The method utilizes constraints and parametric distribution models in a two-step fitting routine involving first the mass-weighted signal and second the number-weighted signal. The method is developed using lognormal and gamma distribution models and tested on experimental PGSE attenuation of the terminal methylene signal and on the sum of all methylene signals of polyethylene glycol in D 2 O. Scaling exponent and dispersity estimates agree with known values in the majority of instances, leading to the potential application of the method to polymers for which characterization is not possible with alternative techniques. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    Science.gov (United States)

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. Copyright 1998 Academic Press.

  17. Rapid prediction of multi-dimensional NMR data sets

    International Nuclear Information System (INIS)

    Gradmann, Sabine; Ader, Christian; Heinrich, Ines; Nand, Deepak; Dittmann, Marc; Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J.; Engelhard, Martin; Baldus, Marc

    2012-01-01

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such “in silico” data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

  18. Rapid prediction of multi-dimensional NMR data sets

    Energy Technology Data Exchange (ETDEWEB)

    Gradmann, Sabine; Ader, Christian [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Heinrich, Ines [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Nand, Deepak [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Dittmann, Marc [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J. [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Engelhard, Martin [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

    2012-12-15

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such 'in silico' data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

  19. UV-vis, IR and 1H NMR spectroscopic studies and characterization of ionic-pair crystal violet-oxytetracycline

    Science.gov (United States)

    Orellana, Sandra; Soto, César; Toral, M. Inés

    2010-01-01

    The present study shows the formation and characterization of the ionic-pair between the antibiotic oxytetracycline and the dye crystal violet in ammonia solution pH 9.0 ± 0.2 extracted into chloroform. The characterization was demonstrated using UV-vis spectrophotometry, 1H NMR, measurement of relaxation times T1 and IR spectroscopy, using a comparison between the signals of individual pure compounds with the signals with the mixture CV-OTC in different alkaline media. The formation of ionic-pair was also corroborated by new signals and chemical shifts. (2D) NMR spectroscopy experiments show that the interaction is electrostatic.

  20. NMR of proteins (4Fe-4S): structural properties and intramolecular electron transfer

    International Nuclear Information System (INIS)

    Huber, J.G.

    1996-01-01

    NMR started to be applied to Fe-S proteins in the seventies. Its use has recently been enlarged as the problems arising from the paramagnetic polymetallic clusters ware overcome. Applications to [4Fe-4S] are presented herein. The information derived thereof deepens the understanding of the redox properties of these proteins which play a central role in the metabolism of bacterial cells. The secondary structure elements and the overall folding of Chromatium vinosum ferredoxin (Cv Fd) in solution have been established by NMR. The unique features of this sequence have been shown to fold as an α helix at the C-terminus and as a loop between two cysteines ligand of one cluster: these two parts localize in close proximity from one another. The interaction between nuclear and electronic spins is a source of additional structural information for (4Fe-AS] proteins. The conformation of the cysteine-ligands, as revealed by the Fe-(S γ -C β -H β )Cys dihedral angles, is related to the chemical shifts of the signals associated with the protons of these residues. The longitudinal relaxation times of the protons depend on their distance to the cluster. A quantitative relationship has been established and used to show that the solution structure of the high-potential ferredoxin from Cv differs significantly from the crystal structure around Phe-48. Both parameters (chemical shifts and longitudinal relaxation times) give also insight into the electronic and magnetic properties of the [4Fe-4S] clusters. The rate of intramolecular electron transfer between the two [4FE-4S] clusters of ferredoxins has been measured by NMR. It is far slower in the case of Cv Fd than for shorter ferredoxins. The difference may be associated with changes in the magnetic and/or electronic properties of one cluster. The strong paramagnetism of the [4Fe-4S] clusters, which originally limited the applicability of NMR to proteins containing these cofactors, has been proven instrumental in affording new

  1. Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

    Science.gov (United States)

    Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

    2013-04-01

    Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

  2. Rheological study of chitosan in solution

    International Nuclear Information System (INIS)

    Silva, Italo Guimaraes Medeiros da; Alves, Keila dos Santos; Balaban, Rosangela de Carvalho

    2009-01-01

    Chitosan is an abundant biopolymer with remarkable physicochemical and biological properties, usually employed in a wide range of applications. It acts as a cationic polyelectrolyte in aqueous acid solutions, leading to unique characteristics. In this work, chitosan was characterized by 1 H NMR and its rheological behavior were studied as function of chitosan sample, shear rate, polymer concentration, ionic strength, time and temperature. In order to calculate rheological parameters and to understand the macromolecular dynamic in solution, the Otswald-de Waele model was fitted. (author)

  3. NMR imaging of osteoarticular pathology

    International Nuclear Information System (INIS)

    Frocrain, L.; Duvauferrier, R.; Gagey, N.

    1987-01-01

    NMR imaging is assuming an increasingly important role in the diagnosis of osteo-articular disorders. Semiological descriptions of the mean pathological disorders of the locomotor system are presented. Some investigation strategies are proposed to compare NMR imaging with other imaging techniques in various pathological states [fr

  4. NMR structure of the glucose-dependent insulinotropic polypeptide fragment, GIP(1-30)amide

    International Nuclear Information System (INIS)

    Alana, Inigo; Hewage, Chandralal M.; G. Malthouse, J. Paul; Parker, Jeremy C.; Gault, Victor A.; O'Harte, Finbarr P.M.

    2004-01-01

    Glucose-dependent insulinotropic polypeptide is an incretin hormone that stimulates insulin secretion and reduces postprandial glycaemic excursions. The glucose-dependent action of GIP on pancreatic β-cells has attracted attention towards its exploitation as a potential drug for type 2 diabetes. Use of NMR or X-ray crystallography is vital to determine the three-dimensional structure of the peptide. Therefore, to understand the basic structural requirements for the biological activity of GIP, the solution structure of the major biologically active fragment, GIP(1-30)amide, was investigated by proton NMR spectroscopy and molecular modelling. The structure is characterised by a full length α-helical conformation between residues F 6 and A 28 . This structural information could play an important role in the design of therapeutic agents based upon GIP receptor agonists

  5. Tautomerism in o-hydroxyanilino-1,4-naphthoquinone derivatives: Structure, NMR, HPLC and density functional theoretic investigations

    Science.gov (United States)

    Bhand, Sujit; Patil, Rishikesh; Shinde, Yogesh; Lande, Dipali N.; Rao, Soniya S.; Kathawate, Laxmi; Gejji, Shridhar P.; Weyhermüller, Thomas; Salunke-Gawali, Sunita

    2016-11-01

    Structure and spectral characteristics of 'Ortho' ((E)-4-hydroxy-2-(2‧-(4‧-R)-hydroxyphenyl)-imino)-naphthalen-1(2H)-one) and 'para' (2-(2‧-(4‧-R)-hydroxyphenyl)-amino)-1,4-naphthoquinone) tautomers of o-hydroxyanilino-1,4-naphthoquinone derivatives (Rdbnd H, 1A; sbnd CH3, 2A; and -Cl, 3A) are investigated using the 1H, 13C, DEPT, gDQCOSY, gHSQCAD NMR, HPLC, cyclic voltammetry techniques combined with the density functional theory. The compound 2A crystallizes in monoclinic space group P21/c. wherein the polymer chain is facilitated via Osbnd H⋯O and Csbnd H⋯O intermolecular hydrogen bonding. Marginal variations in bond distances in quinonoid and aminophenol moieties render structural flexibility to these compounds those in solution exist as exist in 'ortho - para' tautomers. 1H and 13C NMR spectra in DMSO-d6 showed two sets of peaks in all compounds; whereas only the para tautomer of for 1A and 2A, the para tautomer is predominant in CD3CN solution. Further the ortho-para interconversion is accompanied by a large up-field signals for C(3)sbnd H(3) in their 1H and 13C NMR spectra. These inferences are corroborated by the density functional theoretic calculations.

  6. Study on the Effects of Oligo chitosan and Bioliquifert on Two Rice Mutants, NMR 151 and NMR 152

    International Nuclear Information System (INIS)

    Shakinah Salleh; Faiz Ahmad; Sobri Hussein

    2016-01-01

    Nuclear Malaysia has successfully developed two new rice mutants namely NMR 151 and NMR 152. In addition, Nuclear Malaysia has also successfully developed Oligo chitosan and liquid bio fertilizer (Bioliquifert). Oligo chitosan acts as elicitor that has been proven to be very effective in controlling disease infections and improving yield productivity. Bioliquifert on the other hand is a mixture of microbes containing major nutrient-providing microorganisms. The objective of this study is to observe the effects of Oligo chitosan and Bioliquifert on rice mutants, NMR 151 and NMR 152. The treatment was applied on 14 day old seedlings of MR 219, NMR 151 and NMR 152 sowed in 20 cm pots containing silty clay from the paddy soil of Tanjung Karang, Selangor. The seedlings were then placed in the greenhouse at Nuclear Malaysia until it reaches 110 days old. Study was conducted in a Complete Randomized Design (CRD) with 3 replications was used and each replication consisted of three plants. All treatments received compound and single dressing fertilizer as recommended by National Rice Production Package except for Treatment 2 and 3, in which Treatment 2 received Oligo chitosan and Bioliquifert while Treatment 3 only received Bioliquifert. Results on plant height, number of tiller and plant fresh weight are not significantly different for all cultivar except for seed dry weight of NMR 152 and MR 219. (author)

  7. Structural comparison of 1{beta}-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sunagawa, M.; Sasaki, A.; Igarashi, J.-E.; Nishimura, T. [Research Center, Sumitomo Pharmaceuticals Co., Ltd., 3-1-98 Kasugadenaka, Konohanaku, Osaka (Japan)

    1998-04-01

    Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using {sup 1}H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained {beta}-lactam rings in good agreement with the crystallographic data. {sup 1}H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  8. Structural comparison of 1β-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

    International Nuclear Information System (INIS)

    Sunagawa, M.; Sasaki, A.; Igarashi, J.-E.; Nishimura, T.

    1998-01-01

    Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using 1 H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained β-lactam rings in good agreement with the crystallographic data. 1 H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  9. Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.

    Science.gov (United States)

    Deshmukh, Lalit; Schwieters, Charles D; Grishaev, Alexander; Clore, G Marius

    2016-06-03

    Nucleic-acid-related events in the HIV-1 replication cycle are mediated by nucleocapsid, a small protein comprising two zinc knuckles connected by a short flexible linker and flanked by disordered termini. Combining experimental NMR residual dipolar couplings, solution X-ray scattering and protein engineering with ensemble simulated annealing, we obtain a quantitative description of the configurational space sampled by the two zinc knuckles, the linker and disordered termini in the absence of nucleic acids. We first compute the conformational ensemble (with an optimal size of three members) of an engineered nucleocapsid construct lacking the N- and C-termini that satisfies the experimental restraints, and then validate this ensemble, as well as characterize the disordered termini, using the experimental data from the full-length nucleocapsid construct. The experimental and computational strategy is generally applicable to multidomain proteins. Differential flexibility within the linker results in asymmetric motion of the zinc knuckles which may explain their functionally distinct roles despite high sequence identity. One of the configurations (populated at a level of ≈40 %) closely resembles that observed in various ligand-bound forms, providing evidence for conformational selection and a mechanistic link between protein dynamics and function. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Whole-core analysis by 13C NMR

    International Nuclear Information System (INIS)

    Vinegar, H.J.; Tutunjian, P.N.; Edelstein, W.A.; Roemer, P.B.

    1991-01-01

    This paper reports on a whole-core nuclear magnetic resonance (NMR) system that was used to obtain natural abundance 13 C spectra. The system enables rapid, nondestructive measurements of bulk volume of movable oil, aliphatic/aromatic ratio, oil viscosity, and organic vs. carbonate carbon. 13 C NMR can be used in cores where the 1 H NMR spectrum is too broad to resolve oil and water resonances separately. A 5 1/4-in. 13 C/ 1 H NMR coil was installed on a General Electric (GE) CSI-2T NMR imager/spectrometer. With a 4-in.-OD whole core, good 13 C signal/noise ratio (SNR) is obtained within minutes, while 1 H spectra are obtained in seconds. NMR measurements have been made of the 13 C and 1 H density of crude oils with a wide range of API gravities. For light- and medium-gravity oils, the 13 C and 1 H signal per unit volume is constant within about 3.5%. For heavy crudes, the 13 C and 1 H density measured by NMR is reduced by the shortening of spin-spin relaxation time. 13 C and 1 H NMR spin-lattice relaxation times were measured on a suite of Cannon viscosity standards, crude oils (4 to 60 degrees API), and alkanes (C 5 through C 16 ) with viscosities at 77 degrees F ranging from 0.5 cp to 2.5 x 10 7 cp. The 13 C and 1 H relaxation times show a similar correlation with viscosity from which oil viscosity can be estimated accurately for viscosities up to 100 cp. The 13 C surface relaxation rate for oils on water-wet rocks is very low. Nonproton decoupled 13 C NMR is shown to be insensitive to kerogen; thus, 13 C NMR measures only the movable hydrocarbon content of the cores. In carbonates, the 13 C spectrum also contains a carbonate powder pattern useful in quantifying inorganic carbon and distinguishing organic from carbonate carbon

  11. An Inversion Recovery NMR Kinetics Experiment

    OpenAIRE

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a conveni...

  12. Recommendations of the wwPDB NMR Validation Task Force

    Science.gov (United States)

    Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

    2013-01-01

    As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

  13. Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study

    OpenAIRE

    Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.

    2012-01-01

    Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar c...

  14. Fourier transform NMR

    International Nuclear Information System (INIS)

    Hallenga, K.

    1991-01-01

    This paper discusses the concept of Fourier transformation one of the many precious legacies of the French mathematician Jean Baptiste Joseph Fourier, essential for understanding the link between continuous-wave (CW) and Fourier transform (FT) NMR. Although in modern FT NMR the methods used to obtain a frequency spectrum from the time-domain signal may vary greatly, from the efficient Cooley-Tukey algorithm to very elaborate iterative least-square methods based other maximum entropy method or on linear prediction, the principles for Fourier transformation are unchanged and give invaluable insight into the interconnection of many pairs of physical entities called Fourier pairs

  15. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

    2015-08-15

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  16. Nuclear magnetic resonance apparatus having semitoroidal RF coil for use in topical NMR and NMR imaging

    International Nuclear Information System (INIS)

    Fukushima, E.; Assink, R.A.; Roeder, S.B.W.; Gibson, A.A.V.

    1984-01-01

    An improved nuclear magnetic resonance (NMR) apparatus for use in topical magnetic resonance (TMR) spectroscopy and other remote sensing NMR applications includes a semitoroidal radio frequency (rf) coil. The semitoroidal rf coil produces an effective alternating magnetic field at a distance from the poles of the coil, to enable NMR measurements to be taken from selected regions inside an object, particularly human and other living subjects. The semitoroidal rf coil is relatively insensitive to magnetic interference from metallic objects located behind the coil, thereby rendering the coil particularly suited for use in both conventional and superconducting NMR magnets. The semitoroidal NMR coil can be constructed so that it emits little or no excess rf electric field associated with the rf magnetic field, thus avoiding adverse effects due to dielectric heating of the sample or to any other electric field interactions. The coil may be combined with a like orthogonal coil and suitably driven to provide a circularly polarised field; or it may be used in conjunction with a concentrically nested smaller semitoroidal coil to move the maximum field further from the coil assembly. (author)

  17. Hydrothermal reaction of albite and a sodium aluminosilicate glass: A solid-state NMR study

    Science.gov (United States)

    Yang, Wang-hong Alex; Kirkpatrick, R. James

    1989-04-01

    We present here a solid-state NMR study of the structure and chemical composition of the products and mechanisms of the reaction of crystalline low albite and a glass of nearly albite composition with aqueous solutions of pH from 1 to 11 at 250°C. For the crystalline albite, there are no detectable bulk or surface structural changes due to aqueous attack, consistent with the idea that both cation exchange and disruption of the aluminosilicate framework occur only near the mineral/solution interface and that the hydrated surface layer, if it exists, is not more than about 30 Å thick. This reaction occurs by solution/reprecipitation, and its rate decreases with increasing solution pH, supporting the idea that the dissolution of feldspar is initiated by cation-exchange. For the glass, the reaction proceeds by cation exchange of protons for Na +, incorporation of molecular water into the bulk glass, and a small amount of depolymerization of the aluminosilicate framework in the interior of the glass. Cation exchange becomes less important with increasing solution pH. The incorporation of molecular water and cation-exchange cause structural changes in the glass via solidstate adjustment without dissolution/reprecipitation. The large cations in the hydrated glass (Na and K) probably have a shell of water molecules around them, with a maximum average coordination number of six. The secondary phases formed from both albite and the glass are often amorphous and can be well characterized by NMR. The compositional and structural variations of the amorphous phases are important factors in these reactions and cannot be ignored in theoretical models of aluminosilicate dissolution. As expected, the aluminum coordination in the secondary phases changes from six-fold to four-fold as the solution pH increases.

  18. Ions in solution basic principles of chemical interactions

    CERN Document Server

    Burgess, J

    1999-01-01

    This outline of the principles and chemical interactions in inorganic solution chemistry delivers a course module in an area of considerable complexity. Problems with solutions and tutorial hints to test comprehension have been added as a feature to check readers' understanding and assist self-study. Exercises and projects are also provided to help readers deepen and extend their knowledge and understanding. Inorganic solution chemistry is treated thoroughly Emphasis is placed upon NMR, UV-VIS, IR Raman spectroscopy, X-ray diffraction, and such topics as acid-base behaviour, stability constants and kinetics.

  19. Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

    International Nuclear Information System (INIS)

    Hennig, Janosch; Wang, Iren; Sonntag, Miriam; Gabel, Frank; Sattler, Michael

    2013-01-01

    Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.

  20. Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

    Energy Technology Data Exchange (ETDEWEB)

    Hennig, Janosch; Wang, Iren; Sonntag, Miriam [Institute of Structural Biology, Helmholtz Zentrum Muenchen (Germany); Gabel, Frank [Extremophiles and Large Molecular Assemblies Group (ELMA), Institut de Biologie Structurale (IBS) CEA-CNRS-UJF (France); Sattler, Michael, E-mail: sattler@helmholtz-muenchen.de [Institute of Structural Biology, Helmholtz Zentrum Muenchen (Germany)

    2013-05-15

    Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.

  1. Carbon-13 NMR of flavinoids

    International Nuclear Information System (INIS)

    Agrawal, P.K.

    1989-01-01

    The present book has been written with the objective of introducing the organic chemists with the conceptual and experimental basis required for interpretation of 13 C NMR spectra of a flavonoid and to a discussion of general usefulness of the technique in solving flavonoid structural problem. After a brief general introduction to the essential aspects of flavonoids and 13 C NMR spectroscopy, considerable emphasis has been placed in chapter 2 on the various experimental methods and the interpretation of spectral details which enable individual resonance lines to be associated with the appropriate carbons in a molecule. The whole bulk of the literature, published on 13 C NMR of flavonoids in the major journals upto 1986 alongwith some recent references of 1987 has been classified in several categories such as: flavonoids, isflavonoids, other flavonoids, flavonoid glycosides, chalconoids and flavanoids. Each category constitutes a chapter. Finally the last chapter is devoted largely to a discussion for the differentiation of various categories and subcategories of flavonoids and for the establishment of aromatic substitution pattern in these compounds. It should be emphasized that the book is a data book and only concerned with the actual analysis of 13 C NMR spectra, thus a reasonable familiarity with basic instrumentation of 13 C NMR and general pattern of nuclear chemical shifts has been assumed. (author). refs.; figs.; tabs

  2. Phosphorus-31 NMR (nuclear magnetic resonance) analysis of gold plating baths

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.E.

    1990-01-01

    This report describes the nuclear magnetic resonance (NMR) analysis of the gold plating baths in the Micro-Miniature Electronic Assembly department of Allied-Signal Inc., Kansas City Division (KCD). The baths were analyzed for phosphorylated components. In freshly prepared gold plating baths, a 50-percent aqueous solution of aminotrimethylphosphonate (ATMP) is the principal compound observed. As the bath is used in production, the ATMP breaks down and new materials (phosphate, ADMP, and AMMP) are identified. The NMR method was used to monitor the concentrations of the ATMP and breakdown products for a nine-month period. The 225-liter bath had plated approximately 100 square feet of gold during the nine-month period. These results can be used to predict the performance of baths as they are used in production. The accuracy of the analysis is 96 percent for ATMP and 92 percent for phosphate. The precision (relative standard deviation) is 5.2 percent for ATMP and 4.5 percent for phosphate. 1 ref., 5 figs., 2 tabs.

  3. NMR imaging

    International Nuclear Information System (INIS)

    Ouchi, Toshihiro; Steiner, R.E.

    1984-01-01

    Three epidermoid and two dermoid tumours, pathologically proven, were examined by NMR and CT scans. Although most brain tumours have a low signal with a long T 1 , a dermoid cyst and one of the two components of the other dermoid tumour had a high signal and therefore a short T 1 . All three epidermoid tumours had a low signal and a long T 1 . Because of the high level contrast between some of the tumours and cerebrospinal fluid, NMR is helpful to detect the lesion. Neither of the liquid fluid levels in the tumour cysts or floating fat in the subarachnoid space was recognized in one patients, but the fine leakage of the content from the epidermoid cyst into the lateral ventricle was detected on a saturation recovery 1000 image in one case. (author)

  4. Investigations on renal organic and inorganic solutes, in vivo

    International Nuclear Information System (INIS)

    Wolff, S.D.

    1989-01-01

    A basic question in renal physiology is how do the cells of the renal medulla survive the high concentrations of sodium chloride and urea which occur with antidiuresis. The problem is two-fold: (1) urea, being highly permeable to cell membranes, should enter the cell and adversely affect protein function; and (2) inorganic ions, being in much higher concentration extracellularly than intracellularly should dehydrate the cell. If these organic solutes exist in response to high concentrations of sodium chloride and urea, then their content should vary with diuretic state. Two protocols were developed to test the validity of this hypothesis. The first protocol used 31 P-NMR in vivo to monitor GPC content before, during, and after acute diuresis in an exteriorized rabbit kidney model. Changes in sodium distribution and tissue structure were monitored dynamically with 23 Na- and 1 H-NMR imaging, respectively. The second protocol used HPLC to quantitate each of the four organic solutes in renal inner medullary homogenates. Here, the effect of diuretic state and acute diuresis on organic solute content was assessed

  5. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

    Science.gov (United States)

    Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

    2009-01-01

    A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

  6. NMR spectroscopy of coal pyrolysis products

    Energy Technology Data Exchange (ETDEWEB)

    Polonov, V.M.; Kalabin, G.A.; Kushnarev, D.F.; Shevchenko, G.G.

    1985-12-01

    The authors consider the scope for using H 1 and C 13 NMR spectroscopy to describe the products from coal pyrolysis and hydrogenization. The accuracy of the structural information provided by the best NMR methods is also considered. The stuctural parameters derived from H 1 and C 13 NMR spectra are presented. Results demonstrate the high accuracy and sensitivity of the structural information provided by H 1 AND C 13 NMR spectra for coal products. There are substantial structural differences between the soluble products from medium-temperature coking of Cheremkhov coal and high-speed pyrolysis of Kan-Acha coal, and also differences in behavior during hydrogenation. These differences are related to the structure of the organic matter in the initial coal and to differences in the pyrolysis mechanisms.

  7. Structure discrimination for the C-terminal domain of Escherichia coli trigger factor in solution

    International Nuclear Information System (INIS)

    Yao Yong; Bhabha, Gira; Kroon, Gerard; Landes, Mindy; Dyson, H. Jane

    2008-01-01

    NMR measurements can give important information on solution structure, without the necessity for a full-scale solution structure determination. The C-terminal protein binding domain of the ribosome-associated chaperone protein trigger factor is composed of non-contiguous parts of the polypeptide chain, with an interpolated prolyl isomerase domain. A construct of the C-terminal domain of Escherichia coli trigger factor containing residues 113-149 and 247-432, joined by a Gly-Ser-Gly-Ser linker, is well folded and gives excellent NMR spectra in solution. We have used NMR measurements on this construct, and on a longer construct that includes the prolyl isomerase domain, to distinguish between two possible structures for the C-terminal domain of trigger factor, and to assess the behavior of the trigger factor C-terminal domain in solution. Two X-ray crystal structures, of intact trigger factor from E. coli (Ferbitz et al., Nature 431:590-596, 2004), and of a truncated trigger factor from Vibrio cholerae (Ludlam et al., Proc Natl Acad Sci USA 101:13436-13441, 2004) showed significant differences in the structure of the C-terminal domain, such that the two structures could not be superimposed. We show using NMR chemical shifts and long range nuclear Overhauser effects that the secondary and tertiary structure of the E. coli C-terminal domain in solution is consistent with the crystal structure of the E. coli trigger factor and not with the V. cholerae protein. Given the similarity of the amino acid sequences of the E. coli and V. cholerae proteins, it appears likely that the structure of the V. cholerae protein has been distorted as a result of truncation of a 44-amino acid segment at the C-terminus. Analysis of residual dipolar coupling measurements shows that the overall topology of the solution structure is completely inconsistent with both structures. Dynamics analysis of the C-terminal domain using T 1 , T 2 and heteronuclear NOE parameters show that the protein is

  8. High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes

    International Nuclear Information System (INIS)

    Yao, Yong; Dutta, Samit Kumar; Park, Sang Ho; Rai, Ratan; Fujimoto, L. Miya; Bobkov, Andrey A.; Opella, Stanley J.; Marassi, Francesca M.

    2017-01-01

    The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13 C or 1 H detection, have very narrow line widths (0.40–0.60 ppm for 13 C, 0.11–0.15 ppm for 1 H, and 0.46–0.64 ppm for 15 N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1 H-detected solid-state NMR 1 H/ 15 N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1 H/ 15 N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

  9. NMR spectroscopy and drug development

    International Nuclear Information System (INIS)

    Craik, D.; Munro, S.

    1990-01-01

    The use of nuclear magnetic resonance (NMR) spectroscopy for structural and conformational studies on drug molecules, the three-dimensional investigation of proteins structure and their interactions with ligands are discussed. In-vivo NMR studies of the effects of drugs on metabolism in perfused organs and whole animals are also briefly presented. 5 refs., ills

  10. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy; Bontemps, P.; Rikken, Geert L J A

    2011-01-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  11. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy

    2011-09-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  12. Two-dimensional NMR spectroscopy. Applications for chemists and biochemists

    International Nuclear Information System (INIS)

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Two-dimensional nuclear magnetic resonance spectroscopy (2-D NMR) has become a very powerful class of experiments (in the hands of an adept scientist) with broad adaptability to new situations. It is the product of a happy marriage between modern pulse FT-NMR technology, with its large memory and high-speed computers, and the physicists and chemists who love to manipulate spin systems. Basic 2-D experiments are now a standard capability of modern NMR spectrometers, and this timely book intends to make 2-D NMR users of those who are familiar with normal 1-D NMR. The 2-D NMR goal is correlation of the lines of the observed NMR spectrum with other properties of the system. This book deals with applications to high-resolution spectrum analysis, utilizing either coupling between the NMR-active nuclei or chemical exchange to perform the correlation. The coupling can be scalar (through bonds) or direct through space (within 5 A). The coupling may be homonuclear (between like nuclei) or heteronuclear

  13. PSYCHE Pure Shift NMR Spectroscopy.

    Science.gov (United States)

    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.

  14. High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HRMAS NMR) for Studies of Reactive Fabrics

    Science.gov (United States)

    2015-11-01

    spectroscopy (NMR) Self- decontaminating fabric Reactive fabric...reactions of reagents including chemical weapons on materials like concrete, soil , and sand, as well as reactive polymers.3,4,5,6,7 There are...sample. The rotor and cap can be cleaned by rinsing with solvent or decontamination solution and reused. 12.0 DATA ANALYSIS AND CALCULATIONS 12.1

  15. Push-through Direction Injectin NMR Automation

    Science.gov (United States)

    Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the two major spectroscopic techniques successfully used in metabolomics studies. The non-invasive, quantitative and reproducible characteristics make NMR spectroscopy an excellent technique for detection of endogeno...

  16. NMR reaction monitoring in flow synthesis.

    Science.gov (United States)

    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.

  17. Interaction of charged amphiphilic drugs with phosphatidylcholine vesicles studied by NMR

    International Nuclear Information System (INIS)

    Eriksson, L.E.G.

    1987-01-01

    Small unilamellar vesicles from egg phosphatidylcholine in NaCl solutions were exposed to some amphiphilic pharmaca. The aromatic drugs (chlorpromazine, dibucaine, tetracaine, imipramine and propranolol) were in their cationic form of the amines. By 1 H- and 31 P-NMR the membrane signals were observed. In particular, the N-methyl choline proton signals were followed upon drug addition. The intrinsic chemical shift difference (0.02 ppm) between the inner (upfield) and outer choline signals was influenced by the drug concentration. Packing properties of the lipid head groups and ring current shift probably contributed. At very high drug concentration, the vesicles are destroyed. A transformation into a micellar state with a high sample viscosity took place in a narrow concentration range of drug. The anion effects of Cl - were studied from the 35 Cl-NMR linewidth at 9.8 and 39.1 MHz. A continuous increase in the signal linewidth followed upon drug addition to the vesicles. Only chlorpromazine produced a broadening in the absence of vesicles (NaCl blank). The linewidth reflected a critical micelle concentration of this drug around 7 mM in 0.1 M NaCl. The 35 Cl-NMR experiments demonstrated the existence of an anionic counterion effect. This phenomenon should be accounted for when quantitatively analysing drug-membrane interactions in electrostatic terms. (Auth.)

  18. First NMR Experiments in the Hybrid, 40T and beyond: A challenge to traditional NMR instrumentation

    Science.gov (United States)

    Reyes, Arneil P.

    2001-03-01

    The recent commissioning of the continuous 45T hybrid magnet at NHMFL has opened new horizon for science but carried with it new challenges that forced NMR spectroscopists to reevaluate the traditional approach to NMR instrumentation. Very recently, a world record frequency at 1.5GHz has been achieved, signaling the new era of NMR probe designs that may someday blur the distinction between the classic NMR and millimeter-wave spectroscopies. No longer can we ignore stray capacitances and exposed leads in the terrain where every millimeter of cable counts. The challenge brought about by ever increasing fields and consequently, frequency, requirements has stimulated ingenuity among scientists. This is eased by accelerated growth in RF communications and computing technologies that made available advanced devices with more speed, power, bandwidth, noise immunity, flexibility, and complexity in small space at very low costs. Utilization of these devices have been paramount consideration in cutting-edge designs at NHMFL for Condensed Matter NMR and will be described in this talk. I will also discuss a number of first >33T NMR experiments to date utilizing the strength of the field to expose, as well as to induce occurrence of, new physical phenomena in condensed matter and which resulted in better understanding of the physics of materials. This work has been a result of continuing collaboration with P. L Kuhns, W. G. Moulton, W. P. Halperin (NU), and W. G. Clark (UCLA). The NHMFL is supported through the National Science Foundation and the State of Florida.

  19. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Falk, Alexander S.; Siemer, Ansgar B., E-mail: asiemer@usc.edu [Keck School of Medicine of USC, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute (United States)

    2016-11-15

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  20. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    International Nuclear Information System (INIS)

    Falk, Alexander S.; Siemer, Ansgar B.

    2016-01-01

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  1. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

    Science.gov (United States)

    Bingol, Kerem; Brüschweiler, Rafael

    2015-06-05

    A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.

  2. Automated Control of the Organic and Inorganic Composition of Aloe vera Extracts Using (1)H NMR Spectroscopy.

    Science.gov (United States)

    Monakhova, Yulia B; Randel, Gabriele; Diehl, Bernd W K

    2016-09-01

    Recent classification of Aloe vera whole-leaf extract by the International Agency for Research and Cancer as a possible carcinogen to humans as well as the continuous adulteration of A. vera's authentic material have generated renewed interest in controlling A. vera. The existing NMR spectroscopic method for the analysis of A. vera, which is based on a routine developed at Spectral Service, was extended. Apart from aloverose, glucose, malic acid, lactic acid, citric acid, whole-leaf material (WLM), acetic acid, fumaric acid, sodium benzoate, and potassium sorbate, the quantification of Mg(2+), Ca(2+), and fructose is possible with the addition of a Cs-EDTA solution to sample. The proposed methodology was automated, which includes phasing, baseline-correction, deconvolution (based on the Lorentzian function), integration, quantification, and reporting. The NMR method was applied to 41 A. vera preparations in the form of liquid A. vera juice and solid A. vera powder. The advantages of the new NMR methodology over the previous method were discussed. Correlation between the new and standard NMR methodologies was significant for aloverose, glucose, malic acid, lactic acid, citric acid, and WLM (P vera.

  3. Solution structure and dynamics of melanoma inhibitory activity protein

    International Nuclear Information System (INIS)

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  4. O-17 NMR measurement of water

    International Nuclear Information System (INIS)

    Fukazawa, Nobuyuki

    1990-01-01

    Recently, attention has been paid to the various treatment of water and the utilization of water by magnetic treatment, electric field treatment and so on. It has been said that by these treatments, the change in the properties of water arises. The state of this treated water cannot be explained by the properties of water from conventional physical and chemical standpoints. In addition, the method of measurement of whether the change arose or not is not yet determined. It is necessary to establish the method of measurement for the basic state of water. In this study, O-17 NMR which observes the state of water directly at molecular or atomic level was investigated as the method of measuring water. The measurement of O-17 NMR was carried out with a JNR 90Q FT NMR of Fourier transformation type of JEOL Ltd. The experimental method and the results are reported. The result of measurement of the O-17 NMR spectrum for distilled ion exchange water is shown. It is know that it has very wide line width as compared with the NMR spectra of protons and C-13. The relative sensitivity of O-17 observation is about 1/100,000 of that of protons. As to the information on the state of water obtained by O-17 NMR, there are chemical shift and line width. As temperature rose, the line width showed decrease, which seemed to be related to the decrease of hydrogen combination. (K.I.)

  5. Value of NMR logging for heavy oil characterization

    Energy Technology Data Exchange (ETDEWEB)

    Chen, S.; Chen, J.; Georgi, D. [Baker Hughes, Calgary, AB (Canada); Sun, B. [Chevron Energy Technology Co., Calgary, AB (Canada)

    2008-07-01

    Non-conventional, heavy oil fields are becoming increasingly important to the security of energy supplies and are becoming economically profitable to produce. Heavy oil reservoirs are difficult to evaluate since they are typically shallow and the connate waters are very fresh. Other heavy oil reservoirs are oil-wet where the resistivities are not indicative of saturation. Nuclear magnetic resonance (NMR) detects molecular level interactions. As such, it responds distinctively to different hydrocarbon molecules, thereby opening a new avenue for constituent analysis. This feature makes NMR a more powerful technique than bulk oil density or viscosity measurements for characterizing oils, and is the basis for detecting gas in heavy oil fields. NMR logging, which measures fluid in pore space directly, is capable of separating oil from water. It is possible to discern movable from bound water by analyzing NMR logs. The oil viscosity can be also quantified from NMR logs, NMR relaxation time and diffusivity estimates. The unique challenges for heavy oil reservoir characterization for the NMR technique were discussed with reference to the extra-fast decay of the NMR signal in response to extra-heavy oil/tars, and the lack of sensitivity in measuring very slow diffusion of heavy oil molecules. This paper presented various methods for analyzing heavy oil reservoirs in different viscosity ranges. Heavy oil fields in Venezuela, Kazakhstan, Canada, Alaska and the Middle East were analyzed using different data interpretation approaches based on the reservoir formation characteristics and the heavy oil type. NMR direct fluid typing was adequate for clean sands and carbonate reservoirs while integrated approaches were used to interpret extra heavy oils and tars. It was concluded that NMR logs can provide quantitative measures for heavy oil saturation, identify sweet spots or tar streaks, and quantify heavy oil viscosity within reasonable accuracy. 14 refs., 16 figs.

  6. Investigation of zeolites by solid state quadrapole NMR

    International Nuclear Information System (INIS)

    Janssen, R.

    1990-01-01

    The subject of this thesis is the NMR investigation of zeolites. The nature and properties of zeolites are discussed. Some of the basic priniples of NMR techniques on quadrupole nuclei are presented. A special technique, namely a two-dimensional nutation experiment is discussed in detail. The theory of the nutation experiment for quadrupole spin species with spin quantum number 3/2 as well as 5/2 is presented. For both spin spcies the theoretical spectra are compared with experimental results. It is also shown that the nutation expeirment can be performed with several pulse schemes. It is shown how phase-sensitive pure-absorption nutation spectra can be obtained and an NMR-probe is presented that is capable of performing NMR experiments at high (up to 500 degree C) temperatures. The two-dimensional nutation NMR technique has been applied to sodium cations in zeolite NaA. For this purpose a numbre of zeolite samples were prepared that contained different amounts of water. With the aid of nutation NMR the hydration of the zeolite can be studied and conclusions can be drawn about the symmetry of the surrounding of the sodium cations. With the aid of an extension of the nutation NMR experiment: Rotary Echo Nutation NMR, it is shown that in zeolite NaA, in various stages of hydration, the sodium cations or water molecules are mobile. Proof is given by means of high-temperature 23 Na-NMR that dehydrates zeolite NaA undergoes a phase transition at ca. 120 degree C. In a high-temperature NMR investigation of zeolite ZSM-5 it is shown that the sodium ions start to execute motions when the temperature is increased. (author). 198 refs.; 72 figs.; 6 tabs

  7. NMR reaction monitoring in flow synthesis

    Directory of Open Access Journals (Sweden)

    M. Victoria Gomez

    2017-02-01

    Full Text Available 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.

  8. Petrophysical properties of greensand as predicted from NMR measurements

    DEFF Research Database (Denmark)

    Hossain, Zakir; Grattoni, Carlos A.; Solymar, Mikael

    2011-01-01

    ABSTRACT: Nuclear magnetic resonance (NMR) is a useful tool in reservoir evaluation. The objective of this study is to predict petrophysical properties from NMR T2 distributions. A series of laboratory experiments including core analysis, capillary pressure measurements, NMR T2 measurements...... with macro-pores. Permeability may be predicted from NMR by using Kozeny's equation when surface relaxivity is known. Capillary pressure drainage curves may be predicted from NMR T2 distribution when pore size distribution within a sample is homogeneous....

  9. Unified integration intervals for the structural characterization of oil, coal or fractions there of by 1h NMR and 13c NMR

    International Nuclear Information System (INIS)

    Avella, Eliseo; Fierro, Ricardo

    2010-01-01

    Based on an analysis of publications reported between 1972 and 2006, it became clear that there are inaccuracies in the limits of the ranges of integration that the authors assigned to signals in nuclear magnetic resonance (NMR) to the structural characterization of petroleum, coals and their derived fractions, from their hydrogen (1H NMR) and carbon (13C NMR) spectra. Consequently, consolidated limits were determined for the integration of 1H NMR spectra and 13C NMR of these samples using a statistical treatment applied to the limits of integration intervals already published. With these unified limits, correlation NMR charts were developed that are useful for the allocation of the integral at such intervals, and at smaller intervals defined in terms of the intersection between different assignments. Also raised equations needed to establish the integral attributable to specific fragments in an attempt to make a more accurate structural characterization from NMR spectra of oil, coal or fractions derived.

  10. Investigation of uranium (VI) extraction mechanisms from phosphoric and sulfuric media by {sup 31}P-NMR

    Energy Technology Data Exchange (ETDEWEB)

    Fries, B.; Marie, C.; Pacary, V.; Berthon, C.; Miguirditchian, M.; Charbonnel, M.C. [CEA, Centre de Marcoule, Nuclear Energy Divison, RadioChemistry and Processes Department - DRCP, F-30207 Bagnols-sur-Ceze (France); Mokhtari, H. [AREVA Mines, Process and Analysis Department - SEPA, F-87250 Bessines-sur-Gartempe (France)

    2016-07-01

    Phosphate rocks contain uranium (∼1000 ppm on average) and are considered as a secondary source for uranium production. Uranium extraction using DEHCNPB (butyl-1-[N,N-bis(2-ethylhexyl)carbamoyl]nonyl phosphonic acid, a bifunctional cationic extractant) has been studied to better understand mechanism differences depending on the original acidic solution (phosphoric or sulfuric). Solvent extraction batch experiments were carried out and the organic phases were probed using {sup 31}P-NMR. This technique enabled to demonstrate that phosphoric acid is poorly extracted by DEHCNPB ([H{sub 3}PO{sub 4}]{sub org} < 2 mM), using direct quantification in the organic phase by {sup 31}P-NMR spectra integration. Moreover, in the presence of uranium in the initial phosphoric acid solution, uranyl extraction by DEHCNPB competes with H{sub 3}PO{sub 4} extraction. Average stoichiometries of U(VI)-DEHCNPB complexes in organic phases were also determined using slope analysis on uranium distribution data. Uranium seems to be extracted from a phosphoric medium by two extractant molecules, whereas more than three DEHCNPB on average would be necessary to extract uranium from a sulfuric medium. Thus, uranium is extracted according to different mechanisms depending on the nature of the initial solution. (authors)

  11. New methods for the correction of 31P NMR spectra in in vivo NMR spectroscopy

    International Nuclear Information System (INIS)

    Starcuk, Z.; Bartusek, K.; Starcuk, Z. jr.

    1994-01-01

    The new methods for the correction of 31 P NMR spectra in vivo NMR spectroscopy have been performed. A method for the baseline correction of the spectra which represents a combination of time-domain and frequency-domain has been discussed.The method is very fast and efficient for minimization of base line artifacts of biological tissues impact

  12. NMR techniques in the study of cardiovascular structure and functions

    International Nuclear Information System (INIS)

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy? NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance

  13. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

    Science.gov (United States)

    Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

    2015-11-01

    Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Conformational Plasticity of the Cell-Penetrating Peptide SAP As Revealed by Solid-State 19F-NMR and Circular Dichroism Spectroscopies.

    Science.gov (United States)

    Afonin, Sergii; Kubyshkin, Vladimir; Mykhailiuk, Pavel K; Komarov, Igor V; Ulrich, Anne S

    2017-07-13

    The cell-penetrating peptide SAP, which was designed as an amphipathic poly-l-proline helix II (PPII), was suggested to self-assemble into regular fibrils that are relevant for its internalization. Herein we have analyzed the structure of SAP in the membrane-bound state by solid-state 19 F-NMR, which revealed other structural states, in addition to the expected surface-aligned PPII. Trifluoromethyl-bicyclopentyl-glycine (CF 3 -Bpg) and two rigid isomers of trifluoromethyl-4,5-methanoprolines (CF 3 -MePro) were used as labels for 19 F-NMR analysis. The equilibria between different conformations of SAP were studied and were found to be shifted by the substituents at Pro-11. Synchrotron-CD results suggested that substituting Pro-11 by CF 3 -MePro governed the coil-to-PPII equilibrium in solution and in the presence of a lipid bilayer. Using CD and 19 F-NMR, we examined the slow kinetics of the association of SAP with membranes and the dependence of the SAP conformational dynamics on the lipid composition. The peptide did not bind to lipids in the solid ordered phase and aggregated only in the liquid ordered "raft"-like bilayers. Self-association could not be detected in solution or in the presence of liquid disordered membranes. Surface-bound amphipathic SAP in a nonaggregated state was structured as a mixture of nonideal extended conformations reflecting the equilibrium already present in solution, i.e., before binding to the membrane.

  15. 13C-NMR assignment, structure, and dynamics of deoxyoligonucleotides

    International Nuclear Information System (INIS)

    Zanatta, N.; Borer, P.N.; Levy, G.C.

    1986-01-01

    The unique spectral properties of 13 C-NMR for studying nucleic acids and some of the important features of 13 C-NMR in oligonucleotide studies are demostrated. The main difficulty in studying oligonucleotides by 13 C-NMR and recent improvements in NMR instrumentation and advances in oligonucleotide synthesis are presented. The high resolution 13 C-NMR spectra, T 1 relaxation times and NOEs were measured for duplex of the self-complementary oligo-DNAs: d(CG) 3 and d(GGTATACC) are studied. The target of this study is to developed a systematic 13 C-NMR spectral assignment and to investigate the structure and dynamics of these two sequences by this techniques. (M.J.C.) [pt

  16. NMR imaging studies of coal

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Z.R.; Zhang, P.Z.; Ding, G.L.; Li, L.Y.; Ye, C.H. [University of Science and Technology, Beijing (China). Dept. of Chemistry

    1996-06-01

    The permeation transportation and swelling behavior of solvents into coal are investigated by NMR imaging using pyridine-d{sub 5} and acetone-d{sub 6}. Images of coal swollen with deuterated solvents illuminate proton distributions of mobile phases within the coal macromolecular networks. More information about the chemical and physical structure of coal can be obtained using NMR imaging techniques.

  17. Variations of NMR signals by hyperpolarization and ultrasound; Variation von NMR-Signalen durch Hyperpolarisation und Ultraschall

    Energy Technology Data Exchange (ETDEWEB)

    Engelbertz, A.

    2006-07-01

    In this thesis it is described how p-NMR can be applied to metals with verlo low hydrogen concentrations and how a combination of ultrasound and NMR can lead to an improvement of the measureing method. As examples measurements on H{sub 2}O and ethanol are described. (HSI)

  18. NMR characteristics of low-grade glioma. Comparison with CT

    Energy Technology Data Exchange (ETDEWEB)

    Asato, Reinin; Tokuriki, Yasuhiko; Nakano, Yoshihisa; Itoh, Harumi; Torizuka, Kanji; Ueda, Tohru; Yamashita, Junkoh; Handa, Hajime

    1985-08-01

    Sixteen low-grade gliomas were evaluated both with nuclear magnetic resonance (NMR) imaging and with computed tomography (CT). In 13 cases (81%), the NMR images were much better in tissue contrast than the contrast-enhanced CT images. The tumors were shown as well-circumscribed oval lesions in the NMR, though they appeared as ill-defined, irregular, low-attenuation areas in the CT. The extent of the lesion, which was supposed to represent the active tumor tissue, was greater in the NMR than in the CT, because NMR tissue parameters (T/sub 1/, T/sub 2/) are more sensitive to pathological changes in brain tissue than is the X-ray attenuation coefficient. Though, in an optic glioma and a brain-stem astrocytoma, the CT with contrast enhancement displayed the contour of the mass as well as did NMR, it was inferior to the NMR in showing the cephalocaudal extension of the tumors. Calcification does not give a proton NMR signal under the present measuring conditions; thus the calcified cystic wall of a hypothalamic astrocytoma was displayed only in the CT images. In conclusion, the NMR imaging was apparently superior to contrast-enhanced CT in demonstrating the lesions due to low-grade glioma.

  19. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  20. Detergent/nanodisc screening for high-resolution NMR studies of an integral membrane protein containing a cytoplasmic domain.

    Directory of Open Access Journals (Sweden)

    Christos Tzitzilonis

    Full Text Available Because membrane proteins need to be extracted from their natural environment and reconstituted in artificial milieus for the 3D structure determination by X-ray crystallography or NMR, the search for membrane mimetic that conserve the native structure and functional activities remains challenging. We demonstrate here a detergent/nanodisc screening study by NMR of the bacterial α-helical membrane protein YgaP containing a cytoplasmic rhodanese domain. The analysis of 2D [(15N,(1H]-TROSY spectra shows that only a careful usage of low amounts of mixed detergents did not perturb the cytoplasmic domain while solubilizing in parallel the transmembrane segments with good spectral quality. In contrast, the incorporation of YgaP into nanodiscs appeared to be straightforward and yielded a surprisingly high quality [(15N,(1H]-TROSY spectrum opening an avenue for the structural studies of a helical membrane protein in a bilayer system by solution state NMR.

  1. NMR spectroscopic studies of membrane-bound biological systems

    International Nuclear Information System (INIS)

    Hohlweg, W.

    2013-01-01

    In the course of this thesis, biological NMR spectroscopy was employed in studying membrane-bound peptides and proteins, for which structural information is still comparatively hard to obtain. Initial work focused on various model peptides bound to membrane-mimicking micelles, studying the protonation state of arginine in a membrane environment. Strong evidence for a cation-π complex was found in TM7, a peptide which forms the seventh transmembrane helix of subunit a of the vacuolar-type H+-ATPase (V-ATPase). V-ATPase is a physiologically highly relevant proton pump, which is present in intracellular membranes of all eukaryotic organisms, as well as the plasma membrane of several specialized cells. Loss of functional V-ATPase is associated with human diseases such as osteopetrosis, distal renal tubular acidosis or the spreading of cancer. V-ATPase is considered a potential drug target in the treatment of osteoporosis and cancer, or in the development of novel contraceptives. Results from NMR solution structure determination, NMR titration experiments, paramagnetic relaxation enhancement experiments and tryptophan fluorescence spectroscopy confirm the existence of a buried cation-? complex formed between arginine residue R735, which is essential for proton transport, and neighbouring tryptophan and tyrosine residues. In vivo experiments in the yeast Saccharomyces cerevisiae using selective growth tests and fluorescence microscopy showed that formation of the cation-π complex is essential for V-ATPase function. Deletion of both aromatic residues, as well as only the one tryptophan residue leads to growth defects and inability to maintain vacuolar pH homeostasis. These findings shine new light on the still elusive mechanism of proton transport in V-ATPase, and show that arginine R735 may be directly involved in proton transfer across the membrane. (author) [de

  2. NMR in the SPINE Structural Proteomics project.

    Science.gov (United States)

    Ab, E; Atkinson, A R; Banci, L; Bertini, I; Ciofi-Baffoni, S; Brunner, K; Diercks, T; Dötsch, V; Engelke, F; Folkers, G E; Griesinger, C; Gronwald, W; Günther, U; Habeck, M; de Jong, R N; Kalbitzer, H R; Kieffer, B; Leeflang, B R; Loss, S; Luchinat, C; Marquardsen, T; Moskau, D; Neidig, K P; Nilges, M; Piccioli, M; Pierattelli, R; Rieping, W; Schippmann, T; Schwalbe, H; Travé, G; Trenner, J; Wöhnert, J; Zweckstetter, M; Kaptein, R

    2006-10-01

    This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

  3. 1H and 13C NMR studies of palladium(2) and platinium(2) complexes with S-Methyl-L-Cysteine

    International Nuclear Information System (INIS)

    Allain, A.; Jezowska-Trzebiatowska, B.; Kozlowski, H.

    1979-01-01

    Our recent 1 H NMR studies on Pd(2)-S-Methyl-L-Cysteine(SMC) complexes have shown that the use of a conformational analysis to establish the complexed species existing in solution may provide clearer results than considering the proton chemical shift only. However, the use of the vicinal coupling constant of ABC spectrum of αCH-βCH 2 proton unit to estimate the rotational isomer fractions, may contain some ambiguity, especially on the proton assignment of the methylene group. For this reason 13 C NMR method has been applied to study these systems. (author)

  4. Direct 13C NMR Detection in HPLC Hyphenation Mode

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Johansen, Kenneth; Nyberg, Nils

    2012-01-01

    Solid phase extraction (SPE) was introduced as a crucial step in the HPLC-SPE-NMR technique to enable online analyte enrichment from which proton-detected NMR experiments on submicrogram amounts from complex mixtures were possible. However, the significance of direct-detected (13)C NMR experiments...... application of HPLC-SPE-NMR analysis using direct-detected (13)C NMR spectra. HPLC column loading, accumulative SPE trappings, and the effect of different elution solvents were evaluated and optimized. A column loading of approximately 600 mug of a prefractionated triterpenoid mixture, six trappings...

  5. ECG gated NMR-CT for cardiovascular diseases

    International Nuclear Information System (INIS)

    Nishikawa, J.; Machida, K.; Iio, M.; Yoshimoto, N.; Sugimoto, T.; Kawaguchi, H.; Mano, H.

    1984-01-01

    The authors applied NMR-CT to cardiac study with ECG gated technique to evaluate the left ventricular (LV) function and compared it with cardiovascular nuclear medicine study (NM). The NMR-CT machine has resistive air-core magnet with 0.15 Tesla. The saturation recovery image or inversion recovery image were obtained as 256 x 256 matrix and 15 mm in thickness. The study population was ten patients who were evaluated both by NMR image and by NM performed within one week interval. The heart muscle was able to be visualized without any contrast material nor radioisotopes in inversion recovery images, whereas saturation recovery images failed to separate heart muscle from blood pool. The wall motions of LV in both methods were well correlated except for inferior wall. The values of ejection fraction in NMR image were moderately low, but two modalities showed satisfactory correlation (r=0.85). The region of myocardial infarction was revealed as wall thinning and/or wall motion abnormality. It is still preliminary to draw a conclusion, however, it can be said that in the evaluation of LV function, method by NMR might be of equal value to those of NM. It can be certain that eventually gated NMR-CT will become more effective method for various aspects of cardiovascular evaluation

  6. Structural investigations of substituted indolizine derivatives by NMR studies

    International Nuclear Information System (INIS)

    Furdui, Bianca; Dinica, Rodica; Demeunynck, Martine; Druta, Ioan

    2008-01-01

    Owing to the increasing importance of indolizine heterocycles in the field of biology and pharmacology we have synthesized and investigated the obtained heterocycles by NMR techniques. In order to investigate the substituent effects on the spectroscopic properties, a series of indolizine derivatives were studied by 1 H-NMR, 13 C-NMR and 2D NMR (GCOSY, GHMBC and GHMQC spectra). (authors)

  7. Detailed NMR investigation of cyclodextrin-perfluorinated surfactant interactions in aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Weiss-Errico, Mary Jo; O’Shea, Kevin E., E-mail: osheak@fiu.edu

    2017-05-05

    Highlights: • Perfluorochemicals (PFCs) are strongly encapsulated by cyclodextrins (CDs). • Competition studies confirm strong CD:PFC host-guest interactions. • {sup 19}F NMR Spectroscopy demonstrates association constants up to 10{sup 5} M{sup −1}. • Position of CD along PFC chain is elucidated from NMR results. • CD:PFC complex is not disturbed under a variety of water quality conditions. - Abstract: Perfluorochemicals (PFCs) are contaminants of serious concern because of their toxicological properties, widespread presence in drinking water sources, and incredible stability in the environment. To assess the potential application of α-, β-, and γ-cyclodextrins for PFC remediation, we investigated their complexation with linear fluorinated carboxylic acids, sulfonates, and a sulfonamide with carbon backbones ranging from C4-C9. {sup 19}F Nuclear Magnetic Resonance (NMR) spectroscopy studies demonstrated β-CD formed the strongest complexes with these PFCs. The polar head group had a modest influence, but for PFCs with backbones longer than six carbons, strong association constants are observed for 1:1 (K{sub 1:1} ∼ 10{sup 5} M{sup −1}) and 2:1 (K{sub 2:1} ∼ 10{sup 3} M{sup −1}) β-CD:PFC complexes. Excess β-CD can be used to complex 99.5% of the longer chain PFCs. Competition studies with adamantane-carboxylic acid and phenol confirmed the nature and persistence of the β-CD:PFC complex. Detailed analyses of the individual NMR chemical shifts and Job plots indicate the favored positions of the β-CD along the PFC chain. Solution pH, ionic strength, and the presence of humic acid have modest influence on the β-CD:PFC complexes. The strong encapsulation of PFCs by β-CD under a variety of water quality conditions demonstrates the tremendous potential of CD-based materials for the environmental remediation of PFCs.

  8. Quantification of dextrose in model solution by 1H MR spectroscopy at 1.5T

    International Nuclear Information System (INIS)

    Lee, Kyung Hee; Cho, Soon Gu; Kim, Hyung Jin; Suh, Chang Hae; Kim, Yong Seong; Lee, Jung Hee

    2002-01-01

    To evaluate the feasibility of proton magnetic resonance spectroscopy ( 1 H-MRS) using a 1.5T magnetic resonance (MR) imager for quantification of the contents of model solutions. We prepared model solutions of dextrose +water and dextrose +water + ethanol at dextrose concentrations of 0.01% to 50% and 0.01% to 20%, respectively. Using these solutions and a 1.5T MR imager together with a high-resolution nuclear magnetic resonance (NMR) spectroscope, we calculated the ratios of dextrose to water peak, (dextrose +ethanol) to water peak, and (dextrose + ethanol) to ethanol peak, as seen on MR and NMR spectra, analysing the relationships between dextrose concentration and the ratios of peaks, and between the ratios of the peaks seen on MR spectra and those seen on NMR spectra. Changes in the ratios between dextrose concentration and dextrose to water peak, (dextrose + ethanol) to water peak and (dextrose + ethanol) to ethanol peak, as seen on MR spectra, were statistically significant, and there was good linear regression. There was also close correlation between the ratios of the observed on MR and NMR spectra. The results depict the quantification of dextrose concentration according to the ratios of spectral peaks obtained by proton MRS at 1.5T. Using proton MRS at 1.5T, and on the basis of the ratios of spectcal peaks, it was possible to quantify the concentration of dextrose in model solutions of dextrose + water and dextrose + water+ ethanol. The results of this study suggest that for quantifying the contents of biofluids, the use of low-tesla 1 H-MRS is feasible

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

    Science.gov (United States)

    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

  10. NMR study of LaPb2

    International Nuclear Information System (INIS)

    Ueda, K.; Kohara, T.; Yamada, Y.

    1995-01-01

    La and Pb NMR signals were observed in LaPb 2 with a superconducting transition temperature of about 7 K. The width of the Pb NMR spectrum with an asymmetric line shape was rather narrower than those of Er-, Gd- and Ho-Pb 2 . The spin-lattice relaxation time of Pb nuclei was twice longer than that of Pb metal. La NMR spectrum had satellites due to the electric quadrupole interaction. These results show that each local environment at La or Pb site in LaPb 2 compound is uniquely determined, compared with those in randomly substituted alloys. ((orig.))

  11. In Vitro Antioxidant Activity of Chitosan Aqueous Solution: Effect of ...

    African Journals Online (AJOL)

    ... (CS-TPP) and chitosan ethylenediaminetetraacetic acid (CS-EDTA) solution were determined employing various established in vitro system such as superoxide and hydroxyl radicals scavenging, metal ion chelating and reducing power. Their chemical structures were characterized by nuclear magnetic resonance (NMR) ...

  12. Nuclear magnetic resonance (NMR) tomography

    International Nuclear Information System (INIS)

    Skalpe, I.O.

    1984-01-01

    A brief survey of the working principle of the NMR technique in diagnostical medicine is given. Its clinical usefulness for locating tumors, diagnosing various other diseases, such as some mental illnesses and multiple sclerosis, and its possibilities for studying biochemical processes in vivo are mentioned. The price of NMR image scanners and the problems of the strong magnetic field around the machines are mentioned

  13. High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Yong; Dutta, Samit Kumar [Sanford Burnham Prebys Medical Discovery Institute (United States); Park, Sang Ho; Rai, Ratan [University of California San Diego, Department of Chemistry and Biochemistry (United States); Fujimoto, L. Miya; Bobkov, Andrey A. [Sanford Burnham Prebys Medical Discovery Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbp.edu [Sanford Burnham Prebys Medical Discovery Institute (United States)

    2017-03-15

    The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with {sup 13}C or {sup 1}H detection, have very narrow line widths (0.40–0.60 ppm for {sup 13}C, 0.11–0.15 ppm for {sup 1}H, and 0.46–0.64 ppm for {sup 15}N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The {sup 1}H-detected solid-state NMR {sup 1}H/{sup 15}N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR {sup 1}H/{sup 15}N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

  14. NMR-based metabolomics of water-buffalo milk after conventional or biological feeding

    Directory of Open Access Journals (Sweden)

    Pierluigi Mazzei

    2018-02-01

    Full Text Available Abstract Background Biological farming in dairy production is often advocated as one of the most virtuous solutions to the environmental problems of conventional farming while improving the sustainability of production and cattle welfare. However, it is still under debate whether the conversion from conventional to biological farming has an influence on milk composition. In addition, the possible frauds related to biological dairy products call for analytical tools enabling the authentication of products quality and consumers protection. The aim of this work was to determine the composition of milk produced by water-buffaloes and to identify the specific metabolic profiles discriminating a biological from a conventional feeding diet. Methods Liquid-state 1H, 13C, and 31P nuclear magnetic resonance (NMR spectroscopies were used to study milk samples which were supplied during a 2-year-long experimentation by a single dairy farm and sampled from conventionally and biologically fed buffaloes (CFM and BFM, respectively. For each milk sample, we obtained NMR spectra of both raw milk and milk cream fractions comprising neutral lipids and phospholipids. Results The elaboration of multinuclear spectroscopic NMR results by the principal component analysis (PCA enabled the identification of diagnostic differences in the milk composition between CFM and BFM samples. In particular, BFM were characterized by larger content of unsaturated lipids and phosphatidylcholine. Our findings confirmed that the conversion from a conventional to biological feeding regime influenced the buffalo milk composition, with possible implications for sensorial and nutritional properties of dairy products. Finally, the analytical methodology of NMR spectroscopy shown here may be considered as a useful tool to assess the quality and the authenticity of biological milk.

  15. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  16. NMR imaging of the cardiovascular system

    International Nuclear Information System (INIS)

    Canby, R.C.; Evanochko, W.T.; Pohost, G.M.

    1986-01-01

    Proton nuclear magnetic resonance (NMR) imaging permits high-resolution tomographic and three-dimensional images of the human body to be obtained without exposure to ionizing radiation. Such imaging not only yields anatomic resolution comparable to X-ray examinations but also provides a potential means to discriminate between healthy tissue and diseased tissue. This potential is based on certain NMR properties known as relaxation times, which determine, in part, the signal intensity in an image. These properties are related to such factors as the sizes and concentrations of proteins and mobile lipids and the compartmentalization of the protons of water. Although NMR imaging (also called magnetic resonance imaging, MRI) is becoming widely available for clinical use, application to the cardiovascular system, though promising, remains primarily a research tool. Gated proton NMR imaging can generate cardiac images with excellent morphologic detail and contrast; however, its ultimate importance as a cardiovascular diagnostic modality will depend on the development of several unique applications. These applications are discussed in this paper

  17. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

    2008-07-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  18. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    International Nuclear Information System (INIS)

    Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

    2008-01-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1 H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13 C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  19. NMR investigation of acrolein stability in hydroalcoholic solution as a foundation for the valid HS-SPME/GC–MS quantification of the unsaturated aldehyde in beverages

    International Nuclear Information System (INIS)

    Kächele, Martin; Monakhova, Yulia B.; Kuballa, Thomas; Lachenmeier, Dirk W.

    2014-01-01

    Highlights: • Acrolein in hydroalcoholic solution degrades to 1,3,3-propanetriol and 3-hydroxypropionaldehyde. • Hydroquinone (0.2%) at pH 3.0 stabilizes acrolein solutions. • Quantitative HS-SPME/GC–MS determination of acrolein in alcoholic beverages was developed (LOD 14 μg L −1 ). • 6 of 117 samples had acrolein levels above the WHO threshold (1500 μg L −1 ). - Abstract: Acrolein (propenal) is found in many foods and beverages and may pose a health hazard due to its cytotoxicity. Considerable knowledge gaps regarding human exposure to acrolein exist, and there is a lack of reliable analytical methods. Hydroalcoholic dilutions prepared for calibration purposes from pure acrolein show considerable degradation of the compound and nuclear magnetic resonance (NMR) spectroscopy showed that 1,3,3-propanetriol and 3-hydroxypropionaldehyde are formed. The degradation can be prevented by addition of hydroquinone as stabilizer to the calibration solutions, which then show linear concentration-response behaviour required for quantitative analysis. The stabilized calibration solutions were used for quantitative headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC–MS) determination of acrolein in alcoholic beverages with a detection limit of 14 μg L −1 . Of 117 tested alcoholic beverages, 64 were tested positive with the highest incidence in grape marc spirits and whiskey (100%, mean 252 μg L −1 ), followed by fruit spirits (86%, mean 591 μg/L −1 ), tequila (86%, mean 404 μg L −1 ), Asian spirits (43%, mean 54 μg L −1 ) and wine (9%, mean 0.7 μg L −1 ). Acrolein could not be detected in beer, vodka, absinthe and bottled water. Six of the fruit and grape marc spirits had acrolein levels above the World Health Organization (WHO) provisional tolerable concentration of 1.5 mg L −1

  20. NMR investigation of acrolein stability in hydroalcoholic solution as a foundation for the valid HS-SPME/GC–MS quantification of the unsaturated aldehyde in beverages

    Energy Technology Data Exchange (ETDEWEB)

    Kächele, Martin [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Hochschule Mannheim, Paul-Wittsack-Strasse 10, D-68163 Mannheim (Germany); Monakhova, Yulia B. [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Bruker Biospin GmbH, Silbersteifen, 76287 Rheinstetten (Germany); Department of Chemistry, Saratov State University, Astrakhanskaya Street 83, 410012 Saratov (Russian Federation); Kuballa, Thomas [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Lachenmeier, Dirk W., E-mail: lachenmeier@web.de [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Ministry of Rural Affairs and Consumer Protection, Kernerplatz 10, 70182 Stuttgart (Germany)

    2014-04-01

    Highlights: • Acrolein in hydroalcoholic solution degrades to 1,3,3-propanetriol and 3-hydroxypropionaldehyde. • Hydroquinone (0.2%) at pH 3.0 stabilizes acrolein solutions. • Quantitative HS-SPME/GC–MS determination of acrolein in alcoholic beverages was developed (LOD 14 μg L⁻¹. • 6 of 117 samples had acrolein levels above the WHO threshold (1500 μg L⁻¹). Abstract: Acrolein (propenal) is found in many foods and beverages and may pose a health hazard due to its cytotoxicity. Considerable knowledge gaps regarding human exposure to acrolein exist, and there is a lack of reliable analytical methods. Hydroalcoholic dilutions prepared for calibration purposes from pure acrolein show considerable degradation of the compound and nuclear magnetic resonance (NMR) spectroscopy showed that 1,3,3-propanetriol and 3-hydroxypropionaldehyde are formed. The degradation can be prevented by addition of hydroquinone as stabilizer to the calibration solutions, which then show linear concentration-response behaviour required for quantitative analysis. The stabilized calibration solutions were used for quantitative headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC–MS) determination of acrolein in alcoholic beverages with a detection limit of 14 μg L⁻¹. Of 117 tested alcoholic beverages, 64 were tested positive with the highest incidence in grape marc spirits and whiskey (100%, mean 252 μg L⁻¹), followed by fruit spirits (86%, mean 591 μg/L⁻¹), tequila (86%, mean 404 μg L⁻¹), Asian spirits (43%, mean 54 μg L⁻¹) and wine (9%, mean 0.7 μg L⁻¹). Acrolein could not be detected in beer, vodka, absinthe and bottled water. Six of the fruit and grape marc spirits had acrolein levels above the World Health Organization (WHO) provisional tolerable concentration of 1.5 mg L⁻¹.

  1. Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

    Science.gov (United States)

    Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

    2018-04-01

    Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high

  2. Acidity and Structure of Isosaccharinate in Aqueous Solution: A Nuclear Magnetic Resonance Study

    International Nuclear Information System (INIS)

    Cho, Herman M.; Rai, Dhanpat; Hess, Nancy J.; Xia, Yuanxian; Rao, Linfeng

    2003-01-01

    Dilute aqueous solutions of the calcium and sodium salts of -D-isosaccharinate (ISA) have been analyzed by 13C and 1H NMR spectroscopy. The positions of the six 13C ISA NMR lines show a pH dependence that can be used to infer that the most acidic proton is the one associated with the carboxylate group, with a log k0 of -3.27 - -3.36 for the reaction H(ISA) H+ K ISA-

  3. Structural and dynamical characterization of the Miz-1 zinc fingers 5-8 by solution-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, David; Bedard, Mikaeel; Bilodeau, Josee; Lavigne, Pierre, E-mail: pierre.lavigne@usherbrooke.ca [Universite de Sherbrooke, Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Institut de Pharmacologie de Sherbrooke (Canada)

    2013-10-15

    Myc-interacting zinc finger protein-1 (Miz-1) is a BTB/POZ transcription factor that activates the transcription of cytostatic genes, such as p15{sup INK4B} or p21{sup CIP1}. The C-terminus of Miz-1 contains 13 consensus C{sub 2}H{sub 2} zinc finger domains (ZF). ZFs 1-4 have been shown to interact with SMAD3/4, while the remaining ZFs are expected to bind the promoters of target genes. We have noted unusual features in ZF 5 and the linker between ZFs 5 and 6. Indeed, a glutamate is found instead of the conserved basic residue two positions before the second zinc-coordinating histidine on the ZF 5 helix, and the linker sequence is DTDKE in place of the classical TGEKP sequence. In a canonical {beta}{beta}{alpha} fold, such unusual primary structure elements should cause severe electrostatic repulsions. In this context, we have characterized the structure and the dynamics of a Miz-1 construct comprising ZFs 5-8 (Miz 5-8) by solution-state NMR. Whilst ZFs 5, 7 and 8 were shown to adopt the classical {beta}{beta}{alpha} fold for C{sub 2}H{sub 2} ZFs, the number of long-range NOEs was insufficient to define a classical fold for ZF 6. We show by using {sup 15}N-relaxation dispersion experiments that this lack of NOEs is due to the presence of extensive motions on the {mu}s-ms timescale. Since this negatively charged region would have to be located near the phosphodiester backbone in a DNA complex, we propose that in addition to promoting conformational searches, it could serve as a hinge region to keep ZFs 1-4 away from DNA.

  4. Visualising substrate-fingermark interactions: Solid-state NMR spectroscopy of amino acid reagent development on cellulose substrates.

    Science.gov (United States)

    Spindler, Xanthe; Shimmon, Ronald; Roux, Claude; Lennard, Chris

    2015-05-01

    Most spectroscopic studies of the reaction products formed by ninhydrin, 1,2-indanedione-zinc (Ind-Zn) and 1,8-diazafluoren-9-one (DFO) when reacted with amino acids or latent fingermarks on paper substrates are focused on visible absorption or luminescence spectroscopy. In addition, structural elucidation studies are typically limited to solution-based mass spectrometry or liquid nuclear magnetic resonance (NMR) spectroscopy, which does not provide an accurate representation of the fingermark development process on common paper substrates. The research presented in this article demonstrates that solid-state carbon-13 magic angle spinning NMR ((13)C-MAS-NMR) is a technique that can not only be utilised for structural studies of fingermark enhancement reagents, but is a promising technique for characterising the effect of paper chemistry on fingermark deposition and enhancement. The latter opens up a research area that has been under-explored to date but has the potential to improve our understanding of how fingermark secretions and enhancement reagents interact with paper substrates. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Contact replacement for NMR resonance assignment.

    Science.gov (United States)

    Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

    2008-07-01

    Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

  6. NMR characterization of thin films

    Science.gov (United States)

    Gerald II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2010-06-15

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  7. NMR characterization of thin films

    Science.gov (United States)

    Gerald, II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2008-11-25

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  8. Three-dimensional solution structure of lactoferricin B, an antimicrobial peptide derived from bovine lactoferrin.

    Science.gov (United States)

    Hwang, P M; Zhou, N; Shan, X; Arrowsmith, C H; Vogel, H J

    1998-03-24

    The solution structure of bovine lactoferricin (LfcinB) has been determined using 2D 1H NMR spectroscopy. LfcinB is a 25-residue antimicrobial peptide released by pepsin cleavage of lactoferrin, an 80 kDa iron-binding glycoprotein with many immunologically important functions. The NMR structure of LfcinB reveals a somewhat distorted antiparallel beta-sheet. This contrasts with the X-ray structure of bovine lactoferrin, in which residues 1-13 (of LfcinB) form an alpha-helix. Hence, this region of lactoferricin B appears able to adopt a helical or sheetlike conformation, similar to what has been proposed for the amyloidogenic prion proteins and Alzheimer's beta-peptides. LfcinB has an extended hydrophobic surface comprised of residues Phe1, Cys3, Trp6, Trp8, Pro16, Ile18, and Cys20. The side chains of these residues are well-defined in the NMR structure. Many hydrophilic and positively charged residues surround the hydrophobic surface, giving LfcinB an amphipathic character. LfcinB bears numerous similarities to a vast number of cationic peptides which exert their antimicrobial activities through membrane disruption. The structures of many of these peptides have been well characterized, and models of their membrane-permeabilizing mechanisms have been proposed. The NMR solution structure of LfcinB may be more relevant to membrane interaction than that suggested by the X-ray structure of intact lactoferrin. Based on the solution structure, it is now possible to propose potential mechanisms for the antimicrobial action of LfcinB.

  9. Software Library for Bruker TopSpin NMR Data Files

    Energy Technology Data Exchange (ETDEWEB)

    2016-10-14

    A software library for parsing and manipulating frequency-domain data files that have been processed using the Bruker TopSpin NMR software package. In the context of NMR, the term "processed" indicates that the end-user of the Bruker TopSpin NMR software package has (a) Fourier transformed the raw, time-domain data (the Free Induction Decay) into the frequency-domain and (b) has extracted the list of NMR peaks.

  10. DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

    International Nuclear Information System (INIS)

    Gupta, G.; Sarma, M.H.; Sarma, R.H.

    1987-01-01

    A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1 H NMR studies in H 2 O and D 2 O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

  11. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

    Science.gov (United States)

    Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

    2018-02-01

    A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Polymeric proanthocyanidins 13C NMR studies of procyanidins

    Science.gov (United States)

    Lawrence J. Porter; Roger H. Newman; Lai Yeap Foo; Herbert Wong; Richard W. Hemingway

    1982-01-01

    Proanthocyanidin polymers have been shown to consist entirely of flavan-3-ol units by a combination of techniques including 13C n.m.r. spectroscopy. The 13C n.m.r. spectra of the polymers and related molecules are now considered in more detail. Prior to this study UC n.m.r. data has been published of procyanidins and...

  13. Flow units from integrated WFT and NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Kasap, E.; Altunbay, M.; Georgi, D.

    1997-08-01

    Reliable and continuous permeability profiles are vital as both hard and soft data required for delineating reservoir architecture. They can improve the vertical resolution of seismic data, well-to-well stratigraphic correlations, and kriging between the well locations. In conditional simulations, permeability profiles are imposed as the conditioning data. Variograms, covariance functions and other geostatistical indicators are more reliable when based on good quality permeability data. Nuclear Magnetic Resonance (NMR) logging and Wireline Formation Tests (WFT) separately generate a wealth of information, and their synthesis extends the value of this information further by providing continuous and accurate permeability profiles without increasing the cost. NMR and WFT data present a unique combination because WFTs provide discrete, in situ permeability based on fluid-flow, whilst NMR responds to the fluids in the pore space and yields effective porosity, pore-size distribution, bound and moveable fluid saturations, and permeability. The NMR permeability is derived from the T{sub 2}-distribution data. Several equations have been proposed to transform T{sub 2} data to permeability. Regardless of the transform model used, the NMR-derived permeabilities depend on interpretation parameters that may be rock specific. The objective of this study is to integrate WFT permeabilities with NMR-derived, T{sub 2} distribution-based permeabilities and thereby arrive at core quality, continuously measured permeability profiles. We outlined the procedures to integrate NMR and WFT data and applied the procedure to a field case. Finally, this study advocates the use of hydraulic unit concepts to extend the WFT-NMR derived, core quality permeabilities to uncored intervals or uncored wells.

  14. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    International Nuclear Information System (INIS)

    Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek; Lee, Weontae

    2014-01-01

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding

  15. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Sunjin [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Yong Woo; Kim, Woo Taek [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2014-01-10

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.

  16. Solution structure of LC4 transmembrane segment of CCR5.

    Directory of Open Access Journals (Sweden)

    Kazuhide Miyamoto

    Full Text Available CC-chemokine receptor 5 (CCR5 is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1. The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  17. Solution structure of LC4 transmembrane segment of CCR5.

    Science.gov (United States)

    Miyamoto, Kazuhide; Togiya, Kayo

    2011-01-01

    CC-chemokine receptor 5 (CCR5) is a specific co-receptor allowing the entry of human immunodeficiency virus type 1 (HIV-1). The LC4 region in CCR5 is required for HIV-1 entry into the cells. In this study, the solution structure of LC4 in SDS micelles was elucidated by using standard 1H two-dimensional NMR spectroscopy, circular dichroism, and fluorescence quenching. The LC4 structure adopts two helical structures, whereas the C-terminal part remains unstructured. The positions in which LC4 binds to the HIV-1 inhibitory peptide LC5 were determined by docking calculations in addition to NMR data. The poses showed the importance of the hydrophobic interface of the assembled structures. The solution structure of LC4 elucidated in the present work provides a structural basis for further studies on the HIV-1 inhibitory function of the LC4 region.

  18. Prototropic tautomerism of 5-nitrobenzimidazole derivatives in {sup 1}H, {sup 13}C and {sup 15}N NMR spectra; Tautomeria prototropowa pochodnych 5-nitrobenzimidazolu w widmach {sup 1}H, {sup 13}C, {sup 15}N NMR

    Energy Technology Data Exchange (ETDEWEB)

    Wiench, J W; Bocian, W; Stefaniak, L [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

    1994-12-31

    NMR spectra of 5-nitrobenzimidazole derivatives in DMSO solution show the fast exchange of protons. The line broadening in {sup 1}H,{sup 13}C and {sup 15}N spectra have been observed. The interpretation of the spectra has been done basing on chemical shifts values and couplings between nuclei in the investigated derivatives. 3 refs, 2 figs, 3 tabs.

  19. Characterization of natural bentonite by NMR

    International Nuclear Information System (INIS)

    Leite, Sidnei Q.M.; Dieguez, Lidia C.; Menezes, Sonia M.C.; San Gil, Rosane A.S.

    1993-01-01

    Solid state NMR as well as several other instrumental chemical analysis techniques were used in order to characterize two natural occurring bentonite. The methodology is described. The NMR spectra, together with the other used techniques suggest that the observed differences are due to iron inclusions in tetrahedral and octahedral sites

  20. Selective sensitivity enhancement in FT-NMR

    International Nuclear Information System (INIS)

    Farrar, T.C.

    1987-01-01

    In this article the basic two-spin nuclear magnetic resonance (NMR) experiment and the new sensitivity enhancement experiments are reviewed. In part two of this two-part series an overview of two-dimensional NMR experiments will be presented. Part two will appear in the June 1 issue of Analytical Chemistry

  1. NMR-Fragment Based Virtual Screening: A Brief Overview.

    Science.gov (United States)

    Singh, Meenakshi; Tam, Benjamin; Akabayov, Barak

    2018-01-25

    Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

  2. NMR-Fragment Based Virtual Screening: A Brief Overview

    Directory of Open Access Journals (Sweden)

    Meenakshi Singh

    2018-01-01

    Full Text Available Fragment-based drug discovery (FBDD using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

  3. Fluid-Rock Characterization and Interactions in NMR Well Logging

    Energy Technology Data Exchange (ETDEWEB)

    George J. Hirasaki; Kishore K. Mohanty

    2005-09-05

    The objective of this report is to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity. Oil based drilling fluids can have an adverse effect on NMR well logging if it alters the wettability of the formation. The effect of various surfactants on wettability and surface relaxivity are evaluated for silica sand. The relation between the relaxation time and diffusivity distinguishes the response of brine, oil, and gas in a NMR well log. A new NMR pulse sequence in the presence of a field gradient and a new inversion technique enables the T{sub 2} and diffusivity distributions to be displayed as a two-dimensional map. The objectives of pore morphology and rock characterization are to identify vug connectivity by using X-ray CT scan, and to improve NMR permeability correlation. Improved estimation of permeability from NMR response is possible by using estimated tortuosity as a parameter to interpolate between two existing permeability models.

  4. Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons

    International Nuclear Information System (INIS)

    Roder, H.; Wuethrich, K.

    1986-01-01

    A method to be used for experimental studies of protein folding introduced by Schmid and Baldwin, which is based on the competition between amide hydrogen exchange and protein refolding, was extended by using rapid mixing techniques and 1 H NMR to provide site-resolved kinetic information on the early phases of protein structure acquisition. In this method, a protonated solution of the unfolded protein is rapidly mixed with a deuterated buffer solution at conditions assuring protein refolding in the mixture. This simultaneously initiates the exchange of unprotected amide protons with solvent deuterium and the refolding of protein segments which can protect amide groups from further exchange. After variable reaction times the amide proton exchange is quenched while folding to the native form continues to completion. By using 1 H NMR, the extent of exchange at individual amide sites is then measured in the refolded protein. Competition experiments at variable reaction times or variable pH indicate the time at which each amide group is protected in the refolding process. This technique was applied to the basic pancreatic trypsin inhibitor, for which sequence-specific assignments of the amide proton NMR lines had previously been obtained. For eight individual amide protons located in the beta-sheet and the C-terminal alpha-helix of this protein, apparent refolding rates in the range from 15 s-1 to 60 s-1 were observed. These rates are on the time scale of the fast folding phase observed with optical probes

  5. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

    Science.gov (United States)

    Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

    2015-12-01

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  6. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  7. A portable Halbach magnet that can be opened and closed without force: the NMR-CUFF.

    Science.gov (United States)

    Windt, Carel W; Soltner, Helmut; van Dusschoten, Dagmar; Blümler, Peter

    2011-01-01

    Portable equipment for nuclear magnetic resonance (NMR) is becoming increasingly attractive for use in a variety of applications. One of the main scientific challenges in making NMR portable is the design of light-weight magnets that possess a strong and homogeneous field. Existing NMR magnets can provide such magnetic fields, but only for small samples or in small regions, or are rather heavy. Here we show a simple yet elegant concept for a Halbach-type permanent magnet ring, which can be opened and closed with minimal mechanical force. An analytical solution for an ideal Halbach magnet shows that the magnetic forces cancel if the structure is opened at an angle of 35.3° relative to its poles. A first prototype weighed only 3.1 kg, and provided a flux density of 0.57 T with a homogeneity better than 200 ppm over a spherical volume of 5mm in diameter without shimming. The force needed to close it was found to be about 20 N. As a demonstration, intact plants were imaged and water (xylem) flow measured. Magnets of this type (NMR-CUFF = Cut-open, Uniform, Force Free) are ideal for portable use and are eminently suited to investigate small or slender objects that are part of a larger or immobile whole, such as branches on a tree, growing fruit on a plant, or non-metallic tubing in industrial installations. This new concept in permanent-magnet design enables the construction of openable, yet strong and homogeneous magnets, which aside from use in NMR or MRI could also be of interest for applications in accelerators, motors, or magnetic bearings. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  9. Straightforward and complete deposition of NMR data to the PDBe

    International Nuclear Information System (INIS)

    Penkett, Christopher J.; Ginkel, Glen van; Velankar, Sameer; Swaminathan, Jawahar; Ulrich, Eldon L.; Mading, Steve; Stevens, Tim J.; Fogh, Rasmus H.; Gutmanas, Aleksandras; Kleywegt, Gerard J.; Henrick, Kim; Vranken, Wim F.

    2010-01-01

    We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.htmlhttp://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html.

  10. Interaction of the Saccharomyces cerevisiae α-factor with phospholipid vesicles as revealed by proton and phosphorus NMR

    International Nuclear Information System (INIS)

    Jelicks, L.A.; Broido, M.S.; Becker, J.M.; Naider, F.R.

    1989-01-01

    Proton and phosphorus-31 nuclear magnetic resonance ( 1 H and 31 P NMR) studies of the interaction between a tridecapeptide pheromone, the α-factor of Saccharomyces cerevisiae, and sonicated lipid vesicles are reported. 31 P NMR studies demonstrate that there is interaction of the peptide with the phosphorus headgroups, and quasielastic light scattering (QLS) studies indicate that lipid vesicles increase in size upon addition of peptide. Previous solution (aqueous and DMSO) studies from this laboratory indicate that α-factor is highly flexible with only one long-lived identifiable structural feature, a type II β-turn spanning the central portion of the peptide. Two-dimensional (2D) 1 H nuclear Overhauser effect spectroscopy (NOESY) studies demonstrate a marked ordering of the peptide upon interaction with lipid, suggesting a compact N-terminus, in addition to a stabilized β-turn. In contrast to these results in both solution and lipid environment, Wakamatsu et al. proposed a lipid environment conformation, on the basis of one-dimensional transferred NOE studies in D 2 O, which does not include the β-turn

  11. Autonomous driving in NMR.

    Science.gov (United States)

    Perez, Manuel

    2017-01-01

    The automatic analysis of NMR data has been a much-desired endeavour for the last six decades, as it is the case with any other analytical technique. This need for automation has only grown as advances in hardware; pulse sequences and automation have opened new research areas to NMR and increased the throughput of data. Full automatic analysis is a worthy, albeit hard, challenge, but in a world of artificial intelligence, instant communication and big data, it seems that this particular fight is happening with only one technique at a time (let this be NMR, MS, IR, UV or any other), when the reality of most laboratories is that there are several types of analytical instrumentation present. Data aggregation, verification and elucidation by using complementary techniques (e.g. MS and NMR) is a desirable outcome to pursue, although a time-consuming one if performed manually; hence, the use of automation to perform the heavy lifting for users is required to make the approach attractive for scientists. Many of the decisions and workflows that could be implemented under automation will depend on the two-way communication with databases that understand analytical data, because it is desirable not only to query these databases but also to grow them in as much of an automatic manner as possible. How these databases are designed, set up and the data inside classified will determine what workflows can be implemented. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Bentonite pore structure based on SAXS, chloride exclusion and NMR studies

    International Nuclear Information System (INIS)

    Muurinen, A.; Carlsson, T.

    2013-11-01

    Water-saturated bentonite is planned to be used in many countries as an important barrier component in high-level nuclear waste (HLW) repositories. Knowledge about the microstructure of the bentonite and the distribution of water between interlayer and non-interlayer pores is important for modelling of long-term processes. In this work the microstructure of water-saturated samples prepared from Na montmorillonite, Ca-montmorillonite, sodium bentonite MX-80 and calcium bentonite Deponit CaN were studied with nuclear magnetic resonance (NMR) and small-angle xray scattering spectroscopy (SAXS). The sample dry densities ranged between 0.3 and 1.6 g/cm 3 . The NMR technique was used to get information about the volumes of different water types in the bentonite samples. The results were obtained using 1H NMR spin-lattice T 1ρ relaxation time measurements using the short inter-pulse method. The interpretation of the NMR results was made by fitting distributions of exponentials to observed decay curves. The SAXS measurements were used to get information about the size distribution of the interlayer distance of montmorillonite. The chloride porosity measurements and Donnan exclusion calculations were used together with the SAXS results for evaluation of the bentonite microstructure. The NMR studies and SAXS studies coupled with Cl porosity measurements provided very similar pictures of how the porewater is divided in interlayer and non-interlayer water in MX-80 bentonite. In the case where MX-80 of a dry density 1.6 g/cm 3 was equilibrated with 0.1 M NaCl solution, the results indicated an interlayer porosity of 30 % and non-interlayer porosity of 12 %. The interlayer space mainly contained two water layers but also spaces with more water layers were present. The average size of the non-interlayer pores was evaluated to be 120 - 150 A. From the montmorillonite surface area 98 % was interlayer and 2 % non-interlayer. Evaluation of the interlayer and non

  13. Combined chemometric analysis of (1)H NMR, (13)C NMR and stable isotope data to differentiate organic and conventional milk.

    Science.gov (United States)

    Erich, Sarah; Schill, Sandra; Annweiler, Eva; Waiblinger, Hans-Ulrich; Kuballa, Thomas; Lachenmeier, Dirk W; Monakhova, Yulia B

    2015-12-01

    The increased sales of organically produced food create a strong need for analytical methods, which could authenticate organic and conventional products. Combined chemometric analysis of (1)H NMR-, (13)C NMR-spectroscopy data, stable-isotope data (IRMS) and α-linolenic acid content (gas chromatography) was used to differentiate organic and conventional milk. In total 85 raw, pasteurized and ultra-heat treated (UHT) milk samples (52 organic and 33 conventional) were collected between August 2013 and May 2014. The carbon isotope ratios of milk protein and milk fat as well as the α-linolenic acid content of these samples were determined. Additionally, the milk fat was analyzed by (1)H and (13)C NMR spectroscopy. The chemometric analysis of combined data (IRMS, GC, NMR) resulted in more precise authentication of German raw and retail milk with a considerably increased classification rate of 95% compared to 81% for NMR and 90% for IRMS using linear discriminate analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Proton NMR relaxation in hydrous melts

    International Nuclear Information System (INIS)

    Braunstein, J.; Bacarella, A.L.; Benjamin, B.M.; Brown, L.L.; Girard, C.

    1976-01-01

    Pulse and continuous wave NMR measurements are reported for protons in hydrous melts of calcium nitrate at temperatures between -4 and 120 0 C. Although measured in different temperature ranges, spin-lattice (T 1 ) and spin-spin (T 2 ) relaxation times appear to be nearly equal to each other and proportional to the self-diffusion coefficients of solute metal cations such as Cd 2+ . At temperatures near 50 0 C, mean Arrhenius coefficients Δ H/sub T 1 / (kcal/mol) are 7.9, 7.3, and 4.8, respectively, for melts containing 2.8, 4.0, and 8.0 moles of water per mole of calcium nitrate, compared to 4.6 kcal/mol for pure water. Temperature dependence of T 1 and T 2 in Ca(NO 3 ) 2 -2.8 H 2 O between -4 and 120 0 C are non-Arrhenius and can be represented by a Fulcher-type equation with a ''zero mobility temperature'' (T 0 ) of 225 0 K, close to the value of T 0 for solute diffusion, electrical conductance and viscosity. Resolution of the relaxation rates into correlation times for intramolecular (rotational) and intermolecular (translational) diffusional motion is discussed in terms of the Bloembergen-Purcell-Pound and more recent models for dipolar relaxation

  15. Three-dimensional solution structure of Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Gong, Y; Kao, J L; Krishnamoorthi, R

    1995-04-18

    The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made for all the main-chain and most of the side-chain hydrogens. Stereospecific assignments were also made for some of the beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens. The ring conformations of all six prolines in the inhibitor were determined on the basis of 1H-1H vicinal coupling constant patterns; most of the proline ring hydrogens were stereospecifically assigned on the basis of vicinal coupling constant and intraresidue nuclear Overhauser effect (NOE) patterns. Distance constraints were determined on the basis of NOEs between pairs of hydrogens. Dihedral angle constraints were determined from estimates of scalar coupling constants and intraresidue NOEs. On the basis of 727 interproton distance and 111 torsion angle constraints, which included backbone phi angles and side-chain chi 1, chi 2, chi 3, and chi 4 angles, 22 structures were calculated by a distance geometry algorithm and refined by energy minimization and simulated annealing methods. Both main-chain and side-chain atoms are well-defined, except for a loop region, two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 22 individual structures and the mean structure obtained by averaging their coordinates is 0.58 +/- 0.06 A for the main-chain atoms and 1.01 +/- 0.07 A for all the non-hydrogen atoms of residues 3-40 and 49-67. These structures were compared to the X-ray crystallographic structure of another protein of the same inhibitor family-chymotrypsin inhibitor-2 from barley seeds [CI-2; McPhalen, C. A., & James, M. N. G. (1987) Biochemistry 26

  16. nmr spectroscopic study and dft calculations of giao nmr shieldings

    African Journals Online (AJOL)

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    3Department of Physics, Arts and Science Faculty, Dumlupinar University, Kütahya, ... 1H, 13C NMR chemical shifts and 1JCH coupling constants of .... then estimated using the corresponding TMS shieldings calculated in advance at the same.

  17. Two-dimensional NMR spectrometry

    International Nuclear Information System (INIS)

    Farrar, T.C.

    1987-01-01

    This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t 0 ; an evolution period, t 1 ; and a detection period, t 2

  18. 1H-NMR/13C-NMR studies of branched structures in PVC obtained at atmospheric pressure

    International Nuclear Information System (INIS)

    Braun, D.; Holzer, G.; Hjertberg, T.

    1981-01-01

    The 1 H-NMR-spectra of raw poly (vinyl cloride) obtained at atmospheric pressure (U-PVC) have revealed the presence of high concentrations of branches. The content of labile chlorine was determined by reaction with phenole in order to estimate the branch points with tertiary chlorine. The branch length of reductively dehalogenated U-PVC by 13 C-NMR analysis have provided evidence for both short chain branches including chloromethyl groups and 2.4-dichloro-n-butyl groups and long chain branching. For a number of U-polymers the total amount of branching ranges from 7.5 to 13.5/1000 C. The 13 C-NMR measurements point to a ratio of methyl/butyl branches of 1:1 and short chains/long chains of 6:1. (orig.)

  19. Introduction to some basic aspects of NMR

    International Nuclear Information System (INIS)

    Goldman, M.

    1992-01-01

    The principal interactions are reviewed that are experienced by nuclear spins making magnetic resonance feasible and which disturb it in a way that gives access to the properties of bulk matter. The interactions leading to NMR include Zeeman interaction, dipole-dipole interactions, and exchange interactions. Spin-lattice relaxation relevant to NMR is revisited next. It is followed by an overview of spin temperature. Finally, the care of periodic Hamiltonian is discussed in detail as another contribution to NMR. (R.P.) 48 refs., 12 figs

  20. An Inversion Recovery NMR Kinetics Experiment

    Science.gov (United States)

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  1. $\\beta$-NMR of copper isotopes in ionic liquids

    CERN Multimedia

    We propose to test the feasibility of spin-polarization and $\\beta$-NMR studies on several short-lived copper isotopes, $^{58}$ Cu, $^{74}$Cu and $^{75}$Cu in crystals and liquids. The motivation is given by biological studies of Cu with $\\beta$-NMR in liquid samples, since Cu is present in a large number of enzymes involved in electron transfer and activation of oxygen. The technique is based on spin-polarization via optical pumping in the new VITO beamline. We will use the existing lasers, NMR magnet and NMR chambers and we will prepare a new optical pumping system. The studies will be devoted to tests of achieved $\\beta$-asymmetry in solid hosts, the behaviour of asymmetry when increasing vacuum, and finally NMR scans in ionic liquids. The achieved spin polarization will be also relevant for the plans to measure with high precision the magnetic moments of neutron-rich Cu isotopes.

  2. Tensiometric, fluorescence and 1H NMR study of mixed micellization of non-steroidal anti-inflammatory drug sodium salt of ibuprofen in the presence of non-ionic surfactant in aqueous/urea solutions

    International Nuclear Information System (INIS)

    Rub, Malik Abdul; Khan, Farah; Sheikh, Mohmad Shafi; Azum, Naved; Asiri, Abdullah M.

    2016-01-01

    Highlights: • Interaction between (IBF + TX-100) mixtures has been investigated. • (IBF + TX-100) mixtures exhibit synergistic behavior. • Urea increases the surface charge of the micelles resulting halt of the micelles formation. • N agg , K sv and dielectric constant of mixed systems have also been evaluated. • 1 H NMR data suggested that IBF and TX-100 interacts through hydrophobic as well as hydrophillic interaction. - Abstract: The desirable surface/bulk properties for specific applications of drug sodium salt of ibuprofen (IBF) and Triton X-100 (TX-100) can be achieved by adjusting mainly the composition of these systems. The interactions of anionic drug IBF with non-ionic surfactant TX-100 micelles have been investigated using tensiometry, fluorometry and 1 H NMR in aqueous as well in 250 mmol⋅kg −1 urea solutions. Different theoretical models like Clint, Rubingh, and Rosen, etc. were utilized to get information about the nature of interaction between these two in bulk and at the interface. These models disclose that the non-ideal behavior with attractive interaction in bulk and at the interface exists. The steady-state fluorescence quenching study was employed to evaluate micelle aggregation numbers (N agg ), which signify the involvement of surfactant was forever higher compared to IBF. Stern–Volmer binding constants (K sv ), micropolarity (I 1 /I 3 ) and dielectric constant (D exp ) of the mixtures are also obtained using fluorescence method. By the addition of urea raise in the surface charge of the micelles was observed followed by halt of the micellization of drug and surfactant as well as their mixture, therefore cmc values increases followed by decrease in aggregation number. The 1 H NMR resonance intensity variations were paralleled by upfield shifts in the resonance frequencies, due to an increased shielding of IBF happening from closeness of the non-ionic TX-100 surfactant.

  3. Quantification of aluminium-27 NMR spectra of high-surface-area oxides

    International Nuclear Information System (INIS)

    Pearson, R.M.; Schramm, C.M.

    1990-01-01

    This paper discusses the quantitation of 27 Al NMR spectra. It is showns that the so called 'invisible' aluminium atoms seen by recent workers are completely consistent with known continuous wave NMR studies of the 27 Al NMR spectra of high surface area aluminium oxides. The use of pulsed NMR techniques further complicate the quantitative measurement of 27 Al NMR spectra, especially when high resolution NMR spectrometers are used for this purpose. Methods are described which allow both the estimation of aluminium not seen by continuous wave techniques and the amounts of the NMR spectra lost in pulsed work. (author). 24 refs.; 6 figs.; 1 tab

  4. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  5. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP-346487.1 from Streptococcus pneumoniae TIGR4

    Energy Technology Data Exchange (ETDEWEB)

    Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Geralt, Michael; Serrano, Pedro; Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    The NMR structure of the 206-residue protein NP-346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP-346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.

  6. Identification of solution products of lanthanoid (3) diethyldithiocarbamatohexamethyl phosphotriamide compounds from IR, electron and sup 1 H, sup 13 C, sup 31 P NMR absorption spectra. Identifikatsiya produktov rastvoreniya diehtilditiokarbamatogeksametil fosfotriamidnykh soedinenij lantanoidov (3) po IK, ehlektronnym i YaMR sup 1 H, sup 13 C, sup 31 P spektram pogloshcheniya

    Energy Technology Data Exchange (ETDEWEB)

    Skopenko, V V; Savost' yanova, A F; Trachevskij, V V; Gorbalyuk, A D; Sukhan, T A [Kievskij Gosudarstvennyj Univ., Kiev (Ukrainian SSR)

    1991-01-01

    By the methods of conductometry, IR, electron and {sup 1}H, {sup 13}C, {sup 31}P NMR spectroscopy nonaqueous solutions of the compounds (La(S{sub 2}CNEt{sub 2})Hmpa{sub 5})(BPh{sub 4}){sub 2}, Hmpa=OP(NMe{sub 2}){sub 3}; (Ln(S{sub 2}CNEt{sub 2}){sub 2}Hmpa{sub 3})BPh{sub 4}, Ln=Y, La-Lu; (Ln(S{sub 2}CNEt{sub 2}){sub 3}Hmpa{sub 2}), Ln=La-Gd, have been investigated. It is ascertained that bis-dithiocarbamate compounds are dissolved in all the studied solvents with preservation of composition and structure of lanthanide (3) inner coordination sphere. Tris-dithiocarbamates in nonaqueous solutions are subjected to reactions of ligand redistribution according to schemes depending on the solvent nature. In the process of dissolving of lanthanum monodithiocarbamate bond isomerization of dithiocarbamate groups occurs, which is pronounced in splitting of {sup 1}H and {sup 13}C NMR signals.

  7. Use of NMR as an online sensor in industrial processes

    International Nuclear Information System (INIS)

    Andrade, Fabiana Diuk de

    2012-01-01

    Nuclear magnetic resonance (NMR) is one of the most versatile analytical techniques for chemical, biochemical and medical applications. Despite this great success, NMR is seldom used as a tool in industrial applications. The first application of NMR in flowing samples was published in 1951. However, only in the last ten years Flow NMR has gained momentum and new and potential applications have been proposed. In this review we present the historical evolution of flow or online NMR spectroscopy and imaging, and current developments for use in the automation of industrial processes. (author)

  8. A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

    Science.gov (United States)

    Lu, George J; Son, Woo Sung; Opella, Stanley J

    2011-04-01

    A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. NMR study of the possible interaction in solution of angiotensin II with a peptide encoded by angiotensin II complementary RNA

    International Nuclear Information System (INIS)

    Eaton, H.L.; Fesik, S.W.; Austin, R.E.; Martin, S.F.

    1989-01-01

    The potential binding of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) (AII) to a peptide encoded by its complementary RNA (Lys-Gly-Val-Asp-Val-Try-Ala-Val) (IIA) has been studied by monitoring the 1 H NMR spectrum of IIA in aqueous phosphate or Tris·HCl buffer ( 2 H 2 O) as it is titrated with AII. For molar ratios of AII/IIA ranging from 0.2 to 1.8, the NMR spectra are unchanged as compared to the spectra of the isolated peptides. Based on these findings, the K d for the putative biomolecular complex of the two peptides under these conditions is calculated to be >10 -4 M. This result does not support the suggestion of Elton et al. that AII and IIA engage in high-affinity binding (K d ∼ 5 x 10 -8 M) with each other

  10. Characterization of water in hydrated Bombyx mori silk fibroin fiber and films by 2H NMR relaxation and 13C solid state NMR.

    Science.gov (United States)

    Asakura, Tetsuo; Isobe, Kotaro; Kametani, Shunsuke; Ukpebor, Obehi T; Silverstein, Moshe C; Boutis, Gregory S

    2017-03-01

    The mechanical properties of Bombyx mori silk fibroin (SF), such as elasticity and tensile strength, change remarkably upon hydration. However, the microscopic interaction with water is not currently well understood on a molecular level. In this work, the dynamics of water molecules interacting with SF was studied by 2 H solution NMR relaxation and exchange measurements. Additionally, the conformations of hydrated [3- 13 C]Ala-, [3- 13 C]Ser-, and [3- 13 C]Tyr-SF fibers and films were investigated by 13 C DD/MAS NMR. Using an inverse Laplace transform algorithm, we were able to identify four distinct components in the relaxation times for water in SF fiber. Namely, A: bulk water outside the fiber, B: water molecules trapped weakly on the surface of the fiber, C: bound water molecules located in the inner surface of the fiber, and D: bound water molecules located in the inner part of the fiber were distinguishable. In addition, four components were also observed for water in the SF film immersed in methanol for 30s, while only two components for the film immersed in methanol for 24h. The effects of hydration on the conformation of Ser and Tyr residues in the site-specific crystalline and non-crystalline domains of 13 C selectively labeled SF, respectively, could be determined independently. Our measurements provide new insight relating the characteristics of water and the hydration structure of silk, which are relevant in light of current interest in the design of novel silk-based biomaterials. The mechanical properties of Bombyx mori silk fibroin (SF) change remarkably upon hydration. However, the microscopic interaction between SF and water is not currently well understood on a molecular level. We were able to identify four distinct components in the relaxation times for water in SF fiber by 2 H solution NMR relaxation and exchange measurements. In addition, the effects of hydration on the conformation of Ser and Tyr residues in the site-specific crystalline and

  11. Chemical Ligation of Folded Recombinant Proteins: Segmental Isotopic Labeling of Domains for NMR Studies

    Science.gov (United States)

    Xu, Rong; Ayers, Brenda; Cowburn, David; Muir, Tom W.

    1999-01-01

    A convenient in vitro chemical ligation strategy has been developed that allows folded recombinant proteins to be joined together. This strategy permits segmental, selective isotopic labeling of the product. The src homology type 3 and 2 domains (SH3 and SH2) of Abelson protein tyrosine kinase, which constitute the regulatory apparatus of the protein, were individually prepared in reactive forms that can be ligated together under normal protein-folding conditions to form a normal peptide bond at the ligation junction. This strategy was used to prepare NMR sample quantities of the Abelson protein tyrosine kinase-SH(32) domain pair, in which only one of the domains was labeled with 15N Mass spectrometry and NMR analyses were used to confirm the structure of the ligated protein, which was also shown to have appropriate ligand-binding properties. The ability to prepare recombinant proteins with selectively labeled segments having a single-site mutation, by using a combination of expression of fusion proteins and chemical ligation in vitro, will increase the size limits for protein structural determination in solution with NMR methods. In vitro chemical ligation of expressed protein domains will also provide a combinatorial approach to the synthesis of linked protein domains.

  12. 19F NMR studies of 5-fluorouracil-substituted Escherichia coli transfer RNAs: solution structure and codon-anticodon interaction

    International Nuclear Information System (INIS)

    Gollnick, P.D.

    1986-01-01

    19 F NMR was used to study E. coli tRNA 1 /sup Val/, tRNA/sub f//sup Met/, and tRNA/sub m//Met/, in which 5-fluorouracil (FUra) has replaced uracil and uracil-derived minor bases. 19 F NMR spectra of these tRNAs resolve resonances from nearly all the incorporated FUra residues. Each of the three tRNAs can be resolved into two isoaccepting species, termed forms A and B, whose 19 F spectra differ in the shift of one 19 F peak from ca. 4.5 ppm in form B, upfield to -15 ppm in form A. Because the two isoacceptors of each tRNA differ only at one position, the peaks at 4.5 ppm in the spectra of (FUra)tRNA 1 /sup Val/ and (FUra)tRNA/sub m//sup Met/; are assigned to FUra 17 and Fura 20 respectively. Bisulfate modification and pH dependence indicate that 19 F signals in the central region of the spectrum of (FUra)tRNA 1 /sup Val/ correspond to fluorouracils in non-base-paired regions. Photoreaction with psoralen indicates upfield 19 F signals arise from residues in helical environments. Removal of magnesium or addition of NaCl produces major, reversible changes in the 19 F spectrum of fluorinated tRNAs. Studies of manganese and spermine binding to (FUra)tRNA 1 /sup Val/ allow localization of several resonances in the 18 F spectrum to regions near putative binding sites for these ions. Binding of the codon G/sub p/U/sub p/A causes an upfield shift of a 19 F resonance at 3.9 ppm in the spectrum of (FUra)tRNA 1 /sup Val/. G/sub p/U/sub p/A/sub p/A, which is complementary to the anticodon and 5'-adjacent FUra 33, shifts an additional 19 F peak at 4.5 ppm. 1 H NMR and RNase H digestion studies show that the oligonucleotides bind to the anticodon

  13. NMR examinations of the facial skeleton. Pt. 1

    International Nuclear Information System (INIS)

    Grodd, W.; Lenz, M.; Baumann, R.; Schroth, G.

    1984-01-01

    The resolution of NMR and CT was compared using axial sections of the normal anatomic structures of the facial skeleton. Is was shown that NMR was superior in differentiating muscles, tonsils, mucosa, lymph nodes and blood vessels. The demonstration of bone and its differentiation from air-containing spaces is often difficult. Metallic, non-ferromagnetic dental fillings, which cause serious artefacts on CT, do not after NMR. (orig.) [de

  14. Spectroscopic effects in 1H and 13C NMR spectra of 4,4'-di-substituted 3,3'-diquinolines sulfides

    International Nuclear Information System (INIS)

    Pluta, K.

    1994-01-01

    The 1 H and 13 C NMR spectra of 4,4'-disubstituted sulfides of 3,3'-quinolines have been studied in CDCl 3 solutions. The observed spectroscopic effects have been interpreted in terms of molecule structure and configuration. The factors being responsible for the value of spectroscopic effects have been discussed

  15. Nuclear magnetic resonance (NMR) imaging in the diagnosis of liver disease. Differential diagnosis of hepatic tumors and correlation between NMR imaging and histological findings

    Energy Technology Data Exchange (ETDEWEB)

    Ebara, Masaaki; Oto, Masao; Sugiura, Nobuyuki; Kimura, Kunio; Okuda, Kunio; Hirooka, Noboru; Ikehira, Hiroo; Fukuda, Nobuo; Tateno, Yukio

    1984-06-01

    Characteristics of nuclear magnetic resonance (NMR) images for various liver diseases were examined using a 0.1 T resistive NMR imaging unit on 26 patients with liver disease and 10 normal volunteers. Hepatic tumors, including small hepatocellular carcinoma 1.5 cm in diameter, were detected on NMR imaging. Ring sign characteristic of nodular type hepatocellular carcinoma was shown on NMR-CT in 60 % of patients. T/sub 1/ values allowed differential diagnosis of hepatic tumors. There was close correlation between NMR images and histopathological findings. The T/sub 1/ in the liver and spleen was more prolonged in patients with liver cirrhosis than in normal volunteers, with significant differences. (Namekawa, K.).

  16. NMR imaging of soft tissue tumors

    International Nuclear Information System (INIS)

    Laval-Jeantet, M.; Tobolsk, F.; Delepine, N.; Delepine, G.; Roger, B.; Cabanis, E.A.

    1986-01-01

    Preliminary findings on NMR imaging of 30 soft tissue tumors demonstrated the indispensable value of this examination (particularly when a surface antenna is used) for preoperative investigation and diagnosis of tumoral recurrence when compared with other radiologic techniques. The possible potential of NMR imaging for characterization of tissues, apart from lipoma or liposarcoma, cannot be evaluated at the present time [fr

  17. Solid state NMR of spin-1/2 nuclei

    International Nuclear Information System (INIS)

    Wind, R.A.

    1991-01-01

    The detection of nuclear magnetic resonance by Bloch et al. and Purcell and co-workers in 1946 has led to the development of one of the most powerful spectroscopic techniques known today. The reason is that, besides the applied external magnetic field, a nuclear spin also experiences extra local magnetic fields, which are due to surrounding electron clouds (the chemical shift) and other spins. These local fields differ for nuclei located at chemically different positions in a molecule. The result is that an NMR spectrum often consists of several lines, which can be considered to be a fingerprint of the material under investigation an can assist the clarifying its molecular structure. NMR has been especially successful in liquids and liquid like materials, where fast molecular tumblings average out the anisotropies in the local fields, resulting in well-resolved NMR spectra. This paper reports that initially the development of solid-state NMR was less dramatic. Originally, for reasons of sensitivity, attention was focused mainly on 1 H NMR. The result is that the NMR spectrum usually consists of single, broad, featureless line, which, except for special cases such as more or less isolated spin pairs or methyl groups, does not provide much information

  18. NMR Phase Noise in Bitter Magnets

    Science.gov (United States)

    Sigmund, E. E.; Calder, E. S.; Thomas, G. W.; Mitrović, V. F.; Bachman, H. N.; Halperin, W. P.; Kuhns, P. L.; Reyes, A. P.

    2001-02-01

    We have studied the temporal instability of a high field resistive Bitter magnet through nuclear magnetic resonance (NMR). This instability leads to transverse spin decoherence in repeated and accumulated NMR experiments as is normally performed during signal averaging. We demonstrate this effect via Hahn echo and Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation experiments in a 23-T resistive magnet. Quantitative analysis was found to be consistent with separate measurements of the magnetic field frequency fluctuation spectrum, as well as with independent NMR experiments performed in a magnetic field with a controlled instability. Finally, the CPMG sequence with short pulse delays is shown to be successful in recovering the intrinsic spin-spin relaxation even in the presence of magnetic field temporal instability.

  19. NMR spectroscopy

    International Nuclear Information System (INIS)

    Gruenert, J.

    1989-01-01

    The book reviews the applications of NMR-spectroscopy in medicine and biology. The first chapter of about 40 pages summarizes the history of development and explains the chemical and physical fundamentals of this new and non-invasive method in an easily comprehensible manner. The other chapters summarize diagnostic results obtained with this method in organs and tissues, so that the reader will find a systematic overview of the available findings obtained in the various organ systems. It must be noted, however, that ongoing research work and new insight quite naturally will necessitate corrections to be done, as is the case here with some biochemical interpretations which would need adjustment to latest research results. NMR-spectroscopy is able to measure very fine energy differences on the molecular level, and thus offers insight into metabolic processes, with the advantage that there is no need of applying ionizing radiation in order to qualitatively or quantitatively analyse the metabolic processes in the various organ systems. (orig./DG) With 40 figs., 4 tabs [de

  20. NMR studies of proton exchange kinetics in aqueous formaldehyde solutions.

    Science.gov (United States)

    Rivlin, Michal; Eliav, Uzi; Navon, Gil

    2014-05-01

    Aqueous solutions of formaldehyde, formalin, are commonly used for tissue fixation and preservation. Treatment with formalin is known to shorten the tissue transverse relaxation time T2. Part of this shortening is due to the effect of formalin on the water T2. In the present work we show that the shortening of water T2 is a result of proton exchange between water and the major constituent of aqueous solutions of formaldehyde, methylene glycol. We report the observation of the signal of the hydroxyl protons of methylene glycol at 2ppm to high frequency of the water signal that can be seen at low temperatures and at pH range of 6.0±1.5 and, at conditions where it cannot be observed by the single pulse experiment, it can be detected indirectly through the water signal by the chemical exchange saturation transfer (CEST) experiment. The above finding made it possible to obtain the exchange rate between the hydroxyl protons of the methylene glycol and water in aqueous formaldehyde solutions, either using the dispersion of the spin-lattice relaxation rate in the rotating frame (1/T1ρ) or, at the slow exchange regime, from the line width hydroxyl protons of methylene glycol. The exchange rate was ∼10(4)s(-1) at pH 7.4 and 37°C, the activation energy, 50.2kJ/mol and its pH dependence at 1.1°C was fitted to: k (s(-1))=520+6.5×10(7)[H(+)]+3.0×10(9)[OH(-)]. Copyright © 2014. Published by Elsevier Inc.