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Sample records for nmr structural study

  1. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1989-01-01

    This report covers the progress made on the title project during the past reporting period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines the authors are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. The effects of very high MAS rates (>10 kHz) on cross polarization dynamics are also being investigated for similar reasons. The authors have been reinvestigating the prospects of using zero field NMR types of techniques for two dimensional NMR structural analysis of complex organic solids such as coals. Currently MAS spin rates are not sufficiently high to permit zero field in high field NMR for protons in typical organic solids, however they are compatible with {sup 13}C-{sup 13}C dipolar couplings. In collaboration with Dr. Robert Tycko of AT T Bell Laboratories, inventor of the zero field in high field NMR method, the authors have performed the first zero field in high field {sup 13}C NMR experiments. These results are described. 9 refs., 2 figs.

  2. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1989-01-01

    This report covers the progress made on the title project and summarizes the accomplishments for the project period. Four major areas of inquiry have been pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concern how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines we are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. The effects of very high MAS rates (>10 kHz) on cross polarization dynamics are also being investigated for similar reasons. During the last quarter the authors have concentrated on improvements in cross polarization (CP) sequences with a goal of making the CP process insensitive to experimental conditions such as the magic angle spinning (MAS) rate. In order to be able to use fields the order of 7.0 T or higher, CP efficiency must be maintained at MAS rates of over 10 kHz. The standard sequences have severe limitations at these rates which lead to intensity distortions in {sup 13}C CPMAS spectra. Thus in order to be able to take advantage of the increases in sensitivity and resolution that accompany high field operation, improvements in the NMR methods are required. The new sequences the authors are developing will be especially important for quantitative analysis of coal structure by {sup 13}C solid state NMR at high field strengths. 13 refs., 7 figs., 2 tabs.

  3. Structural Studies of Biological Solids Using NMR

    NASA Astrophysics Data System (ADS)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  4. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1988-01-01

    This report covers the progress made on the title project during the current reporting period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines we are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. This quarter we have focused on variable temperature spin lattice relaxation measurements for several of the Argonne coals. 5 figs.

  5. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1988-01-01

    This report covers the progress made on the title project during the current reporting period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines we are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. This quarter we have focussed on spin lattice relaxation measurements for several of the Argonne coals. 2 figs., 1 tab.

  6. NMR studies of protein structure and dynamics

    NASA Astrophysics Data System (ADS)

    Kay, Lewis E.

    2011-12-01

    Recent advances in solution NMR spectroscopy have significantly extended the spectrum of problems that can now be addressed with this technology. In particular, studies of proteins with molecular weights on the order of 100 kDa are now possible at a level of detail that was previously reserved for much smaller systems. An example of the sort of information that is now accessible is provided in a study of malate synthase G, a 723 residue enzyme that has been a focal point of research efforts in my laboratory. Details of the labeling schemes that have been employed and optimal experiments for extraction of structural and dynamics information on this protein are described. NMR studies of protein dynamics, in principle, give insight into the relation between motion and function. A description of deuterium-based spin relaxation methods for the investigation of side chain dynamics is provided. Examples where millisecond (ms) time scale dynamics play an important role and where relaxation dispersion NMR spectroscopy has been particularly informative, including applications involving the membrane enzyme PagP and mutants of the Fyn SH3 domain that fold on a ms time scale, are presented.

  7. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1990-01-01

    This report covers the progress made on the title project and summarizes the accomplishments for the project period. Four major areas of inquiry have been pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines the authors are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. The effects of very high MAS rates (>10 kHz) on cross polarization dynamics are also being investigated for similar reasons. The authors have concentrated on a theoretical treatment of pairs of tightly coupled spin {1/2} nuclei under magic angle spinning conditions. The average Hamiltonian theory developed here is required for a quantitative understanding of two dimensional NMR experiments of such spin pairs in solids. These experiments in turn provide a means of determining connectivities between resonances in solid state NMR spectra. Development of these techniques will allow us to establish connectivities between functional components in coals. The complete description of these spin dynamics has turned out to be complex, and is necessary to provide a foundation upon which such experiments may be quantitatively interpreted in complex mixtures such as coals. 25 refs., 4 figs., 3 tabs.

  8. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1989-01-01

    This report covers the progress made on the title project and summarizes the accomplishments for the project period. Four major areas of inquiry have been pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coal models. Along the same lines the author are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. The effects of very high MAS rates (>10 kHz) on cross polarization dynamics are also being investigated for similar reasons. During the last quarter the authors has concentrated on improvements in cross polarization (CP) sequences with a goal of making the CP process insensitive to experimental conditions such as the Hartmann-Hahn mismatch. It has been found that the usual theories of CP are incorrect, and that the CP process is very heterogeneous in nature. This has significant implications on methods typically used in quantifying {sup 13}C CPMAS spectra of coals. 19 refs., 11 figs.

  9. Isotope labeling for NMR studies of macromolecular structure and interactions

    SciTech Connect

    Wright, P.E.

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  10. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1992-05-27

    This report covers the progress made on the title project for the project period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed a delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  11. NMR techniques in the study of cardiovascular structure and functions

    SciTech Connect

    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.

  12. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1997-03-01

    This report covers the progress made on the title project for the project period. The study of coal chemical structure is a vital component of research efforts to develop better chemical utilization of coals, and for furthering our basic understanding of coal geochemistry. In this grant we are addressing several structural questions pertaining to coals with advances in state of the art solids NMR methods. Our goals are twofold. First, we are interested in developing new methods that will enable us to measure important structural parameters in whole coals not directly accessible by other techniques. In parallel with these efforts we will apply these NMR methods in a study of the chemical differences between gas-sourcing and oil-sourcing coals. The NMR methods work will specifically focus on determination of the number and types of methylene groups, determination of the number and types of methane groups, identification of carbons adjacent to nitrogen and sites with exchangeable protons, and methods to more finely characterize the distribution of hydrogen in coals. The motivation for investigating these specific structural features of coals arises from their relevance to the chemical reactivity of coals, and their suitability for possible correlations with the oil sourcing potential of some types of coals. The coals to be studied and contrasted include oil-prone coals from Australia and Indonesia, those comprising the Argonne Premium Coal Sample bank, and other relevant samples. In this report period we have focused our work on 1 segment of the program. Our last report outlined progress in using our NMR editing methods with higher field operation where higher magic angle spinning rates are required. Significant difficulties were identified, and these have been the main subject of study during the most recent granting period.

  13. NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs

    PubMed Central

    Jeong, Ji-Ho; Kim, Ji-Sun; Choi, Sung-Sub; Kim, Yongae

    2016-01-01

    Lactophoricin (LPcin), a component of proteose peptone (113–135) isolated from bovine milk, is a cationic amphipathic antimicrobial peptide consisting of 23 amino acids. We designed a series of N- or C-terminal truncated variants, mutated analogs, and truncated mutated analogs using peptide-engineering techniques. Then, we selected three LPcin analogs of LPcin-C8 (LPcin-YK1), LPcin-T2WT6W (LPcin-YK2), and LPcin-T2WT6W-C8 (LPcin-YK3), which may have better antimicrobial activities than LPcin, and successfully expressed them in E. coli with high yield. We elucidated the 3D structures and topologies of the three LPcin analogs in membrane environments by conducting NMR structural studies. We investigated the purity of the LPcin analogs and the α-helical secondary structures by performing 1H-15N 2D HSQC and HMQC-NOESY liquid-state NMR spectroscopy using protein-containing micelle samples. We measured the 3D structures and tilt angles in membranes by conducting 15N 1D and 2D 1H-15N SAMMY type solid-state NMR spectroscopy with an 800 MHz in-house-built 1H-15N double-resonance solid-state NMR probe with a strip-shield coil, using protein-containing large bicelle samples aligned and confirmed by molecular-dynamics simulations. The three LPcin analogs were found to be curved α-helical structures, with tilt angles of 55–75° for normal membrane bilayers, and their enhanced activities may be correlated with these topologies. PMID:26789765

  14. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1997-09-01

    This report covers the progress made on the title project for the project period. The study of coal chemical structure is a vital component of research efforts to develop better chemical utilization of coals, and for furthering our basic understanding of coal geochemistry. In this grant we are addressing several structural questions pertaining to coals with advances in state of the art solids NMR methods. The main activity during this granting period was a completion of a detailed comparative analysis of the suite of spectral editing techniques developed in our laboratory for this purpose. The appended report is a manuscript being submitted to the Journal of Magnetic Resonance on this subject.

  15. Solid-State NMR Studies of Amyloid Fibril Structure

    NASA Astrophysics Data System (ADS)

    Tycko, Robert

    2011-05-01

    Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid-state nuclear magnetic resonance (NMR) methods have the unique capability of providing detailed structural constraints for amyloid fibrils, sufficient for the development of full molecular models. In this article, recent progress in the application of solid-state NMR to fibrils associated with Alzheimer's disease, prion fibrils, and related systems is reviewed, along with relevant developments in solid-state NMR techniques and technology.

  16. NMR Study of Organic Counterion Binding to Perfluorinated Micellar Structures

    NASA Astrophysics Data System (ADS)

    Bossev, Dobrin; Matsumoto, Mustuo; Nakahara, Masaru

    2008-03-01

    In this study we have applied our previously developed NMR method to study the adsorption of tetramethylammonium (TMA^+) and tetraethylammonium (TEA^+) counterions to micelles formed by perfluorooctylsulfonate (FOS^-) surfactant in water at 30 C. These two counterions induce formation of threadlike surfactant structures that result in well pronounced viscoelastic properties of the solution. To selectively probe the degree of counterion binding we have used ^1H and ^19F NMR chemical shifts and self-diffusion coefficients that are sensitive to the Stern and diffuse double layers, respectively. The competitive adsorption of TMA^+ and TEA^+ was examined as a function of the TMA^+/TEA^+ ratio at a constant FOS^- concentration of 100 mM. The two counterions were found to form Stern layer around the FOS^- micelles with comparable packing; about one counterion per two micellized FOS molecules. When mixed at intermediate proportions, however, the TEA^+ counterion shows preferential binding; the concentration of TEA^+ in the Stern layer is found to be twice higher than that of TMA^+ at equal total respective concentrations in the solution. These results are discussed in terms of counterion size and hydrophobicity and presented in parallel with those that involved the smaller and more hydrophilic lithium counterion.

  17. NMR structural studies of PECVD amorphous silicon films

    NASA Astrophysics Data System (ADS)

    Cull, Thomas Sidley, Jr.

    The properties of plasma enhanced chemical vapor deposition (PECVD) amorphous semiconductor films vary depending upon preparation conditions and doping. Hydrogenated amorphous silicon films (a-Si:H) have some properties that make these films desirable for use in solar cells and photoreceptor devices. Maximizing electronic and structural properties of such films is key to their success. Nuclear magnetic resonance, and in particular deuterium magnetic resonance (DMR) for a-Si:H,D films, is a useful means to study the morphology of such samples. The location and motions of hydrogen and the chemically equivalent deuterium within an amorphous semiconductor film can be observed with NMR. The information from the NMR studies can be correlated with electronic properties studies to determine whether a given sample would make a successful photovoltaic device. This thesis focuses on three aspects of study: comparison of two samples that differ in the bias applied to the substrate upon which the amorphous films were grown; derivation of relaxation parameters for covalently bonded deuterium; development of a new pulse sequence "incremental spin echo double resonance (SEDOR)" to study the number of unlike spins that contribute to the local field of a given nuclei. Four significant conclusions can be drawn. First, the electronic quality as measured by the photoresponse product etamutau correlates with the broad Gaussian DMR spectral feature which arises from molecular hydrogen in sites that restrict motion. Second, the relaxation of nuclear magnetization under extreme inhomogeneous broadening can be modeled very well as the relaxation without spin diffusion to faster relaxing species within a sample. Third, incremental SEDOR has either a quantum mechanical or classical behavior depending upon the length of the pulse spacing in comparison to the spin-spin relaxation time. Fourth, the local field at the hydrogen of an HD pair within an a-Si:H,D sample is determined on average by

  18. Practical applications of hydrostatic pressure to refold proteins from inclusion bodies for NMR structural studies.

    PubMed

    Ogura, Kenji; Kobashigawa, Yoshihiro; Saio, Tomohide; Kumeta, Hiroyuki; Torikai, Shinnosuke; Inagaki, Fuyuhiko

    2013-06-01

    Recently, the hydrostatic pressure refolding method was reported as a practical tool for solubilizing and refolding proteins from inclusion bodies; however, there have been only a few applications for protein structural studies. Here, we report the successful applications of the hydrostatic pressure refolding method to refold proteins, including the MOE-2 tandem zinc-finger, the p62 PB1 domain, the GCN2 RWD domain, and the mTOR FRB domain. Moreover, the absence of aggregation and the correct folding of solubilized protein samples were evaluated with size exclusion chromatography and NMR experiments. The analyses of NMR spectra for MOE-2 tandem zinc-finger and GCN2 RWD further led to the determination of tertiary structures, which are consistent with those from soluble fractions. Overall, our results indicate that the hydrostatic pressure method is effective for preparing samples for NMR structural studies.

  19. Silver metallation of hen egg white lysozyme: X-ray crystal structure and NMR studies.

    PubMed

    Panzner, Matthew J; Bilinovich, Stephanie M; Youngs, Wiley J; Leeper, Thomas C

    2011-12-14

    The X-ray crystal structure, NMR binding studies, and enzyme activity of silver(I) metallated hen egg white lysozyme are presented. Primary bonding of silver is observed through His15 with secondary bonding interactions coming from nearby Arg14 and Asp87. A covalently bound nitrate completes a four coordinate binding pocket.

  20. NMR Studies of Peroxidases.

    NASA Astrophysics Data System (ADS)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  1. A comprehensive NMR structural study of Titan aerosol analogs: Implications for Titan's atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    He, Chao; Smith, Mark A.

    2014-11-01

    Titan has a thick atmosphere composed primarily of nitrogen and methane. Complex organic chemistry induced by solar ultraviolet radiation and energetic particles, takes place in Titan's upper atmosphere, producing an optically thick reddish brown carbon based haze encircling this moon. The chemistry in Titan's atmosphere and its resulting chemical structures are still not fully understood in spite of a great many efforts being made. In our previous work, we have investigated the structure of the 13C and 15N labeled, simulated Titan haze aerosols (tholin) by NMR and identified several dominant small molecules in the tholin. Here we report our expanded structural investigation of the bulk of the tholin by more comprehensive NMR study. The NMR results show that the tholin materials are dominated by heavily nitrogenated compounds, in which the macromolecular structures are highly branched polymeric or oligomeric compounds terminated in methyl, amine, and nitrile groups. The structural characteristic suggest that the tholin materials are formed via different copolymerization or incorporation mechanisms of small precursors, such as HCN, CH2dbnd NH, NH3 and C2H2. This study helps to understand the formation process of nitrogenated organic aerosols in Titan's atmosphere and their prebiotic implications.

  2. Advanced solids NMR studies of coal structure and chemistry. Progress report, March 1 - September 1, 1996

    SciTech Connect

    Zilm, K.W.

    1996-12-31

    This report covers the progress made on the title project for the project period. The study of coal chemical structure is a vital component of research efforts to develop better chemical utili- zation of coals, and for furthering our basic understanding of coal geochemistry. In this grant we are addressing several structural questions pertaining to coals with advances in state of the art solids NMR methods. Our goals are twofold. First, we are interested in developing new methods that will enable us to measure important structural parameters in whole coals not directly accessible by other techniques. In parallel with these efforts we will apply these NNM methods in a study of the chemical differences between gas-sourcing and oil-sourcing coals. The NMR methods work will specifically focus on determination of the number and types of methylene groups, determination of the number and types of methine groups, identification of carbons adjacent to nitrogen and sites with exchangeable protons, and methods to more finely characterize the distribution of hydrogen in coals. We will also develop NMR methods for probing coal macropore structure using hyperpolarized {sup 29}Xe as a probe, and study the molecular dynamics of what appear to be mobile, CH{sub 2} rich, long chain hydrocarbons. The motivation for investigating these specific structural features of coals arises from their relevance to the chemical reactivity of coals, and their suitability for possible correlations with the oil sourcing potential of some types of coals. The coals to be studied and contrasted include oil-prone coals from Australia and Indonesia, those comprising the Argonne Premium Coal Sample bank, and other relevant samples.

  3. Theoretical and experimental IR, Raman and NMR spectra in studying the electronic structure of 2-nitrobenzoates

    NASA Astrophysics Data System (ADS)

    Świsłocka, R.; Samsonowicz, M.; Regulska, E.; Lewandowski, W.

    2007-05-01

    The influence of lithium, sodium, potassium, rubidium and cesium on the electronic system of the 2-nitrobenzoic acid (2-NBA) was studied. Optimized geometrical structures of studied compounds were calculated by HF, B3PW91, B3LYP methods using 6-311++G ∗∗ basis set. The theoretical IR and NMR spectra were obtained. The vibrational (FT-IR, FT-Raman) and NMR ( 1H and 13C) spectra for 2-nitrobenzoic acid salts of alkali metals were also recorded. The assignment of vibrational spectra was done. Characteristic shifts of band wavenumbers and changes in band intensities along the metal series were observed. Good correlation between the wavenumbers of the vibrational bands in the IR and Raman spectra for 2-nitrobenzoates (2-NB) and ionic potential, electronegativity, atomic mass and affinity of metals were found. The chemical shifts of protons and carbons ( 1H, 13C NMR) in the series of studied alkali metal 2-nitrobenzoates were observed too. The calculated parameters were compared to experimental characteristic of studied compounds.

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

    SciTech Connect

    Volkman, Brian Finley

    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. Structural analysis of molybdo-zinc-phosphate glasses: Neutron scattering, FTIR, Raman scattering, MAS NMR studies

    NASA Astrophysics Data System (ADS)

    Renuka, C.; Shinde, A. B.; Krishna, P. S. R.; Reddy, C. Narayana

    2016-08-01

    Vitreous samples were prepared in the xMoO3-17ZnO-(83-x) NaPO3 with 35 ≥ x ≥ 55 glass forming system by energy efficient microwave heating method. Structural evolution of the vitreous network was monitored as a function of composition by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), Raman scattering, Magic Angle Spin Nuclear magnetic resonance (MAS NMR) and Neutron scattering. Addition of MoO3 to the ZnO-NaPO3 glass leads to a pronounced increase in glass transition temperature (Tg) suggesting a significant increase in network connectivity and strength. In order to analyze FTIR and Raman scattering, a simple structural model is presented to rationalize the experimental observations. A number of structural units are formed due to network modification, and the resulting glass may be characterized by a network polyhedral with different numbers of unshared corners. 31P MAS NMR confirms a clear distinction between structural species having 3, 2, 1, 0 bridging oxygens (BOs). Further, Neutron scattering studies were used to probe the structure of these glasses. The result suggests that all the investigated glasses have structures based on chains of four coordinated phosphate and six coordinated molybdate units, besides, two different lengths of P-O bonds in tetrahedral phosphate units that are assigned to bonds of the P-atom with terminal and bridging oxygen atoms.

  6. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  7. High-resolution /sup 1/H NMR study of the solution structure of alamethicin

    SciTech Connect

    Esposito, G.; Carver, J.A.; Boyd, J.; Campbell, I.D.

    1987-02-24

    A /sup 1/H NMR study of the peptide alamethicin, which forms voltage-gated ion channels in membranes, is described. The molecule was studied in methanol as a function of temperature and pH. A complete assignment of the spectra is given, including several stereospecific assignments. Alamethicin was found to have a structure substantially similar to the crystal although, in solution, the C-terminal dipeptide adopts a somewhat extended conformation. The overall conformation was insensitive to the ionization of the side chain of the ionizable group, Glu-18.

  8. NMR Studies of the Structure and Function of the HIV-1 5'-Leader.

    PubMed

    Keane, Sarah C; Summers, Michael F

    2016-12-21

    The 5'-leader of the human immunodeficiency virus type 1 (HIV-1) genome plays several critical roles during viral replication, including differentially establishing mRNA versus genomic RNA (gRNA) fates. As observed for proteins, the function of the RNA is tightly regulated by its structure, and a common paradigm has been that genome function is temporally modulated by structural changes in the 5'-leader. Over the past 30 years, combinations of nucleotide reactivity mapping experiments with biochemistry, mutagenesis, and phylogenetic studies have provided clues regarding the secondary structures of stretches of residues within the leader that adopt functionally discrete domains. More recently, nuclear magnetic resonance (NMR) spectroscopy approaches have been developed that enable direct detection of intra- and inter-molecular interactions within the intact leader, providing detailed insights into the structural determinants and mechanisms that regulate HIV-1 genome packaging and function.

  9. NMR Studies of the Structure and Function of the HIV-1 5′-Leader

    PubMed Central

    Keane, Sarah C.; Summers, Michael F.

    2016-01-01

    The 5′-leader of the human immunodeficiency virus type 1 (HIV-1) genome plays several critical roles during viral replication, including differentially establishing mRNA versus genomic RNA (gRNA) fates. As observed for proteins, the function of the RNA is tightly regulated by its structure, and a common paradigm has been that genome function is temporally modulated by structural changes in the 5′-leader. Over the past 30 years, combinations of nucleotide reactivity mapping experiments with biochemistry, mutagenesis, and phylogenetic studies have provided clues regarding the secondary structures of stretches of residues within the leader that adopt functionally discrete domains. More recently, nuclear magnetic resonance (NMR) spectroscopy approaches have been developed that enable direct detection of intra- and inter-molecular interactions within the intact leader, providing detailed insights into the structural determinants and mechanisms that regulate HIV-1 genome packaging and function. PMID:28009832

  10. Structural studies of PCU-hydrazones: NMR spectroscopy, X-ray diffractions, and DFT calculations

    NASA Astrophysics Data System (ADS)

    Veljković, Jelena; Šekutor, Marina; Molčanov, Krešimir; Lo, Rabindranath; Ganguly, Bishwajit; Mlinarić-Majerski, Kata

    2011-06-01

    In this article we present a detailed structural investigation for the configurational isomers of PCU-hydrazones. The structural characterization of these hydrazones was performed using NMR spectroscopy, X-ray diffraction analysis and theoretical calculations. The single crystal X-ray structures of PCU-hydrazones 6B and 6C have been solved and used to conclusively confirm the characterization obtained via NMR spectra of a particular isomer. Nuclear magnetic shielding values calculated for 6A-C using DFT calculations were correlated with the experimentally determined chemical shifts. The computed results were found to be in good agreement with the observed 13C NMR values. The computed NMR results helped to ascertain the isomers of PCU-hydrazones 4A-C.

  11. Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Erickson, J.W.; Abad-Zapatero, C.

    1988-11-01

    A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P/sub 2/ and P/sub 3/ sites) of a tightly bound inhibitor of porcine pepsin have bene determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions.

  12. Protein-Inhibitor Interaction Studies Using NMR

    PubMed Central

    Ishima, Rieko

    2015-01-01

    Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies. PMID:26361636

  13. Structural studies of the activation of the two component receiver domain NTRC by multidimensional heteronuclear NMR

    SciTech Connect

    Nohaile, Michael James

    1996-05-01

    Multidimensional heteronuclear NMR spectroscopy was used to investigate the N-terminal domain of the transcriptional enhancer NTRC (NiTrogen Regulatory protein C). This domain belongs to the family of receiver domains of two-component regulatory systems involved in signal transduction. Phosphorylation of NTRC at D54 leads to an activated form of the molecule which stimulates transcription of genes involved in nitrogen regulation. Three and four dimensional NMR techniques were used to determine an intermediate resolution structure of the unphosphorylated, inactive form of the N-terminal domain of NTRC. The structure is comprised of five α-helices and a five-stranded β-sheet in a (β/α)5 topology. Analysis of the backbone dynamics of NTRC indicate that helix 4 and strand 5 are significantly more flexible than the rest of the secondary structure of the protein and that the loops making up the active site are flexible. The short lifetime of phospho-NTRC hampers the study of this form. However, conditions for determining the resonance assignments and, possibly, the three dimensional structure of phosphorylated NTRC have been obtained. Tentative assignments of the phosphorylated form indicate that the majority of the changes that NTRC experiences upon phosphorylation occur in helix 3, strand 4, helix 4, strand 5, and the loop between strand 5 and helix 5 (the 3445 face of NTRC) as well as near the site of phosphorylation. In order to examine a stable, activated form of the protein, constitutively active mutants of NTRC were investigated.

  14. Porous Structure of Pharmaceutical Tablets Studied Using PGSTE-NMR Technique

    NASA Astrophysics Data System (ADS)

    Porion, Patrice; Tchoreloff, Pierre; Busignies, Virginie; Leclerc, Bernard; Evesque, Pierre

    2009-06-01

    The compaction of pharmaceutical tablets at high pressure (250 MPa) is a complex process that depends on the nature of the chemical compound. The purpose of this work is to characterize the porous structure of tablets obtained by uniaxial compaction, the most used process in pharmaceutical technology. First, three pharmaceutical excipients (microcrystalline cellulose, lactose and anhydrous calcium phosphate) were compacted and their compressibility properties determined. Secondly, the study of the self-diffusion process of a molecular fluid inside the pore space was performed by using pulsed-gradient stimulated-echo (PGSTE) NMR method, for tablets compacted under various pressure, in the directions perpendicular and parallel to the compaction axis. The results are used to determine the tortuosity factor and the anisotropy of the porous space of such compacted materials.

  15. 15N NMR study of nitrate ion structure and dynamics in hydrotalcite-like compounds

    USGS Publications Warehouse

    Hou, X.; James, Kirkpatrick R.; Yu, P.; Moore, D.; Kim, Y.

    2000-01-01

    We report here the first nuclear magnetic resonance (NMR) spectroscopic study of the dynamical and structural behavior of nitrate on the surface and in the interlayer of hydrotalcite-like compounds (15NO3--HT). Spectroscopically resolvable surface-absorbed and interlayer NO3- have dramatically different dynamical characteristics. The interlayer nitrate shows a well defined, temperature independent uniaxial chemical shift anisotropy (CS A) powder pattern. It is rigidly held or perhaps undergoes rotation about its threefold axis at all temperatures between -100 ??C and +80 ??C and relative humidities (R.H.) from 0 to 100% at room temperature. For surface nitrate, however, the dynamical behavior depends substantially on temperature and relative humidity. Analysis of the temperature and R.H. dependences of the peak width yields reorieritational frequencies which increase from essentially 0 at -100 ??C to 2.6 ?? 105 Hz at 60 ??C and an activation energy of 12.6 kJ/mol. For example, for samples at R.H. = 33%, the surface nitrate is isotropically mobile at frequencies greater than 105 Hz at room temperature, but it becomes rigid or only rotates on its threefold axis at -100 ??C. For dry samples and samples heated at 200 ??C (R.H. near 0%), the surface nitrate is not isotropically averaged at room temperature. In contrast to our previous results for 35Cl--containing hydrotalcite (35Cl--HT), no NMR detectable structural phase transition is observed for 15NO3--HT. The mobility of interlayer nitrate in HT is intermediate between that of carbonate and chloride.

  16. NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds.

    PubMed

    Ortegón-Reyna, David; Garcías-Morales, Cesar; Padilla-Martínez, Itzia; García-Báez, Efren; Aríza-Castolo, Armando; Peraza-Campos, Ana; Martínez-Martínez, Francisco

    2013-12-31

    An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.

  17. Two dimensional NMR and NMR relaxation studies of coal structure. Progress report, September 13, 1991--December 31, 1991

    SciTech Connect

    Zilm, K.W.

    1992-05-27

    This report covers the progress made on the title project for the project period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed a delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  18. Two dimensional NMR and NMR relaxation studies of coal structure. Progress report, January 1, 1992--March 31, 1992

    SciTech Connect

    Zilm, K.W.

    1992-07-01

    This report covers the progress made on the title project for the project period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed at delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  19. A structural study of epoxidized natural rubber (ENR-50) and its cyclic dithiocarbonate derivative using NMR spectroscopy techniques.

    PubMed

    Hamzah, Rosniza; Bakar, Mohamad Abu; Khairuddean, Melati; Mohammed, Issam Ahmed; Adnan, Rohana

    2012-09-12

    A structural study of epoxidized natural rubber (ENR-50) and its cyclic dithiocarbonate derivative was carried out using NMR spectroscopy techniques. The overlapping (1)H-NMR signals of ENR-50 at δ 1.56, 1.68-1.70, 2.06, 2.15-2.17 ppm were successfully assigned. In this work, the <(13)C-NMR chemical shift assignments of ENR-50 were consistent to the previously reported work. A cyclic dithiocarbonate derivative of ENR-50 was synthesized from the reaction of purified ENR-50 with carbon disulfide (CS(2)), in the presence of 4-dimethylaminopyridine (DMAP) as catalyst at reflux temperature. The cyclic dithiocarbonate formation involved the epoxide ring opening of the ENR-50. This was followed by insertion of the C-S moiety of CS(2) at the oxygen attached to the quaternary carbon and methine carbon of epoxidized isoprene unit, respectively. The bands due to the C=S and C-O were clearly observed in the FTIR spectrum while the (1)H-NMR spectrum of the derivative revealed the peak attributed to the methylene protons had split. The (13)C-NMR spectrum of the derivative further indicates two new carbon peaks arising from the >C=S and quaternary carbon of cyclic dithiocarbonate. All other (1)H- and (13)C-NMR chemical shifts of the derivative remain unchanged with respect to the ENR-50.

  20. NMR studies of ordered structures and valence states in the successive valence-transition system EuPtP

    NASA Astrophysics Data System (ADS)

    Mito, T.; Nishitani, K.; Koyama, T.; Muta, H.; Maruyama, T.; Pristáš, G.; Ueda, K.; Kohara, T.; Mitsuda, A.; Sugishima, M.; Wada, H.

    2014-11-01

    We have studied EuPtP, which undergoes two successive valence transitions at TA˜240 K and TB˜200 K by 31P-nuclear magnetic resonance (NMR) measurements. From the analysis of NMR spectra, we obtained plausible ordered structures and Eu valence states in three phases divided by TA and TB. These ordered structures well explain observed inequivalent P sites and the intensity ratio of the NMR spectra arising from these P sites. The results are also in good accordance with mean Eu valence measured by the x-ray absorption spectroscopy. We also discuss Eu 4 f states and the origin of the transitions from the measurements of nuclear spin lattice relaxation rate and hyperfine coupling constant.

  1. T1BT* structural study of an anti-plasmodial peptide through NMR and molecular dynamics

    PubMed Central

    2013-01-01

    Background T1BT* is a peptide construct containing the T1 and B epitopes located in the 5’ minor repeat and the 3’ major repeat of the central repeat region of the Plasmodium falciparum circumsporozoite protein (CSP), respectively, and the universal T* epitope located in the C-terminus of the same protein. This peptide construct, with B = (NANP)3, has been found to elicit antisporozoite antibodies and gamma-interferon-screening T-cell responses in inbred strains of mice and in outbred nonhuman primates. On the other hand, NMR and CD spectroscopies have identified the peptide B’ = (NPNA)3 as the structural unit of the major repeat in the CSP, rather than the more commonly quoted NANP. With the goal of assessing the structural impact of the NPNA cadence on a proven anti-plasmodial peptide, the solution structures of T1BT* and T1B’T* were determined in this work. Methods NMR spectroscopy and molecular dynamics calculations were used to determine the solution structures of T1BT* and T1B’T*. These structures were compared to determine the main differences and similarities between them. Results Both peptides exhibit radically different structures, with the T1B’T* showing strong helical tendencies. NMR and CD data, in conjunction with molecular modelling, provide additional information about the topologies of T1BT* and T1B’T*. Knowing the peptide structures required to elicit the proper immunogenic response can help in the design of more effective, conformationally defined malaria vaccine candidates. If peptides derived from the CSP are required to have helical structures to interact efficiently with their corresponding antibodies, a vaccine based on the T1B’T* construct should show higher efficiency as a pre-erythrocyte vaccine that would prevent infection of hepatocytes by sporozoites. PMID:23506240

  2. Protein NMR structures refined without NOE data.

    PubMed

    Ryu, Hyojung; Kim, Tae-Rae; Ahn, SeonJoo; Ji, Sunyoung; Lee, Jinhyuk

    2014-01-01

    The refinement of low-quality structures is an important challenge in protein structure prediction. Many studies have been conducted on protein structure refinement; the refinement of structures derived from NMR spectroscopy has been especially intensively studied. In this study, we generated flat-bottom distance potential instead of NOE data because NOE data have ambiguity and uncertainty. The potential was derived from distance information from given structures and prevented structural dislocation during the refinement process. A simulated annealing protocol was used to minimize the potential energy of the structure. The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. Among them, 50 structures were used as a training set to find the optimal "width" parameter in the flat-bottom distance potential functions. In the validation set (the other 84 structures), most of the 12 quality assessment scores of the refined structures were significantly improved (total score increased from 1.215 to 2.044). Moreover, the secondary structure similarity of the refined structure was improved over that of the original structure. Finally, we demonstrate that the combination of two energy potentials, statistical torsion angle potential (STAP) and the flat-bottom distance potential, can drive the refinement of NMR structures.

  3. Layered structure of room-temperature ionic liquids in microemulsions by multinuclear NMR spectroscopic studies.

    PubMed

    Falcone, R Dario; Baruah, Bharat; Gaidamauskas, Ernestas; Rithner, Christopher D; Correa, N Mariano; Silber, Juana J; Crans, Debbie C; Levinger, Nancy E

    2011-06-06

    Microemulsions form in mixtures of polar, nonpolar, and amphiphilic molecules. Typical microemulsions employ water as the polar phase. However, microemulsions can form with a polar phase other than water, which hold promise to diversify the range of properties, and hence utility, of microemulsions. Here microemulsions formed by using a room-temperature ionic liquid (RTIL) as the polar phase were created and characterized by using multinuclear NMR spectroscopy. (1)H, (11)B, and (19)F NMR spectroscopy was applied to explore differences between microemulsions formed by using 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]) as the polar phase with a cationic surfactant, benzylhexadecyldimethylammonium chloride (BHDC), and a nonionic surfactant, Triton X-100 (TX-100). NMR spectroscopy showed distinct differences in the behavior of the RTIL as the charge of the surfactant head group varies in the different microemulsion environments. Minor changes in the chemical shifts were observed for [bmim](+) and [BF(4)](-) in the presence of TX-100 suggesting that the surfactant and the ionic liquid are separated in the microemulsion. The large changes in spectroscopic parameters observed are consistent with microstructure formation with layering of [bmim](+) and [BF(4)](-) and migration of Cl(-) within the BHDC microemulsions. Comparisons with NMR results for related ionic compounds in organic and aqueous environments as well as literature studies assisted the development of a simple organizational model for these microstructures.

  4. Aggregation properties and structural studies of anticancer drug Irinotecan in DMSO solution based on NMR measurements

    NASA Astrophysics Data System (ADS)

    D'Amelio, N.; Aroulmoji, V.; Toraldo, A.; Sundaraganesan, N.; Anbarasan, P. M.

    2012-04-01

    Irinotecan is an antitumor drug mostly used in the treatment of colorectal cancer. Its efficacy is influenced by the chemical state of the molecule undergoing chemical equilibria, metabolic changes and photodegradation. In this work, we describe the chemical equilibria of the drug in dimethyl sulfoxide (DMSO). The energetic barrier for hindered rotation around the bond connecting the piperidino—piperidino moiety with the camptothecin-like fragment was evaluated. Furthermore, we showed how the molecule aggregates in DMSO solution forming dimeric species able to prevent its degradation. The equilibrium constant for self-aggregation was determined by NMR based on the assumption of the isodesmic model. The formation of a dimer was highlighted by NMR diffusion ordered spectroscopy (NMR-DOSY) experiments at the concentrations used. Structural features of the complex were inferred by NOE and 13C chemical shift data. Molecular modelling of the complex driven by experimental data, lead to a structure implying the formation of two hydrogen bonds involving the lactone ring whose opening is one of the main causes of drug degradation. This species is probably responsible for the improved stability of the drug at concentrations higher than 1 mM.

  5. NMR studies of isotopically labeled RNA

    SciTech Connect

    Pardi, A.

    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.

  6. Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.

    PubMed

    Dagenais, Pierre; Girard, Nicolas; Bonneau, Eric; Legault, Pascale

    2017-04-06

    Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate. The recent publications of high-resolution structures of the VS ribozyme, obtained by NMR spectroscopy and X-ray crystallography, offer an opportunity to integrate the data and closely examine the structural and dynamic properties of this model RNA system. Notably, these investigations provide a valuable example of the divide-and-conquer strategy for structural and dynamic characterization of a large RNA, based on NMR structures of several individual subdomains. The success of this divide-and-conquer approach reflects the modularity of RNA architecture and the great care taken in identifying the independently-folding modules. Together with previous biochemical and biophysical characterizations, the recent NMR and X-ray studies provide a coherent picture into how the VS ribozyme recognizes its stem-loop substrate. Such in-depth characterization of this RNA enzyme will serve as a model for future structural and engineering studies of dynamic RNAs and may be particularly useful in planning divide-and-conquer investigations. For further resources related to this article, please visit the WIREs website.

  7. Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins.

    PubMed

    Zhang, Jiapu; Zhang, Yuanli

    2014-02-07

    Prion diseases, traditionally referred to as transmissible spongiform encephalopathies (TSEs), are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep and goats, bovine spongiform encephalopathy (BSE or mad-cow disease) in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)), and the conversion of PrP(C) to PrP(Sc) is believed to involve conformational change from a predominantly α-helical protein to one rich in β-sheet structure. Such a conformational change may be amenable to study by molecular dynamics (MD) techniques. For rabbits, classical studies show that they have a low susceptibility to be infected by PrP(Sc), but recently it was reported that rabbit prions can be generated through saPMCA (serial automated Protein Misfolding Cyclic Amplification) in vitro and the rabbit prion is infectious and transmissible. In this paper, we first do a detailed survey on the research advances of rabbit prion protein (RaPrP) and then we perform MD simulations on the NMR and X-ray molecular structures of rabbit prion protein wild-type and mutants. The survey shows to us that rabbits were not challenged directly in vivo with other known prion strains and the saPMCA result did not pass the test of the known BSE strain of cattle. Thus, we might still look rabbits as a prion resistant species. MD results indicate that the three α-helices of the wild-type are stable under the neutral pH environment (but under low pH environment the three α-helices have been unfolded into β-sheets), and the three α-helices of the mutants (I214V and S173N) are unfolded into rich β-sheet structures under

  8. Wheat-germ cell-free production of prion proteins for solid-state NMR structural studies.

    PubMed

    Noirot, Claire; Habenstein, Birgit; Bousset, Luc; Melki, Ronald; Meier, Beat H; Endo, Yaeta; Penin, François; Böckmann, Anja

    2011-04-30

    The expression of soluble, functional protein on a preparative scale poses a central challenge for structural studies. Cell-free protein expression has become a valuable alternative to cell-based methods, and allows today the expression of milligram quantities of protein. Its use is particularly attractive for NMR studies as it allows a multitude of isotopic labeling schemes. We have implemented and further developed protocols to prepare cell-free extracts from wheat germ to produce recombinant protein for solid-state NMR studies. Furthermore, we established the Renilla luciferase model to optimise and evaluate extract quality, and report first productions of the prions Ure2p and HET-s devoted to structural studies currently ongoing in our laboratories.

  9. Structural Studies of Ethylene-1-Octene and Ethylene-Norbornene Random Copolymers by NMR and WAXD

    NASA Astrophysics Data System (ADS)

    Mowery, Daniel; Carrilero, Isabel; Alamo, Rufina

    2003-03-01

    The properties of two series of melt-quenched, random ethylene copolymers (comonomer content < 15 moldiscussed. Changes in the crystallite properties with increasing comonomer content, including crystallite thickness reduction from ^13C T1 NMR relaxation times and chain packing from the line widths of crystal NMR spectra, were found to be independent of comonomer type. Analyses of the non-crystalline regions revealed differences. Copolymers with norbornene showed a larger reduction in the peak position of the WAXD amorphous halo relative to copolymers with the same content of 1-octene. The NMR resonance of the amorphous CH2 backbone units was broader in the copolymers with norbornene. Both observations are due to significant conformational differences in the non-crystalline chains with different comonomer type. Interestingly, the overall decrease in ^13C T1 times of the amorphous CH2 backbone units with increasing comonomer content was the same for both copolymer systems. Hence, in the range of comonomer content studied, the rates of fast motions for ethylene segments in the backbone are independent of comonomer type.

  10. Structural study of synthetic mica montmorillonite by means of 2D MAS NMR experiments

    NASA Astrophysics Data System (ADS)

    Alba, M. D.; Castro, M. A.; Chain, P.; Naranjo, M.; Perdigón, A. C.

    2005-07-01

    Syn-1, is a synthetic mica montmorillonite interstratified mineral that forms one of the standard clay samples in the Clay Minerals Society Source Clays Project. However, there are still controversies regarding some structural aspects such as the interlayer composition or the location of the extra-aluminium determined by chemical analysis. The main objective of this paper is to shed light on those structural aspects that affect the reactivity of the interstratified minerals. For this purpose, we have used 1 H 29 Si and 1 H 27Al HETCOR MAS NMR to show that it is likely that the interlayer space of the beidellite part is composed of ammonium ions whereas ammonium and aluminium ions are responsible for the charge balance in the mica type layer.

  11. A multinuclear solid state NMR spectroscopic study of the structural evolution of disordered calcium silicate sol-gel biomaterials.

    PubMed

    Lin, Zhongjie; Jones, Julian R; Hanna, John V; Smith, Mark E

    2015-01-28

    Disordered sol-gel prepared calcium silicate biomaterials show significant, composition dependent ability to bond with bone. Bone bonding is attributed to rapid hydroxycarbonate apatite (HCA) formation on the glass surface after immersion in body fluid (or implantation). Atomic scale details of the development of the structure of (CaO)x(SiO2)1-x (x = 0.2, 0.3 and 0.5) under heat treatment and subsequent dissolution in simulated body fluid (SBF) are revealed through a multinuclear solid state NMR approach using one-dimensional (17)O, (29)Si, (31)P and (1)H. Central to this study is the combination of conventional static and magic angle spinning (MAS) and two-dimensional (2D) triple quantum (3Q) (17)O NMR experiments that can readily distinguish and quantify the bridging (BOs) and non-bridging (NBOs) oxygens in the silicate network. Although soluble calcium is present in the sol, the (17)O NMR results reveal that the sol-gel produced network structure is initially dominated by BOs after gelation, aging and drying (e.g. at 120 °C), indicating a nanoscale mixture of the calcium salt and a predominantly silicate network. Only once the calcium salt is decomposed at elevated temperatures do the Ca(2+) ions become available to break BO. Apatite forming ability in SBF depends strongly on the surface OH and calcium content. The presence of calcium aids HCA formation via promotion of surface hydration and the ready availability of Ca(2+) ions. (17)O NMR shows the rapid loss of NBOs charge balanced by calcium as it is leached into the SBF. The formation of nanocrystalline, partially ordered HCA can be detected via(31)P NMR. This data indicates the importance of achieving the right balance of BO/NBO for optimal biochemical response and network properties.

  12. 29Si NMR study of structural ordering in aluminosilicate geopolymer gels.

    PubMed

    Duxson, Peter; Provis, John L; Lukey, Grant C; Separovic, Frances; van Deventer, Jannie S J

    2005-03-29

    A systematic series of aluminosilicate geopolymer gels was synthesized and then analyzed using 29Si magic-angle spinning nuclear magnetic resonance (MAS NMR) in combination with Gaussian peak deconvolution to characterize the short-range ordering in terms of T-O-T bonds (where T is Al or Si). The effect of nominal Na2O/(Na2O + K2O) and Si/Al ratios on short-range network ordering was quantified by deconvolution of the 29Si MAS NMR spectra into individual Gaussian peaks representing different Q4(mAl) silicon centers. The deconvolution procedure developed in this work is applicable to other aluminosilicate gel systems. The short-range ordering observed here indicates that Loewenstein's Rule of perfect aluminum avoidance may not apply strictly to geopolymeric gels, although further analyses are required to quantify the degree of aluminum avoidance. Potassium geopolymers appeared to exhibit a more random Si/Al distribution compared to that of mixed-alkali and sodium systems. This work provides a quantitative account of the silicon and aluminum ordering in geopolymers, which is essential for extending our understanding of the mechanical strength, chemical and thermal stability, and fundamental structure of these systems.

  13. NMR cryoporometry characterisation studies of the relation between drug release profile and pore structural evolution of polymeric nanoparticles

    PubMed Central

    Gopinathan, Navin; Yang, Bin; Lowe, John P.; Edler, Karen J.; Rigby, Sean P.

    2014-01-01

    PLGA/PLA polymeric nanoparticles could potentially enhance the effectiveness of convective delivery of drugs, such as carboplatin, to the brain, by enabling a more sustained dosage over a longer time than otherwise possible. However, the link between the controlled release nanoparticle synthesis route, and the subsequent drug release profile obtained, is not well-understood, which hinders design of synthesis routes and availability of suitable nanoparticles. In particular, despite pore structure evolution often forming a key aspect of past theories of the physical mechanism by which a particular drug release profile is obtained, these theories have not been independently tested and validated against pore structural information. Such validation is required for intelligent synthesis design, and NMR cryoporometry can supply the requisite information. Unlike conventional pore characterisation techniques, NMR cryoporometry permits the investigation of porous particles in the wet state. NMR cryoporometry has thus enabled the detailed study of the evolving, nanoscale structure of nanoparticles during drug release, and thus related pore structure to drug release profile in a way not done previously for nanoparticles. Nanoparticles with different types of carboplatin drug release profiles were compared, including burst release, and various forms of delayed release. ESEM and TEM images of these nanoparticles also provided supporting data showing the rapid initial evolution of some nanoparticles. Different stages, within a complex, varying drug release profile, were found to be associated with particular types of changes in the nanostructure which could be distinguished by NMR. For a core-coat nanoparticle formulation, the development of smaller nanopores, following an extended induction period with no structural change, was associated with the onset of substantial drug release. This information could be used to independently validate the rationale for a particular synthesis

  14. Molecular structure and spectroscopic analysis of homovanillic acid and its sodium salt - NMR, FT-IR and DFT studies

    NASA Astrophysics Data System (ADS)

    Samsonowicz, M.; Kowczyk-Sadowy, M.; Regulska, E.; Lewandowski, W.

    2014-01-01

    The estimation of the electronic charge distribution in metal complex or salt allows to predict what kind of deformation of the electronic system of ligand would undergo during complexation. It also permits to make more precise interpretation of mechanism by which metals affect the biochemical properties of ligands. The influence of sodium cation on the electronic system of homovanillic acid was studied in this paper. Optimized geometrical structures of studied compounds were calculated by B3LYP/6-311++G** method. Mulliken, MK and ChelpG atomic charges were analyzed. The theoretical NMR and IR spectra were obtained. 1H and 13C NMR as well as FT-IR and FT-Raman spectra of studied compounds were also recorded and analyzed. The calculated parameters are compared with experimental characteristics of these molecules.

  15. Molecular structure and spectroscopic analysis of homovanillic acid and its sodium salt--NMR, FT-IR and DFT studies.

    PubMed

    Samsonowicz, M; Kowczyk-Sadowy, M; Regulska, E; Lewandowski, W

    2014-01-24

    The estimation of the electronic charge distribution in metal complex or salt allows to predict what kind of deformation of the electronic system of ligand would undergo during complexation. It also permits to make more precise interpretation of mechanism by which metals affect the biochemical properties of ligands. Theinfluence ofsodium cation on the electronic system of homovanillic acid was studied in this paper. Optimized geometrical structures of studied compounds were calculated by B3LYP/6-311++G(**) method. Mulliken, MK and ChelpG atomic charges were analyzed. The theoretical NMR and IR spectra were obtained. (1)H and (13)C NMR as well as FT-IR and FT-Raman spectra of studied compounds were also recorded and analyzed. The calculated parameters are compared with experimental characteristics of these molecules.

  16. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  17. Glassy carbons from poly(furfuryl alcohol) copolymers: structural studies by high-resolution solid-state NMR techniques

    SciTech Connect

    Eckert, H.; Levendis, Y.A.; Flagan, R.C.

    1988-08-25

    The chemical structure of glass carbon particles produced from poly(furfuryl alcohol) copolymers is studied by /sup 13/C cross-polarization/magic-angle spinning (CP-MAS) NMR and high-speed /sup 1/H MAS NMR. In agreement with earlier proposals, /sup 13/C NMR spectra confirm the buildup of a highly unsaturated system at the expense of furan rings and aliphatic carbon atoms, and upon heating to 800 K this conversion is essentially complete. Successive carbonization by air oxidation or pyrolysis at temperatures up to 1600 K is reflected in a gradual decrease of the /sup 13/C chemical shift from ca. 130 to 115 ppm versus tetramethylsilane. /sup 1/H MAS NMR is used to detect and quantitate the amount of residual C-bonded hydrogen species at various stages of the carbonization process. In addition, these spectra show intense, narrow resonances due to sorbed H/sub 2/O molecules, which resonate over a wide range of chemical shifts (between 2.5 and /minus/8 ppm versus tetramethylsilane). In analogy with effects observed by Tabony and co-workers for molecules adsorbed above the basal plane of graphite, the upfield shifts observed for water sorbed in the glassy carbons of the present study are attributed to the large susceptibility anisotropy of submicroscopically ordered, turbostratic, or partially graphitized regions of the samples. The extent of this ordering is inversely correlated with the absolute content of residual C-bonded hydrogen species and depends mainly on the temperature of pyrolysis, whereas the oxygen content of the heating atmosphere and the composition of the initial polymeric material appear to be of secondary importance. The results suggest that sorbed H/sub 2/O molecules can function as sensitive NMR chemical shift probes for the initial stages of crystallization processes in glassy carbons.

  18. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions

    PubMed Central

    Gizachew, Dawit; Dratz, Edward

    2011-01-01

    Protein-protein interactions control signaling, specific adhesion and many other biological functions. The three dimensional structures of the interfaces and bound ligand can be approached with Tr-NOESY NMR, which can be applied to much larger proteins than conventional NMR and requires less concentrated protein. However, it is not clear how accurately the structures of protein-bound peptides can be determined by Tr-NOESY. We studied the structure of a biotin-mimetic peptide (FSHPQNT) bound to streptavidin, since the x-ray structure of the complex is available to 1.74Å resolution and we found that conditions could be adjusted so that the off-rates were fast enough for Tr-NOESY NMR. The off-rate was determined with 19F NMR, using a para-fluoro-phenylalanine analog of the peptide. A new criterion for a lower limit on kinetic off-rate was found, which allowed accurate structure determination at a slower off-rate. Non-specific binding of the peptide to streptavidin was not significant, since biotin blocked the peptide Tr-NOESY. Protein mediation for the long range peptide Tr-NOESY cross-peaks was corrected by a Tr-NOESY/ROESY averaging procedure. The protein-bound structure of the peptide was determined by Tr-NOESY constrained and simulated annealing. The structure deduced from the NMR was close to the x-ray structure. PMID:21294848

  19. Multinuclear NMR study of the solution structure and reactivity of tris(trimethylsilyl)methyllithium and its iodine ate complex.

    PubMed

    Reich, Hans J; Sikorski, William H; Sanders, Aaron W; Jones, Amanda C; Plessel, Kristin N

    2009-01-16

    The extreme steric bulk of tris(trimethylsilyl)methyl derivatives (1-X) provides interesting structural and dynamic behavior for study. Dynamic NMR studies on 1-SePh and 1-I showed restricted rotation around the C-Si bonds of each trimethylsilyl groups. An extensive multinuclear NMR study of natural abundance and (6)Li and (13)C enriched 1-Li revealed three species in THF-containing solvents, a dimer 1T, and two monomers, the contact ion pair 1C, and solvent separated ion pair 1S. Observed barriers for interconversion of 1-Li aggregates were unusually high (DeltaG(double dagger) ca. 9 kcal/mol for exchange of 1S and 1C, DeltaG(double dagger)(41) = 16.4 kcal/mol for exchange of 1T with 1C and 1S), allowing for study of reactivity of each aggregate individually. We can show that 1S is at least 50 times as reactive as 1C and at least 5 x 10(10) times as reactive as 1T toward MeI. The large difference in reactivity allowed further study on the mechanism of the lithium-iodine exchange of 1-I with 1-Li and characterization of the intermediate iodine ate complex 4. Additional calibrations are presented for the sensitive yet chemically inert (13)C NMR chemical shift thermometer 1-H.

  20. Deuterium NMR study of structural and dynamic properties of horseradish peroxidase

    SciTech Connect

    La Mar, G.N.; Thanabal, V.; Johnson, R.D.; Smith, K.M.; Parish, D.W.

    1989-04-05

    High field deuterium NMR spectra have been recorded for various horseradish peroxidase complexes reconstituted with hemins possessing specific 2H labels. The line width of the 2H NMR signals of deuteroheme reconstituted-horseradish peroxidase (HRP) and its cyano complex for the immobilized skeletal 2-2H and 4-2H labels yield the overall protein rotational correlation time (22 ms at 55 degrees C), which is consistent with expectations based on molecular weight. Meso-2H4 labels yield broad (1.3 kHz) signals just upfield from the diamagnetic protein envelope for HRP, and in the central portion of the protein envelope for the CN- ligated resting state HRP. Meso-2H4-labeled mesohemin-reconstituted HRP exhibits a similar signal but shifted further upfield by approximately 10 ppm. The net upfield meso-H hyperfine shifts confirm a five-coordinate structure for resting state HRP. 2Ha resonances for essentially rotationally immobile vinyl groups were detected in both resting state HRP and CN- ligated resting state HRP. Heme methyl-2H-labeling yields relatively narrow lines (approximately 80 Hz) indicative of effective averaging of the quadrupolar relaxation by rapid methyl rotation. Thus the 2H line width of rapidly rotating methyls in hemoproteins can be used effectively to determine the overall protein tumbling rate. Preliminary 2H experiments in meso-2H4-labeled compound I do not support large pi spin density at these positions on the porphyrin cation radical, and argue for a a1u rather than a a2u orbital ground state.

  1. NMR studies of the surface structure and dynamics of semiconductor nanocrystals

    NASA Astrophysics Data System (ADS)

    Sachleben, Joseph R.; Wooten, E. Wrenn; Emsley, Lyndon; Pines, Alexander; Colvin, Vicki L.; Alivisatos, A. Paul

    1992-10-01

    1H NMR studies of thiophenol capping groups on cadmium sulfide nanocrystals demonstrate that the coverage of the capping molecule depends on the size of the nanocrystal. Data are presented which show that as the size of the nanocrystal increases, the coverage of thiophenol decreases. In addition, information about the overall tumbling of the nanocrystal and the motion of the capping groups relative to the surface can be obtained from linewidth studies, indicating that the rotation of the capping groups is hindered in the smaller nanocrystals ( r≈12 Å) and becomes less so in larger nanocrystals ( r≈20 Å). The coverage data are related to the electronic properties of this important class of compounds.

  2. Monolignol acylation and lignin structure in some nonwoody plants: a 2D NMR study.

    PubMed

    Martínez, Angel T; Rencoret, Jorge; Marques, Gisela; Gutiérrez, Ana; Ibarra, David; Jiménez-Barbero, Jesús; del Río, José C

    2008-11-01

    Lignins from three nonwoody angiosperms were analyzed by 2D NMR revealing important differences in their molecular structures. The Musa textilis milled-wood-lignin (MWL), with a syringyl-to-guaiacyl (S/G) ratio of 9, was strongly acylated (near 85% of side-chains) at the gamma-carbon by both acetates and p-coumarates, as estimated from (1)H-(13)C correlations in C(gamma)-esterified and C(gamma)-OH units. The p-coumarate H(3,5)-C(3,5) correlation signal was completely displaced by acetylation, and disappeared after alkali treatment, indicating that p-coumaric acid was esterified maintaining its free phenolic group. By contrast, the Cannabis sativa MWL (S/G approximately 0.8) was free of acylating groups, and the Agave sisalana MWL (S/G approximately 4) showed high acylation degree (near 80%) but exclusively with acetates. Extensive C(gamma)-acylation results in the absence (in M. textilis lignin) or low abundance (4% in A. sisalana lignin) of beta-beta' resinol linkages, which require free C(gamma)-OH to form the double tetrahydrofuran ring. However, minor signals revealed unusual acylated beta-beta' structures confirming that acylation is produced at the monolignol level, in agreement with chromatographic identification of gamma-acetylated sinapyl alcohol among the plant extractives. In contrast, resinol substructures involved 22% side-chains in the C.sativa MWL. The ratio between beta-beta' and beta-O-4' side-chains in these and other MWL varied from 0.32 in C.sativa MWL to 0.02 in M. textilis MWL, and was inversely correlated with the degree of acylation. The opposite was observed for the S/G ratio that was directly correlated with the acylation degree. Monolignol acylation is discussed as a mechanism potentially involved in the control of lignin structure.

  3. Regenerated silk fibers: Structural studies and solid state NMR techniques for efficient multiple distance determinations in proteins

    NASA Astrophysics Data System (ADS)

    Liivak, Oskar

    2000-09-01

    Material Science is the science of understanding the relationship between the molecular level structure of a material and its macroscopic properties. Such research requires both the ability to determine molecular structure and the ability to control and modify the molecular structure. The present research into silks, especially the dragline silk from the spider Nephila clavipes , is occurring at a time when these two criteria are beginning to be met for proteins like spider silk. Genetic engineering has evolved to the point where material scientists have full control over the primary sequence of amino acids that comprise proteins. In addition, solid state nuclear magnetic resonance (NMR) techniques exist which allow us to probe molecular structure. This work applies solid state NMR to the study of the structure of silk fibers. In particular, we focus on techniques of fiber regeneration from solution. The purpose is not only to develop the techniques by which genetically engineered fibers could be spun into fibers for mass production but also as a tool into fundamental silk research. Results on these regenerated fibers show a correlation between the fraction of the silk's alanine residues which are in the β-sheet conformation and the ultimate tensile strength of the fibers. In addition, in a clever mating of the fiber regeneration technique and the solid state NMR distance measurement experiment, rotational echo double resonance (REDOR), we investigate the supramolecular topology of the alanine β-sheet crystals. Even though the REDOR technique has failings for the complicated ISn spin systems found in the silk samples, a qualitative analysis does indicate that the β-sheet crystals are intermolecular. Finally, we investigate a new class of REDOR-like experiments which are designed to overcome the failings of REDOR in ISn spin systems. Experimental data is shown to validate these ideas. An alternate pulse sequence is also introduced and verified with experimental

  4. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

    PubMed

    Reddy, Jithender G; Hosur, Ramakrishna V

    2014-03-01

    Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.

  5. A structural study of fentanyl by DFT calculations, NMR and IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Asadi, Zahra; Esrafili, Mehdi D.; Vessally, Esmail; Asnaashariisfahani, Manzarbanou; Yahyaei, Saeideh; Khani, Ali

    2017-01-01

    N-(1-(2-phenethyl)-4-piperidinyl-N-phenyl-propanamide (fentanyl) is synthesized and characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy and elemental analyses. The geometry optimization is performed using the B3LYP and M06 density functionals with 6-311 + G(d) and 6-311++G(d,p) basis sets. The complete assignments are performed on the basis of the potential energy distribution (PED) of the all vibrational modes. Almost a nice correlation is found between the calculated 13C chemical shifts and experimental data. The frontier molecular orbitals and molecular electrostatic potential of fentanyl are also obtained.

  6. Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.

    PubMed

    Zhang, Jiapu; Wang, Feng; Zhang, Yuanli

    2015-01-01

    Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer and elk, and humans. But for rabbits, studies have shown that they have a low susceptibility to be infected by prion diseases. This paper does molecular dynamics (MD) studies of rabbit NMR structures (of the wild type and its two mutants of two surface residues), in order to understand the specific mechanism of rabbit prion proteins (RaPrP(C)). Protein surface electrostatic charge distributions are specially focused to analyze the MD trajectories. This paper can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrP(C); this may be useful for the medicinal treatment of prion diseases.

  7. Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

    NASA Astrophysics Data System (ADS)

    Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

    2013-01-01

    The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

  8. Structural and Nutritional Properties of Pasta from Triticum monococcum and Triticum durum Species. A Combined ¹H NMR, MRI, and Digestibility Study.

    PubMed

    Pasini, Gabriella; Greco, Fulvia; Cremonini, Mauro A; Brandolini, Andrea; Consonni, Roberto; Gussoni, Maristella

    2015-05-27

    The aim of the present study was to characterize the structure of two different types of pasta, namely Triticum turgidum ssp. durum (cv. Saragolla) and Triticum monococcum ssp. monococcum (cv. Monlis), under different processing conditions. MRI analysis and NMR spectroscopy (i.e., T1 and T2 NMR relaxation times and diffusion parameters) were conducted on pasta, and (1)H NMR spectroscopic analysis of the chemical compounds released by pasta samples during the cooking process was performed. In addition, starch digestibility (enzimatically determined) was also investigated. The NMR results indicated that Saragolla pasta has a more compact structure, ascribed to pasta network and in particular to different technological gluten properties, that mainly determine the lower ability of Monlis pasta in binding water. These results correlate well with the lower rate of starch hydrolysis measured for Monlis pasta compared to Saragolla when both are dried at high temperature.

  9. An NMR study of structure and dynamics of hydrated poly (aspartic acid) sodium salt

    NASA Astrophysics Data System (ADS)

    Wang, Pixin; Ando, Isao

    1998-06-01

    High-resolution 13C CP/MAS NMR and pulse 1H NMR experiments were carried out for hydrated poly(aspartic acid) sodium salt, in order to investigate the conformation and molecular motion of the polymer. From these experimental results, it is found that the main-chain conformation of poly(aspartic acid) sodium salt which takes an α-helix form in the dry state is not drastically affected by an addition of water. In the 13C CP/MAS NMR spectrum, a new peak at ca. 184 ppm appears, which comes from the formation of hydrogen bond between the carbonyl carbon of the side chains and water, and the intensity of the peak is associated with the water content. The 13C spin-lattice relaxation time ( T1) experiments show that the T1 values for the individual carbons of the polymer are decreased with an increase in the water content. This shows that the mobility of the polymer is increased with an increase in the water content. Further, the 1H spin-spin relaxation time ( T2) experiments show that the polymer has the two or three components with different molecular motion. With an increase in the water content or temperature, the T2 values of hydrated PAANa are increased. This shows that the molecular motion is increased. In the high water content, the polymer has a signal component in the molecular motion. This shows that the polymer is uniformly hydrated.

  10. Dipolar-dephasing 13C NMR studies of decomposed wood and coalified xylem tissue: Evidence for chemical structural changes associated with defunctionalization of lignin structural units during coalification

    USGS Publications Warehouse

    Hatcher, P.G.

    1988-01-01

    A series of decomposed and coalified gymnosperm woods was examined by conventional solid-state 13C nuclear magnetic resonance (NMR) and by dipolar-dephasing NMR techniques. The results of these NMR studies for a histologically related series of samples provide clues as to the nature of codification reactions that lead to the defunctionalization of lignin-derived aromatic structures. These reactions sequentially involve the following: (1) loss of methoxyl carbons from guaiacyl structural units with replacement by hydroxyls and increased condensation; (2) loss of hydroxyls or aryl ethers with replacement by hydrogen as rank increases from lignin to high-volatile bituminous coal; (3) loss of alkyl groups with continued replacement by hydrogen. The dipolar-dephasing data show that the early stages of coalification in samples examined (lignin to lignite) involve a decreasing degree of protonation on aromatic rings and suggest that condensation is significant during coalification at this early stage. An increasing degree of protonation on aromatic rings is observed as the rank of the sample increases from lignite to anthracite.

  11. Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Wolniak, Michał; Tomczyk, Michał; Gudej, Jan; Wawer, Iwona

    2006-12-01

    Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. 13C NMR spectra were recorded for solution and solid phase. 13C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1 dbnd O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10 sbnd OH⋯O dbnd C or C10 sbnd OH⋯OCH 3).

  12. First X-ray structural characterization of isatin Schiff base derivative. NMR and theoretical conformational studies

    NASA Astrophysics Data System (ADS)

    Davidovich, Pavel; Novikova, Daria; Tribulovich, Vyacheslav; Smirnov, Sergey; Gurzhiy, Vlad; Melino, Gerry; Garabadzhiu, Alexander

    2014-10-01

    Isatin (1H-indole-2,3-dione) is an endogenous natural compound under intense development in medicinal chemistry. Here, we characterize isatin Schiff base derivative by X-ray crystallography. We describe a derivative that crystallizes E-isomer form in the triclinic space group P 1bar;a = 5.9580 (4) Å, b = 8.4184 (7) Å, c = 14.1801 (14) Å, α = 73.962 (8)°, β = 83.184 (7)°, γ = 81.143 (6)°. NMR data show that E-conformer interconverts to the Z-conformer when dissolved, this equilibrium weakly depends on the solvent type. The Z-isomer geometry and the energetics of ΔEE-Z interconversion barriers were determined by quantum chemical calculations. The isomers are further characterized by means of FT-IR and UV-Vis spectroscopy.

  13. Preservation of bilayer structure in human erythrocytes and erythrocyte ghosts after phospholipase treatment. A 31P-NMR study.

    PubMed

    van Meer, G; de Kruijff, B; op den Kamp, J A; van Deenen, L L

    1980-02-15

    1. Fresh human erythrocytes were treated with lytic and non-lytic combinations of phospholipases A2, C and sphingomyelinase. The 31P-NMR spectra of ghosts derived from such erythrocytes show that, in all cases, the residual phospholipids and lysophospholipids remain organized in a bilayer configuration. 2. A bilayer configuration of the (lyso)phospholipids was also observed after treatment of erythrocyte ghosts with various phospholipases even in the case that 98% of the phospholipid was converted into lysophospholipid (72%) and ceramides (26%). 3. A slightly decreased order of the phosphate group of phospholipid molecules, seen as reduced effective chemical shift anisotropy in the 31P-NMR spectra, was found following the formation of diacyglycerols and ceramides in the membrane of intact erythrocytes. Treatment of ghosts always resulted in an extensive decrease in the order of the phosphate groups. 4. The results allow the following conclusions to made: a. Hydrolysis of phospholipids in intact red cells and ghosts does not result in the formation of non-bilayer configuration of residual phospholipids and lysophospholipids. b. Haemolysis, which is obtained by subsequent treatment of intact cells with sphingomyelinase and phospholipase A2, or with phospholipase C, cannot be ascribed to the formation of non-bilayer configuration of phosphate-containing lipids. c. Preservation of bilayer structure, even after hydrolysis of all phospholipid, shows that other membrane constitutents, e.g. cholesterol and/or membrane proteins play an important role in stabilizing the structure of the erythrocyte membrane. d. A major prerequisite for the application of phospholipases in lipid localization studies, the preservation of a bilayer configuration during phospholipid hydrolysis, is met for the erythrocyte membrane.

  14. Local structure and molecular motions in imidazolium hydrogen malonate crystal as studied by 2H and 13C NMR

    NASA Astrophysics Data System (ADS)

    Mizuno, M.; Chizuwa, M.; Umiyama, T.; Kumagai, Y.; Miyatou, T.; Ohashi, R.; Ida, T.; Tansho, M.; Shimizu, T.

    2015-04-01

    The local structure and molecular motion of the imidazolium hydrogen malonate crystal were investigated using solid-state 2H and 13C NMR. The imidazolium ion undergoes isotropic rotation, which is correlated with a defect in the crystal, as observed by 2H NMR broadline spectra above 263 K. A 180∘ flip of the imidazolium ion in the regular site was observed from 2H NMR quadrupole Carr-Purcell-Meiboom-Gill (QCPMG) spectra. The Grotthuss mechanism was accompanied by a 180∘ flip of the imidazolium ion in regular sites. Moreover, the proton transfer associated with the imidazolium ion of the defective crystal is important for proton conductivity of the imidazolium hydrogen malonate crystal.

  15. NMR study on the quasi one-dimensional quantum spin magnet with ladder structure

    NASA Astrophysics Data System (ADS)

    Kobori, Shohei; Matsui, Kazuki; Kuwahara, Hideki; Goto, Takayuki; Zhang, Xiao; Nakano, Yuki; Nishihara, Sadafumi; Inoue, Katsuya; Sasaki, Takahiko

    2016-12-01

    The two-legged spin ladder Cu(CO3)0.5(ClO4)(H2O)0.5(NH3)2.5 consists of a rung formed by two Cu(II)'s and of a spacing molecule CO3^{2-} between each two rungs. The non-centrosymmetric shape of CO3^{2-} molecule brings a slight bond alternation along the leg, and hence the system can be considered as an alternating spin chain, which is confirmed so far by the temperature dependence of magnetic susceptibility. In order to investigate its spin state at low temperatures, we have performed experiments of 1H-NMR, magnetization and specific heat under wide range of magnetic field, and have found the critical diverging of longitudinal relaxation rate 1/ T 1, the spectral broadening and the lambda-type anomaly in specific heat at T N≃ 3.4 K, indicating the existence of long range magnetic order. In paramagnetic state well above T N, 1/ T 1 showed a power-law temperature dependence, suggesting the realization of Tomonaga Luttinger liquid state.

  16. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

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

  17. sup 31 P and sup 2 H NMR studies of structure and motion in bilayers of phosphatidylcholine and phosphatidylethanolamine

    SciTech Connect

    Ghosh, R. )

    1988-10-04

    The structural and motional properties of mixed bilayers of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) have been examined by using wide-line {sup 31}P, {sup 14}N, and {sup 2H} NMR. {sup 2}H and {sup 14}N NMR data showed that in mixed bilayers containing both PC and PE the conformations of the head-group moieties are essentially identical with those observed for bilayers containing a single phospholipid species. Equimolar amounts of cholesterol induce also only a small change in head-group conformation. For all phospholipid mixtures studied, the {sup 31}P T{sub 1} relaxation was homogeneous over the whole powder spectrum and could be fitted to a single-exponential decay. The {sup 31}P vs temperature profiles were analyzed by a simple correlation model. The presence of equimolar amounts of PE containing either the same (POPE) or a different (Escherichia coli PE) fatty acid composition had essentially no effect on the rate of rotational diffusion of the phosphate groups, with the correlation time being found to be 0.68 ns at 20{degree}C. The presence of equimolar amounts of cholesterol decreased the correlation time to 0.65 ns, and also the activation energy was reduced to 22.6 kJ mol{sup {minus}1}. The authors interpret the decrease in activation energy as being due to the spacing effect of cholesterol which reduces the H-bonding interactions between head-groups, allowing them to rotate more freely. For all cases examined, the rotational diffusion of the phosphate moieties was slower than that observed for the rigid glycerol backbone of the molecule, the latter probably corresponding to overall phospholipid rotation.

  18. Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

    SciTech Connect

    Kalbitzer, H.R.; Neidig, K.P. ); Hengstenberg, W. )

    1991-11-19

    Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earlier in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.

  19. Study of electrostatic potential surface distribution of wild-type plastocyanin Synechocystis solution structure determined by homonuclear NMR.

    PubMed

    Monleón, Daniel; Celda, Bernardo

    2003-10-01

    Plastocyanin is a small (approximately 10 kDa), type I blue copper protein that works as an electron donor to photosystem I from cytochrome f in both chloroplast systems and in some strains of cyanobacteria. Comparative studies of the kinetic mechanisms of plastocyanins in different organisms show that the electron transfer from photosystem I happens by simple collision in cyanobacteria but through a intermediate transition complex in green algae and superior plants. Previous work has proved that this effect cannot be explained by structural variations across the different plastocyanins but it can be explained by differences in the electrostatic potential distribution at the protein surface. In that case, minor conformational errors at the amino acid side chain level may imply an important effect in the electrostatic potential distribution calculation. In this work we present a high resolution study of side chain conformation by homonuclear NMR for the reduced wild-type plastocyanin Synechocystis using intensity ratios for 2D-NOESY and 2D-H,H-TOCSY cross peaks at different mixing times. We also present the corresponding comparison with different plastocyanin structures and the effect in the electrostatic potential distribution at the protein surface. We discuss the importance of indirect J-coupling information from TOCSY-type experiments as complement for intraresidue distances derived from NOESY experiments in the determination of side chain orientation and stereo-specific assignments.

  20. Structural transformation and physical properties of a hydrogel-forming peptide studied by NMR, transmission electron microscopy, and dynamic rheometer.

    PubMed

    Huang, Hongzhou; Herrera, Alvaro I; Luo, Zhiping; Prakash, Om; Sun, Xiuzhi S

    2012-09-05

    Peptide-based hydrogels are attractive biological materials. Study of their self-assembly pathways from their monomer structures is important not only for undertaking the rational design of peptide-based materials, but also for understanding their biological functions and the mechanism of many human diseases relative to protein aggregation. In this work, we have monitored the conformation, morphological, and mechanical properties of a hydrogel-forming peptide during hydrogelation in different dimethylsulfoxide (DMSO)/H(2)O solutions. The peptide shows nanofiber morphologies in DMSO/H(2)O solution with a ratio lower than 4:1. Increased water percentage in the solution enhanced the hydrogelation rate and gel strength. One-dimensional and two-dimensional proton NMR and electron microscopy studies performed on the peptide in DMSO/H(2)O solution with different ratios indicate that the peptide monomer tends to adopt a more helical structure during the hydrogelation as the DMSO/H(2)O ratio is reduced. Interestingly, at the same DMSO/H(2)O ratio, adding Ca(2+) not only promotes peptide hydrogelation and gel strength, but also leads to special shear-thinning and recovery properties of the hydrogel. Without changing the peptide conformation, Ca(2+) binds to the charged Asp residues and induces the change of interfiber interactions that play an important role in hydrogel properties.

  1. Combined experimental and theoretical studies on the X-ray crystal structure, FT-IR, 1H NMR, 13C NMR, UV-Vis spectra, NLO behavior and antimicrobial activity of 2-hydroxyacetophenone benzoylhydrazone.

    PubMed

    Sheikhshoaie, Iran; Ebrahimipour, S Yousef; Sheikhshoaie, Mahdeyeh; Rudbari, Hadi Amiri; Khaleghi, Moj; Bruno, Giuseppe

    2014-04-24

    A Schiff base ligand, 2-hydroxyacetophenone benzoylhydrazone (HL) was synthesized and fully characterized with FT-IR, elemental analyses, UV-Vis, (1)H NMR and (13)C NMR spectra. DFT calculations using B3LYP/6-31+G(d,p) and PW91/DZP are performed to optimize the molecular geometry. Optimized structures are used to calculate FT-IR, UV-Vis, (1)H NMR and (13)C NMR spectra of the compound. Also the energies of the frontier molecular orbitals (FMOs) have been determined. The results obtained from the optimization and spectral analyses are in good agreement with the experimental data. To investigate non-linear optical properties, the electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) were computed. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the compound can be a good candidate of nonlinear optical materials. In addition, the minimal inhibitory concentration (MIC) of this compound against Staphylococcus aureus, and Candida albicans was determined.

  2. NMR Studies of Structure-Reactivity Relationships in Carbonyl Reduction: A Collaborative Advanced Laboratory Experiment

    ERIC Educational Resources Information Center

    Marincean, Simona; Smith, Sheila R.; Fritz, Michael; Lee, Byung Joo; Rizk, Zeinab

    2012-01-01

    An upper-division laboratory project has been developed as a collaborative investigation of a reaction routinely taught in organic chemistry courses: the reduction of carbonyl compounds by borohydride reagents. Determination of several trends regarding structure-activity relationship was possible because each student contributed his or her results…

  3. Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

    SciTech Connect

    Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V.

    2016-01-21

    Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.

  4. Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

    NASA Astrophysics Data System (ADS)

    Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V.

    2016-01-01

    Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.

  5. Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids.

    PubMed

    Kharkov, B B; Chizhik, V I; Dvinskikh, S V

    2016-01-21

    Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.

  6. NMR studies on the structure and dynamics of lac operator DNA

    SciTech Connect

    Lee, S.C.

    1985-01-01

    Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with a maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.

  7. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  8. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations.

    PubMed

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as "pau branco". Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The (13)C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d,p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  9. Structural studies of the exopolysaccharide from Lactobacillus plantarum C88 using NMR spectroscopy and the program CASPER.

    PubMed

    Fontana, Carolina; Li, Shengyu; Yang, Zhennai; Widmalm, Göran

    2015-01-30

    Some lactic acid bacteria, such as those of the Lactobacillus genus, have the ability to produce exopolysaccharides (EPSs) that confer favorable physicochemical properties to food and/or beneficial physiological effects on human health. In particular, the EPS of Lactobacillus plantarum C88 has recently demonstrated in vitro antioxidant activity and, herein, its structure has been investigated using NMR spectroscopy and the computer program CASPER (Computer Assisted Spectrum Evaluation of Regular polysaccharides). The pentasaccharide repeating unit of the O-deacetylated EPS consists of a trisaccharide backbone, →4)-α-D-Galp-(1→2)-α-D-Glcp-(1→3)-β-D-Glcp-(1→, with terminal D-Glc and D-Gal residues (1.0 and 0.8 equiv per repeating unit, respectively) extending from O3 and O6, respectively, of the →4)-α-D-Galp-(1→ residue. In the native EPS an O-acetyl group is present, 0.85 equiv per repeating unit, at O2 of the α-linked galactose residue; thus the repeating unit of the EPS has the following structure: →4)[β-D-Glcp-(1→3)][β-D-Galp-(1→6)]α-D-Galp2Ac-(1→2)-α-D-Glcp-(1→3)-β-D-Glcp-(1→. These structural features, and the chain length (∼10(3) repeating units on average, determined in a previous study), are expected to play an important role in defining the physicochemical properties of the polymer.

  10. Use of solid-state 13C NMR in structural studies of humic acids and humin from Holocene sediments

    USGS Publications Warehouse

    Hatcher, P.G.; VanderHart, D.L.; Earl, W.L.

    1980-01-01

    13C NMR spectra of solid humic substances in Holocene sediments have been obtained using cross polarization with magic-angle sample spinning techniques. The results demonstrate that this technique holds great promise for structural characterizations of complex macromolecular substances such as humin and humic acids. Quantifiable distinctions can be made between structural features of aquatic and terrestrial humic substances. The aliphatic carbons of the humic substances are dominant components suggestive of input from lipid-like materials. An interesting resemblance is also noted between terrestrial humic acid and humin spectra. ?? 1980.

  11. Protein structure determination from NMR chemical shifts.

    PubMed

    Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

    2007-06-05

    NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

  12. Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT-GIAO calculations

    NASA Astrophysics Data System (ADS)

    Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona

    2009-09-01

    Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.

  13. Studying Cellulose Fiber Structure by SEM, XRD, NMR and Acid Hydrolysis

    SciTech Connect

    Zhao, Haibo; Kwak, Ja Hun; Zhang, Z. Conrad; Brown, Heather M.; Arey, Bruce W.; Holladay, John E.

    2007-03-21

    Cotton linters were partially hydrolyzed in dilute acid and the morphology of remaining macrofibrils studied with Scanning Electron Microscopy (SEM) under various magnifications. The crystal region (microfibril bundles) in the macrofibrils was not altered by hydrolysis, and only amorphous cellulose was hydrolyzed and leached out from the macrofibrils. The diameter of microfibril bundles was 20-30 nm after the amorphous cellulose was removed by hydrolysis. XRD experiments confirm the unaltered diameter of the microfibrils after hydrolysis. The strong stability of these microfibril bundles in hydrolysis limits both the total sugar monomer yield and the size of nano particles or rods produced in hydrolysis. The large surface potential on the remaining microfibril bundles drives the agglomeration of macrofibrils.

  14. 14N and 81Br quadrupolar nuclei as sensitive NMR Probes of n-alkyltrimethylammonium bromide crystal structures. An experimental and theoretical study.

    PubMed

    Alonso, Bruno; Massiot, Dominique; Florian, Pierre; Paradies, Henrich H; Gaveau, Philippe; Mineva, Tzonka

    2009-09-03

    This is the first time a comprehensive study has been carried out on n-alkyltrimethylammonium bromide salts using (14)N and (81)Br solid state NMR, X-ray diffraction, and theoretical calculations. The investigation represents a necessary step toward further (14)N and (81)Br NMR characterization of the environment of cationic and anionic groups in materials, accounting for the amphiphilic properties of cationic surfactants. The NMR spectra of five C(x)H(2x+1)(CH(3))(3)N(+)Br(-) polycrystalline samples with different n-alkyl chain lengths (x = 1, 12, 14, 16, 18) were recorded and modeled. The (14)N and (81)Br quadrupolar coupling interaction parameters (C(Q), eta(Q)) were also estimated from spectrum modeling and from computer simulation. The obtained results were discussed in depth making use of the experimental and reoptimized crystal structures. In the study, both (14)N and (81)Br nuclei were found to be sensitive probes for small structural variations. The parameters which influence the NMR properties the most are mobility, deviation of C-N-C bond angles from T(d) angles, and variations in r(N-Br) distances.

  15. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus

    SciTech Connect

    Huang Ribo; Du Qishi Wang Chenghua; Chou, K.-C.

    2008-12-26

    The long-sought three-dimensional structure of the M2 proton channel of influenza A virus was successfully determined recently by the high-resolution NMR [J.R. Schnell, J.J. Chou, Structure and mechanism of the M2 proton channel of influenza A virus, Nature 451 (2008) 591-595]. Such a milestone work has provided a solid structural basis for studying drug-resistance problems. However, the action mechanism revealed from the NMR structure is completely different from the traditional view and hence prone to be misinterpreted as 'conflicting' with some previous biological functional studies. To clarify this kind of confusion, an in-depth analysis was performed for these functional studies, particularly for the mutations D44N, D44A and N44D on position 44, and the mutations on positions 27-38. The analyzed results have provided not only compelling evidences to further validate the NMR structure but also very useful clues for dealing with the drug-resistance problems and developing new effective drugs against H5N1 avian influenza virus, an impending threat to human beings.

  16. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  17. Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14

    SciTech Connect

    Albright, Seth; Chen Bin; Holbrook, Kristen; Jain, Nitin U.

    2008-04-04

    CD14 functions as a key pattern recognition receptor for a diverse array of Gram-negative and Gram-positive cell-wall components in the host innate immune response by binding to pathogen-associated molecular patterns (PAMPs) at partially overlapping binding site(s). To determine the potential contribution of CD14 residues in this pattern recognition, we have examined using solution NMR spectroscopy, the binding of three different endotoxin ligands, lipopolysaccharide, lipoteichoic acid, and a PGN-derived compound, muramyl dipeptide to a {sup 15}N isotopically labeled 152-residue N-terminal fragment of sCD14 expressed in Pichia pastoris. Mapping of NMR spectral changes upon addition of ligands revealed that the pattern of residues affected by binding of each ligand is partially similar and partially different. This first direct structural observation of the ability of specific residue combinations of CD14 to differentially affect endotoxin binding may help explain the broad specificity of CD14 in ligand recognition and provide a structural basis for pattern recognition. Another interesting finding from the observed spectral changes is that the mode of binding may be dynamically modulated and could provide a mechanism for binding endotoxins with structural diversity through a common binding site.

  18. γ-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state (19)F-NMR peptide studies.

    PubMed

    Kubyshkin, Vladimir; Afonin, Sergii; Kara, Sezgin; Budisa, Nediljko; Mykhailiuk, Pavel K; Ulrich, Anne S

    2015-03-21

    γ-(4S)-Trifluoromethyl proline was synthesised according to a modified literature protocol with improved yield on a multigram scale. Conformational properties of the amide bond formed by the amino acid were characterised using N-acetyl methyl ester model. The amide populations (s-trans vs. s-cis) and thermodynamic parameters of the isomerization were found to be similar to the corresponding values for intact proline. Therefore, the γ-trifluoromethyl proline was suggested as a structurally low-disturbing proline substitution in peptides for their structural studies by (19)F-NMR. Indeed, the exchange of native proline for γ-trifluoromethyl proline in the peptide antibiotic gramicidin S was shown to preserve the overall amphipathic peptide structure. The utility of the amino acid as a selective (19)F-NMR label was demonstrated by observing the re-alignment of the labelled gramicidin S in oriented lipid bilayers.

  19. Biosynthesis, molecular structure, and domain architecture of potato suberin: a (13)C NMR study using isotopically labeled precursors.

    PubMed

    Yan, B; Stark, R E

    2000-08-01

    Although suberin in potato wound periderm is known to be a polyester containing long-chain fatty acids and phenolics embedded within the cell wall, many aspects of its molecular structure and polymer-polymer connectivities remain elusive. The present work combines biosynthetic incorporation of site-specifically (13)C-enriched acetates and phenylalanines with one- and two-dimensional solid-state (13)C NMR spectroscopic methods to monitor the developing suberin polymer. Exogenous acetate is found to be incorporated preferentially at the carboxyl end of the aliphatic carbon chains, suggesting addition during the later elongation steps of fatty acid synthesis. Carboxyl-labeled phenylalanine precursors provide evidence for the concurrent development of phenolic esters and of monolignols typical of lignin. Experiments with ring-labeled phenylalanine precursors demonstrate a predominance of sinapyl and guaiacyl structures among suberin's phenolic moieties. Finally, the analysis of spin-exchange (solid-state NOESY) NMR experiments in ring-labeled suberin indicates distances of no more than 0.5 nm between pairs of phenolic and oxymethine carbons, which are attributed to the aromatic-aliphatic polyester and the cell wall polysaccharide matrix, respectively. These results offer direct and detailed molecular information regarding the insoluble intermediates of suberin biosynthesis, indicate probable covalent linkages between moieties of its polyester and polysaccharide domains, and yield a clearer overall picture of this agriculturally important protective material.

  20. Molecular structure of quinuclidine betaine hydrate studied by X-ray diffraction, DFT, FTIR, Raman, NMR methods

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2009-03-01

    A new quinuclidine betaine (1-carboxymethyl-quinuclidinium inner salt), QNB, has been synthesized and characterized by X-ray diffraction, FTIR, NMR, and Raman spectra, and DFT calculations. QNB crystallized as monohydrate in monoclinic space group P2 1/n. Two water molecules link two QNB molecules into a cyclic system by two O-H···O hydrogen bonds of 2.731(1) and 2.760(1) Å. The optimized structure of (QNB·H 2O) 2 by the B3LYP/6-31G(d,p) method is more bent than in the crystal. The FTIR spectrum of the solid compound is consistent with the X-ray structure.

  1. Complete structure of the cell surface polysaccharide of Streptococcus oralis C104: A 600-MHz NMR study

    SciTech Connect

    Abeygunawardana, C.; Bush, C.A. ); Cisar, J.O. )

    1991-09-03

    Specific lectin-carbohydrate interactions between certain oral streptococci and actinomyces contribute to the microbial colonization of teeth. The receptor molecules of Streptococcus oralis, 34, ATCC 10557, and Streptococcus mitis J22 for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii are antigenically distinct polysaccharides, each formed by a different phosphodiester-linked oligosaccharide repeating unit. Receptor polysaccharide was isolated form S. oralis C104 cells and was shown to contain galactose, N-acetylgalactosamine, ribitol, and phosphate with molar ratios of 4:1:1:1. The {sup 1}H NMR spectrum of the polysaccharide shows that it contains a repeating structure. The individual sugars in the repeating unit were identified by {sup 1}H coupling constants observed in E-COSY and DQF-COSY spectra. NMR methods included complete resonance assignments ({sup 1}H and {sup 13}C) by various homonuclear and heteronuclear correlation experiments that utilize scalar couplings. Sequence and linkage assignments were obtained from the heteronuclear multiple-bond correlation (HMBC) spectrum. This analysis shows that the receptor polysaccharide of S. oralis C104 is a ribitol teichoic acid polymer composed of a linear hexasaccharide repeating unit containing two residues each of galactopyranose and galactofuranose and a residue each of GalNAc and ribitol joined end to end by phosphodiester linkages.

  2. [Study of the structure and dynamics of a chimeric variant of the SH3 domain (SHA-Bergerac) by NMR spectroscopy].

    PubMed

    Prokhorov, D A; Timchenko, M A; Kudrevatykh, Iu A; Fediukina, D V; Gushchina, L V; Khristoforov, V S; Filimonov, V V; Kutyshenko, V P

    2008-01-01

    A structural-dynamic study of one of the chimeric proteins (SHA) belonging to the SH3-Bergerac family and containing the KATANGKTYE sequence instead of the N47D48 beta-turn in the spectrin SH3 domain was carried out by high resolution NMR spectroscopy. The spatial structure of the protein was determined and its dynamics in solution was investigated on the basis of the NMR data. The elongation of the SHA polypeptide chain in comparison with the WT-SH3 original protein (by ~17%) exerts practically no effect on the general topology of the molecule. The presence of a stable beta-hairpin in the region of insertion was confirmed. This hairpin was shown to have a higher mobility in comparison with other regions of the protein.

  3. Investigation of structure, vibrational and NMR spectra of oxycodone and naltrexone: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Tavakol, Hossein; Esfandyari, Maryam; Taheri, Salman; Heydari, Akbar

    2011-08-01

    In this work, two important opioid antagonists, naltrexone and oxycodone, were prepared from thebaine and were characterized by IR, 1H NMR and 13C NMR spectroscopy. Moreover, computational NMR and IR parameters were obtained using density functional theory (DFT) at B3LYP/6-311++G** level of theory. Complete NMR and vibrational assignment were carried out using the observed and calculated spectra. The IR frequencies and NMR chemical shifts, determined experimentally, were compared with those obtained theoretically from DFT calculations, showed good agreements. The RMS errors observed between experimental and calculated data for the IR absorptions are 85 and 105 cm -1, for the 1H NMR peaks are 0.87 and 0.17 ppm and for those of 13C NMR are 5.6 and 5.3 ppm, respectively for naltrexone and oxycodone.

  4. High-resolution, high-pressure NMR studies of proteins.

    PubMed Central

    Jonas, J; Ballard, L; Nash, D

    1998-01-01

    Advanced high-resolution NMR spectroscopy, including two-dimensional NMR techniques, combined with high pressure capability, represents a powerful new tool in the study of proteins. This contribution is organized in the following way. First, the specialized instrumentation needed for high-pressure NMR experiments is discussed, with specific emphasis on the design features and performance characteristics of a high-sensitivity, high-resolution, variable-temperature NMR probe operating at 500 MHz and at pressures of up to 500 MPa. An overview of several recent studies using 1D and 2D high-resolution, high-pressure NMR spectroscopy to investigate the pressure-induced reversible unfolding and pressure-assisted cold denaturation of lysozyme, ribonuclease A, and ubiquitin is presented. Specifically, the relationship between the residual secondary structure of pressure-assisted, cold-denatured states and the structure of early folding intermediates is discussed. PMID:9649405

  5. A new Schiff base compound N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone): synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, 1H NMR and 13C NMR spectra.

    PubMed

    Saheb, Vahid; Sheikhshoaie, Iran

    2011-10-15

    The Schiff base compound, N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone) (NDHA) is synthesized through the condensation of 2-hydroxylacetophenone and 2,2-dimethyl 1,3-amino propane in methanol at ambient temperature. The yellow crystalline precipitate is used for X-ray single-crystal determination and measuring Fourier transform infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP, PBEPBE and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the FTIR, (1)H NMR and (13)C NMR spectra of the compound. Time-dependent density functional theory (TDDFT) method is used to calculate the UV-visible spectrum of NDHA. Vibrational frequencies are determined experimentally and compared with those obtained theoretically. Vibrational assignments and analysis of the fundamental modes of the compound are also performed. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR and (13)C NMR chemical shifts calculated by all DFT methods are consistent with the experimental data. However, the NMR shielding tensors computed at the B3LYP/6-31+G(d,p) level of theory are in better agreement with experimental (1)H NMR and (13)C NMR spectra. The electronic absorption spectrum calculated at the B3LYP/6-31+G(d,p) level by using TD-DFT method is in accordance with the observed UV-visible spectrum of NDHA. In addition, some quantum descriptors of the molecule are calculated and conformational analysis is performed and the results were compared with the crystallographic data.

  6. NMR Structures of Membrane Proteins in Phospholipid Bilayers

    PubMed Central

    Radoicic, Jasmina; Lu, George J.; Opella, Stanley J.

    2014-01-01

    Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins; especially those accomplished with the proteins in phospholipid bilayer environments where they function. PMID:25032938

  7. The interaction of vanadia with sepiolite. Structural studies by sup 51 V solid-state NMR and Raman spectroscopy

    SciTech Connect

    Occelli, M.L. ); Maxwell, R.S.; Eckert, H. )

    1992-09-01

    The interaction of vanadium with sepiolite, a layered magnesium silicate used to stabilize cracking catalysts against metal contaminants in crude oils, is investigated. To this end, field-dependent {sup 51}V wideline, magic-angle-spinning (MAS), and nutation NMR studies, together with X-ray diffraction (XRD) and laser Raman spectroscopy (LRS) results, are reported on sepiolite samples impregnated with a solution of vanadyl naphthenate in benzene. These results are discussed in connection with benchmark NMR data of crystallographically well-defined model compounds in the MgO-V{sub 2}O{sub 5} system. When heated near 760 C in the presence of steam, sepiolite decomposes into enstatite (MgSiO{sub 3}) and silica. If the hydrothermal treatment is repeated in the presence of vanadium, a disordered microcrystalline phase {alpha}-Mg{sub 2}V{sub 2}O{sub 7}. An MgV{sub 2}O{sub 6}-like, distorted octahedral environment is present only in samples with very high surface coverages and can be suppressed by choosing multiple-step over single-step impregnation.

  8. Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

    PubMed Central

    2015-01-01

    A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

  9. Protein structure determination with paramagnetic solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Jaroniec, Christopher P

    2013-09-17

    Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2

  10. [NMR study of complex formation of aromatic ligands with heptadeoxynucleotide 5'-d(GCGAAGC) forming stable hairpin structure in aqueous solution].

    PubMed

    Veselkov, A N; Eaton, R J; Semanin, A V; Pakhomov, V I; Dymant, L N; Karavaev, L; Davies, D V

    2002-01-01

    Complex formation of hairpin-producing heptadeoxynucleotide 5'-d(GCGAAGC) with aromatic molecules: acridine dye proflavine and anthracycline antibiotic daunomycin was studied by one-dimensional 1H NMR and two-dimensional correlation 1H-1H (2M-TOCSY, 2M-NOESY), 1H-31P (2M-HMBC) NMR spectroscopy (500 and 600 MHz) in aqueous solution. Concentration and temperature dependences for the chemical shifts of ligand protons were measured, molecular models of equilibrium in solution were developed, and equilibrium thermodynamic parameters for the formation of intercalation complexes were calculated. Spatial structures of dye and antibiotic complexes with the heptamer hairpin were constructed on the basis of 2M-NOE data and the calculated values of limiting chemical shifts of ligand protons.

  11. Dynamic structures of intact chicken erythrocyte chromatins as studied by 1H-31P cross-polarization NMR.

    PubMed Central

    Akutsu, H; Nishimoto, S; Kyogoku, Y

    1994-01-01

    The dynamic properties of DNA in intact chicken erythrocyte cells, nuclei, nondigested chromatins, digested soluble chromatins, H1, H5-depleted soluble chromatins and nucleosome cores were investigated by means of single-pulse and 1H-31P cross-polarization NMR. The temperature dependence of the phosphorus chemical shift anisotropy was identical for the former three in the presence of 3 mM MgCl2, suggesting that the local higher order structure is identical for these chromatins. The intrinsic phosphorus chemical shift anisotropy of the nucleosome cores was -159 ppm. The chemical shift anisotropy of DNA in the chromatins can be further averaged by the motion of the linker DNA. The spin-lattice relaxation time in the rotating frame of the proton spins (T1p) of the nondigested chromatins was measured at various locking fields. The result was analyzed on the assumption of the isotropic motion to get a rough value of the correlation time of the motion efficient for the relaxation, which was eventually ascribed to the segmental motion of the linker DNA with restricted amplitude. The 30 nm filament structure induced by NaCl was shown to be dynamically different from that induced by MgCl2. Side-by-side compaction of 30-nm filaments was suggested to be induced in the MgCl2 concentration range higher than 0.3 mM. Biological significance of the dynamic structure was discussed in connection with the results obtained. PMID:7948693

  12. Two-dimensional 1H-NMR study of the spatial structure of neurotoxin II from Naja naja oxiana.

    PubMed

    Golovanov, A P; Lomize, A L; Arseniev, A S; Utkin, Y N; Tsetlin, V I

    1993-05-01

    The spatial structure of neurotoxin II from the venom of the central Asian cobra Naja naja oxiana was determined by two-dimensional 1H-NMR techniques and computational analysis. Nearly complete proton resonance assignments for 61 amino acid residues have been made using two-dimensional (2D) homonuclear total correlated spectroscopy, 2D homonuclear double-quantum-filtered correlated spectroscopy and 2D homonuclear NOE spectroscopy (NOESY) experiments. The cross-peak volumes in NOESY spectra spin-spin coupling constants of vicinal protons NH-C alpha H and C alpha H-C beta H and the observation of slow deuterium exchange of amide protons were used to define local structure and a set of constraints for distance geometry program DIANA. The average root-mean-square deviations are 53 pm for backbone heavy atoms and 118 pm for all heavy atoms of 19 final neurotoxin II conformations. The spatial structure is characterized by a short double-stranded (residues 1-5 and 13-17) and a triple-stranded (residues 22-30, 33-41 and 50-54) antiparallel beta-sheets.

  13. A novel tridentate Schiff base dioxo-molybdenum(VI) complex: synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, ¹H NMR and ¹³C NMR spectra.

    PubMed

    Saheb, Vahid; Sheikhshoaie, Iran; Stoeckli-Evans, Helen

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound.

  14. Structure of 6-hydroxy-1-methylquinolinium chloride hydrate studied by X-ray, DFT calculations, FTIR and NMR spectroscopes

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Komasa, A.; Ratajczak-Sitarz, M.; Katrusiak, A.; Koput, J.; Dega-Szafran, Z.; Szafran, M.

    2010-12-01

    The crystal structure of 6-hydroxy-1-methylquinolinium chloride hydrate ( 1), 6QBWHCl, is monoclinic, space group P2 1/ n and Z = 4. 1-Methyl-6-oxyquinolinium betaine, 6QB, is protonated and its OH group participates in a moderate hydrogen bond with water molecule (O(1)-H⋯O(W1) = 2.636(2) Å). The water molecule is further connected by a hydrogen bond to chloride ion (O(W1)-H(W2)⋯Cl(1) = 3.090(3) Å). Structures of five complexes ( 2- 6) have been optimized by the B3LYP/6-311G(d, p) level of theory and the results have been compared with the X-ray data of 1. Linear correlations between the experimental 1H and 13C NMR chemical shifts ( δexp) of complexes 2- 5 and the magnetic isotropic shielding constants ( σcal) calculated by the GIAO/B3LYP/6-311G(d, p) approach, using the screening solvation model (COSMO), δexp = a + bσcal, are reported. The probable assignments of the anharmonic experimental solid state vibrational frequencies of anhydrous complex, 6QBHCl, based on the calculated B3LYP/6-311G(d, p) harmonic frequencies have been proposed.

  15. Ion pairs of indobenzimidazolo cyanines: a structural study based on conductivity, absorption, fluorescence and 1H-NMR

    NASA Astrophysics Data System (ADS)

    Tatikolov, Aleksandr S.; Ishchenko, Aleksandr A.; Ghelli, Stefano; Ponterini, Glauco

    1998-11-01

    Asymmetric benzimidazolo carbo, di- and tricarbocyanines form ion pairs of the solvent-separated and contact types with different counterions in tetrahydrofuran, toluene and toluene-nitrile mixtures. The dissociation constants of the ion pairs in tetrahydrofuran, evaluated from conductivity data, do not depend on the length of the polymethine chain and show only a small decrease with decreasing counterion size. The absorption and fluorescence excitation spectra of the contact ion pairs exhibit a pronounced hypsochromic shift with respect to the solvated ions and the solvent-separated ion pairs. 1H-NMR experiments have provided information about the electronic structures of the ions of both the asymmetric dyes and the corresponding symmetric carbocyanines. They have also revealed different preferred anion locations in the contact ion pairs of the symmetric indocarbocyanine on one hand, and of the benzimidazolo carbocyanine and the asymmetric dyes on the other. This structural difference is suggested to be a cause of the observed opposite effects of ion pairing on the isomerization kinetics of the two groups of dyes.

  16. 17O NMR studies of local structure and phase evolution for materials in the Y 2Ti 2O 7-ZrTiO 4 binary system

    NASA Astrophysics Data System (ADS)

    Palumbo, John L.; Schaedler, Tobias A.; Peng, Luming; Levi, Carlos G.; Grey, Clare P.

    2007-07-01

    17O MAS NMR and XRD studies of precursor-derived Y 1.6Zr 0.4Ti 2O 7.2 and Y 1.2Zr 0.8Ti 2O 7.4 have been performed to investigate the development of local and long-range order in these materials as they evolve from a metastable amorphous state upon heating. Zirconium titanate (ZrTiO 4) was also investigated to help interpret the 17O NMR spectra of the ternary compositions. Consistent with earlier studies, crystallization was observed at 800 °C to form a fluorite structure and a small amount of rutile; weak broad reflections were also observed which were ascribed to the presence of small pyrochlore-like ordered domains or particles within the fluorite phase. As the temperature was increased further, the sizes of these domains grew along with the concentration of rutile. At the highest temperature studied (1300 °C), the reflections of the thermodynamic phases, pyrochlore and zirconium titanate (ZrTiO 4), dominated the XRD pattern. The 17O NMR spectra revealed a series of different peaks that were assigned to different 3- and 4-coordinate O local environments. The data were consistent with the formation of a metastable phase Y 2-xZr xTi 2-yZr yO 7+x with pyrochlore-like ordering but with Zr substitution on both cation sites of the pyrochlore structure. At low temperatures, doping on the A (Y 3+) sites predominates (i.e., x> y), consistent with the fact that the pyrochlore develops out of a more disordered fluorite-like, phase. As the temperature is raised, the Zr doping on the A site decreases and the metastable phase at this temperature can now be written as Y 2-x'Zr x'Ti 2-y'Zr y'O 7+x' (i.e., x'< y'); TiO 2 is also observed, consistent with this suggestion. At high temperatures, doping on the B site decreases and the resonances due to the stoichiometric pyrochlore yttrium titanate (Y 2Ti 2O 7) dominate the NMR spectra. Weaker 17O NMR resonances due zirconium titanate (ZrTiO 4) are also observed.

  17. Improving the quality of protein structures derived by NMR spectroscopy.

    PubMed

    Spronk, Christian A E M; Linge, Jens P; Hilbers, Cornelis W; Vuister, Geerten W

    2002-03-01

    Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in terms of good quality of local- and overall geometry. Recent surveys indicate that structures solved by NMR-spectroscopy normally are of lower precision than high-resolution X-ray structures. Here, we present a refinement protocol that improves the quality of protein structures determined by NMR-spectroscopy to the level of those determined by high resolution X-ray crystallography in terms of local geometry. The protocol was tested on experimental data of the proteins IL4 and Ubiquitin and on simulated data of the protein Crambin. In almost all aspects, the protocol yielded better results in terms of accuracy and precision. Independent validation of the results for Ubiquitin, using residual dipolar couplings, indicates that the ensemble of NMR structure is substantially improved by the protocol.

  18. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.

    PubMed

    Mao, Binchen; Tejero, Roberto; Baker, David; Montelione, Gaetano T

    2014-02-05

    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.

  19. Modification of structure and digestibility of chestnut starch upon cooking: a solid state (13)C CP MAS NMR and enzymatic degradation study.

    PubMed

    Pizzoferrato, L; Rotilio, G; Paci, M

    1999-10-01

    The modification of starch, which is the major component of the polysaccharide fraction of chestnuts (Castanea sativa), has been studied from the point of view of structure and digestibility to understand the modifications induced by cooking and, specifically, by the Maillard reaction. The study was carried out by enzymatic degradation kinetics, monitoring the glucose released upon time, and by solid state (13)C CP MAS NMR, which has the potential of monitoring the solid state phase changes occurring upon chemical modification due to the cooking process. Results obtained reveal that large changes are induced in the macromolecular structure of starchy materials and that these changes are correlated with changes of digestibility in terms of enzymatic degradation resistance. In the system studied, the extension of the Maillard reaction is not such as to exert a significant influence on structure and/or digestibility of chestnut starch.

  20. High-Resolution NMR Studies of Human Tissue Factor

    PubMed Central

    Nuzzio, Kristin M.; Watt, Eric D.; Boettcher, John M.; Gajsiewicz, Joshua M.; Morrissey, James H.; Rienstra, Chad M.

    2016-01-01

    In normal hemostasis, the blood clotting cascade is initiated when factor VIIa (fVIIa, other clotting factors are named similarly) binds to the integral membrane protein, human tissue factor (TF). The TF/fVIIa complex in turn activates fX and fIX, eventually concluding with clot formation. Several X-ray crystal structures of the soluble extracellular domain of TF (sTF) exist; however, these structures are missing electron density in functionally relevant regions of the protein. In this context, NMR can provide complementary structural information as well as dynamic insights into enzyme activity. The resolution and sensitivity for NMR studies are greatly enhanced by the ability to prepare multiple milligrams of protein with various isotopic labeling patterns. Here, we demonstrate high-yield production of several isotopically labeled forms of recombinant sTF, allowing for high-resolution NMR studies both in the solid and solution state. We also report solution NMR spectra at sub-mM concentrations of sTF, ensuring the presence of dispersed monomer, as well as the first solid-state NMR spectra of sTF. Our improved sample preparation and precipitation conditions have enabled the acquisition of multidimensional NMR data sets for TF chemical shift assignment and provide a benchmark for TF structure elucidation. PMID:27657719

  1. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy.

    PubMed

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu

    2017-01-23

    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  2. Novel phthalocyaninatobis(alkylcarboxylato)silicon(IV) compounds: NMR data and X-ray structures to study the spacing provided by long hydrocarbon tails that enhance their solubility.

    PubMed

    Sosa-Sánchez, Jose L; Sosa-Sánchez, Arturo; Farfán, Norberto; Zamudio-Rivera, Luis S; López-Mendoza, Gerson; Pérez Flores, Javier; Beltrán, Hiram I

    2005-07-04

    The reaction between trans-PcSiCl2 (1) and the potassium salts of six fatty acids (2 a-2 f) led to the trans-PcSi[OOC(CH2)nCH3]2 compounds (3 a-3 f), which were characterised by elemental analysis, IR, UV/Vis and 1H, 13C, and 29Si NMR spectroscopy. From a detailed study of the NMR spectra, the strong anisotropic currents of the Pc macrocycle were found to have an effect on up to the sixth methylenic group. As expected, the length of the hydrocarbon tail does not affect the chemical shift of the 29Si nucleus of any of the compounds, appearing at around -222.6. The structures of PcSi[OOC(CH2)nCH3]2, where n = 7, 10, 12, 13 and 20, were determined by X-ray crystallography. All the compounds were found to be triclinic with a P1 space group. In all cases the observed crystallographic pseudosymmetry is Ci and the asymmetric unit consists of half a molecule. The silicon atom is at the centre of a distorted octahedron and hence its coordination number is six. The carboxylate fragments are in a trans configuration with respect to the Pc macrocycle. The supramolecular structures are discussed in detail herein. The correlation between the 1H NMR chemical shifts and the position of the corresponding carbon atoms in the hydrocarbon tail reveals that the dicarboxylate substituents exhibit a spacer-like behaviour that enhances the solubility. A detailed study of the tail variable allowed us to evaluate the loss of radial shielding along the Pc2- ligand.

  3. Desktop NMR for structure elucidation and identification of strychnine adulteration.

    PubMed

    Singh, Kawarpal; Blümich, Bernhard

    2017-03-27

    Elucidating the structure of complex molecules is difficult at low magnetic fields due to the overlap of different peak multiplets and second-order coupling effects. This is even more challenging for rigid molecules with small chemical shift differences and with prochiral centers. Since low-field NMR spectroscopy is sometimes presumed as restricted to the analysis of only small and simple molecules, this paper aims at countering this misconception: it demonstrates the use of low-field NMR spectroscopy in chemical forensics for identifying strychnine and its counterions by exploring the chemical shift as a signature in different 1D (1)H and (13)C experiments. Hereby the applied methodologies combine various 1D and 2D experiments such as 1D (1)H, (13)C, DEPT, and 2D COSY, HETCOR, HSQC, HMBC and J-resolved spectroscopy to elucidate the molecular structure and skeleton of strychnine at 1 Tesla. Strychnine is exemplified here, because it is a basic precursor in the chemistry of natural products and is employed as a chemical weapon and as a doping agent in sports including the Olympics. In our study, the molecular structure of the compound could be identified either with a 1D experiment at high magnetic field or with HMBC and HSQC experiments at 1 T. In conclusion, low-field NMR spectroscopy enables the chemical elucidation of the strychnine structure through a simple click with a computer mouse. In situations where a high-field NMR spectrometer is unavailable, compact NMR spectrometers can nevertheless generate knowledge of the structure, important for identifying the different chemical reaction mechanisms associated with the molecule. Desktop NMR is a cost-effective viable option in chemical forensics. It can prove adulteration and identify the origin of different strychnine salts, in particular, the strychnine free base, strychnine hemisulphate and strychnine hydrochloride. The chemical shift signatures report the chemical structure of the molecules due to the impact

  4. Native dynamics from diversity in NMR structures

    NASA Astrophysics Data System (ADS)

    Lammert, Heiko; Onuchic, Jose

    2015-03-01

    Protein function relies on the characteristic dynamics that arise in the protein's unique native structure, controlled by the smooth, funneled energy landscape evolved to enable fast and reliable folding. Structure-based models draw on energy landscape theory to build an ideally funneled energy landscape only from a protein's native structure. Simplified interactions of homogeneous strength are used to eliminate energetic frustration. The dynamics of the model are controlled by geometric constraints imposed by the native fold. The energy landscapes of many actual proteins are smooth enough to let such unfrustrated models describe their folding mechanisms. But conflicting functional demands upon the sequence may introduce sufficient frustration into the energetics to affect the dynamics. For such cases heterogeneous interactions can be optimized based on additional data. We use the diversity among the conformations deposited in a set of NMR structures to estimate the extent of fluctuations in the native state to build an improved model of protein S6. Qualitative modifications bring the observed mechanism into agreement with experiment, and matching of the entire fluctuation profile leads to similar contact maps as optimization based on either phi-values of sequence data.

  5. Interfaces in polymer nanocomposites - An NMR study

    NASA Astrophysics Data System (ADS)

    Böhme, Ute; Scheler, Ulrich

    2016-03-01

    Nuclear Magnetic Resonance (NMR) is applied for the investigation of polymer nanocomposites. Solid-state NMR is applied to study the modification steps to compatibilize layered double hydroxides with non-polar polymers. 1H relaxation NMR gives insight on the polymer dynamics over a wide range of correlation times. For the polymer chain dynamics the transverse relaxation time T2 is most suited. In this presentation we report on two applications of T2 measurements under external mechanical stress. In a low-field system relaxation NMR studies are performed in-situ under uniaxial stress. High-temperature experiments in a Couette cell permit the investigation of the polymer dynamics in the melt under shear flow.

  6. X-ray, FT-IR, NMR and PM5 structural studies and antibacterial activity of unexpectedly stable salinomycin-benzotriazole intermediate ester

    NASA Astrophysics Data System (ADS)

    Huczyński, Adam; Janczak, Jan; Antoszczak, Michał; Stefańska, Joanna; Brzezinski, Bogumil

    2012-08-01

    The unexpectedly stable benzotriazole ester of salinomycin (SAL-HOBt) - an intermediate product of the amidation reaction of salinomycin has been isolated and structurally characterised (using a single crystal) by X-ray, FT-IR, NMR and semiempirical methods. The results of the X-ray and spectroscopic studies demonstrated that this intermediate ester exist in the solid state and in solution exclusively as the stable O-acyl form. The molecular structure of SAL-HOBt is stabilised by relatively weak intramolecular hydrogen bonds. The PM5 calculation of possible structures of SAL-HOBt has shown that the O-acyl form is more energetically favourable than its N-oxide-N-acyl isomers. The antimicrobial tests show that SAL-HOBt is active against Gram-positive bacteria and clinical isolates methicillin-resistant Staphylococcus aureus (MIC = 1-2 μg/ml).

  7. Probing the atomic structure of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1): Insights from high-resolution solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Park, S. Y.; Lee, S. K.

    2015-12-01

    Probing the structural disorder in multi-component silicate glasses and melts with varying composition is essential to reveal the change of macroscopic properties in natural silicate melts. While a number of NMR studies for the structure of multi-component silicate glasses and melts including basaltic and andesitic glasses have been reported (e.g., Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125; Park and Lee, Geochim. Cosmochim. Acta, 2014, 26, 42), many challenges still remain. The composition of multi-component basaltic melts vary with temperature, pressure, and melt fraction (Kushiro, Annu. Rev. Earth Planet. Sci., 2001, 71, 107). Especially, the eutectic point (the composition of first melt) of nepheline-forsterite-quartz (the simplest model of basaltic melts) moves with pressure from silica-saturated to highly undersaturated and alkaline melts. The composition of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1, the xenolith from Kilbourne Hole) also vary with pressure. In this study we report experimental results for the effects of composition on the atomic structure of Na2O-MgO-Al2O3-SiO2 (NMAS) glasses in nepheline (NaAlSiO4)-forsterite (Mg2SiO4)-quartz (SiO2) eutectic composition and basaltic glasses generated by partial melting of upper mantle peridotite (KLB-1) using high-resolution multi-nuclear solid-state NMR. The Al-27 3QMAS (triple quantum magic angle spinning) NMR spectra of NMAS glasses in nepheline-forsterite-quartz eutectic composition show only [4]Al. The Al-27 3QMAS NMR spectra of KLB-1 basaltic glasses show mostly [4]Al and a non-negligible fraction of [5]Al. The fraction of [5]Al, the degree of configurational disorder, increases from 0 at XMgO [MgO/(MgO+Al2O3)]=0.55 to ~3% at XMgO=0.79 in KLB-1 basaltic glasses while only [4]Al are observed in nepheline-forsterite-quartz eutectic composition. The current experimental results provide that the fraction of [5]Al abruptly increases by the effect of

  8. Shedding new light on ZnCl2-mediated addition reactions of Grignard reagents to ketones: structural authentication of key intermediates and diffusion-ordered NMR studies.

    PubMed

    Armstrong, David R; Clegg, William; García-Alvarez, Pablo; McCall, Matthew D; Nuttall, Lorraine; Kennedy, Alan R; Russo, Luca; Hevia, Eva

    2011-04-11

    Building on recent advances in synthesis showing that the addition of inorganic salts to Grignard reagents can greatly enhance their performance in alkylation reactions to ketones, this study explores the reactions of EtMgCl with benzophenone in the presence of stoichiometric or catalytic amounts of ZnCl(2) with the aim of furthering the understanding of the role and constitution of the organometallic species involved in these transformations. Investigations into the metathesis reactions of three molar equivalents of EtMgCl with ZnCl(2) led to the isolation and characterisation (X-ray crystallography and (1)H and (13)C NMR spectroscopy) of novel magnesium "zinc-rich" zincate [{(THF)(6)Mg(2)Cl(3)}(+){Zn(2)Et(5)}(-)] (1), whose complicated constitution in THF solutions was assessed by variable-temperature (1)H DOSY NMR studies. Compound 1 reacted with one equivalent of benzophenone to yield magnesium magnesiate [{(THF)(6)Mg(2)Cl(3)}(+){Mg(2)(OC(Et)Ph(2))(2)Cl(3)(THF)}(-)] (3), whose structure was determined by X-ray crystallography. (1)H NMR monitoring of this reaction showed two equivalents of ZnEt(2) formed as a co-product, which together with the "magnesium only constitution" of 3 provides experimental insights into how zinc can be efficiently recycled in these reactions, and therefore used catalytically. The chemoselectivity of this reaction can be rationalised in terms of the synergic effect of magnesium and zinc and contrasts with the results obtained when benzophenone was allowed to react with EtMgCl in the absence of ZnCl(2), where the reduction of the ketone takes place preferentially. The reduction product [{(THF)(5)Mg(3)Cl(4){OC(H)Ph(CF(3))}(2)] (4) obtained from the reaction of EtMgCl with 2,2,2-trifluoroacetophenone was established by X-ray crystallography and multinuclear ((1)H, (13)C and (19)F) NMR spectroscopy. Compounds 3 and 4 exhibit new structural motifs in magnesium chemistry having MgCl(2) integrated within their constitution, which highlights

  9. Studies on silicon NMR characterization and kinetic modeling of the structural evolution of siloxane-based materials and their applications in drug delivery and adsorption

    NASA Astrophysics Data System (ADS)

    Ambati, Jyothirmai

    This dissertation presents studies of the synthetic processes and applications of siloxane-based materials. Kinetic investigations of bridged organoalkoxysilanes that are precursors to organic-inorganic hybrid polysilsesquioxanes are a primary focus. Quick gelation despite extensive cyclization is found during the polymerization of bridged silane precursors except for silanes with certain short bridges. This work is an attempt to characterize and understand some of the distinct features of bridged silanes using experimental characterization, kinetic modeling and simulation. In addition to this, the dissertation shows how the properties of siloxane-materials can be engineered for drug delivery and adsorption. The phase behavior of polymerizing mixtures is first investigated to identify the solutions that favor kinetic characterization. Microphase separation is found to cause gradual loss of NMR signal for certain initial compositions. Distortionless Enhancement by Polarization Transfer 29Si NMR is employed to identify the products of polymerization of some short-bridged silanes under no signal loss conditions. This technique requires knowing indirect 29Si-1H scalar coupling constants which sometimes cannot be measured due to second-order effects. However, the B3LYP density functional method with 6-31G basis set is found to predict accurate 29Si- 1H coupling constants of organoalkoxysilanes and siloxanes. The scalar coupling constants thus estimated are employed to resolve non-trivial coupled NMR spectra and quantitative kinetic modeling is performed using the DEPT Si NMR transients. In order to investigate the role of the organic bridging group, the structural evolution of bridged and non-bridged silanes are compared using Monte Carlo simulations. Kinetic and simulation models suggest that cyclization plays a key role right from the onset of polymerization for bridged silanes even more than in non-bridged silanes. The simulations indicate that the carbosiloxane

  10. NMR Methods to Study Dynamic Allostery

    PubMed Central

    Grutsch, Sarina; Brüschweiler, Sven; Tollinger, Martin

    2016-01-01

    Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach. PMID:26964042

  11. Dynamics and Structure in Good Glass Formers LiCl-RH2O: A NMR and Quasielastic Neutron Scattering Study

    NASA Astrophysics Data System (ADS)

    Maurin, P.; Dupuy-Philon, J.; Jal, J.; Asahi, N.; Kamiyama, T.; Kawamura, J.; Nakamura, Y.

    The temperature behaviour of the self-diffusion coefficient and of the spin-lattice correlation time have been analysed from QENS and NMR experiments performed on LiCl-6H2O and LiCl-4H2O. Those results throw some light to primary and secondary relaxation time behaviour in these systems.

  12. Microgram-scale protein structure determination by NMR.

    PubMed

    Aramini, James M; Rossi, Paolo; Anklin, Clemens; Xiao, Rong; Montelione, Gaetano T

    2007-06-01

    Using conventional triple-resonance nuclear magnetic resonance (NMR) experiments with a 1 mm triple-resonance microcoil NMR probe, we determined near complete resonance assignments and three-dimensional (3D) structure of the 68-residue Methanosarcina mazei TRAM protein using only 72 mug (6 microl, 1.4 mM) of protein. This first example of a complete solution NMR structure determined using microgram quantities of protein demonstrates the utility of microcoil-probe NMR technologies for protein samples that can be produced in only limited quantities.

  13. Cell-free expression of the APP transmembrane fragments with Alzheimer's disease mutations using algal amino acid mixture for structural NMR studies.

    PubMed

    Bocharova, Olga V; Urban, Anatoly S; Nadezhdin, Kirill D; Bocharov, Eduard V; Arseniev, Alexander S

    2016-07-01

    Structural investigations need ready supply of the isotope labeled proteins with inserted mutations n the quantities sufficient for the heteronuclear NMR. Though cell-free expression system has been widely used in the past years, high startup cost and complex compound composition prevent many researches from the developing this technique, especially for membrane protein production. Here we demonstrate the utility of a robust, cost-optimized cell-free expression technique for production of the physiologically important transmembrane fragment of amyloid precursor protein, APP686-726, containing Alzheimer's disease mutations in the juxtamembrane (E693G, Arctic form) and the transmembrane parts (V717G, London form, or L723P, Australian form). The protein cost was optimized by varying the FM/RM ratio as well as the amino acid concentration. We obtained the wild-type and mutant transmembrane fragments in the pellet mode of continuous exchange cell-free system consuming only commercial algal mixture of the (13)C,(15)N-labeled amino acids. Scaling up analytical tests, we achieved milligram quantity yields of isotope labeled wild-type and mutant APP686-726 for structural studies by high resolution NMR spectroscopy in membrane mimicking environment. The described approach has from 5 to 23-fold cost advantage over the bacterial expression methods described earlier and 1.5 times exceeds our previous result obtained with the longer APP671-726WT fragment.

  14. Structure and disorder in iron-bearing sodium silicate glasses and melts: High-resolution 29Si and 17O solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Kim, H.; Lee, S.

    2012-12-01

    Understanding of the effect of iron content on the structure (Si coordination environment and the degree of polymerization) of iron-bearing silicate melts and glasses is essential for studying their macroscopic properties and diverse geological processes in Earth's interior. Although the recent advances in high-resolution solid-state NMR techniques provide detailed structural information of a diverse iron-free oxide glasses with varying composition (e.g., Lee, P. Natl. Acad. Sci. USA., 2011, 108, 6847; Lee and Sung, Chem. Geol., 2008, 256, 326; Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125; Lee et al., Phys. Rev., 103, 095501, 2009), their application to iron-bearing silicate glasses has a limited usefulness in resolving atomic configurations due to the effect of paramagnetic cation (i.e., Fe) on the NMR spectra. Here, we report the first ^{29}Si and ^{17}O NMR spectra for sodium-iron silicate glasses with varying iron content (Na_{2}O-Fe_{2}O_{3}-SiO_{2} glasses, up to 34.60 wt% Fe_{2}O_{3}), revealing previously unknown details of iron-induced changes in structure and disorder. While signal intensity decreases and peak width increases exponentially with increasing iron content [=Fe_{2}O_{3}/(Na_{2}O+Fe_{2}O_{3})], ^{29}Si MAS NMR spectra for sodium-iron silicate glasses present the slight peak shift and an asymmetrical peak broadening toward higher Q^{n} species with increasing iron content. This result implies an increase in the degree of polymerization with increasing iron content. Additionally, ^{29}Si spin-relaxation time (T_{1}) for the glasses decreases with increasing of iron content by several orders of magnitude. ^{17}O 3QMAS NMR spectra for the glasses show well-resolved non-bridging oxygen (NBO, Na-O-Si) and bridging oxygen (BO, Si-O-Si) even at relatively high iron content, providing the first direct experimental estimation of the degree of polymerization. In sodium-iron silicate glasses, the fraction of NBO decreases with increasing iron

  15. Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study.

    PubMed Central

    van den Hoogen, Y T; van Beuzekom, A A; de Vroom, E; van der Marel, G A; van Boom, J H; Altona, C

    1988-01-01

    Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex. NMR and model-building studies were performed on the duplex (CUGGUGCGG).(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (approximately equal to 0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles zeta/alpha. An energy-minimized model of the duplex, which fits the present collection of data, is presented. PMID:3387215

  16. NMR studies of nucleic acid dynamics

    NASA Astrophysics Data System (ADS)

    Al-Hashimi, Hashim M.

    2013-12-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.

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

    PubMed

    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.

  18. NMR studies of cation transport across membranes

    SciTech Connect

    Shochet, N.R.

    1985-01-01

    /sup 23/Na NMR Studies of cation transport across membranes were conducted both on model and biological membranes. Two ionophores, the carrier monensin and the channel-former gramicidin, were chosen to induce cation transport in large unilamellar phosphatidylcholine vesicles. The distinction between the NMR signals arising from the two sides of the membrane was achieved by the addition of an anionic paramagnetic shift reagent to the outer solution. The kinetics of the cation transport across the membrane was observed simultaneously monitoring the changes in the /sup 23/Na NMR signals of both compartments. Two mathematical models were developed for the estimation of the transport parameters of the monensin- and gramicidin-induced cation transport. The models were able to fit the experimental data very well. A new method for the estimation of the volume trapped inside the vesicles was developed. The method uses the relative areas of the intra- and extravesicular NMR signals arising from a suspension of vesicles bathed in the same medium they contain, as a measure for the relative volumes of these compartments. Sodium transport across biological membranes was studied by /sup 23/ NMR, using suspensions of cultured nerve cells. The sodium influx through voltage-gated channels was studied using the channel modifier batrachotoxin in combination with scorpion toxin.

  19. Combined experimental and quantum chemical studies on spectroscopic (FT-IR, FT-Raman, UV-Vis, and NMR) and structural characteristics of quinoline-5-carboxaldehyde

    NASA Astrophysics Data System (ADS)

    Kumru, Mustafa; Altun, Ahmet; Kocademir, Mustafa; Küçük, Vesile; Bardakçı, Tayyibe; Şaşmaz, İbrahim

    2016-12-01

    Comparative experimental and theoretical studies have been performed on the structure and spectral (FT-IR, FT-Raman, UV-Vis and NMR) features of quinoline-5-carboxaldehyde. Quantum chemical calculations have been carried out at Hartree-Fock and density functional B3LYP levels with the triple-zeta 6-311++G** basis set. Two stable conformers of quinoline-5-carboxaldehyde arising from the orientation of the carboxaldehyde moiety have been located at the room temperature. The energetic separation of these conformers is as small as 2.5 kcal/mol with a low transition barrier (around 9 kcal/mol). Therefore, these conformers are expected to coexist at the room temperature. Several molecular characteristics of quinoline-5-carboxaldehyde obtained through B3LYP and time-dependent B3LYP calculations, such as conformational stability, key geometry parameters, vibrational frequencies, IR and Raman intensities, UV-Vis vertical excitation energies and the corresponding oscillator strengths have been analyzed. The 1H and 13C NMR chemical shifts of quinoline-5-carboxaldehyde were also investigated.

  20. NMR studies of chiral P,S-chelate platinum, rhodium, and iridium complexes and the X-ray structure of a palladium(II) allyl derivative

    SciTech Connect

    Albinati, A.; Eckert, J.; Pregosin, P.; Ruegger, H.; Salzmann, R.; Stoessel, C.

    1997-02-18

    Several Rh(I), Ir(III), and Pt(II) complexes of the chiral P,S-bidentate ligand 2 have been prepared and characterized. Detailed two-dimensional NMR studies show that (i) the boat-type chelate ring and the stereogenic sulfur center can invert rapidly at ambient temperature and (ii) the sulfur donor may dissociate, essentially destroying the chiral pocket. The solid-state structure of [Pt({eta}{sup 3}-C{sub 3}H{sub 5})(2)]PF{sub 6} (3) has been determined and the sulfur substituent shown to have an axial orientation. The six-membered chelate ring takes up a boat-like conformation. As shown by an X-ray diffraction study for 3, and via incoherent inelastic neutron scattering (IINS) measurements for the Pd analog, 4, the OH group is remote from the metal atom. 42 refs., 11 figs., 6 tabs.

  1. Structural characterization, solvent effects on nuclear magnetic shielding tensors, experimental and theoretical DFT studies on the vibrational and NMR spectra of 3-(acrylamido)phenylboronic acid

    NASA Astrophysics Data System (ADS)

    Alver, Özgür; Kaya, Mehmet Fatih; Dikmen, Gökhan

    2015-12-01

    Structural elucidation of 3-(acrylamido)phenylboronic acid (C9H10BNO3) was carried out with 1H, 13C and HETCOR NMR techniques. Solvent effects on nuclear magnetic shielding tensors were examined with deuterated dimethyl sulfoxide, acetone, methanol and water solvents. The correct order of appearance of carbon and hydrogen atoms on NMR scale from highest magnetic field region to the lowest one were investigated using different types of theoretical levels and the details of the levels were presented in this study. Stable structural conformers and vibrational band analysis of the title molecule (C9H10BNO3) were studied both experimental and theoretical viewpoints using FT-IR, Raman spectroscopic methods and density functional theory (DFT). FT-IR and Raman spectra were obtained in the region of 4000-400 cm-1, and 3700-10 cm-1, respectively. Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d, p) basis set was included in the search for optimized structures and vibrational wavenumbers. Experimental and theoretical results show that after application of a suitable scaling factor density functional B3LYP method resulted in acceptable results for predicting vibrational wavenumbers except OH and NH stretching modes which is most likely arising from increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges those of which are not fully taken into consideration in theoretical processes. To make a more quantitative vibrational assignments, potential energy distribution (PED) values were calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.

  2. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    PubMed Central

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano

    2016-01-01

    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 15N-1H 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 (DP) 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. PMID:26081575

  3. NMR and structural features of noble-metal fluorides

    SciTech Connect

    Gabuda, S.P.; Zemskov, S.V.

    1987-11-01

    NMR studies are reported on the structures of binary and other noble-metal fluorides. Revised measurements have been made on /sup 19/F chemical shifts and the anisotropy in them. A relationship is considered between the screening tensor for /sup 19/F and the electronic structure of the molecule or ion containing the noble-metal cation in the electronic configuration d/sup 6/, d/sup 8/, or d/sup 10/. The observed anomalous shifts in this class of compound are explained qualitatively in terms of paired electrons in filled d shells affecting the result within the framework of the classical theory of magnetic nuclear screening.

  4. Studies of Structure and Dynamics of Light Harvesting Complex 1 of R. Sphaeroides by Solid State NMR

    SciTech Connect

    McDermott, Ann E

    2014-11-14

    Studies of the structure and dynamics of a light harvesting complex from photosynthetic bacteria are described. Using Nuclear Magnetic Resonance methods, we explored the idea that optical properties are modulated via a conformational switch in the BChl chromophores, in a way that provides benefits for the efficiency of energy conversion.

  5. (17)O NMR Investigation of Water Structure and Dynamics.

    PubMed

    Keeler, Eric G; Michaelis, Vladimir K; Griffin, Robert G

    2016-08-18

    The structure and dynamics of the bound water in barium chlorate monohydrate were studied with (17)O nuclear magnetic resonance (NMR) spectroscopy in samples that are stationary and spinning at the magic-angle in magnetic fields ranging from 14.1 to 21.1 T. (17)O NMR parameters of the water were determined, and the effects of torsional oscillations of the water molecule on the (17)O quadrupolar coupling constant (CQ) were delineated with variable temperature MAS NMR. With decreasing temperature and reduction of the librational motion, we observe an increase in the experimentally measured CQ explaining the discrepancy between experiments and predictions from density functional theory. In addition, at low temperatures and in the absence of (1)H decoupling, we observe a well-resolved (1)H-(17)O dipole splitting in the spectra, which provides information on the structure of the H2O molecule. The splitting arises because of the homogeneous nature of the coupling between the two (1)H-(17)O dipoles and the (1)H-(1)H dipole.

  6. Isoxazole derivatives of alpha-pinene isomers: Synthesis, crystal structure, spectroscopic characterization (FT-IR/NMR/GC-MS) and DFT studies

    NASA Astrophysics Data System (ADS)

    Eryılmaz, Serpil; Gül, Melek; İnkaya, Ersin; Taş, Murat

    2016-03-01

    In this paper, the alpha-pinene isoxazole derivatives (3a-b-c, 4a-b) were synthesized via 1,3-dipolar cycloaddition and characterized with FT-IR, 1H NMR, 13C NMR and GC-MS. Isoxazole (C21H23NO) compound (4a) 6,6,7a,-trimethyl-3-(naphthalen-2-yl)-3a,4,5,6,7,7a-hexahydro-5,7-methanobenzo[d] was characterized by X-ray single crystal diffraction technique. The compound crystallizes in the monoclinic space group P 212121, with Z = 4. The molecular geometry of the compound was optimized by applying Density Functional Theory (DFT/B3LYP) method with 6-31G(d,p) and 6-311 + G(d,p) basis sets in the ground state and geometric parameters were compared with the X-ray analysis results of the structure. Results of the experimental FT-IR and NMR spectral analysis were examined in order to determine the compliance with vibrational frequencies, 1H NMR and 13C NMR chemical shifts values by using the Gauge-Independent Atomic Orbital (GIAO) method calculated over the optimized structure. Besides molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behaviour and Mulliken charge analysis of the (4a) compound were computed with the same method in gas phase, theoretically.

  7. Multidimensional solid-state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C-labeled Arabidopsis primary cell walls

    SciTech Connect

    Dick-Perez, Marilu; Wang, Tuo; Salazar, Andre; Zabotina, Olga A.; Hong, Mei

    2012-07-08

    Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high-resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic-angle-spinning (MAS) solid-state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with 13C and their NMR spectra were compared. Recent 13C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D 13C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. 13C spin–lattice relaxation times and 1H rotating-frame spin–lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near-native conditions. Copyright © 2012 John Wiley & Sons, Ltd.

  8. Synthesis, Infra-red, CP/MAS-NMR characterization, structural study and electrical properties of the bis(4-amino-2-chloropyridinium) tetrachlorozincate (II) monohydrate

    NASA Astrophysics Data System (ADS)

    Karâa, Najla; Hamdi, Besma; Ben Salah, Abdelhamid; Zouari, Ridha

    2013-10-01

    Single crystals of the new ionic salt bis(4-amino-2-chloropyridinium) tetrachlorozincate (II) monohydrate, (C5H6N2Cl)2 ZnCl4ṡH2O, were grown by slow evaporation from aqueous solution at room temperature. The compound was characterized by IR, thermal analysis (TGA-DSC), single crystal X-ray diffraction, CP/MAS-NMR and impedance spectroscopy. The structure (4-amino-2-chloropyridinium)2 ZnCl4·H2O, [(CAP)2ZnCl4·H2O], consists of isolated H2O, isolated [ZnCl4]2- tetrahedral anions and 4-amino-2-chloropyridinium [C5H6N2Cl] + cations, CAP, which are connected together via N-H⋯Cl, N-H⋯O ((N: pyridinium) and (N: amine)), O-H⋯Cl and C-H⋯Cl hydrogen bonds. Cation-cation, offset-face-to-face interactions (π-π stacking) between identical antiparallel CAP (aromatic-aromatic), in which they may be effective in the stabilization of the crystal structure. Solid state CP/MAS-NMR spectra showed five isotropic resonances, 13C, confirming the solid state structure determined by X-ray diffraction. Impedance spectroscopy study, reported for a single crystal, revealed that the conduction in the material was due to a hopping process. This work aims to reveal the thermal properties of a new zinc (II) based organic-inorganic hybrid and the conductivity properties that these compounds exhibit.

  9. Atomic structure and dehydration mechanism of amorphous silica: Insights from 29Si and 1H solid-state MAS NMR study of SiO2 nanoparticles

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Na; Lee, Sung Keun

    2013-11-01

    larger than those in 14 nm amorphous silica nanoparticles. Dehydration of 7 nm amorphous silica nanoparticles occurs at a lower temperature than that of 14 nm amorphous silica nanoparticles. 29Si MAS NMR results show that a possible simultaneous dehydroxylation can also occur with removal of the hydrogen bonded silanol in the 7 nm silica nanoparticles. The energy penalty of dehydroxylation estimated from 29Si MAS NMR spectra varies with Q species and is smaller in 7 nm than in 14 nm amorphous silica nanoparticles. These results demonstrate that the particle size of nanoparticles plays an important role in controlling the hydrogen contents, and thus overall hydrogen bond strength of hydroxyl groups and atomic structure of silanols can control dehydroxylation of amorphous silica nanoparticles. The structural information and mechanistic details obtained from the current study provide insights into the structure of hydrous species and dehydration mechanisms in crystalline and amorphous silicates in diverse geological settings, highlighting usually unknown effects of particle size on the dehydration processes.

  10. Effect of Sterol Structure on Chain Ordering of an Unsaturated Phospholipid: A 2H-NMR Study of POPC/Sterol Membranes

    NASA Astrophysics Data System (ADS)

    Shaghaghi, Mehran; Thewalt, Jenifer; Zuckermann, Martin

    2012-10-01

    The physical properties of biological membranes are considerably altered by the presence of sterols. In particular, sterols help to maintain the integrity of the cell by adjusting the fluidity of the plasma membrane. Cholesterol is in addition an important component of lipid rafts which are hypothesized to compartmentalize the cell membrane surface thereby making it possible for certain proteins to function. Using 2H-NMR spectroscopy, we studied the effect of a series of different sterols on the chain ordering of POPC, an unsaturated phospholipid present in eukaryotic cell membranes. We were able to assigned specific roles to the structural differences between the sterols by comparing the manner in which they affect the average lipid chain conformation of POPC.

  11. Structural and spectroscopic (UV-Vis, IR, Raman, and NMR) characteristics of anisaldehydes that are flavoring food additives: A density functional study in comparison with experiments

    NASA Astrophysics Data System (ADS)

    Altun, Ahmet; Swesi, O. A. A.; Alhatab, B. S. S.

    2017-01-01

    The molecular structures, vibrational spectra (IR and Raman), electronic spectra (UV-Vis and DOS), and NMR spectra (13C and 1H) of p-anisaldehyde, m-anisaldehyde, and o-anisaldehyde have been studied by using the B3LYP density functional and the 6-311++G** basis set. While p-anisaldehyde has been found to contain two stable conformers at room temperature, m-anisaldehyde and o-anisaldehyde contain four stable conformers. In agreement with the calculated ground-state energetics and small transition barriers, the comparison of the experimental and calculated spectra of the anisaldehydes indicates equilibrium between all conformers at room temperature. However, the two conformers of o-anisaldehyde, in which the methoxy group lies out of the ring plane, are too rare at the equilibrium. The equilibrium conditions of the conformers of the anisaldehyde isomers have been shown readily accessible through UV-Vis and 13C NMR spectral studies but requiring very detailed vibrational analyses. The effect of the solvent has been found to red-shift the electronic absorption bands and to make the anisaldehydes more reactive and soft. Molecular electrostatic potential maps of the anisaldehydes show that their oxygen atoms are the sites for nucleophilic reactivity. Compared with the most sophisticated NBO method, ESP charges have been found mostly reliable while Mulliken charges fail badly with the present large 6-311++G** basis set. The present calculations reproduce not only the experimental spectral characteristics of the anisaldehydes but also reveal their several structural features.

  12. Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

    SciTech Connect

    Trueba, Alondra Torres; Kroon, Maaike C.; Peters, Cor J.; Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A.; Alavi, Saman

    2014-06-07

    Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH{sub 3}F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. {sup 13}C NMR chemical shifts of a CH{sub 3}F/CH{sub 4}/TBME sH hydrate and a temperature analysis of the {sup 2}H NMR powder lineshapes of a CD{sub 3}F/THF sII and CD{sub 3}F/TBME sH hydrate, displayed evidence that the populations of CH{sub 4} and CH{sub 3}F in the D and D{sup ′} cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH{sub 3}F and TBME/CH{sub 4} sH hydrates showed that the presence of CH{sub 3}F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH{sub 3}F and THF/CH{sub 4} sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH{sub 3}F molecules between adjacent small cages.

  13. NMR studies on effects of temperature, pressure, and fluorination on structures and dynamics of alcohols in liquid and supercritical states.

    PubMed

    Tsukahara, Takehiko; Harada, Masayuki; Tomiyasu, Hiroshi; Ikeda, Yasuhisa

    2008-10-09

    We measured 1H NMR chemical shifts (delta H) and 1H and 2H NMR spin-lattice relaxation times (1H- and 2H-T1) of methanol, ethanol, 2-propanol, 2,2,2-trifluoroethanol, and 1,1,1,3,3,3-hexafluoro-2-propanol in the temperature range from 298 to 673 K at reduced pressures ( Pr = P/ Pc) of 1.22 and 3.14. The delta H values showed that the degree (X HB) of hydrogen bonding decreased in the order of methanol > ethanol >2-propanol > H2O, and that the hydrogen bonding was much affected by fluorination, because of the intramolecular H-F interactions in supercritical (sc) states. Moreover, 1H- T 1 measurements revealed that the relaxation processes of OH groups in nonfluoroalcohols are controlled by dipole-dipole (DD) and spin-rotation (SR) mechanisms below and above the critical temperature (Tc), while the cross-correlation effects connected with intramolecular DD interactions between a carbon atom and an adjacent proton played an important role for hydrocarbon groups (CHn, n = 1-3) under sc conditions. This interpretation was also supported by two other results. The first is that the intramolecular H-F interactions strongly inhibit the internal rotation of CH and CH2 groups of sc fluoroalcohols, and the second is that the molecular reorientational correlation times (tauc(D)) obtained from 2H- T 1 values of deuterated hydrocarbon groups (CDn ) at temperatures above T c have significantly less temperature dependence than those of OD groups. Actually, the apparent activation energy (DeltaEa) for molecular reorientational motions in sc alcohols was smaller compared with liquid alcohols, being about 1 order of magnitude.

  14. Structure, Topology and Tilt of Cell-Signaling Peptides Containing Nuclear Localization Sequences in Membrane Bilayers Determined by Solid-State NMR and Molecular Dynamics Simulation Studies

    PubMed Central

    Ramamoorthy, Ayyalusamy; Kandasamy, Senthil K.; Lee, Dong-Kuk; Kidambi, Srikanth; Larson, Ronald G.

    2008-01-01

    Cell-signaling peptides have been extensively used to transport functional molecules across the plasma membrane into living cells. These peptides consist of a hydrophobic sequence and a cationic nuclear localization sequence (NLS). It has been assumed that the hydrophobic region penetrates through the hydrophobic lipid bilayer and delivers the NLS inside the cell. To better understand the transport mechanism of these peptides, in this study, we investigated the structure, orientation, tilt of the peptide relative to the bilayer normal, and the membraneinteraction of two cell-signaling peptides, SA and SKP. Results from CD and solid-state NMR experiments combined with molecular dynamics simulations suggest that the hydrophobic region is helical and has a transmembrane orientation with the helical axis tilted away from the bilayer normal. The influence of the hydrophobic mismatch, between the hydrophobic length of the peptide and the hydrophobic thickness of the bilayer, on the tilt angle of the peptides was investigated using thicker POPC and thinner DMPC bilayers. NMR experiments showed that the hydrophobic domain of each peptide has a tilt angle of 15±3° in POPC, while in DMPC 25±3° and 30±3° tilts were observed for SA and SKP peptides respectively. These results are in good agreement with molecular dynamics simulations, which predicts a tilt angle of 13.3° (SA in POPC), 16.4° (SKP in POPC), 22.3° (SA in DMPC) and 31.7° (SKP in POPC). These results and simulations on the hydrophobic fragment of SA or SKP suggest that the tilt of helices increases with a decrease in the bilayer thickness without changing the phase, order, and structure of the lipid bilayers. PMID:17240980

  15. Solid-state MAS NMR, TEM, and TGA studies of structural hydroxyl groups and water in nanocrystalline apatites prepared by dry milling.

    PubMed

    Pajchel, Lukasz; Kolodziejski, Waclaw

    2013-01-01

    A series of nanocrystalline calcium hydroxyapatites was prepared by dry milling and characterized using proton and (31)P MAS NMR, TEM, and TGA methods. The samples contained stubby rod-shaped crystals, which length and width varied in the 130-30 and 95-20 nm ranges, respectively. It was confirmed that concentration of structural hydroxyl groups in nanocrystalline apatites decreases with the decreasing crystal size. In the series of the studied apatites, the decrease was from 86 to ca. 50 % in reference to stoichiometric apatite. Water was found in the surface hydrated layer and in the c-axis channels, in which compartments existed as adsorbed and structural, respectively. Molecules of the adsorbed water were capable of moving from the crystal surface into the lattice c-axis channels of apatite. This process introduced considerable structural disorder within and around those channels and reduced the content of the structural hydroxyl groups, particularly in the region underneath the apatite crystal surface.

  16. Natural abundance 17O, 6Li NMR and molecular modeling studies of the solvation structures of lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane liquid electrolytes

    SciTech Connect

    Wan, Chuan; Hu, Mary Y.; Borodin, Oleg; Qian, Jiangfeng; Qin, Zhaohai; Zhang, Ji-Guang; Hu, Jian Zhi

    2016-03-01

    Natural abundance 17O and 6Li NMR experiments, quantum chemistry and molecular dynamics studies were employed to investigate the solvation structures of Li+ at various concentrations of LiFSI in DME electrolytes in an effort to solve this puzzle. It was found that the chemical shifts of both 17O and 6Li changed with the concentration of LiFSI, indicating the changes of solvation structures with concentration. For the quantum chemistry calculations, the coordinated cluster LiFSI(DME)2 forms at first, and its relative ratio increases with increasing LiFSI concentration to 1 M. Then the solvation structure LiFSI(DME) become the dominant component. As a result, the coordination of forming contact ion pairs between Li+ and FSI- ion increases, but the association between Li+ and DME molecule decreases. Furthermore, at LiFSI concentration of 4 M the solvation structures associated with Li+(FSI-)2(DME), Li+2(FSI-)(DME)4 and (LiFSI)2(DME)3 become the dominant components. For the molecular dynamics simulation, with increasing concentration, the association between DME and Li+ decreases, and the coordinated number of FSI- increases, which is in perfect accord with the DFT results. These results provide more insight on the fundamental mechanism on the very high CE of Li deposition in these electrolytes, especially at high current density conditions.

  17. Natural abundance 17O, 6Li NMR and molecular modeling studies of the solvation structures of lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane liquid electrolytes

    NASA Astrophysics Data System (ADS)

    Wan, Chuan; Hu, Mary Y.; Borodin, Oleg; Qian, Jiangfeng; Qin, Zhaohai; Zhang, Ji-Guang; Hu, Jian Zhi

    2016-03-01

    Natural abundance 17O and 6Li NMR experiments, quantum chemistry and molecular dynamics studies were employed to investigate the solvation structures of Li+ at various concentrations of LiFSI in DME electrolytes. It was found that the chemical shifts of both 17O and 6Li changed with the concentration of LiFSI, indicating the changes of solvation structures with concentration. For the quantum chemistry calculations, the coordinated cluster LiFSI(DME)2 forms at first, and its relative ratio increases with increasing LiFSI concentration to 1 M. Then the solvation structure LiFSI(DME) become the dominant component. As a result, the coordination of forming contact ion pairs between Li+ and FSI- ion increases, but the association between Li+ and DME molecule decreases. Furthermore, at LiFSI concentration of 4 M the solvation structures associated with Li+(FSI-)2(DME), Li+2(FSI-)(DME)4 and (LiFSI)2(DME)3 become the dominant components. For the molecular dynamics simulation, with increasing concentration, the association between DME and Li+ decreases, and the coordinated number of FSI- increases, which is in perfect accord with the DFT results.

  18. Structural biology applications of solid state MAS DNP NMR.

    PubMed

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance.

  19. Structural biology applications of solid state MAS DNP NMR

    NASA Astrophysics Data System (ADS)

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance.

  20. A multinuclear static NMR study of geopolymerisation

    SciTech Connect

    Favier, Aurélie; Habert, Guillaume; Roussel, Nicolas; D'Espinose de Lacaillerie, Jean-Baptiste

    2015-09-15

    Geopolymers are inorganic binders obtained by alkali activation of aluminosilicates. While the structure of geopolymers is now well understood, the details of the geopolymerisation reaction and their impact on the rheology of the paste remain uncertain. In this work, we follow the elastic properties of a paste made with metakaolin and sodium silicate solution. After the first sharp increase of elastic modulus occurring a few hundred of seconds after mixing and related to the heterogeneous formation of an alumina–silicate gel with a molar ratio Si/Al < 4 located at the grains boundaries, we focus on the progressive increase in elastic modulus on a period of few hours during the setting of the geopolymer. In this study, we combine the study of rheological properties of the paste with {sup 23}Na, {sup 27}Al and {sup 29}Si static NMR measurement in order to better understand the origin of this second increase in elastic modulus. Our results show that, after a few hours, Al and Na evolution in the liquid phase are concomitant. This suggests the precipitation of an aluminosilicate phase where Al is in tetrahedral position and Na compensates the charge. Furthermore, Si speciation confirms this result and allows us to identify the precipitation of a product, which has a chemical composition close to the final composition of geopolymer. This study provides strong evidence for a heterogeneous formation of an aluminosilicate glass directly from the first gel and the silicate solution without the need for a reorganisation of Gel 1 into Gel 2.

  1. Attachment of Pseudomonas putida onto differently structured kaolinite minerals: a combined ATR-FTIR and 1H NMR study.

    PubMed

    Vasiliadou, Ioanna A; Papoulis, Dimitris; Chrysikopoulos, Constantinos V; Panagiotaras, Dionisios; Karakosta, Eleni; Fardis, Michael; Papavassiliou, Georgios

    2011-06-01

    The attachment of Pseudomonas (P.) putida onto well (KGa-1) and poorly (KGa-2) crystallized kaolinite was investigated in this study. Batch experiments were carried out to determine the attachment isotherms of P. putida onto both types of kaolinite particles. The attachment process of P. putida onto KGa-1 and KGa-2 was adequately described by a Langmuir isotherm. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy and Nuclear Magnetic Resonance were employed to study the attachment mechanisms of P. putida. Experimental results indicated that KGa-2 presented higher affinity and attachment capacity than KGa-1. It was shown that electrostatic interactions and clay mineral structural disorders can influence the attachment capacity of clay mineral particles.

  2. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    SciTech Connect

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG))centerreverse arrowdot)d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.

  3. Chemo-enzymatic synthesis of selectively ¹³C/¹⁵N-labeled RNA for NMR structural and dynamics studies.

    PubMed

    Alvarado, Luigi J; Longhini, Andrew P; LeBlanc, Regan M; Chen, Bin; Kreutz, Christoph; Dayie, T Kwaku

    2014-01-01

    for the synthesis of gram quantities of nucleotides with >80% yields while using a limited number of enzymes, six at most. The unavailability of selectively labeled ribose and base precursors had prevented the effective use of this versatile method until now. Recently, we combined an improved organic synthetic approach that selectively places (13)C/(15)N labels in the pyrimidine nucleobase (either (15)N1, (15)N3, (13)C2, (13)C4, (13)C5, or (13)C6 or any combination) with a very efficient enzymatic method to couple ribose with uracil to produce previously unattainable labeling patterns (Alvarado et al., 2014). Herein we provide detailed steps of both our chemo-enzymatic synthesis of custom nucleotides and their incorporation into RNAs with sizes ranging from 29 to 155 nt and showcase the dramatic improvement in spectral quality of reduced crowding and narrow linewidths. Applications of this selective labeling technology should prove valuable in overcoming two major obstacles, chemical shift overlap of resonances and associated rapid signal loss due to line broadening, that have impeded studying the structure and dynamics of large RNAs such as full-length riboswitches larger than the ~25 nt median size of RNA NMR structures found in the PDB.

  4. A combined solid-state NMR and synchrotron x-ray diffraction powder study on the structure of the antioxidant(+)-catechin 4.5 hydrate.

    SciTech Connect

    Harper, J. K.; Doebbler, J. A.; Jaccques, E.; Grant, D. M.; Von Dreele, R. B.; Univ. of Utah

    2010-03-10

    Analyses combining X-ray powder diffraction (XRD) and solid-state NMR (SSNMR) data can now provide crystal structures in challenging powders that are inaccessible by traditional methods. The flavonoid catechin is an ideal candidate for these methods, as it has eluded crystallographic characterization despite extensive study. Catechin was first described nearly two centuries ago, and its powders exhibit numerous levels of hydration. Here, synchrotron XRD data provide all heavy-atom positions in (+)-catechin 4.5-hydrate and establish the space group as C2. SSNMR data ({sup 13}C tensor and {sup 1}H/{sup 13}C correlation) complete the conformation by providing catechin's five OH hydrogen orientations. Since 1903, this phase has been erroneously identified as a 4.0 hydrate, but XRD and density data establish that this discrepancy is due to the facile loss of the water molecule located at a Wyckoff special position in the unit cell. A final improvement to heavy-atom positions is provided by a geometry optimization of bond lengths and valence angles with XRD torsion angles held constant. The structural enhancement in this final structure is confirmed by the significantly improved fit of computed {sup 13}C tensors to experimental data.

  5. Crystal and molecular structure studies of (Z)-N-methyl-C-4-substituted phenyl nitrones by XRD, DFT, FTIR and NMR methods

    NASA Astrophysics Data System (ADS)

    Lasri, Jamal; Eltayeb, Naser Eltaher; Haukka, Matti; Alghamdi, Yousef

    2017-01-01

    (Z)-N-methyl-C-4-substituted phenyl nitrones -O+N(Me)=C(H)R (Z-2a R = 4-ClC6H4, Z-2b R = 4-NO2C6H4, Z-2c R = 4-CH3OC6H4) were synthesized and characterized by elemental analyses, FTIR, 1H, 13C and DEPT-135 NMR spectroscopy and also by single crystal X-ray diffraction (in the case of Z-2a and Z-2b). The geometries of the nitrone molecules Z-2a, Z-2b and Z-2c and their E-isomers; (E)-N-methyl-C-4-chlorophenyl nitrone E-2a, (E)-N-methyl-C-4-nitrophenyl nitrone E-2b and (E)-N-methyl-C-4-methoxyphenyl nitrone E-2c were optimized using density functional theory (DFT) at the B3LYP/6-311++G(d,p) level of theory. The theoretical vibrational frequencies obtained by DFT calculations are in good agreement with the experimental values. The electronics structures were described in terms of the distribution of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Gauge independent atomic orbital (GIAO) method was used to calculate the NMR spectra, the correlation between the calculated and experimental chemical shifts is mostly in the range of 0.94-0.97 for 1H, whereas, the correlation for 13C is 0.99. Thermodynamics study showed that the Z-isomer is favoured than E-isomer with energy barrier of 7.1, 7.2 and 7.1 kcal/mol for Z-2a, Z-2b and Z-2c, respectively. The abundance of the most stable species Z-isomers is equal to 99.99% for all three compounds at 298 K in gas phase.

  6. Study of cultured fibroblasts in vivo using NMR

    SciTech Connect

    Karczmar, G.S.

    1984-08-01

    The goal was to study the compartmentation of phosphorylated glycolytic intermediates in intact Chicken Embryo Fibroblasts (CEFs) using /sup 31/P NMR at 109 MHz. A technique for maintaining functional cells at high densities in an NMR magnet is described. Signals were detected from cytoplasmic inorganic phosphate (P/sub i/), ATP, NAD, NADH, phosphorylcholine and phosphorylethanolamine. The effect of external glucose on cytoplasmic pools of phosphates was studied. When cells were perfused with glucose-free medium the rate of glycolysis decreased, the amplitudes of the ATP resonances decreased, and the P/sub i/ intensity increased. The quantity of NMR-detectable P/sub i/ produced was significantly greater than the quantity of NMR-detectable ATP which was lost. Experiments with /sup 32/P labeled P/sub i/ showed that as the concentration of glucose in the medium was increase, the amount of phosphate sequestered in the cells increased. We conclude that there is a pool of P/sub i/ which is not detected by high resolution NMR and that the size of this pool increases as the rate of glycolysis increase. Longtitudinal relaxation times of intracellular phosphates in normal, transformed, and primary CEFs were measured. The results demonstrate that relaxation times of phosphates are sensitive to structural and metabolic changes which occur when cells are grown in culture. 59 references. 31 figures.

  7. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

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

  8. Structural investigations on betacyanin pigments by LC NMR and 2D NMR spectroscopy.

    PubMed

    Stintzing, Florian C; Conrad, Jürgen; Klaiber, Iris; Beifuss, Uwe; Carle, Reinhold

    2004-02-01

    Four betacyanin pigments were analysed by LC NMR and subjected to extensive NMR characterisation after isolation. Previously, low pH values were applied for NMR investigations of betalains resulting in rapid degradation of the purified substances thus preventing extensive NMR studies. Consequently, up to now only one single (13)C NMR spectrum of a betalain pigment, namely that of neobetanin (=14,15-dehydrobetanin), was available. Because of its sufficient stability under highly acidic conditions otherwise detrimental for betacyanins, this pigment remained an exemption. Since betalains are most stable in the pH range of 5-7, a new solvent system has been developed allowing improved data acquisition through improved pigment stability at near neutral pH. Thus, not only (1)H, but for the first time also partial (13)C data of betanin, isobetanin, phyllocactin and hylocerenin isolated from red-purple pitaya [Hylocereus polyrhizus (Weber) Britton & Rose, Cactaceae] could be indirectly obtained by gHSQC- and gHMQC-NMR experiments.

  9. Reactions of bis[bis(trimethylsilyl)amido] zinc with amides of sulfonimidic acids. Crystal structure and NMR studies of bischelate zinc complex

    NASA Astrophysics Data System (ADS)

    Guzyr, Olexandr I.; Markovskii, Leonid N.; Povolotskii, Mark I.; Roesky, Herbert W.; Chernega, Alexander N.; Rusanov, Eduard B.

    2006-05-01

    Reactions of bis[bis(trimethylsilyl)amido] zinc with amides of sulfonimidic acids are leading to the corresponding bischelate complexes 1- 3. Compounds 1- 3 were characterized by means of NMR spectroscopy and elemental analysis. The X-ray analysis of [ p-MeC 6H 4S(O)(N t-Bu) 2] 2Zn ( 3) demonstrates a tetrahedral environment of the Zn atom in the solid state and dynamic 1H NMR studies showed interconvention between two conformers in solution at high temperatures.

  10. Probing the structural disorder of basalts and slab-driven andesite melts: Insights from high-resolution solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Park, S.; Lee, S.

    2012-12-01

    Whereas the structure of multi-component silicate melts has strong implication for the properties of natural silicate melts and relevant magmatic processes in Earth's mantle and crust, little is known about their atomic structures due to lack of suitable experimental probes of multi-component amorphous oxides. Although most of the progress in melt structure has been made for relatively simple binary and ternary silicate glasses, recent advances in high-resolution solid-state NMR (nuclear magnetic resonance) unveil previously unknown structural details of multi-component silicate melts (Lee, S. K. and Sung, S., Chem. Geol., 2008, 256, 326; Lee et al., P. Natl. Acad. Sci. USA., 2011, 108, 6847; Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125). In this study we report experimental results on the effects of composition. atomic structure of CaO-MgO-Al_{2} O_{3} -SiO_{2} (CMAS) glasses in diopside (CaMgSi_{2}O_{6}) and Ca-tschermakite (CaAl_{2}SiO_{6}) join and glass in the diopside-anorthite eutectic composition (Di_{64}An_{36})—model systems for basaltic melts—using solid-state NMR. We also report the first high-resolution experimental results on the atomic structure of CaO-MgO-Na_{2}O-Al_{2}O_{3}-SiO_{2} (CMNAS) glasses in diopside and jadeite (NaAlSi_{2}O_{6}) join, and glass in the natural phonolite composition (CaO: MgO: Na_{2}O: K_{2}O: Al_{2}O_{3}: SiO_{2}= 1.4: 8.0: 9.0: 3.8: 13: 64 mol%), a model system for slab driven andesite melts. The Al-27 3QMAS (triple quantum magic angle spinning) NMR spectra of CMAS glasses in diopside-Ca-tschermakite join show predominant ^{[4]}Al and a non-negligible fraction of ^{[5]}Al. Approximately 3.3% of ^{[5]}Al is observed for Di_{64}An_{36} glass. The Al-27 3QMAS NMR spectra of CMNAS glasses in diopside and jadeite join show mostly ^{[4]}Al and a non-negligible fraction of ^{[5]}Al (X_{Diopside}=0.75, the mole fraction of diopside content). While the C_{q} (quadrupolar coupling constant) of ^{[4]}Al for glasses in

  11. From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry

    NASA Astrophysics Data System (ADS)

    Simpson, A.

    2009-04-01

    NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

  12. High-Field NMR Studies of Molecular Recognition and Structure-Function Relationships in Antimicrobial Piscidins at the Water-Lipid Bilayer Interface

    SciTech Connect

    Chekmenev, Eduard Y.; Jones, Shiela M.; Nikolayeva, Yelena; Vollmar, Breanna S.; Wagner, Timothy J.; Gorkov, Peter L.; Brey, William W.; Manion, Mckenna N.; Daugherty, Kenneth C.; Cotten, Myriam L.

    2006-04-26

    Piscidins are the first amphipathic, cationic, antimicrobial peptides (ACAPs) to be found in the mast cells of fish, and they are believed to play a crucial role in the fight against many aquatic infections.1 Many ACAPs have been characterized functionally, and some models for their mechanism of action exist, including the barrel-stave model, the wormhole model, the carpet mechanism, and the intracellular activation of fatal pathways.2-9 Much information remains to be learned about the details of their structure, initial interactions with membranes, and the ultimate mechanism for disrupting cellular function. To this end, we employed solid-state NMR (ssNMR) to probe the structure and topology of isotopically labeled piscidins in the membrane-bound state.

  13. A consensus on protein structure accuracy in NMR?

    PubMed

    Billeter, Martin

    2015-02-03

    The precision of an NMR structure may be manipulated by calculation parameters such as calibration factors. Its accuracy is, however, a different issue. In this issue of Structure, Buchner and Güntert present "consensus structure bundles," where precision analysis allows estimation of accuracy.

  14. Local structures of polar wurtzites Zn1-xMgxO studied by raman and 67Zn/25Mg NMR spectroscopies and by total neutron scattering

    SciTech Connect

    Proffen, Thomas E; Kim, Yiung- Il; Cadars, Sylvian; Shayib, Ramzy; Feigerle, Charles S; Chmelka, Bradley F; Seshadri, Ram

    2008-01-01

    Research in the area of polar semiconductor heterostructures has been growing rapidly, driven in large part by interest in two-dimensional electron gas (2DEG) systems. 2DEGs are known to form at heterojunction interfaces that bear polarization gradients. They can display extremely high electron mobilities, especially at low temperatures, owing to spatial confinement of carrier motions. Recent reports of 2DEG behaviors in Ga{sub 1-x}Al{sub x}N/GaN and Zn{sub 1-x}Mg{sub x}O/ZnO heterostructures have great significance for the development of quantum Hall devices and novel high-electron-mobility transistors (HEMTs). 2DEG structures are usually designed by interfacing a polar semiconductor with its less or more polar alloys in an epitaxial manner. Since the quality of the 2DEG depends critically on interface perfection, as well as the polarization gradient at the heterojunction, understanding compositional and structural details of the parent and alloy semiconductors is an important component in 2DEG design and fabrication. Zn{sub 1-x}Mg{sub x}O/ZnO is one of the most promising heterostructure types for studies of 2DEGs, due to the large polarization of ZnO, the relatively small lattice mismatch, and the large conduction band offsets in the Zn{sub 1-x}Mg{sub x}O/ZnO heterointerface. Although 2DEG formation in Zn{sub 1-x}Mg{sub x}O/ZnO heterostructures have been researched for some time, a clear understanding of the alloy structure of Zn{sub 1-x}Mg{sub x}O is currently lacking. Here, we conduct a detailed and more precise study of the local structure of Zn{sub 1-x}Mg{sub x}O alloys using Raman and solid-state nuclear magnetic resonance (NMR), in conjunction with neutron diffraction techniques.

  15. Solution structures of cyclosporin a and its complex with dysprosium(III) in SDS micelles: NMR and molecular dynamics studies.

    PubMed

    Bernardi, Francesca; D'Amelio, Nicola; Gaggelli, Elena; Molteni, Elena; Valensin, Gianni

    2008-01-24

    Cyclosporin A (CsA) is a cyclic naturally occurring peptide used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is due to the formation of a complex with cyclophilin A (Cyp), in which the cis 9MeLeu-10MeLeu amide bond of CsA assumes a trans conformation. The mechanism of the conformational inversion has not been delineated, but it has been postulated that metal ions binding induces a conformational change that enables CsA to bind Cyp. In this work, we solved the structures of CsA in sodium dodecyl sulfate (SDS) micelles (which enhance its solubility and mimic the hydrophobic environment clinically used for drug delivery) and its complex with Dy(III) ion, whose coordination chemistry is frequently used to reproduce the effect of Ca(II). The paramagnetic properties of Dy(III) allowed us to build up a structure using proton relaxation enhancements, which remains stable in a MD simulation in the micelle environment.

  16. The dynamic duo: Combining NMR and small angle scattering in structural biology

    PubMed Central

    Hennig, Janosch; Sattler, Michael

    2014-01-01

    Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution. PMID:24687405

  17. Solid state and solution properties of lanthanide(III) complexes of a tetraiminodiphenolate macrocyclic ligand. X-ray structure, 1H NMR and luminescence spectral studies

    NASA Astrophysics Data System (ADS)

    Bag, Pradip; Dutta, Supriya; Flörke, Ulrich; Nag, Kamalaksha

    2008-11-01

    The lanthanide(III) complexes of composition [Ln(LH 2)(H 2O) 3Cl]Cl 2 (Ln = La-Lu and Y, 1- 15) derived from the tetraiminodiphenolate macrocyclic ligand L 2- have been prepared and characterized. In these compounds, the two uncoordinated imine nitrogens of the macrocycle are protonated and hydrogen-bonded with the metal-bound phenolate oxygens and thereby provide a zwitterionic structure to the ligand. The X-ray crystal structure of the compounds of La and Nd have been determined and they are found to be isostructural. The coordination polyhedra for the eight-coordinated metal centre in the complex cation [Ln(N 2O 2)(O 3Cl)] 2+ can be described as distorted square antiprism. Intermolecular hydrogen-bondings involving the three coordinated water molecules and the two uncoordinated chloride ions give rise to the 2-D network in which the chlorides are triply hydrogen-bridged and the water molecules are doubly hydrogen-bridged. Moreover, the aromatic rings in this network are involved in π-π interaction in two different ways. 1H NMR spectra of the complexes in (CD 3) 2SO have been studied. The spectral assignments for the paramagnetic complexes of Ce-Eu have been made from { 1H- 1H} COSY spectra and longitudinal relaxation time ( T1) measurements. It is inferred that the complex species [Ln(LH 2){(CD 3) 2SO} 4] 3+ that exist in solution are isostructural for the compounds of La-Eu. The contact and pseudo-contact contribution to the isotropic paramagnetic shifts in the complexes of Ce-Eu have been estimated. The luminescence spectra of the complexes of La, Sm, Eu and Tb have been studied in methanol-ethanol (1:4) glassy matrix and in the solid state at 77 K, and the quantum yields have been estimated.

  18. Theoretical and experimental study of inclusion complexes formed by isoniazid and modified β-cyclodextrins: 1H NMR structural determination and antibacterial activity evaluation.

    PubMed

    Teixeira, Milena G; de Assis, João V; Soares, Cássia G P; Venâncio, Mateus F; Lopes, Juliana F; Nascimento, Clebio S; Anconi, Cleber P A; Carvalho, Guilherme S L; Lourenço, Cristina S; de Almeida, Mauro V; Fernandes, Sergio A; de Almeida, Wagner B

    2014-01-09

    Me-β-cyclodextrin (Me-βCD) and HP-β-cyclodextrin (HP-βCD) inclusion complexes with isoniazid (INH) were prepared with the aim of modulating the physicochemical and biopharmaceutical properties of the guest molecule, a well-known antibuberculosis drug. The architectures of the complexes were initially proposed according to NMR data Job plot and ROESY followed by density functional theory (DFT) calculations of (1)H NMR spectra using the PBE1PBE functional and 6-31G(d,p) basis set, including the water solvent effect with the polarizable continuum model (PCM), for various inclusion modes, providing support for the experimental proposal. An analysis of the (1)H NMR chemical shift values for the isoniazid (H6',8' and H5',9') and cyclodextrins (H3,5) C(1)H hydrogens, which are known to be very adequately described by the DFT methodology, revealed them to be extremely useful, promptly confirming the inclusion complex formation. An included mode which describes Me-βCD partially enclosing the hydrazide group of the INH is predicted as the most favorable supramolecular structure that can be used to explain the physicochemical properties of the encapsulated drug. Antibacterial activity was also evaluated, and the results indicated the inclusion complexes are a potential strategy for tuberculosis treatment.

  19. Crystal structure, NMR study, dielectric relaxation and AC conductivity of a new compound [Cd3(SCN)2Br6(C2H9N2)2]n

    NASA Astrophysics Data System (ADS)

    Saidi, K.; Kamoun, S.; Ayedi, H. Ferid; Arous, M.

    2013-11-01

    The crystal structure, the 13C NMR spectroscopy and the complex impedance have been carried out on [Cd3(SCN)2Br6(C2H9N2)2]n. Crystal structure shows a 2D polymeric network built up of two crystallographically independent cadmium atoms with two different octahedral coordinations. This compound exhibits a phase transition at (T=355±2 K) which has been characterized by differential scanning calorimetry (DSC), X-rays powder diffraction, AC conductivity and dielectric measurements. Examination of 13C CP/MAS line shapes shows indirect spin-spin coupling (14N and 13C) with a dipolar coupling constant of 1339 Hz. The AC conductivity of this compound has been carried out in the temperature range 325-376 K and the frequency range from 10-2 Hz to 10 MHz. The impedance data were well fitted to two equivalent electrical circuits. The results of the modulus study reveal the presence of two distinct relaxation processes. One, at low frequency side, is thermally activated due to the ionic conduction of the crystal and the other, at higher frequency side, gradually disappears when temperature reaches 355 K which is attributed to the localized dipoles in the crystal. Moreover, the temperature dependence of DC-conductivity in both phases follows the Arrhenius law and the frequency dependence of σ(ω,T) follows Jonscher's universal law. The near values of activation energies obtained from the conductivity data and impedance confirm that the transport is through the ion hopping mechanism.

  20. Fe57 NMR and spin structure of manganese ferrite

    NASA Astrophysics Data System (ADS)

    Štěpánková, H.; Sedlák, B.; Chlan, V.; Novák, P.; Šimša, Z.

    2008-03-01

    NMR of Fe57 in five MnFe2O4 single crystals with different degrees of inversion was measured in liquid He temperature. At the zero external field, two lines originating from Fe3+ ions on the octahedral sites are observed at 68.7 and 71.1MHz , while the line at 72.0MHz , the amplitude of which increases with increasing inversion, is ascribed to Fe3+ ions on the tetrahedral sites. Measurement in the external field shows that the spin structure is in accord with the Goodenough-Kanamori rules. This contradicts to an abnormal spin structure which Shim [Phys. Rev. B 75, 134406 (2007)] proposed recently on the basis of Fe57 NMR measured in polycrystalline manganese ferrite. Reinterpretation of the NMR in polycrystalline compounds is given.

  1. Solid State NMR Studies of Energy Conversion and Storage Materials

    NASA Astrophysics Data System (ADS)

    Jankuru Hennadige, Sohan Roshel De Silva

    NMR (Nuclear magnetic resonance) spectroscopy is utilized to study energy conversion and storage materials. Different types of NMR techniques including Magic Angle Spinning, Cross-polarization and relaxation measurement experiments were employed. Four different projects are discussed in this dissertation. First, three types of CFx battery materials were investigated. Electrochemical studies have demonstrated different electrochemical performances by one type, delivering superior performance over the other two. 13C and 19F MAS NMR techniques are employed to identify the atomic/molecular structural factors that might account for differences in electrochemical performance among different types. Next as the second project, layered polymer dielectrics were investigated by NMR. Previous studies have shown that thin film capacitors are improved by using alternate layers of two polymers with complementary properties: one with a high breakdown strength and one with high dielectric constant as opposed to monolithic layers. 13C to 1H cross-polarization techniques were used to investigate any inter-layer properties that may cause the increase in the dielectric strength. The third project was to study two types of thermoelectric materials. These samples were made of heavily doped phosphorous and boron in silicon by two different methods: ball-milled and annealed. These samples were investigated by NMR to determine the degree of disorder and obtain insight into the doping efficiency. The last ongoing project is on a lithium-ion battery system. The nature of passivating layers or the solid electrolyte interphase (SEI) formed on the electrodes surface is important because of the direct correlation between the SEI and the battery life time/durability. Multinuclear (7Li, 19F, 31P) techniques are employed to identify the composition of the SEI formation of both positive and negative electrodes.

  2. COCO: a simple tool to enrich the representation of conformational variability in NMR structures.

    PubMed

    Laughton, Charles A; Orozco, Modesto; Vranken, Wim

    2009-04-01

    NMR structures are typically deposited in databases such as the PDB in the form of an ensemble of structures. Generally, each of the models in such an ensemble satisfies the experimental data and is equally valid. No unique solution can be calculated because the experimental NMR data is insufficient, in part because it reflects the conformational variability and dynamical behavior of the molecule in solution. Even for relatively rigid molecules, the limited number of structures that are typically deposited cannot completely encompass the structural diversity allowed by the observed NMR data, but they can be chosen to try and maximize its representation. We describe here the adaptation and application of techniques more commonly used to examine large ensembles from molecular dynamics simulations, to the analysis of NMR ensembles. The approach, which is based on principal component analysis, we call COCO ("Complementary Coordinates"). The COCO approach analyses the distribution of an NMR ensemble in conformational space, and generates a new ensemble that fills "gaps" in the distribution. The method is very rapid, and analysis of a 25-member ensemble and generation of a new 25 member ensemble typically takes 1-2 min on a conventional workstation. Applied to the 545 structures in the RECOORD database, we find that COCO generates new ensembles that are as structurally diverse-both from each other and from the original ensemble-as are the structures within the original ensemble. The COCO approach does not explicitly take into account the NMR restraint data, yet in tests on selected structures from the RECOORD database, the COCO ensembles are frequently good matches to this data, and certainly are structures that can be rapidly refined against the restraints to yield high-quality, novel solutions. COCO should therefore be a useful aid in NMR structure refinement and in other situations where a richer representation of conformational variability is desired-for example in

  3. Rapid structure elucidation of drug degradation products using mechanism-based stress studies in conjunction with LC-MS(n) and NMR spectroscopy: identification of a photodegradation product of betamethasone dipropionate.

    PubMed

    Lin, Mingxiang; Li, Min; Buevich, Alexei V; Osterman, Rebecca; Rustum, Abu M

    2009-10-15

    Betamethasone dipropionate is an active pharmaceutical ingredient (API) that is used in various dosage forms of finished products for the treatment of inflammatory disorders. An unknown degradant was observed during a solution stability study of betamethasone dipropionate. An approach that combines LC-MS(n), mechanism-based stress studies, semi-preparative HPLC purification and structure elucidation by NMR spectroscopy was used to identify the unknown species. The key step of this approach is the design of relevant stress studies based on the plausible degradation mechanism that is revealed by the informative LC-MS(n) analysis. The appropriately designed mechanism-based stress studies not only verify the degradation mechanism but also produce enough quantities of the unknown species for further structure elucidation/confirmation by NMR spectroscopy. With this strategy, the unknown degradant was rapidly identified as lumibetametasone dipropionate, a photodegradation product of betamethasone dipropionate.

  4. On-line NMR detection of microgram quantities of heparin-derived oligosaccharides and their structure elucidation by microcoil NMR.

    PubMed

    Korir, Albert K; Larive, Cynthia K

    2007-08-01

    The isolation and purification of sufficient quantities of heparin-derived oligosaccharides for characterization by NMR is a tedious and time-consuming process. In addition, the structural complexity and microheterogeneity of heparin makes its characterization a challenging task. The improved mass-sensitivity of microcoil NMR probe technology makes this technique well suited for characterization of mass-limited heparin-derived oligosaccharides. Although microcoil probes have poorer concentration sensitivity than conventional NMR probes, this limitation can be overcome by coupling capillary isotachophoresis (cITP) with on-line microcoil NMR detection (cITP-NMR). Strategies to improve the sensitivity of on-line NMR detection through changes in probe design and in the cITP-NMR experimental protocol are discussed. These improvements in sensitivity allow acquisition of cITP-NMR survey spectra facilitating tentative identification of unknown oligosaccharides. Complete structure elucidation for microgram quantities of the purified material can be carried out through acquisition of 2D NMR spectra using a CapNMR microcoil probe.

  5. A new salen base 5-(phenylazo)-N-(2-amino pyridine) salicyliden Schiff base ligand: synthesis, experimental and density functional studies on its crystal structure, FTIR, 1H NMR and 13C NMR spectra.

    PubMed

    Sheikhshoaie, Iran; Saheb, Vahid

    2010-12-01

    A novel Schiff base ligand 5-(phenylazo)-N-(2-amino pyridine) salicyliden is prepared through the condensation of 5-(phenylazo) salicylaldehyde and 2-amino pyridine in methanol at room temperature. The orange crystalline precipitate is used for X-ray crystallography and measuring Fourier transform (FTIR), 1H NMR and 13C NMR spectra. Density functional theory (DFT) calculations at the B3LYP, MPWB1K and B3PW91 levels of theory is used to optimize the geometry and calculate the FTIR, 1H NMR and 13C NMR spectra of the compound. The vibrational frequencies determined experimentally are compared with those obtained theoretically and a vibrational assignment and analysis of the fundamental modes of the compound is performed. We found that the MPWB1K method predicts low vibrational frequencies better than the commonly used B3LYP method. Although the B3PW91 method overestimates the 1H NMR chemical shifts, the values computed at the B3LYP level of theory are in accordance with experimental 1H NMR spectrum. However, both B3LYP and B3PW91 methods tend to overestimate 13C NMR chemical shifts. In addition, a few quantum descriptors of the molecule are calculated and conformational analysis is performed and the result was compared with crystallographic data.

  6. Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study.

    PubMed

    Do, Ngoc Quang; Phan, Anh Tuân

    2012-11-12

    Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.

  7. Quantum Chemical Study of the Solvent Effect on the Anticancer Active Molecule of Iproplatin: Structural, Electronic, and Spectroscopic Properties (IR, 1H NMR, UV)

    NASA Astrophysics Data System (ADS)

    Sadeghi, N.; Ghiasi, R.; Fazaeli, R.; Jamehbozorgi, S.

    2017-01-01

    The structural, electronic, and spectroscopic properties of the anticancer active molecule of iproplatin were investigated in the gas and liquid phases. Based on the polarizable continuum model (PCM), the solvent effect on the structural parameters, frontier orbitals, and spectroscopic parameters of the complex was investigated. The results indicate that the polarity of solvents plays a significant role in the structure and pro perties of the complex. 1H and 13C NMR chemical shifts were calculated using the Gauge-invariant atomic orbital (GIAO) method. Pt-Cl and Pt-OH bonds were investigated through a vibrational analysis. Moreover, time dependent density functional theory (TD-DFT) was used to calculate the energy, oscillatory strength, and wavelength absorption maximum (λmax) of electronic transitions and its nature within the complex.

  8. NMR monitoring of the SELEX process to confirm enrichment of structured RNA.

    PubMed

    Amano, Ryo; Aoki, Kazuteru; Miyakawa, Shin; Nakamura, Yoshikazu; Kozu, Tomoko; Kawai, Gota; Sakamoto, Taiichi

    2017-03-21

    RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 10(15) different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.

  9. X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

    NASA Astrophysics Data System (ADS)

    Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

    1990-10-01

    The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

  10. NMR study suggests a major role for Arg111 in maintaining the structure and dynamical properties of type II human cellular retinoic acid binding protein.

    PubMed

    Wang, L; Yan, H

    1998-09-15

    The solution structure of a site-directed mutant of type-II human cellular retinoic acid binding protein (CRABPII) with Arg111 replaced by methionine (R111M) has been determined by NMR spectroscopy. The sequential assignments of the 1H and 15N resonances of apo-R111M were established by multinuclear multidimensional NMR. The solution structure was calculated from 2302 distance restraints and 77 phi dihedral restraints derived from the NMR data. The root-mean-square deviation of the ensemble of 28 refined conformers that represent the structure from the mean coordinate set derived from them was 0.54 +/- 0.26 and 0.98 +/- 0.23 A for the backbone atoms and all heavy atoms, respectively. The solution structure of apo-R111M is similar to that of wild-type apo-CRABPII. However, there are significant conformational differences between the two proteins, localized mainly to three segments (Leu19-Ala36, Glu73-Cys81, and Leu99-Pro105) clustered around the ligand entrance more than 17 A away from the point mutation. In apo-R111M, all the three segments move toward the center of the ligand entrance so that the opening of the ligand-binding pocket in apo-R111M is much smaller than that in wild-type apo-CRABPII. Furthermore, the ligand-binding pocket of apo-R111M, especially the ligand entrance, is much less flexible than that of apo-CRABPII. Surprisingly, apo-R111M is more similar to holo-CRABPII than to apo-CRABPII in both structure and dynamical properties. The conformational and dynamical changes caused by the mutation are similar to those induced by binding of RA, although the magnitudes of the changes caused by the mutation are smaller than those induced by binding of RA. The results suggest that Arg111 plays a critical role in determining the structure and dynamical properties of CRABPII.

  11. Solid state NMR studies of materials for energy technology

    NASA Astrophysics Data System (ADS)

    Nambukara Kodiweera Arachchilage, Chandana K.

    Presented in this dissertation are NMR investigations of the dynamical and structural properties of materials for energy conversion and storage devices. 1H and 2H NMR was used to study water and methanol transportation in sulfonated poly(arylene ether ketone) based membranes for direct methanol fuel cells (DMFC). These results are presented in chapter 3. The amount of liquid in the membrane and ion exchange capacity (IEC) are two main factors that govern the dynamics in these membranes. Water and methanol diffusion coefficients also are comparable. Chapters 4 and 5 are concerned with 31P and 1H NMR in phosphoric acid doped PBI membranes (para-PBI and 2OH-PBI) as well as PBI membranes containing ionic liquids (H3PO4/PMIH2PO4/PBI). These membranes are designed for higher-temperature fuel cell operation. In general, stronger short and long range interactions were observed in the 2OH-PBI matrix, yielding reduced proton transport compared to that of para-PBI. In the case of H3PO4/PMIH2PO 4/PBI, both conductivity and diffusion are higher for the sample with molar ratio 2/4/1. Finally, chapter 6 is devoted to the 31P NMR MAS study of phosphorus-containing structural groups on the surfaces of micro/mesoporous activated carbons. Two spectral features were observed and the narrow feature identifies surface phosphates while the broad component identifies heterogeneous subsurface phosphorus environments including phosphate and more complex structure multiple P-C, P-N and P=N bonds.

  12. Multidimensional HRMAS NMR: a platform for in vivo studies using intact bacterial cells.

    PubMed

    Li, Wei

    2006-07-01

    In vivo analysis in whole cell bacteria, especially the native tertiary structures of the bacterial cell wall, remains an unconquered frontier. The current understanding of bacterial cell wall structures has been based on destructive analysis of individual components. These in vitro results may not faithfully reflect the native structural and conformational information. Multidimensional High Resolution Magic Angle Spinning NMR (HRMAS NMR) has evolved to be a powerful technique in a variety of in vivo studies, including live bacterial cells. Existing studies of HRMAS NMR in bacteria, technical consideration of its successful application, and current limitations in studying true human pathogens are briefly reviewed in this report.

  13. Proton NMR studies of functionalized nanoparticles in aqueous environments

    NASA Astrophysics Data System (ADS)

    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

  14. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-05

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

  15. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  16. Protein structure estimation from NMR data by matrix completion.

    PubMed

    Li, Zhicheng; Li, Yang; Lei, Qiang; Zhao, Qing

    2017-02-06

    Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage. Then we use matrix completion to calculate the protein structure from the obtained incomplete distance matrix. We apply the accelerated proximal gradient algorithm to solve the corresponding optimization problem. Furthermore, the recovery error of our method is analyzed, and its efficiency is demonstrated by several practical examples.

  17. A community resource of experimental data for NMR / X-ray crystal structure pairs.

    PubMed

    Everett, John K; Tejero, Roberto; Murthy, Sarath B K; Acton, Thomas B; Aramini, James M; Baran, Michael C; Benach, Jordi; Cort, John R; Eletsky, Alexander; Forouhar, Farhad; Guan, Rongjin; Kuzin, Alexandre P; Lee, Hsiau-Wei; Liu, Gaohua; Mani, Rajeswari; Mao, Binchen; Mills, Jeffrey L; Montelione, Alexander F; Pederson, Kari; Powers, Robert; Ramelot, Theresa; Rossi, Paolo; Seetharaman, Jayaraman; Snyder, David; Swapna, G V T; Vorobiev, Sergey M; Wu, Yibing; Xiao, Rong; Yang, Yunhuang; Arrowsmith, Cheryl H; Hunt, John F; Kennedy, Michael A; Prestegard, James H; Szyperski, Thomas; Tong, Liang; Montelione, Gaetano T

    2016-01-01

    We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.

  18. Phase boundaries, structural characteristics, and NMR spectra of ionic liquid-in-oil microemulsions containing double chain surface active ionic liquid: a comparative study.

    PubMed

    Rao, Vishal Govind; Mandal, Sarthak; Ghosh, Surajit; Banerjee, Chiranjib; Sarkar, Nilmoni

    2013-02-07

    A method developed for the first time, to create a huge number of ionic liquid (IL)-in-oil microemulsions has been discussed in our earlier publication (Rao, V. G.; Ghosh, S.; Ghatak, C.; Mandal, S.; Brahmachari, U.; Sarkar, N. J. Phys. Chem. B 2012, 116, 2850-2855). Here, we present facile methods to adjust the structural parameters of microemulsions using different ionic liquids (ILs) as additives (polar phase). We have characterized ILs/[C(4)mim][AOT]/benzene ternary system by performing a phase behavior study, dynamic light scattering (DLS) measurements, and (1)H NMR measurements. The IL loading capacity of microemulsions (area of single phase region) (i) increases with increase in alkyl chain length of cation of ILs and follows the trend [C(6)mim][TF(2)N] > [C(4)mim][TF(2)N] > [C(2)mim][TF(2)N], (ii) increases with decrease in cation anion interaction strength of added ILs and follows the trend [C(4)mim][TF(2)N] > [C(4)mim][PF(6)] > [C(4)mim][BF(4)]. So depending on the IL used, the amount of IL within the core of microemulsions can be easily manipulated to directly affect the size of aggregates in microemulsions. The size increase with increasing R value (R value is defined as the molar ratio of RTILs to [C(4)mim][AOT]) was found to be maximum in the case of [C(2)mim][TF(2)N]/[C(4)mim][AOT]/benzene microemulsions and follows the trend [C(2)mim][TF(2)N] > [C(4)mim][TF(2)N] > [C(6)mim][TF(2)N]. However, the size increase was almost the same with increase in R value in the case of ILs with different anions. The most promising fact about IL-in-oil microemulsions is their high thermal stability compared to that of aqueous microemulsions, so we investigated the effect of temperature on size of aggregates in microemulsions at R = 1.0. It is evident from dynamic light scattering measurements that the aggregates in microemulsions remain monodisperse in nature with increasing temperature, and in all the cases, the size of aggregates in microemulsions decreases with

  19. Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment

    PubMed Central

    Tompa, Peter; Han, Kyou-Hoon; Bokor, Mónika; Kamasa, Pawel; Tantos, Ágnes; Fritz, Beáta; Kim, Do-Hyoung; Lee, Chewook; Verebélyi, Tamás; Tompa, Kálmán

    2016-01-01

    Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501] PMID:27418282

  20. Effects of nucleotide binding to LmrA: A combined MAS-NMR and solution NMR study.

    PubMed

    Hellmich, Ute A; Mönkemeyer, Leonie; Velamakanni, Saroj; van Veen, Hendrik W; Glaubitz, Clemens

    2015-12-01

    ABC transporters are fascinating examples of fine-tuned molecular machines that use the energy from ATP hydrolysis to translocate a multitude of substrates across biological membranes. While structural details have emerged on many members of this large protein superfamily, a number of functional details are still under debate. High resolution structures yield valuable insights into protein function, but it is the combination of structural, functional and dynamic insights that facilitates a complete understanding of the workings of their complex molecular mechanisms. NMR is a technique well-suited to investigate proteins in atomic resolution while taking their dynamic properties into account. It thus nicely complements other structural techniques, such as X-ray crystallography, that have contributed high-resolution data to the architectural understanding of ABC transporters. Here, we describe the heterologous expression of LmrA, an ABC exporter from Lactococcus lactis, in Escherichia coli. This allows for more flexible isotope labeling for nuclear magnetic resonance (NMR) studies and the easy study of LmrA's multidrug resistance phenotype. We use a combination of solid-state magic angle spinning (MAS) on the reconstituted transporter and solution NMR on its isolated nucleotide binding domain to investigate consequences of nucleotide binding to LmrA. We find that nucleotide binding affects the protein globally, but that NMR is also able to pinpoint local dynamic effects to specific residues, such as the Walker A motif's conserved lysine residue.

  1. Double rotation NMR studies of zeolites and aluminophosphate molecular sieves

    SciTech Connect

    Jelinek, Raz

    1993-07-01

    Goal is to study the organization and structures of guest atoms and molecules and their reactions on internal surfaces within pores of zeolites and aluminophosphate molecular sieves. 27Al and 23Na double rotation NMR (DOR) is used since it removes the anisotropic broadening in NMR spectra of quadrupolar nuclei, thus increasing resolution. This work concentrates on probing aluminum framework atoms in aluminophosphate molecular sieves and sodium extra framework cations in porous aluminosilicates. In aluminophosphates, ordering and electronic environments of the framework 27Al nuclei are modified upon adsorption of water molecules within the channels; a relation is sought between the sieve channel topology and the organization of adsorbed water, as well as the interaction between the Al nuclei and the water molecules. Extra framework Na+ cations are directly involved in adsorption processes and reactions in zeolite cavities.

  2. Stereochemistry and solid-state structure of an intrinsically chiral meso-patterned porphyrin: case study by NMR and single-crystal X-ray diffraction analysis.

    PubMed

    Yang, Liguo; Zhou, Yang; Zhu, Mengliang; Zhao, Luyang; Wei, Liye; Bian, Yongzhong

    2013-10-04

    A C1-symmerical meso-substituted ABCD-type porphyrin, [5-phenyl-10-(2-hydroxynaphthyl)-15-(4-hydroxyphenyl)porphyrinato]zinc(II) (1), has been synthesized and characterized. The molecular structure of 1 has been determined by single-crystal X-ray diffraction analysis. The complex 1 crystallizes in a triclinic system with one pair of enantiomeric molecules per unit cell. Resolution of the racemic mixture has been achieved by chiral HPLC techniques. In particular, the absolute configurations of the enantiomers have been assigned from NMR spectroscopic analysis with L-Phe-OMe as the chiral solvating agent (CSA). The assignments have also been unambiguously confirmed by single-crystal X-ray diffraction analysis. The present results suggest that the CSA-NMR anisotropy strategy is applicable for the stereochemistry determination of chiral host-guest complexes with multiple intermolecular interactions. In addition, the multiple intermolecular interactions between the enantiomerically pure porphyrin S-1 and L-Phe-OMe are proved in the solid state by single-crystal X-ray diffraction analysis.

  3. Crystal structure and theoretical study of IR and 1H and 13C NMR spectra of cordatin, a natural product with antiulcerogenic activity

    NASA Astrophysics Data System (ADS)

    Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Muller, Adolfo H.; Secco, Ricardo De S.; Peris, Gabriel; Llusar, Rosa

    Cordatin is a furan diterpenoid with a clerodane skeleton isolated from Croton palanostigma Klotzsch (Euphorbiaceae). This natural product shows significant antiulcerogenic activity, similar to cimetidine (Tagamet®), a compound used for the treatment of peptic ulcers. The crystal structure of cordatin was obtained by X-ray diffraction and its geometrical parameters were compared with theoretical calculations at the B3LYP theory level. The IR and NMR (1H and 13C chemical shifts and coupling constants) spectra were obtained and compared with the theoretical calculations. The B3LYP theory level, with the 6-31G(d,p) and 6-311G(d,p) basis set, provided IR absorption values close to the experimental data. Moreover, theoretical NMR parameters obtained in both gas phase and chloroform solvent at the B3PW91/DGDZVP, B3LYP/6-311+G(2d,p), and B3PW91/6-311+G(2d,p) levels showed good correlations with the experimental results.

  4. Microslot NMR probe for metabolomics studies.

    PubMed

    Krojanski, Hans Georg; Lambert, Jörg; Gerikalan, Yilmaz; Suter, Dieter; Hergenröder, Roland

    2008-11-15

    A NMR microprobe based on microstrip technology suitable for investigations of volume-limited samples in the low nanoliter range was designed. NMR spectra of sample quantities in the 100 pmol range can be obtained with this probe in a few seconds. The planar geometry of the probe is easily adaptable to the size and geometry requirements of the samples.

  5. Study on molecular structure, spectroscopic investigation (IR, Raman and NMR), vibrational assignments and HOMO-LUMO analysis of L-sodium folinate using DFT: a combined experimental and quantum chemical approach.

    PubMed

    Li, Linwei; Cai, Tiancheng; Wang, Zhiqiang; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2014-01-01

    In the present work, an exhaustive conformational search of N-[4-[[(2-amino-5-formyl-(6S)-3,4,5,6,7,8-hexahydro-4-oxo-6-pteridinyl)methyl]amino]benzoyl]-L-glutamic acid disodium salt (L-SF) has been preformed. The optimized structure of the molecule, vibrational frequencies and NMR spectra studies have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (d, p) basis set. IR and FT-Raman spectra for L-SF have been recorded in the region of 400-4000 cm(-1) and 100-3500 cm(-1), respectively. 13C and 1H NMR spectra were recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule were calculated based on the gauge-independent atomic orbital (GIAO) method. Finally all of the calculation results were applied to simulate IR, Raman, 1H NMR and 13C NMR spectrum of the title compound which showed excellent agreement with observed spectrum. Furthermore, reliable vibrational assignments which have been made on the basis of potential energy distribution (PED) and characteristic vibratinonal absorption bands of the title compound in IR and Raman have been figured out. HOMO-LUMO energy and Mulliken atomic charges have been evaluated, either.

  6. Solid state NMR studies of gels derived from low molecular mass gelators.

    PubMed

    Nonappa; Kolehmainen, E

    2016-07-13

    Since its invention more than six decades ago, nuclear magnetic resonance (NMR) spectroscopy has evolved as an inevitable part of chemical as well as structural analysis of small molecules, polymers, biomaterials and hybrid materials. In the solution state, due to the increased viscosity of complex viscoelastic fluids such as gels, liquid crystals and other soft materials, the rate of molecular tumbling is reduced, which in turn affects the chemical shift anisotropy, dipolar and quadrupolar interactions. As a consequence the solution state NMR spectra show broad lines, and therefore, extracting detailed structural information is a challenging task. In this context, solid state (SS) NMR has the ability to distinguish between a minute amount of polymorphic forms, conformational changes, and the number of non-equivalent molecules in an asymmetric unit of a crystal lattice, and to provide both qualitative as well as quantitative analytical data with a short-range order. Therefore, SS NMR has continued to evolve as an indispensable tool for structural analysis and gave birth to a new field called NMR crystallography. Solid state cross polarization (CP) and high resolution (HR) magic angle spinning (MAS) NMR spectroscopy has been used to study weak interactions in polymer gels. However, the application of SS NMR spectroscopy to study gels derived from low molecular weight gelators has been limited until recently. In this review, we will focus on the importance of solid state NMR spectroscopy in understanding and elucidating the structure of supramolecular gels derived from low molecular weight gelators with selected examples.

  7. Solid state NMR studies of gels derived from low molecular mass gelators

    PubMed Central

    Kolehmainen, E.

    2016-01-01

    Since its invention more than six decades ago, nuclear magnetic resonance (NMR) spectroscopy has evolved as an inevitable part of chemical as well as structural analysis of small molecules, polymers, biomaterials and hybrid materials. In the solution state, due to the increased viscosity of complex viscoelastic fluids such as gels, liquid crystals and other soft materials, the rate of molecular tumbling is reduced, which in turn affects the chemical shift anisotropy, dipolar and quadrupolar interactions. As a consequence the solution state NMR spectra show broad lines, and therefore, extracting detailed structural information is a challenging task. In this context, solid state (SS) NMR has the ability to distinguish between a minute amount of polymorphic forms, conformational changes, and the number of non-equivalent molecules in an asymmetric unit of a crystal lattice, and to provide both qualitative as well as quantitative analytical data with a short-range order. Therefore, SS NMR has continued to evolve as an indispensable tool for structural analysis and gave birth to a new field called NMR crystallography. Solid state cross polarization (CP) and high resolution (HR) magic angle spinning (MAS) NMR spectroscopy has been used to study weak interactions in polymer gels. However, the application of SS NMR spectroscopy to study gels derived from low molecular weight gelators has been limited until recently. In this review, we will focus on the importance of solid state NMR spectroscopy in understanding and elucidating the structure of supramolecular gels derived from low molecular weight gelators with selected examples. PMID:27374054

  8. Structure of model peptides based on Nephila clavipes dragline silk spidroin (MaSp1) studied by 13C cross polarization/magic angle spinning NMR.

    PubMed

    Yang, Mingying; Nakazawa, Yasumoto; Yamauchi, Kazuo; Knight, David; Asakura, Tetsuo

    2005-01-01

    To obtain detailed structural information for spider dragline spidroin (MaSp1), we prepared three versions of the consensus peptide GGLGGQGAGAAAAAAGGAGQGGYGGLGSQGAGR labeled with 13C at six different sites. The 13C CP/MAS NMR spectra were observed after treating the peptides with different reagents known to alter silk protein conformations. The conformation-dependent 13C NMR chemical shifts and peak deconvolution were used to determine the local structure and the fractional compositions of the conformations, respectively. After trifluoroacetic acid (solvent)/diethyl ether (coagulant) treatment, the N-terminal region of poly-Ala (PLA) sequence, Ala8 and Ala10, adopted predominantly the alpha-helix with a substantial amount of beta-sheet. The central region, Ala15, Ala18, and Leu26, and C-terminal region, Ala31, of the peptide were dominated by either 3(1)-helix or alpha-helix. There was no indication of beta-sheet, although peak broadening indicates that the torsion angle distribution is relatively large. After 9 M LiBr/dialysis treatment, three kinds of conformation, beta-sheet, random coil, and 3(1)-helix, appeared, in almost equal amounts of beta-sheet and random coil conformations for Ala8 and Ala10 residues and distorted 3(1)-helix at the central region of the peptide. In contrast, after formic acid/methanol and 8 M urea/acetonitrile treatments, all of the local structure tends to beta-sheet, although small amounts of random coil are also observed. The peak pattern of the Ala Cbeta carbon after 8 M urea/acetonitrile treatment is similar to the corresponding patterns of silk fiber from Bombyx mori and Samia cynthia ricini. We also synthesized a longer 13C-labeled peptide containing two PLA blocks and three Gly-rich blocks. After 8 M urea/acetonitrile treatment, the conformation pattern was closely similar to that of the shorter peptide.

  9. NMR spectroscopic study of organic phosphate esters coprecipitated with calcite

    NASA Astrophysics Data System (ADS)

    Phillips, Brian L.; Zhang, Zelong; Kubista, Laura; Frisia, Silvia; Borsato, Andrea

    2016-06-01

    Organic phosphorus incorporated in calcite during laboratory precipitation experiments and in natural cave deposits was investigated by solid-state NMR spectroscopy. For calcite precipitated in the presence of organic phosphoesters of varying size and functionality, solid-state 31P{1H} CP/MAS NMR shows that the phosphoesters were incorporated intact into the solid. Systematic changes in the 31P NMR chemical shift of the phosphate group were observed between the solid phosphoester and that incorporated in the solid precipitate, yielding 31P NMR chemical shifts of the coprecipitates in the range of +1.8 to -2.2 ppm. These chemical shifts are distinct from that of similarly prepared calcite coprecipitated with inorganic phosphate, 3.5 ppm. Only minor changes were noted in the phosphoester 31P chemical shift anisotropy (CSA) which suggests no significant change in the local structure of the phosphate group, which is dominated by C-O-P bonding. Close spatial proximity of the organic phosphate group to calcite structural components was revealed by 31P/13C rotational echo double resonance (REDOR) experiments for coprecipitates prepared with 13C-labeled carbonate. All coprecipitates showed significant 31P dephasing effects upon 13C-irradiation, signaling atomic-scale proximity to carbonate carbon. The dephasing rate for smaller organophosphate molecules is similar to that observed for inorganic phosphate, whereas much slower dephasing was observed for larger molecules having long and/or bulky side-chains. This result suggests that small organic molecules can be tightly enclosed within the calcite structure, whereas significant structural disruption required to accommodate the larger organic molecules leads to longer phosphate-carbonate distances. Comparison of 31P NMR spectroscopic data from the synthetic coprecipitates with those from calcite moonmilk speleothems indicates that phosphorus occurs mainly as inorganic orthophosphate in the natural deposits, although small

  10. NMR solution structures of actin depolymerizing factor homology domains

    PubMed Central

    Goroncy, Alexander K; Koshiba, Seizo; Tochio, Naoya; Tomizawa, Tadashi; Sato, Manami; Inoue, Makato; Watanabe, Satoru; Hayashizaki, Yoshihide; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

    2009-01-01

    Actin is one of the most conserved proteins in nature. Its assembly and disassembly are regulated by many proteins, including the family of actin-depolymerizing factor homology (ADF-H) domains. ADF-H domains can be divided into five classes: ADF/cofilin, glia maturation factor (GMF), coactosin, twinfilin, and Abp1/drebrin. The best-characterized class is ADF/cofilin. The other four classes have drawn much less attention and very few structures have been reported. This study presents the solution NMR structure of the ADF-H domain of human HIP-55-drebrin-like protein, the first published structure of a drebrin-like domain (mammalian), and the first published structure of GMF β (mouse). We also determined the structures of mouse GMF γ, the mouse coactosin-like domain and the C-terminal ADF-H domain of mouse twinfilin 1. Although the overall fold of the five domains is similar, some significant differences provide valuable insights into filamentous actin (F-actin) and globular actin (G-actin) binding, including the identification of binding residues on the long central helix. This long helix is stabilized by three or four residues. Notably, the F-actin binding sites of mouse GMF β and GMF γ contain two additional β-strands not seen in other ADF-H structures. The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF β and GMF γ. PMID:19768801

  11. NMR structure of the myristylated feline immunodeficiency virus matrix protein.

    PubMed

    Brown, Lola A; Cox, Cassiah; Baptiste, Janae; Summers, Holly; Button, Ryan; Bahlow, Kennedy; Spurrier, Vaughn; Kyser, Jenna; Luttge, Benjamin G; Kuo, Lillian; Freed, Eric O; Summers, Michael F

    2015-04-30

    Membrane targeting by the Gag proteins of the human immunodeficiency viruses (HIV types-1 and -2) is mediated by Gag's N-terminally myristylated matrix (MA) domain and is dependent on cellular phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. To determine if other lentiviruses employ a similar membrane targeting mechanism, we initiated studies of the feline immunodeficiency virus (FIV), a widespread feline pathogen with potential utility for development of human therapeutics. Bacterial co-translational myristylation was facilitated by mutation of two amino acids near the amino-terminus of the protein (Q5A/G6S; myrMAQ5A/G6S). These substitutions did not affect virus assembly or release from transfected cells. NMR studies revealed that the myristyl group is buried within a hydrophobic pocket in a manner that is structurally similar to that observed for the myristylated HIV-1 protein. Comparisons with a recent crystal structure of the unmyristylated FIV protein [myr(-)MA] indicate that only small changes in helix orientation are required to accommodate the sequestered myr group. Depletion of PI(4,5)P2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5)P2 cellular signaling system to direct intracellular Gag trafficking during virus assembly.

  12. NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein

    PubMed Central

    Brown, Lola A.; Cox, Cassiah; Baptiste, Janae; Summers, Holly; Button, Ryan; Bahlow, Kennedy; Spurrier, Vaughn; Kyser, Jenna; Luttge, Benjamin G.; Kuo, Lillian; Freed, Eric O.; Summers, Michael F.

    2015-01-01

    Membrane targeting by the Gag proteins of the human immunodeficiency viruses (HIV types-1 and -2) is mediated by Gag’s N-terminally myristylated matrix (MA) domain and is dependent on cellular phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. To determine if other lentiviruses employ a similar membrane targeting mechanism, we initiated studies of the feline immunodeficiency virus (FIV), a widespread feline pathogen with potential utility for development of human therapeutics. Bacterial co-translational myristylation was facilitated by mutation of two amino acids near the amino-terminus of the protein (Q5A/G6S; myrMAQ5A/G6S). These substitutions did not affect virus assembly or release from transfected cells. NMR studies revealed that the myristyl group is buried within a hydrophobic pocket in a manner that is structurally similar to that observed for the myristylated HIV-1 protein. Comparisons with a recent crystal structure of the unmyristylated FIV protein [myr(-)MA] indicate that only small changes in helix orientation are required to accommodate the sequestered myr group. Depletion of PI(4,5)P2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5)P2 cellular signaling system to direct intracellular Gag trafficking during virus assembly. PMID:25941825

  13. Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions.

    PubMed Central

    Popenda, M; Biala, E; Milecki, J; Adamiak, R W

    1997-01-01

    Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were determined and refined using an iterative relaxation matrix procedure (IRMA) and the restrained MD simulation. Both duplexes form half-turn, right-handed helices with several conformational features which deviate significantly from a canonical A-RNA structure. Duplexes are characterised as having C3'-endo sugar pucker, very low base-pair rise and high helical twist and inclination angles. Helices are overwound with <10 bp per turn. There is limited inter-strand guanine stacking for CG steps. Within CG steps of both duplexes, the planes of the inter-strand cytosines are not parallel while guanines are almost parallel. For the GC steps this pattern is reversed. The 2'-O-methyl groups are spatially close to the 5'-hydrogens of neighbouring residues from the 3'-side and are directed towards the minor groove of 2'-O-Me(CGCGCG)2 forming a hydrophobic layer. Solution structures of both duplexes are similar; the effect of 2'-O-methylation on the parent RNA structure is small. This suggests that intrinsic properties imposed by alternating CG base pairs govern the overall conformation of both duplexes. PMID:9358170

  14. Two dimensional and zero field NMR studies of coal structure: Progress report for the period April 1, 1986-June 30, 1986

    SciTech Connect

    Zilm, K.W.

    1986-10-01

    This report covers the progress made on the title project during the last quarter. During the last three months we have concentrated on further developing zero field NMR methods so that they can be applied to coal structure problems. Designs for both shuttling and pulsed field ZFNMR systems have been finalized and construction about halfway completed. Circuits for driving the fast pulsed field and bucking field coils are completed and described herein. Test results for the piston shuttle and ZFNMR probe are also described. For the pulsed field system we have set up the power supplies neccesary to drive the pulsed magnet. The final configuration of this system is also described in this report. 5 figs.

  15. X-ray structure, NMR and stability-in-solution study of 6-(furfurylamino)-9-(tetrahydropyran-2-yl)purine - A new active compound for cosmetology

    NASA Astrophysics Data System (ADS)

    Walla, Jan; Szüčová, Lucie; Císařová, Ivana; Gucký, Tomáš; Zatloukal, Marek; Doležal, Karel; Greplová, Jarmila; Massino, Frank J.; Strnad, Miroslav

    2010-06-01

    The crystal and molecular structure of 6-(furfurylamino)-9-(tetrahydropyran-2-yl)purine ( 1) was determined at 150(2) K. The compound crystallizes in monoclinic P2 1/ c space group with a = 10.5642(2), b = 13.6174(3), c = 10.3742(2) Å, V = 1460.78(5) Å 3, Z = 4, R( F) = for 3344 unique reflections. The purine moiety and furfuryl ring are planar and the tetrahydropyran-2-yl is disordered in the ratio 1:3, probably due to the chiral carbon atom C(17). The individual 1H and 13C NMR signals were assigned by 2D correlation experiments such as 1H- 1H COSY and ge-2D HSQC. Stability-in-solution was determined in methanol/water in acidic pH (3-7).

  16. In-Cell Solid-State NMR: An Emerging Technique for the Study of Biological Membranes

    PubMed Central

    Warnet, Xavier L.; Arnold, Alexandre A.; Marcotte, Isabelle; Warschawski, Dror E.

    2015-01-01

    Biological molecular processes are often studied in model systems, which simplifies their inherent complexity but may cause investigators to lose sight of the effects of the molecular environment. Information obtained in this way must therefore be validated by experiments in the cell. NMR has been used to study biological cells since the early days of its development. The first NMR structural studies of a protein inside a cell (by solution-state NMR) and of a membrane protein (by solid-state NMR) were published in 2001 and 2011, respectively. More recently, dynamic nuclear polarization, which has been used to enhance the signal in solid-state NMR, has also been applied to the study of frozen cells. Much progress has been made in the past 5 years, and in this review we take stock of this new technique, which is particularly appropriate for the study of biological membranes. PMID:26682804

  17. NMR-Metabolic Methodology in the Study of GM Foods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 1H NMR methodology used in the study of genetically modified (GM) foodstuff is discussed. The study of transgenic lettuce (Lactuca sativa cv "Luxor") over-expressing the KNAT1 gene from Arabidopsis is presented as a novel study-case. The 1H NMR metabolic profiling was carried out. Twenty-two wat...

  18. The structural plasticity of heparan sulfate NA-domains and hence their role in mediating multivalent interactions is confirmed by high-accuracy 15N-NMR relaxation studies

    PubMed Central

    Mobli, Mehdi; Nilsson, Mathias

    2007-01-01

    Considering the biological importance of heparan sulfate (HS) and the significant activity of its highly-sulfated regions (S-domains), the paucity of known functions for the non-sulfated NA-domains is somewhat puzzling. It has been suggested that chain dynamics within the NA-domains are the key to their functional role in HS. In this study, we investigate this hypothesis using state-of-the-art nuclear magnetic resonance (NMR) experiments at multiple frequencies. To resolve the problem of severe overlap in 1H-NMR spectra of repetitive polysaccharides from proteoglycans, we have prepared oligosaccharides with the chemical structure of HS NA-domains containing the 15N nucleus, which has enough chemical shift dispersion to probe the central residues of octasaccharides at atomic resolution using 600 MHz NMR. By performing NMR relaxation experiments at three magnetic-field strengths, high quality data on internal dynamics and rotational diffusion was obtained. Furthermore, translational diffusion could also be measured by NMR using pulse field gradients. These experimental data were used, in concert with molecular dynamics simulations, to provide information on local molecular shape, greatly aiding our relaxation analyses. Our results, which are more accurate than those presented previously, confirm the higher flexibility of the NA-domains as compared with reported data on S-domains. It is proposed that this flexibility has two functional roles. First, it confers a greater area of interaction from the anchoring point on the core protein for the bioactive S-domains. Secondly, it allows multiple interactions along the same HS chain that are dynamically independent of each other. Electronic Supplementary Material The online version of this article (doi:10.1007/s10719-007-9081-9) contains supplementary material, which is available to authorized users. PMID:18080183

  19. NMR studies of multiphase flows II

    SciTech Connect

    Altobelli, S.A.; Caprihan, A.; Fukushima, E.

    1995-12-31

    NMR techniques for measurements of spatial distribution of material phase, velocity and velocity fluctuation are being developed and refined. Versions of these techniques which provide time average liquid fraction and fluid phase velocity have been applied to several concentrated suspension systems which will not be discussed extensively here. Technical developments required to further extend the use of NMR to the multi-phase flow arena and to provide measurements of previously unobtainable parameters are the focus of this report.

  20. NMR Studies of Molecular Orientation and Dynamics in Spider silk

    NASA Astrophysics Data System (ADS)

    Michal, Carl; Eles, Philip

    2004-05-01

    Spider dragline silk has a unique combination of strength and extensibility that has been difficult to achieve in synthetic polymer fibres and has inspired industrial efforts to produce genetically engineered analogues. In light of these efforts elsewhere, we describe solid-state NMR experiments that elucidate the molecular structure and dynamics of this remarkable material. These experiments include the use of a 2-D exchange NMR experiment known as DECODER in which the sample is reoriented through a discrete angle during the mixing time. This experiment allows a reconstruction of the orientation distribution of the protein backbone. Our data is well described by a two-component distribution where the protein backbones of both components are preferentially aligned along the silk fibre. This experiment is also sensitive to molecular motion on a wide range of time-scales, and is employed to study changes in the silk as a function of fibre extension and hydration. Hydrated silk undergoes a remarkable phenomena known as supercontraction where fibres shrink by up to 50% in length while swelling in diameter. DECODER NMR of fully and partially supercontracted silk reveals that supercontraction occurs through a process of local phase transitions where water disrupts inter- and intra-chain hydrogen bonds.

  1. NMR-based simulation studies of Pf1 coat protein in explicit membranes.

    PubMed

    Cheng, Xi; Jo, Sunhwan; Marassi, Francesca M; Im, Wonpil

    2013-08-06

    As time- and ensemble-averaged measures, NMR observables contain information about both protein structure and dynamics. This work represents a computational study to extract such information for membrane proteins from orientation-dependent NMR observables: solid-state NMR chemical shift anisotropy and dipolar coupling, and solution NMR residual dipolar coupling. We have performed NMR-restrained molecular dynamics simulations to refine the structure of the membrane-bound form of Pf1 coat protein in explicit lipid bilayers using the recently measured chemical shift anisotropy, dipolar coupling, and residual dipolar coupling data. From the simulations, we have characterized detailed protein-lipid interactions and explored the dynamics. All simulations are stable and the NMR restraints are well satisfied. The C-terminal transmembrane (TM) domain of Pf1 finds its optimal position in the membrane quickly (within 6 ns), illustrating efficient solvation of TM domains in explicit bilayer environments. Such rapid convergence also leads to well-converged interaction patterns between the TM helix and the membrane, which clearly show the interactions of interfacial membrane-anchoring residues with the lipids. For the N-terminal periplasmic helix of Pf1, we identify a stable, albeit dynamic, helix orientation parallel to the membrane surface that satisfies the amphiphatic nature of the helix in an explicit lipid bilayer. Such detailed information cannot be obtained solely from NMR observables. Therefore, the present simulations illustrate the usefulness of NMR-restrained MD refinement of membrane protein structure in explicit membranes.

  2. Chemical structure and heterogeneity differences of two lignins from loblolly pine as investigated by advanced solid-state NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advanced solid-state NMR was employed to investigate differences in chemical structure and heterogeneity between milled wood lignin (MWL) and residual enzyme lignin (REL). Wiley and conventional milled woods were also studied. The advanced NMR techniques included 13C quantitative direct polarization...

  3. Chemical Equilibrium in Supramolecular Systems as Studied by NMR Spectrometry

    ERIC Educational Resources Information Center

    Gonzalez-Gaitano, Gustavo; Tardajos, Gloria

    2004-01-01

    Undergraduate students are required to study the chemical balance in supramolecular assemblies constituting two or more interacting species, by using proton NMR spectrometry. A good knowledge of physical chemistry, fundamentals of chemical balance, and NMR are pre-requisites for conducting this study.

  4. Solution structure of DAPI selectively bound in the minor groove of a DNA T.T mismatch-containing site: NMR and molecular dynamics studies.

    PubMed Central

    Trotta, E; Paci, M

    1998-01-01

    The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer [d(GCGATTCGC)]2, containing a central T.T mismatch, has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics and molecular dynamics computations including relaxation matrix refinement. The results show that the DAPI molecule binds in the minor groove of the central region 5'-ATT-3' of the DNA oligomer, which predominantly adopts a duplex structure with a global right-handed B-like conformation. In the final models of the complex, the DAPI molecule is located nearly isohelical with its NH indole proton oriented towards the DNA helix axis and forming a bifurcated hydrogen bond with the carbonyl O2 groups of a mismatched T5 and the T6 residue of the opposite strand. Mismatched thymines adopt a wobble base pair conformation and are found stacked between the flanking base pairs, inducing only minor local conformational changes in global duplex structure. In addition, no other binding mechanisms were observed, showing that minor groove binding of DAPI to the mismatch-containing site is favoured in comparison with any other previously reported interaction with G.C sequences. PMID:9753740

  5. Molecular organization in the native state of woody tissue: Studies of tertiary structure using the Raman microprobe Solid State [sup 13]C NMR and biomimetic tertiary aggregates

    SciTech Connect

    Atalla, R.H.

    1992-01-01

    A number of new approaches to the study of native wood tissue complementary to our earlier Raman spectroscopy including solid state [sup 13]C NMR and X-ray diffractometry. A wide variety of native cellulosic tissues were examined which led to the generation of biomimetic tertiary aggregates which simulate states of aggregation characteristic of cell walls. We have also explored charge transport characteristics of lignified tissue. Our Raman spectroscopic studies have advanced our understanding of key spectral features and confirmed the variability of the patterns of orientation of lignin reported earlier. A major effort was dedicated to assessing the contributions of electronic factors such as conjugation and the resonance Raman effect to enhancement of the spectra features associated with lignin. We have now established a solid foundation for spectral mapping of different regions in cell walls.

  6. /sup 19/F NMR studies of 5-fluorouracil-substituted Escherichia coli transfer RNAs: solution structure and codon-anticodon interaction

    SciTech Connect

    Gollnick, P.D.

    1986-01-01

    /sup 19/F NMR was used to study E. coli tRNA/sub 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. /sup 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 /sup 19/F spectra differ in the shift of one /sup 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/sub 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 /sup 19/F signals in the central region of the spectrum of (FUra)tRNA/sub 1//sup Val/ correspond to fluorouracils in non-base-paired regions. Photoreaction with psoralen indicates upfield /sup 19/F signals arise from residues in helical environments. Removal of magnesium or addition of NaCl produces major, reversible changes in the /sup 19/F spectrum of fluorinated tRNAs. Studies of manganese and spermine binding to (FUra)tRNA/sub 1//sup Val/ allow localization of several resonances in the /sup 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 /sup 19/F resonance at 3.9 ppm in the spectrum of (FUra)tRNA/sub 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 /sup 19/F peak at 4.5 ppm. /sup 1/H NMR and RNase H digestion studies show that the oligonucleotides bind to the anticodon.

  7. Protein NMR Structure Refinement based on Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Ikeya, Teppei; Ikeda, Shiro; Kigawa, Takanori; Ito, Yutaka; Güntert, Peter

    2016-03-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a tool to investigate threedimensional (3D) structures and dynamics of biomacromolecules at atomic resolution in solution or more natural environments such as living cells. Since NMR data are principally only spectra with peak signals, it is required to properly deduce structural information from the sparse experimental data with their imperfections and uncertainty, and to visualize 3D conformations by NMR structure calculation. In order to efficiently analyse the data, Rieping et al. proposed a new structure calculation method based on Bayes’ theorem. We implemented a similar approach into the program CYANA with some modifications. It allows us to handle automatic NOE cross peak assignments in unambiguous and ambiguous usages, and to create a prior distribution based on a physical force field with the generalized Born implicit water model. The sampling scheme for obtaining the posterior is performed by a hybrid Monte Carlo algorithm combined with Markov chain Monte Carlo (MCMC) by the Gibbs sampler, and molecular dynamics simulation (MD) for obtaining a canonical ensemble of conformations. Since it is not trivial to search the entire function space particularly for exploring the conformational prior due to the extraordinarily large conformation space of proteins, the replica exchange method is performed, in which several MCMC calculations with different temperatures run in parallel as replicas. It is shown with simulated data or randomly deleted experimental peaks that the new structure calculation method can provide accurate structures even with less peaks, especially compared with the conventional method. In particular, it dramatically improves in-cell structures of the proteins GB1 and TTHA1718 using exclusively information obtained in living Escherichia coli (E. coli) cells.

  8. Structural determination of larger proteins using stable isotope labeling and NMR spectroscopy

    SciTech Connect

    Unkefer, C.; Hernandez, G.; Springer, P.; Trewhella, J.; Blumenthal, D.; Lidstrom, M.

    1996-04-01

    The project sought to employ stable isotope labeling and NMR spectroscopy to study protein structures and provide insight into important biochemical problems. A methylotrophic bacterial expression system has been developed for uniform deuterium and carbon-13 labeling of proteins for structural studies. These organisms grow using methanol as the sole source of carbon and energy. Because isotopically labeled methanol is relatively inexpensive, the methylotrophs are ideal for expressing proteins labeled uniformly with deuterium and/or carbon-13. This expression system has been employed to prepare deuterated troponin C. NMR spectroscopy measurements have been made on the inhibitory peptide from troponin I (residues 96--115), both as the free peptide and the peptide complexed with deuterated troponin C. Proton-NMR spectroscopy resonance-signal assignments have been made for the free peptide.

  9. Effect of iron content on the structure and disorder of iron-bearing sodium silicate glasses: A high-resolution 29Si and 17O solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Kim, Hyo-Im; Sur, Jung Chul; Lee, Sung Keun

    2016-01-01

    increase with iron content and that Fe3+ is predominantly a network-former. The 17O NMR spectra suggest a moderate degree of preferential partitioning of iron between NBO and BO clusters. The present results bear strong promise for studying iron-bearing silicate glasses using solid-state NMR techniques, constraining the effect of iron content on the degree of polymerization. The observed changes in atomic structures of iron-bearing sodium silicate glasses will be helpful for unraveling atomic origins of the properties of natural silicate melts.

  10. NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus).

    PubMed Central

    Torres, A M; Kini, R M; Selvanayagam, N; Kuchel, P W

    2001-01-01

    A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait (Bungarus candidus), was determined by (1)H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for the 20 calculated structures and the mean structure is 0.47 A (1 A=0.1 nm) for all residues and 0.24 A for the well-defined region that spans residues 23-58. Secondary-structural elements include two antiparallel beta-sheets characterized by two and four strands. According to recent X-ray analysis, bucandin adopts a typical three-finger loop motif and yet it has some peculiar characteristics that set it apart from other common alpha-neurotoxins. The presence of a fourth strand in the second antiparallel beta-sheet had not been observed before in three-finger toxins, and this feature was well represented in the NMR structure. Although the overall fold of the NMR structure is similar to that of the X-ray crystal structure, there are significant differences between the two structures that have implications for the pharmacological action of the toxin. These include the extent of the beta-sheets, the conformation of the region spanning residues 42-49 and the orientation of some side chains. In comparison with the X-ray structure, the NMR structure shows that the hydrophobic side chains of Trp(27) and Trp(36) are stacked together and are orientated towards the tip of the middle loop. The NMR study also showed that the two-stranded beta-sheet incorporated in the first loop, as defined by residues 1-22, and the C-terminus from Asn(59), is probably flexible relative to the rest of the molecule. On the basis of the dispositions of the hydrophobic and hydrophilic side chains, the structure of bucandin is clearly different from those of cytotoxins. PMID:11736642

  11. Understanding NMR Multiplet Structure with WinDNMR

    NASA Astrophysics Data System (ADS)

    Bampos, N.; Vidal-Ferran, A.

    2000-01-01

    Interpreting the information encoded in the structure of a multiplet representing a nucleus (e.g., a proton) in nuclear magnetic resonance (NMR) spectroscopy allows us to construct a detailed picture of the molecule to which the nucleus belongs. To gain this understanding, we can employ interactive, user-friendly software packages (such as WinDNMR) on a conventional personal computer to investigate the effect of changing the constituent coupling constants on the appearance of a multiplet. As an example, a multiplet representing a proton coupled to three neighboring environments (four-spin system) is treated in detail. Exercises similar to those presented in this work could be incorporated into a practical component of a course dealing with the basic theoretical concepts of one-dimensional NMR spectroscopy.

  12. NMR studies of two spliced leader RNAs using isotope labeling

    SciTech Connect

    Lapham, J.; Crothers, D.M.

    1994-12-01

    Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

  13. Al NMR study of molten aluminum oxide compounds and mixtures, measured at ultra high temperatures.

    NASA Astrophysics Data System (ADS)

    Piwowarczyk, J.; Marzke, R. F.; Wolf, G. H.; Petuskey, W. T.; Takulapalli, B.

    2002-10-01

    The technique of ultra high-temperature nuclear magnetic resonance (NMR) has provided insight into the chemical structure and properties of molten aluminum-bearing refractory ceramics, at temperatures in excess of 2000 ^oC. Through application of standard NMR measurements we have studied molten aluminum-bearing ceramics via ^27Al NMR. We have measured spin-lattice (T_1) and spin-spin (T_2) relaxation times, have studied Al-O-P chemical bonding within molten aluminua-monazite (Al_2O3 + LaPO_4) samples and have begun to measure Al diffusivity as a function of temperature and composition. To overcome the limitations of standard NMR heating systems a specially designed NMR probe was developed. Application of levitation technology and a laser heating system permit controlled, containerless heating of samples over a wide range of temperatures. Supported by NSF DMR 0116361, DMR 9818133 and by Research Corp. RA 0276

  14. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

    PubMed

    Zook, James; Mo, Gina; Sisco, Nicholas J; Craciunescu, Felicia M; Hansen, Debra T; Baravati, Bobby; Cherry, Brian R; Sykes, Kathryn; Wachter, Rebekka; Van Horn, Wade D; Fromme, Petra

    2015-06-02

    Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines.

  15. Dynamics of Antibody Domains Studied by Solution NMR

    PubMed Central

    Vu, Bang K.; Walsh, Joseph D.; Dimitrov, Dimiter S.; Ishima, Rieko

    2012-01-01

    Information on local dynamics of antibodies is important to evaluate stability, to rationally design variants, and to clarify conformational disorders at the epitope binding sites. Such information may also be useful for improved understanding of antigen recognition. NMR can be used for characterization of local protein dynamics at the atomic level through relaxation measurements. Due to the complexity of the NMR spectra, an extensive use of this method is limited to small protein molecules, for example, antibody domains and some scFv. Here, we describe a protocol that was used to study the dynamics of an antibody domain in solution using NMR. We describe protein preparation for NMR studies, NMR sample optimization, signal assignments, and dynamics experiments. PMID:19252840

  16. Accurate NMR structures through minimization of an extended hybrid energy.

    PubMed

    Nilges, Michael; Bernard, Aymeric; Bardiaux, Benjamin; Malliavin, Thérèse; Habeck, Michael; Rieping, Wolfgang

    2008-09-10

    The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.

  17. NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

    PubMed

    Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

    2011-05-01

    Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB), Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio., (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR, 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

  18. Synthesis, crystal structure, NMR study and AC conductivity of [(C3H7)4N]2Cd2ClF5 compound

    NASA Astrophysics Data System (ADS)

    Hajji, Rachid; Oueslati, Abderrazak; Body, Monique; Hlel, Faouzi

    2015-08-01

    The [(C3H7)4N]2Cd2ClF5 compound was crystallized in the triclinic system with space group P1. The crystal structure consists of organic-inorganic layers, stacked along direction. The organic part consists of two cations types. The inorganic layer is made up of Cd2ClF5 dimmers composed of two in-equivalent irregular tetrahedra sharing one edge (Cl-F). The MAS NMR spectra showed two, three and five isotropic resonances relative to 111Cd, 13C and 19F nuclei, respectively. DSC measurement disclosed a phase transition at around 380 K. The impedance spectroscopy and AC electrical conductivity measurements of our compound were taken from 209 Hz to 5 MHz over the temperature range of 350-381 K. Nyquist plots ( Z″ vs Z') show semicircle arcs at different temperatures, and an electrical equivalent circuit has been proposed to explain the impedance results. The circuits consist of the parallel combination of bulk resistance ( R), capacitance ( C) and fractal capacitance (CPE). The conductivity σ p follows the Arrhenius relation. The near value of activation energies obtained from the conductivity data and circuit equivalent confirms that the transport is through hopping mechanism. The analysis of the experimental data shows that the reorientation motion of [N(C3H7)4]+ cations and/or [Cd2ClF5]2- anions is probably responsible for the observed conductivity.

  19. Protein Structural Studies by Paramagnetic Solid-State NMR Spectroscopy Aided by a Compact Cyclen-Type Cu(II) Binding Tag

    PubMed Central

    Sengupta, Ishita; Gao, Min; Arachchige, Rajith J.; Nadaud, Philippe S.; Cunningham, Timothy F.; Saxena, Sunil; Schwieters, Charles D.; Jaroniec, Christopher P.

    2014-01-01

    Paramagnetic relaxation enhancements (PREs) are a rich source of structural information in protein solid-state NMR spectroscopy. Here we demonstrate that PRE measurements in natively diamagnetic proteins are facilitated by a thiol-reactive compact, cyclen-based, high-affinity Cu2+ binding tag, 1-(2-(pyridin-2-yldisulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (TETAC), that overcomes the key shortcomings associated with the use of larger, more flexible metal-binding tags. Using the TETAC-Cu2+ K28C mutant of B1 immunoglobulin-binding domain of protein G as a model, we find that amino acid residues located within ~10 Å of the Cu2+ center experience considerable transverse PREs leading to severely attenuated resonances in 2D 15N-13C correlation spectra. For more distant residues, electron-nucleus distances are accessible via quantitative measurements of longitudinal PREs, and we demonstrate such measurements for 15N-Cu2+ distances up to ~20 Å. PMID:25432438

  20. Introducing NMR to a General Chemistry Audience: A Structural-Based Instrumental Laboratory Relating Lewis Structures, Molecular Models, and [superscript 13]C NMR Data

    ERIC Educational Resources Information Center

    Pulliam, Curtis R.; Pfeiffer, William F.; Thomas, Alyssa C.

    2015-01-01

    This paper describes a first-year general chemistry laboratory that uses NMR spectroscopy and model building to emphasize molecular shape and structure. It is appropriate for either a traditional or an atoms-first curriculum. Students learn the basis of structure and the use of NMR data through a cooperative learning hands-on laboratory…

  1. High-Throughput NMR Assessment of the Tertiary Structure of Food Allergens

    PubMed Central

    Alessandri, Stefano; Sancho, Ana; Vieths, Stefan; Mills, Clare E. N.; Wal, Jean-Michel; Shewry, Peter R.; Rigby, Neil; Hoffmann-Sommergruber, Karin

    2012-01-01

    Background In vitro component-resolved diagnosis of food allergy requires purified allergens that have to meet high standards of quality. These include the authentication of their conformation, which is relevant for the recognition by specific IgE antibodies from allergic patients. Therefore, highly sensitive and reliable screening methods for the analysis of proteins/allergens are required to assess their structural integrity. In the present study one-dimensional 1H Nuclear Magnetic Resonance (1D 1H-NMR) analysis was adopted for the assessment of overall structural and dynamic properties and authentication of a set of relevant food allergens, including non-specific lipid transfer proteins from apple, peach and hazelnut, 7/8S seed storage globulins from hazelnut and peanut, 11S seed storage globulins from hazelnut and peanut, caseins from cows' and goats' milk and tropomyosin from shrimp. Methodology/Principal Findings Two sets of 1D 1H-NMR experiments, using 700 MHz and 600 MHz instruments at 298 K were carried out to determine the presence and the extent of tertiary structure. Structural similarity among members of the individual allergen families was also assessed and changes under thermal stress investigated. The nuclear magnetic resonance (NMR) results were compared with structural information available either from the literature, Protein Data Bank entries, or derived from molecular models. Conclusions/Significance 1D 1H-NMR analysis of food allergens allowed their classification into molecules with rigid, extended and ordered tertiary structures, molecules without a rigid tertiary structure and molecules which displayed both features. Differences in thermal stability were also detected. In summary, 1D 1H-NMR gives insights into molecular fold of proteins and offers an independent method for assessing structural properties of proteins. PMID:22768312

  2. Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

    PubMed

    Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

    2012-06-06

    Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data.

  3. High-resolution solid-state NMR study of the effect of composition on network connectivity and structural disorder in multi-component glasses in the diopside and jadeite join: Implications for structure of andesitic melts

    NASA Astrophysics Data System (ADS)

    Park, Sun Young; Lee, Sung Keun

    2014-12-01

    The structural evolution of andesitic melts with varying compositions remains one of the unsolved questions in high-temperature geochemistry and petrology. In this article, we report the structural details of model andesitic glasses [CaO-MgO-Na2O-Al2O3-SiO2 (CMNAS)] in the diopside (CaMgSi2O6) and jadeite (NaAlSi2O6) join using high-resolution, multi-nuclear, solid-state nuclear magnetic resonance (NMR). The 27Al NMR spectra of CMNAS glasses confirm that [4]Al is dominant. While a minor fraction of [5]Al is observed, its presence is only prevalent in the glasses with higher Ca-Mg content. Topological disorder in the glass network also tends to increase with Ca-Mg content as evidenced by the increase in the quadrupolar coupling constant (Cq) of [4]Al for glasses with increasing diopside contents (XDiopside). Despite the complex nature of the glasses studied here (with five oxide components), the 17O 3QMAS NMR spectra resolve diverse bridging oxygens (BOs) and non-bridging oxygens (NBOs), from which the degree of Al avoidance among framework cations (Si and Al) and preferential proximity among non-network cations (Ca2+, Mg2+, and Na+) and each oxygen site can be estimated: presence of Al-O-Al in jadeite glass implies a violation of the Al-avoidance rule in the glasses and the decrease in the fraction of NBOs with increasing XDiopside is consistent with a decrease in their viscosity. Analysis of the peak position of {Ca, Mg}-mixed NBOs, along with the absence of Na-NBO peak, and the peak shape of Si-O-Al reveals preferential partitioning of Ca2+ and Mg2 into NBOs and the proximity of Na+ to BOs. The fraction of highly coordinated Al has been linked to thermodynamic and transport properties of the melts. Considering all the experimental Al coordination environments available in the literature, together with the current experimental studies, we attempt to establish the relationship between the fractions of highly coordinated Al and composition, particularly average

  4. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    DOE PAGES

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; ...

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

  5. NMR studies in chemistry. I. Organometallic tin and geramanium compounds. II. The sorbitol pathway in intact lenses

    SciTech Connect

    Williams, W.F.

    1985-01-01

    Nuclear magnetic resonance spectroscopy has been utilized in the study of two very different chemical problems. The bonding and structure of various cyclopropyl derivatives of tin and germanium has been investigated by means of Sn-119, Ge-73, C-13, and H-1 NMR spectroscopy. Intact rabbit lenses have also been studied using NMR spectroscopy with regard to diabetic cataract formation. C-13 and P-31 NMR spectroscopies have been utilized in the study of the sorbitol pathway and aldose reductase inhibition.

  6. NMR studies of metallic tin confined within porous matrices

    SciTech Connect

    Charnaya, E. V.; Tien, Cheng; Lee, M. K.; Kumzerov, Yu. A.

    2007-04-01

    {sup 119}Sn NMR studies were carried out for metallic tin confined within synthetic opal and porous glass. Tin was embedded into nanoporous matrices in the melted state under pressure. The Knight shift for liquid confined tin was found to decrease with decreasing pore size. Correlations between NMR line shapes, Knight shift, and pore filling were observed. The melting and freezing phase transitions of tin under confinement were studied through temperature dependences of NMR signals upon warming and cooling. Melting of tin within the opal matrix agreed well with the liquid skin model suggested for small isolated particles. The influence of the pore filling on the melting process was shown.

  7. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  8. Boric acid, “carbonic” acid, and N-containing oxyacids in aqueous solution: Ab initio studies of structure, pKa, NMR shifts, and isotopic fractionations

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    2005-12-01

    B(OH) 3 and CO 2 are acidic species of considerable geochemical importance, yet the microscopic nature of the acid dissociation reactions for these B and C species is not well understood. Quantum mechanical methods have recently been applied to the direct ab initio calculation of p Ka values for many organic and inorganic weak acids, but the B and C acids have not yet been considered in detail. In the present study, p Ka values are calculated quantum mechanically for the oxyacids B(OH) 3, H 2CO 3 and HNO 3, which have experimental first p Ka values of 9.2, 6.4 and -1.3, respectively. We calculate the gas-phase reaction free energies at the highly accurate CBS-QB3 ab initio quantum mechanical level and reaction free energies of hydration using a polarizable continuum method. Using a thermodynamic cycle corresponding to the simple dissociation process HA A - + H +, in aqueous solution, we calculate p Ka values of 21.6, 3.8 to 2.2 and -0.8 for the three oxyacids mentioned above, closely matching experiment only for HNO 3. The discrepancies with experiment arise from the more complex nature of the acid dissociation process for B(OH) 3, which involves the addition of H 2O to B(OH) 3 and formation of the B(OH) 4- anion, and from the instability of hypothetical H 2CO 3 compared to the proper hydrated reactant complex CO 2. . . H 2O. When the proper microscopic description of the reactants and products is used the calculated p Ka values for the three acids become 11.1, 7.2 and -0.8, in considerably better agreement with experiment for B(OH) 3 and CO 2. . . H 2O. Thus p Ka calculations using this approach are accurate enough to give information on the actual acid species present in solution and the details of their acid dissociation processes at the microscopic level. 11B and 13C-NMR chemical shifts are also calculated for the various species and compared to experiment. By comparison of our calculations with experiment it is apparent that the 13C-NMR chemical shift has

  9. Some nitrogen-14 NMR studies in solids

    SciTech Connect

    Pratum, T.K.

    1983-11-01

    The first order quadrupolar perturbation of the /sup 14/N NMR spectrum yields information regarding the static and dynamic properties of the surrounding electronic environment. Signal to noise problems caused by long /sup 14/N longitudinal relaxation times (T/sub 1/) and small equilibrium polarizations are reduced by rotating frame cross polarization (CP) experiments between /sup 14/N and /sup 1/H. Using quadrupolar echo and CP techniques, the /sup 14/N quadrupolar coupling constants (e/sup 2/qQ/h) and asymmetry parameters (eta) have been obtained for a variety of tetraalkylammonium compounds by observation of their quadrupolar powder patterns at various temperatures. For choline chloride and iodide the /sup 14/N NMR powder patterns exhibit the effects of anisotropic molecular motion, while choline bromide spectra show no such effects.

  10. Stacking structure of confined 1-butanol in SBA-15 investigated by solid-state NMR spectroscopy.

    PubMed

    Lin, Yun-Chih; Chou, Hung-Lung; Sarma, Loka Subramanyam; Hwang, Bing-Joe

    2009-10-12

    Understanding the complex thermodynamic behavior of confined amphiphilic molecules in biological or mesoporous hosts requires detailed knowledge of the stacking structures. Here, we present detailed solid-state NMR spectroscopic investigations on 1-butanol molecules confined in the hydrophilic mesoporous SBA-15 host. A range of NMR spectroscopic measurements comprising of (1)H spin-lattice (T(1)), spin-spin (T(2)) relaxation, (13)C cross-polarization (CP), and (1)H,(1)H two-dimensional nuclear Overhauser enhancement spectroscopy ((1)H,(1)H 2D NOESY) with the magic angle spinning (MAS) technique as well as static wide-line (2)H NMR spectra have been used to investigate the dynamics and to observe the stacking structure of confined 1-butanol in SBA-15. The results suggest that not only the molecular reorientation but also the exchange motions of confined molecules of 1-butanol are extremely restricted in the confined space of the SBA-15 pores. The dynamics of the confined molecules of 1-butanol imply that the (1)H,(1)H 2D NOESY should be an appropriate technique to observe the stacking structure of confined amphiphilc molecules. This study is the first to observe that a significant part of confined 1-butanol molecules are orientated as tilted bilayered structures on the surface of the host SBA-15 pores in a time-average state by solid-state NMR spectroscopy with the (1)H,(1)H 2D NOESY technique.

  11. Structure and reactivity of lithium amides. /sup 6/Li, /sup 13/C, and /sup 15/N NMR spectroscopic studies and colligative measurements of lithium diphenylamide and lithium diphenylamide-lithium bromide complex solvated by tetrahydrofuran

    SciTech Connect

    DePue, J.S.; Collum, D.B.

    1988-08-03

    /sup 6/Li, /sup 13/C, and /sup 15/N NMR spectroscopic studies of lithium diphenylamide in THF/hydrocarbon solutions (THF = tetrahydrofuran) detected two different species. /sup 6/Li and /sup 15/N NMR spectroscopic studies of (/sup 6/Li, /sup 15/N)lithium diphenylamide showed the species observed at low THF concentrations to be a cyclic oligomer. Structural analogies provided strong support for a dimer while colligative measurements at 0/degrees/C indicated the dimer to be di- or trisolvated. On the basis of the observed mass action effects, the species appearing at intermediate THF concentrations is assigned as a contact or solvent-separated ion-paired monomer. Lithium diphenylamide forms a 1:1 adduct with lithium bromide at low THF concentrations. A combination of /sup 6/Li-/sup 15/N double labeling studies and colligative measurements supports a trisolvated cyclic mixed dimer structure. Although detailed spectroscopic studies at elevated THF concentrations were precluded by high fluctionality, the similarity of the /sup 13/C chemical shifts of lithium diphenylamide in the presence and absence of lithium bromide provide indirect evidence that the mixed dimer undergoes a THF concentration dependent dissociation to the monomeric amide and free lithium bromide. 24 references, 9 figures, 2 tables.

  12. Intercalation complex of proflavine with DNA: Structure and dynamics by solid-state NMR

    SciTech Connect

    Tang, Pei; Juang, Chilong; Harbison, G.S. )

    1990-07-06

    The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallel to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.

  13. Probing the surface structure of divalent transition metals using surface specific solid-state NMR spectroscopy.

    PubMed

    Mason, Harris E; Harley, Stephen J; Maxwell, Robert S; Carroll, Susan A

    2012-03-06

    Environmental and geochemical systems containing paramagnetic species could benefit by using nuclear magnetic resonance (NMR) spectroscopy due to the sensitivity of the spectral response to small amounts paramagnetic interactions. In this study, we apply commonly used solid-state NMR spectroscopic methods combined with chemometrics analysis to probe sorption behavior of the paramagnetic cations Cu(2+) and Ni(2+)at the amorphous silica surface. We exploit the unique properties of paramagnets to derive meaningful structural information in these systems at low, environmentally relevant cation surface loadings by comparing the NMR response of sorption samples to paramagnetic free samples. These data suggest that a simple sorption model where the cation sorbs as inner sphere complexes at negatively charged, deprotonated silanol sites is appropriate. These results help constrain sorption models that are used to describe metal fate and transport.

  14. NMR Studies of Dynamic Biomolecular Conformational Ensembles

    PubMed Central

    Torchia, Dennis A.

    2015-01-01

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

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

    PubMed

    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.

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

    PubMed Central

    Horst, Reto; Wüthrich, Kurt

    2016-01-01

    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 [2H, 15N]-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 [15N, 1H]-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. PMID:27077076

  17. NMR structure of the human Mediator MED25 ACID domain.

    PubMed

    Bontems, François; Verger, Alexis; Dewitte, Frédérique; Lens, Zoé; Baert, Jean-Luc; Ferreira, Elisabeth; de Launoit, Yvan; Sizun, Christina; Guittet, Eric; Villeret, Vincent; Monté, Didier

    2011-04-01

    MED25 (ARC92/ACID1) is a 747 residues subunit specific to higher eukaryote Mediator complex, an essential component of the RNA polymerase II general transcriptional machinery. MED25 is a target of the Herpes simplex virus transactivator protein VP16. MED25 interacts with VP16 through a central MED25 PTOV (Prostate tumour overexpressed)/ACID (Activator interacting domain) domain of unknown structure. As a first step towards understanding the mechanism of recruitment of transactivation domains by MED25, we report here the NMR structure of the MED25 ACID domain. The domain architecture consists of a closed β-barrel with seven strands (Β1-Β7) and three α-helices (H1-H3), an architecture showing similarities to that of the SPOC (Spen paralog and ortholog C-terminal domain) domain-like superfamily. Preliminary NMR chemical shift mapping showed that VP16 H2 (VP16C) interacts with MED25 ACID through one face of the β-barrel, defined by strands B4-B7-B6.

  18. NMR studies on polyphosphide Ce6Ni6P17

    NASA Astrophysics Data System (ADS)

    Koyama, T.; Yamada, H.; Ueda, K.; Mito, T.; Aoyama, Y.; Nakano, T.; Takeda, N.

    2016-02-01

    We report the result of 31P nuclear magnetic resonance (NMR) studies on Ce6Ni6P17. The observed NMR spectra show a Lorentzian-type and an asymmetric shapes, reflecting the local symmetry around each P site in the cubic unit cell. We have identified the observed NMR lines corresponding to three inequivalent P sites and deduced the temperature dependence of the Knight shift for each site. The Knight shifts increase with decreasing temperature down to 1.5 K, indicating a localized spin system of Ce6Ni6P17. Antiferromagnetic correlation between 4f spins is suggested from the negative sign of the Weiss-temperature.

  19. Solution-state (15)N NMR spectroscopic study of alpha-C-phycocyanin: implications for the structure of the chromophore-binding pocket of the cyanobacterial phytochrome Cph1.

    PubMed

    Hahn, Janina; Kühne, Ronald; Schmieder, Peter

    2007-12-17

    The detailed structure of the chromophore-binding pocket in phytochrome proteins and the structural changes associated with its photocycle are still matters of debate. Insight into the structure and dynamics of the binding pocket has been gained through the comparison of a (15)N NMR spectrum of alpha-C-phycocyanin, which is often used as a model system for the study of phytochromes, with the previously described (15)N NMR spectrum of the cyanobacterial phytochrome Cph1. The former spectrum supports the hypothesis that all four nitrogen atoms of the alpha-C-phycocyanin chromophore are protonated, in analogy with the proposed protonation state for the P(r) and P(fr) forms of Cph1. The spectra show that the chromophores in both proteins exhibit a distinct dynamic behavior, as also indicated by a NOESY spectrum of Cph1. Finally, stereochemical arguments and a Cph1 homology model support the hypothesis that the chromophore in Cph1 is most likely in the ZZZssa conformation in the P(r) form of the protein.

  20. Infrared spectroscopy as a tool to characterise starch ordered structure--a joint FTIR-ATR, NMR, XRD and DSC study.

    PubMed

    Warren, Frederick J; Gidley, Michael J; Flanagan, Bernadine M

    2016-03-30

    Starch has a heterogeneous, semi-crystalline granular structure and the degree of ordered structure can affect its behaviour in foods and bioplastics. A range of methodologies are employed to study starch structure; differential scanning calorimetry, (13)C nuclear magnetic resonance, X-ray diffraction and Fourier transform infrared spectroscopy (FTIR). Despite the appeal of FTIR as a rapid, non-destructive methodology, there is currently no systematically defined quantitative relationship between FTIR spectral features and other starch structural measures. Here, we subject 61 starch samples to structural analysis, and systematically correlate FTIR spectra with other measures of starch structure. A hydration dependent peak position shift in the FTIR spectra of starch is observed, resulting from increased molecular order, but with complex, non-linear behaviour. We demonstrate that FTIR is a tool that can quantitatively probe short range interactions in starch structure. However, the assumptions of linear relationships between starch ordered structure and peak ratios are overly simplistic.

  1. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.

    PubMed

    Giambaşu, George M; York, Darrin M; Case, David A

    2015-05-01

    RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.

  2. Structure, phase transitions, 55Mn NMR, 57Fe Mössbauer studies and magnetoresistive properties of La0.6Sr0.3Mn1.1-xFexO3

    NASA Astrophysics Data System (ADS)

    Pashchenko, A. V.; Pashchenko, V. P.; Revenko, Yu. F.; Prokopenko, V. K.; Shemyakov, A. A.; Levchenko, G. G.; Pismenova, N. E.; Kitaev, V. V.; Gufan, Yu. M.; Sil'cheva, A. G.; Dyakonov, V. P.

    2014-11-01

    The influence of substitution of Fe ions for manganese on the structure, phase transitions, magnetoresistance, 55Mn NMR and 57Fe Mössbauer spectra in the ceramic La0.6Sr0.3Mn1.1-xFexO3 (x=0-0.15) samples has been studied by X-ray diffraction, electron microscopy, magnetic, 55Mn NMR and 57Fe Mössbauer methods. The real rhombohedral perovskite structure (R3barc) is established to contain the different valence manganese ions (Mn3+ and Mn4+), anion and cation vacancies as well as nanostructural clusters with Mn2+ located in the A-sites. Temperature dependences of the a lattice parameter, a(T), demonstrate the anomalies near the Curie temperature, Tc. Wide asymmetric 55Mn NMR spectra confirm the high frequency electron double exchange between Mn3+ and Mn4+ ions and irregularity of their surrounding by other ions and defects. According to the Mössbauer spectroscopy data, Fe3+ ions (~80%) substitute for Mn3+ and partially Mn4+ in the B-positions. The rest of Fe3+ (Fe2+) ions and clusters with Mn2+ are located in the A-positions. The temperatures of metal-semiconductor and ferromagnet-paramagnet phase transitions are reduced with increasing x, and the magnetic irregularity increases due to the weakening high-frequency Mn3+↔Mn4+ double exchange by Fe3+ ions. The amount of ferromagnetic phase is also reduced. The anomalous hysteresis is interpreted as a result of anisotropy of exchange interaction between the ferromagnetic matrix and antiferromagnetic cluster containing MnA2+ ions. The phase diagram demonstrates the strong correlated interrelation among magnetic, transport and magnetoresistance properties.

  3. Benchmark Theoretical and Experimental Study on (15)N NMR Shifts of Oxidatively Damaged Guanine.

    PubMed

    Dračínský, Martin; Šála, Michal; Klepetářová, Blanka; Šebera, Jakub; Fukal, Jiří; Holečková, Veronika; Tanaka, Yoshiyuki; Nencka, Radim; Sychrovský, Vladimír

    2016-02-11

    The (15)N NMR shifts of 9-ethyl-8-oxoguanine (OG) were calculated and measured in liquid DMSO and in crystal. The OG molecule is a model for oxidatively damaged 2'-deoxyguanosine that occurs owing to oxidative stress in cell. The DNA lesion is repaired with human 8-oxoguanine glycosylase 1 (hOGG1) base-excision repair enzyme, however, the exact mechanism of excision of damaged nucleobase with hOGG1 is currently unknown. This benchmark study on (15)N NMR shifts of OG aims their accurate structural interpretation and calibration of the calculation protocol utilizable in future studies on mechanism of hOGG1 enzyme. The effects of NMR reference, DFT functional, basis set, solvent, structure, and dynamics on calculated (15)N NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on (15)N NMR shifts of OG in liquid was calculated employing molecular dynamics. The B3LYP method with Iglo-III basis used for B3LYP optimized geometry with 6-311++G(d,p) basis and including effects of solvent and molecular dynamic was the calculation protocol used for calculation of (15)N NMR shifts of OG. The NMR shift of N9 nitrogen of OG was particularly studied because the atom is involved in an N-glycosidic bond that is cleaved with hOGG1. The change of N9 NMR shift owing to oxidation of 9-ethylguanine (G) measured in liquid was -27.1 ppm. The calculated N9 NMR shift of OG deviated from experiment in crystal and in liquid by 0.45 and 0.65 ppm, respectively. The calculated change of N9 NMR shift owing to notable N9-pyramidalization of OG in one previously found polymorph was 20.53 ppm. We therefore assume that the pyramidal geometry of N9 nitrogen that could occur for damaged DNA within hOGG1 catalytic site might be detectable with (15)N NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of (15)N NMR shifts of oxidatively damaged guanine DNA residue.

  4. Solid-state 207Pb NMR studies of mixed lead halides, PbFX (X=Cl, Br, or I).

    PubMed

    Glatfelter, Alicia; Dybowski, Cecil; Kragten, David D; Bai, Shi; Perry, Dale L; Lockard, Jenny

    2007-04-01

    Solid-state 207Pb NMR studies have been conducted on mixed lead(II) halides of the type PbFX, where X=Cl, Br, or I. NMR data for the mixed halides are compared to the solid-state NMR data for the divalent, binary lead halides, PbX2 (X=F, Cl, Br, I). The NMR data are evaluated in the context of the structures of the compounds and the effects of the mixed halides on the electronic structure of the divalent lead. Data sets for the mixed halides are discussed and compared to those for the regular lead(II) halides.

  5. From precursors to non-oxide ceramics: Pyrolytic mechanisms studied by NMR

    SciTech Connect

    Sigmund, W.M.; Aldinger, F.; Feike, M.; Spiess, H.W.

    1996-12-31

    The pyrolysis of a poly ethylsilazane was studied using a CO{sub 2}-laser beam heated solid state MAS-NMR probe head. Chemical structures of the intermediate stages could be identified. The analogy of the pyrolysis evolution for the following two different methods could be shown: (A) in an inert gas furnace conventionally prepared and (B) laser irradiated in the NMR probe head under magic-angle spinning (MAS) conditions. Samples prepared by method A were studied by {sup 29}Si MAS-NMR and samples prepared by method B were studied with an appropriate cross polarization time by {sup 29}Si CP-MAS-NMR. Both experiments showed the same mechanisms for the pyrolysis as the polymer is transformed into a Si{sub 3}N{sub 4}/C ceramic.

  6. Diamond Deposition and Defect Chemistry Studied via Solid State NMR

    DTIC Science & Technology

    1994-06-30

    same integrated NMR signal, regardless of its chemical environment, provided complete spin-lattice relaxation occurs between averages 3 . Gem -quality...occurs between averages, and broadening from years, a large research effort has been devoted to the study paramagnetic centers is insignificant. Gem ...information on the distribution and motion mond’s durability very attractive. However, while gem - of hydrogen can be obtained from the solid-state NMR

  7. NMR study of strontium binding by a micaceous mineral.

    PubMed

    Bowers, Geoffrey M; Ravella, Ramesh; Komarneni, Sridhar; Mueller, Karl T

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na(4)Mg(6)Al(4)Si(4)O(20)F(4). Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 degrees C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a (1)H-(87)Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by (87)Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct (87)Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  8. NMR Study of Strontium Binding by a Micaceous Mineral

    SciTech Connect

    Bowers, Geoffrey M.; Ravella, Ramesh; Komarneni, S.; Mueller, Karl T.

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na4Mg6Al4Si4O20F4. Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 °C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a 1H-87Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by 87Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct 87Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  9. Recent progress in solid-state NMR studies of drugs confined within drug delivery systems.

    PubMed

    Skorupska, Ewa; Jeziorna, Agata; Kazmierski, Slawomir; Potrzebowski, Marek J

    2014-01-01

    Recent progress in the application of solid-state NMR (SS NMR) spectroscopy in structural studies of active pharmaceutical ingredients (APIs) embedded in different drug carriers is detailed. This article is divided into sections. The first part reports short characterization of the nanoparticles and microparticles that can be used as drug delivery systems (DDSs). The second part shows the applicability of SS NMR to study non-steroidal anti-inflammatory drugs (NSAIDs). In this section, problems related to API-DDS interactions, morphology, local molecular dynamics, nature of inter- or intramolecular connections, and pore filling are reviewed for different drug carriers (e.g. mesoporous silica nanoparticles (MSNs), cyclodextrins, polymeric matrices and others). The third and fourth sections detail the recent applications of SS NMR for searching for antibiotics and anticancer drugs confined in zeolites, MSNs, amorphous calcium phosphate and other carriers.

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

    PubMed

    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.

  11. The nociceptin pharmacophore site for opioid receptor binding derived from the NMR structure and bioactivity relationships.

    PubMed

    Orsini, Michael J; Nesmelova, Irina; Young, Helen C; Hargittai, Balazs; Beavers, Mary Pat; Liu, Jingchun; Connolly, Peter J; Middleton, Steven A; Mayo, Kevin H

    2005-03-04

    Nociceptin, a 17 amino acid opioid-like peptide that has an inhibitory effect on synaptic transmission in the nervous system, is involved in learning, memory, attention, and emotion and is also implicated in the perception of pain and visual, auditory, and olfactory functions. In this study, we investigated the NMR solution structure of nociceptin in membrane-like environments (trifluoroethanol and SDS micelles) and found it to have a relatively stable helix conformation from residues 4-17 with functionally important N-terminal residues being folded aperidoically on top of the helix. In functional assays for receptor binding and calcium flux, alanine-scanning variants of nociceptin indicated that functionally important residues generally followed helix periodicity, consistent with the NMR structural model. Structure-activity relationships allowed identification of pharmacophore sites that were used in small molecule data base searches, affording hits with demonstrated nociceptin receptor binding affinities.

  12. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements.

    PubMed

    Hennig, Janosch; Warner, Lisa R; Simon, Bernd; Geerlof, Arie; Mackereth, Cameron D; Sattler, Michael

    2015-01-01

    Biological activity in the cell is predominantly mediated by large multiprotein and protein-nucleic acid complexes that act together to ensure functional fidelity. Nuclear magnetic resonance (NMR) spectroscopy is the only method that can provide information for high-resolution three-dimensional structures and the conformational dynamics of these complexes in solution. Mapping of binding interfaces and molecular interactions along with the characterization of conformational dynamics is possible for very large protein complexes. In contrast, de novo structure determination by NMR becomes very time consuming and difficult for protein complexes larger than 30 kDa as data are noisy and sparse. Fortunately, high-resolution structures are often available for individual domains or subunits of a protein complex and thus sparse data can be used to define their arrangement and dynamics within the assembled complex. In these cases, NMR can therefore be efficiently combined with complementary solution techniques, such as small-angle X-ray or neutron scattering, to provide a comprehensive description of the structure and dynamics of protein complexes in solution. Particularly useful are NMR-derived paramagnetic relaxation enhancements (PREs), which provide long-range distance restraints (ca. 20Å) for structural analysis of large complexes and also report on conformational dynamics in solution. Here, we describe the use of PREs from sample production to structure calculation, focusing on protein-RNA complexes. On the basis of recent examples from our own research, we demonstrate the utility, present protocols, and discuss potential pitfalls when using PREs for studying the structure and dynamic features of protein-RNA complexes.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Kupka, Teobald; Wieczorek, Piotr P

    2016-01-15

    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 (1)H and (13)C 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.

  15. Selectively labeling the heterologous protein in Escherichia coli for NMR studies: a strategy to speed up NMR spectroscopy.

    PubMed

    Almeida, F C; Amorim, G C; Moreau, V H; Sousa, V O; Creazola, A T; Américo, T A; Pais, A P; Leite, A; Netto, L E; Giordano, R J; Valente, A P

    2001-01-01

    Nuclear magnetic resonance is an important tool for high-resolution structural studies of proteins. It demands high protein concentration and high purity; however, the expression of proteins at high levels often leads to protein aggregation and the protein purification step can correspond to a high percentage of the overall time in the structural determination process. In the present article we show that the step of sample optimization can be simplified by selective labeling the heterologous protein expressed in Escherichia coli by the use of rifampicin. Yeast thioredoxin and a coix transcription factor Opaque 2 leucine zipper (LZ) were used to show the effectiveness of the protocol. The (1)H/(15)N heteronuclear correlation two-dimensional NMR spectrum (HMQC) of the selective (15)N-labeled thioredoxin without any purification is remarkably similar to the spectrum of the purified protein. The method has high yields and a good (1)H/(15)N HMQC spectrum can be obtained with 50 ml of M9 growth medium. Opaque 2 LZ, a difficult protein due to the lower expression level and high hydrophobicity, was also probed. The (15)N-edited spectrum of Opaque 2 LZ showed only the resonances of the protein of heterologous expression (Opaque 2 LZ) while the (1)H spectrum shows several other resonances from other proteins of the cell lysate. The demand for a fast methodology for structural determination is increasing with the advent of genome/proteome projects. Selective labeling the heterologous protein can speed up NMR structural studies as well as NMR-based drug screening. This methodology is especially effective for difficult proteins such as hydrophobic transcription factors, membrane proteins, and others.

  16. Selectively Labeling the Heterologous Protein in Escherichia coli for NMR Studies: A Strategy to Speed Up NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Almeida, F. C. L.; Amorim, G. C.; Moreau, V. H.; Sousa, V. O.; Creazola, A. T.; Américo, T. A.; Pais, A. P. N.; Leite, A.; Netto, L. E. S.; Giordano, R. J.; Valente, A. P.

    2001-01-01

    Nuclear magnetic resonance is an important tool for high-resolution structural studies of proteins. It demands high protein concentration and high purity; however, the expression of proteins at high levels often leads to protein aggregation and the protein purification step can correspond to a high percentage of the overall time in the structural determination process. In the present article we show that the step of sample optimization can be simplified by selective labeling the heterologous protein expressed in Escherichia coli by the use of rifampicin. Yeast thioredoxin and a coix transcription factor Opaque 2 leucine zipper (LZ) were used to show the effectiveness of the protocol. The 1H/15N heteronuclear correlation two-dimensional NMR spectrum (HMQC) of the selective 15N-labeled thioredoxin without any purification is remarkably similar to the spectrum of the purified protein. The method has high yields and a good 1H/15N HMQC spectrum can be obtained with 50 ml of M9 growth medium. Opaque 2 LZ, a difficult protein due to the lower expression level and high hydrophobicity, was also probed. The 15N-edited spectrum of Opaque 2 LZ showed only the resonances of the protein of heterologous expression (Opaque 2 LZ) while the 1H spectrum shows several other resonances from other proteins of the cell lysate. The demand for a fast methodology for structural determination is increasing with the advent of genome/proteome projects. Selective labeling the heterologous protein can speed up NMR structural studies as well as NMR-based drug screening. This methodology is especially effective for difficult proteins such as hydrophobic transcription factors, membrane proteins, and others.

  17. Prion protein NMR structures of chickens, turtles, and frogs

    PubMed Central

    Calzolai, Luigi; Lysek, Dominikus A.; Pérez, Daniel R.; Güntert, Peter; Wüthrich, Kurt

    2005-01-01

    The NMR structures of the recombinant prion proteins from chicken (Gallus gallus; chPrP), the red-eared slider turtle (Trachemys scripta; tPrP), and the African clawed frog (Xenopus laevis; xlPrP) are presented. The amino acid sequences of these prion proteins show ≈30% identity with mammalian prion proteins. All three species form the same molecular architecture as mammalian PrPC, with a long, flexibly disordered tail attached to the N-terminal end of a globular domain. The globular domain in chPrP and tPrP contains three α-helices, one short 310-helix, and a short antiparallel β-sheet. In xlPrP, the globular domain includes three α-helices and a somewhat longer β-sheet than in the other species. The spatial arrangement of these regular secondary structures coincides closely with that of the globular domain in mammalian prion proteins. Based on the low sequence identity to mammalian PrPs, comparison of chPrP, tPrP, and xlPrP with mammalian PrPC structures is used to identify a set of essential amino acid positions for the preservation of the same PrPC fold in birds, reptiles, amphibians, and mammals. There are additional conserved residues without apparent structural roles, which are of interest for the ongoing search for physiological functions of PrPC in healthy organisms. PMID:15647366

  18. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: a combined experimental and theoretical study.

    PubMed

    Arivazhagan, M; Gayathri, R

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ(*) and π(*) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra.

  19. NMR study of small molecule adsorption in MOF-74-Mg

    NASA Astrophysics Data System (ADS)

    Lopez, M. G.; Canepa, Pieremanuele; Thonhauser, T.

    2013-04-01

    We calculate the carbon nuclear magnetic resonance (NMR) shielding for CO2 and the hydrogen shieldings for both H2 and H2O inside the metal organic framework MOF-74-Mg. Our ab initio calculations are at the density functional theory level using the van der Waals including density functional vdW-DF. The shieldings are obtained while placing the small molecules throughout the structure, including the calculated adsorption site for various loading scenarios. We then explore relationships between loading, rotational and positional characteristics, and the NMR shieldings for each adsorbate. Our NMR calculations show a change in the shielding depending on adsorbate, position, and loading in a range that is experimentally observable. We further provide a simple model for the energy and the NMR shieldings throughout the cavity of the MOF. By providing this mapping of shielding to position and loading for these adsorbates, we argue that NMR probes could be used to provide additional information about the position at which these small molecules bind within the MOF, as well as the loading of the adsorbed molecule.

  20. FT-IR, FT-Raman, UV, NMR spectra and molecular structure investigation of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Therasa Alphonsa, A.; Loganathan, C.; Athavan Alias Anand, S.; Kabilan, S.

    2015-11-01

    This work presents the characterization of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine (HDE) by quantum chemical calculations and spectral techniques. The structure was investigated by FT-IR, FT-Raman, UV-vis and NMR techniques. The geometrical parameters and energies have been obtained from Density functional theory (DFT) B3LYP (6-31G (d, p)) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-independent atomic orbital method (GIAO). The electronic properties such as excitation energies, wavelength, HOMO, LUMO energies performed by Time dependent density functional theory (TD-DFT) results complements with the experimental findings. NBO analysis has been performed for analyzing charge delocalization throughout the molecule. The calculation results were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. To provide information about the interactions between human cytochrome protein and the novel compound theoretically, docking studies were carried out using Schrödinger software.

  1. Molecular structure, spectroscopic (FT-IR, FT Raman, UV, NMR and THz) investigation and hyperpolarizability studies of 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Kumar, Rajesh; Kumar, Amit; Deval, Vipin; Gupta, Archana; Tandon, Poonam; Patil, P. S.; Deshmukh, Prathmesh; Chaturvedi, Deepika; Watve, J. G.

    2017-02-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of the chalcone derivative 3-(2-Chloro-6-fluorophenyl)-1-(2-thienyl) prop-2-en-1-one (2C6F2SC) is reported. Initial geometry generated from single crystal X-ray diffraction parameters was minimized at DFT level employing B3LYP/6-311++G (d,p) without any constraint to the potential energy surface. The molecule has been characterized using various experimental techniques FT-IR, FT-Raman, UV-Vis, 1H NMR, TD-THz and the spectroscopic data have been analyzed theoretically by Density Functional Theory (DFT) method. Harmonic vibrational frequencies were calculated theoretically using the optimized ground state geometry and the spectra were interpreted by means of potential energy distribution. Time Dependent Density Functional Theory (TD-DFT) has been used to calculate energies, absorption wavelengths, oscillator strengths of electronic singlet-singlet transitions. The calculated energy and oscillator strength complement with the experimental findings. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. Good correlations between the experimental 1H NMR chemical shifts and calculated GIAO shielding tensors were found. Stability of the molecule, hyperconjugative interactions and charge delocalization has been analyzed by natural bond orbital (NBO) analysis. The first order hyperpolarizability (β) of this molecular system and related properties (μ, <α> and Δα) have been calculated using the finite-field approach.

  2. Structural study of (±) ethyl 3-acyloxy-1-azabicyclo[2.2.2]octane-3-carboxylates by 1H, 13C NMR spectroscopy, X-ray crystallography and DFT calculations

    NASA Astrophysics Data System (ADS)

    Arias-Pérez, M. S.; Cosme, A.; Gálvez, E.; Morreale, A.; Sanz-Aparicio, J.; Fonseca, I.

    2006-05-01

    1H, 13C NMR spectroscopy and DFT/B3LYP calculations were applied to investigate the conformational preferences of the ethoxycarbonyl and acyloxy groups of some α-acyloxyesters derived from (±) ethyl 3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylate. The crystal structure of (±) ethyl 3-diphenylacetoxy-1-azabicyclo[2.2.2]octane-3-carboxylate was determined by X-ray diffraction. To correlate between calculated conformations and the structure in solution, NMR chemical shifts calculations were also performed using the GIAO approach. It has been found that the lowest energetic conformer computed gives the greatest correspondance with experimental solution and solid state data.

  3. NMR study of non-structural proteins--part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).

    PubMed

    Makrynitsa, Garyfallia I; Ntonti, Dioni; Marousis, Konstantinos D; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2015-10-01

    Macro domains consist of 130-190 amino acid residues and appear to be highly conserved in all kingdoms of life. Intense research on this field has shown that macro domains bind ADP-ribose and other similar molecules, but their exact function still remains intangible. Macro domains are highly conserved in the Alphavirus genus and the Venezuelan equine encephalitis virus (VEEV) is a member of this genus that causes fatal encephalitis to equines and humans. In this study we report the high yield recombinant expression and preliminary solution NMR study of the macro domain of VEEV. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure predicted by TALOS+. The protein shows a unique mixed α/β-fold.

  4. Sol-gel synthesis, phase composition, morphological and structural characterization of Ca10(PO4)6(OH)2: XRD, FTIR, SEM, 3D SEM and solid-state NMR studies

    NASA Astrophysics Data System (ADS)

    Kareiva, Simonas; Klimavicius, Vytautas; Momot, Aleksandr; Kausteklis, Jonas; Prichodko, Aleksandra; Dagys, Laurynas; Ivanauskas, Feliksas; Sakirzanovas, Simas; Balevicius, Vytautas; Kareiva, Aivaras

    2016-09-01

    Aqueous sol-gel chemistry route based on ammonium-hydrogen phosphate as the phosphorus precursor, calcium acetate monohydrate as source of calcium ions, and 1,2-ethylendiaminetetraacetic acid (EDTA), or 1,2-diaminocyclohexanetetracetic acid (DCTA), or tartaric acid (TA), or ethylene glycol (EG), or glycerol (GL) as complexing agents have been used to prepare calcium hydroxyapatite (Ca10(PO4)6(OH)2, CHAp). The phase transformations, composition, and structural changes in the polycrystalline samples were studied by infrared spectroscopy (FTIR), X-ray powder diffraction analysis (XRD), and scanning electron microscopy (SEM). The local short-range (nano- and mezo-) scale effects in CHAp were studied using solid-state NMR spectroscopy. The spatial 3D data from the SEM images of CHAp samples obtained by TA, EG and GL sol-gel routes were recovered for the first time to our knowledge.

  5. NMR Structure Note: PHD Domain from Human SHPRH

    PubMed Central

    Machado, Luciana E. F.; Pustovalova, Yulia; Kile, Andrew C.; Pozhidaeva, Alexandra; Cimprich, Karlene A.; Almeida, Fabio C. L.; Bezsonova, Irina; Korzhnev, Dmitry M.

    2013-01-01

    SHPRH (SNF2, histone linker, PHD, RING, helicase) is a SWI2/SNF2-family ATP-dependent chromatin remodeling factor, and one of E3 ubiquitin ligases responsible for Ubc13-Mms2-dependent K63 poly-ubiquitination of PCNA (proliferating cell nuclear antigen) that promotes error-free DNA damage tolerance in eukaryotes. In contrast to its functional homologues, S. cerevisiae Rad5 and human HLTF (helicase like transcription factor), SHPRH contains a PHD (plant homeodomain) finger embedded in the ‘minor’ insert region of the core helicase-like domain. PHD fingers are often found in proteins involved in chromatin remodeling and transcription regulation, and are generally considered as ‘readers’ of methylation state of histone tails, primarily the lysine 4 (K4) residue of histone H3 (H3K4). Here we report the solution NMR structure of the SHPRH PHD domain and investigate whether this domain is capable of recognizing H3K4 modifications. The domain adopts a canonical PHD-finger fold with a central two-stranded anti-parallel β-sheet flanked on both sides by the two interleaved zinc-binding sites. Despite the presence of a subset of aromatic residues characteristic for PHD-fingers that preferentially bind methylated H3K4, NMR titration experiments reveal that SHPRH PHD does not specifically interact with the H3-derived peptides irrespective of K4 methylation. This result suggests that the SHPRH PHD domain might have evolved a different function other than recognizing histone modifications. PMID:23907177

  6. The NMR study of biologically active metallated alkanol ammoinium ionic liquids

    NASA Astrophysics Data System (ADS)

    Ushakov, I. A.; Voronov, V. K.; Adamovich, S. N.; Mirskov, R. G.; Mirskova, A. N.

    2016-01-01

    The 1H, 13C, 15N, and 111Cd NMR spectra of a series of metallated alkanol ammonium ionic liquids (MAIL) series [n N(CH2CH2OH;)3M]+ · mX-, where M = Cd, Mg, Zn, Fe, Rh; X = Cl, OOCCH3, obtained in a wide range of temperatures of the studied samples, have been analyzed. It is found that, under biomimetic conditions (H2O, 25 °C), the compounds studied exist as mono- bi- and the tricyclic structures, which are in equilibrium. Shift of the equilibrium depends upon nature of a metal and effects all the parameters of the NMR spectra. Peculiarities of ligand exchange, typical for the studied compounds, have been studied in a wide range of temperatures. It is found that the NMR data can be used to control structure of the compounds formed in the course of synthesis.

  7. NMR structure of a gemcitabine-substituted model Okazaki fragment.

    PubMed

    Konerding, David; James, Thomas L; Trump, Eric; Soto, Ana Maria; Marky, Luis A; Gmeiner, William H

    2002-01-22

    Gemcitabine (2'-deoxy-2',2'-difluorodeoxycytidine; dFdC) is a potent anticancer drug that exerts cytotoxic activity, in part, through incorporation of the nucleoside triphosphate dFdCTP into DNA and perturbations to DNA-mediated processes. The structure of a model Okazaki fragment containing a single dFdC substitution, [GEM], was determined using NMR spectroscopy and restrained molecular dynamics to understand structural distortions that may be induced in replicating DNA resulting from dFdC substitution. The electrostatic surface of [GEM] was also computed to determine how the geminal difluoro group of dFdC perturbs DNA electrostatics. The stability of [GEM] was investigated using temperature-dependent UV spectroscopy. dFdC adopted a C3'-endo conformation in [GEM] and decreased the melting temperature of the duplex by 4.3 degrees C. dFdC substitution did not decrease helical stacking among adjacent purines in the DNA duplex region. dFdC substitution substantially altered the electrostatic properties of the model Okazaki fragment, with increased electron density in the vicinity of the geminal difluoro group. The results are consistent with dFdC substitution altering the structural, electrostatic, and thermodynamic properties of DNA and interfering in DNA-mediated processes. Interference in DNA-mediated processes due to dFdC substitution likely contributes to the anticancer activity of dFdC.

  8. Two dimensional and zero field NMR studies of coal structure: Final progress report, including the period July 1, 1987 to September 30, 1987

    SciTech Connect

    Zilm, K.W.

    1987-12-01

    This report covers the progress made on the title project during the last quarter and summarizes the accomplishments for the project period. During the last three months we have completed a full analysis of the limitations of our ADIPSHIFT 2D NMR experiment that we have developed to determine the distribution of functional types of carbon in coals. This is an extensive piece of work and will provide a firm foundation for the application of the method to complex organic solids in the future. A particularly useful graphical analysis is described for use with unknowns such as coals. 17 refs.

  9. High‐Resolution NMR Determination of the Dynamic Structure of Membrane Proteins

    PubMed Central

    Jaremko, Mariusz; Jaremko, Łukasz; Villinger, Saskia; Schmidt, Christian D.; Griesinger, Christian; Becker, Stefan

    2016-01-01

    Abstract 15N spin‐relaxation rates are demonstrated to provide critical information about the long‐range structure and internal motions of membrane proteins. Combined with an improved calculation method, the relaxation‐rate‐derived structure of the 283‐residue human voltage‐dependent anion channel revealed an anisotropically shaped barrel with a rigidly attached N‐terminal helix. Our study thus establishes an NMR spectroscopic approach to determine the structure and dynamics of mammalian membrane proteins at high accuracy and resolution. PMID:27461260

  10. A palladium(II) complex containing both carbonyl and imine oxime ligands: Crystal structure, experimental and theoretical UV-vis, IR and NMR studies

    NASA Astrophysics Data System (ADS)

    Kaya, Yunus; Icsel, Ceyda; Yilmaz, Veysel T.; Buyukgungor, Orhan

    2013-05-01

    A new palladium(II) complex, [Pd(ppeieo)(inap)]·DMSO (ppeieo = (1E,2E)-phenyl-[(1-phenylethyl)imino]-ethanal oxime and inap = isonitrosoacetophenone) has been synthesized and characterized by elemental analysis, UV-vis, IR, NMR. X-ray diffraction analysis of the DMSO solvate of the complex shows that the palladium(II) ion is coordinated in a distorted square-planar geometry by ppeieo and inap, which is formed during the hydrolysis of ppeieo. DFT (B3LYP/LANL2DZ) calculations on the complex have been carried out to correlate geometry and spectroscopic properties such as electronic, vibrational and NMR chemical shifts. The complete vibrational frequency assignments were made and the calculation results were applied to simulate infrared spectra of the title compound which shows good agreement with observed spectra. The calculated HOMO and LUMO energies show that several transitions including the π → π* and charge transfer occur within the molecule. The chemical shifts reasonably correspond to the calculated spectra.

  11. A palladium(II) complex containing both carbonyl and imine oxime ligands: crystal structure, experimental and theoretical UV-vis, IR and NMR studies.

    PubMed

    Kaya, Yunus; Icsel, Ceyda; Yilmaz, Veysel T; Buyukgungor, Orhan

    2013-05-01

    A new palladium(II) complex, [Pd(ppeieo)(inap)]·DMSO (ppeieo=(1E,2E)-phenyl-[(1-phenylethyl)imino]-ethanal oxime and inap=isonitrosoacetophenone) has been synthesized and characterized by elemental analysis, UV-vis, IR, NMR. X-ray diffraction analysis of the DMSO solvate of the complex shows that the palladium(II) ion is coordinated in a distorted square-planar geometry by ppeieo and inap, which is formed during the hydrolysis of ppeieo. DFT (B3LYP/LANL2DZ) calculations on the complex have been carried out to correlate geometry and spectroscopic properties such as electronic, vibrational and NMR chemical shifts. The complete vibrational frequency assignments were made and the calculation results were applied to simulate infrared spectra of the title compound which shows good agreement with observed spectra. The calculated HOMO and LUMO energies show that several transitions including the π→π(*) and charge transfer occur within the molecule. The chemical shifts reasonably correspond to the calculated spectra.

  12. Molecular structure, FT-IR, FT-Raman, NMR studies and first order molecular hyperpolarizabilities by the DFT method of mirtazapine and its comparison with mianserin

    NASA Astrophysics Data System (ADS)

    Sagdinc, Seda G.; Sahinturk, Ayse Erbay

    2013-03-01

    Mirtazapine (±)-1,2,3,4,10,14b-hexahydro-2-methylpyrazino(2,1-a)pyrido(2,3-c)(2)benzazepine is a compound with antidepressant therapeutic effects. It is the 6-aza derivative of the tetracyclic antidepressant mianserin (±)-2-methyl-1,2,3,4,10,14b-hexahydrodibenzo[c,f]pyrazino[1,2-a]azepine. The FT-IR and FT-Raman spectra of mirtazapine have been recorded in 4000-400 cm-1 and 3500-10 cm-1, respectively. The optimized geometry, energies, nonlinear optical properties, vibrational frequencies, 13C, 1H and 15N NMR chemical shift values of mirtazapine have been determined using the density functional theory (DFT/B3LYP) method. A comparison of the experimental and theoretical results of mirtazapine indicates that the density-functional B3LYP method is able to provide satisfactory results for predicting vibrational and NMR properties. The experimental and calculated results for mirtazapine have also been compared with mianserin.

  13. Structural investigation of aluminium doped ZnO nanoparticles by solid-state NMR spectroscopy.

    PubMed

    Avadhut, Yamini S; Weber, Johannes; Hammarberg, Elin; Feldmann, Claus; Schmedt auf der Günne, Jörn

    2012-09-07

    The electrical conductivity of aluminium doped zinc oxide (AZO, ZnO:Al) materials depends on doping induced defects and grain structure. This study aims at relating macroscopic electrical conductivity of AZO nanoparticles with their atomic structure, which is non-trivial because the derived materials are heavily disordered and heterogeneous in nature. For this purpose we synthesized AZO nanoparticles with different doping levels and narrow size distribution by a microwave assisted polyol method followed by drying and a reductive treatment with forming gas. From these particles electrically conductive, optically transparent films were obtained by spin-coating. Characterization involved energy-dispersive X-ray analysis, wet chemical analysis, X-ray diffraction, electron microscopy and dynamic light scattering, which provided a basis for a detailed structural solid-state NMR study. A multinuclear ((27)Al, (13)C, (1)H) spectroscopic investigation required a number of 1D MAS NMR and 2D MAS NMR techniques (T(1)-measurements, (27)Al-MQMAS, (27)Al-(1)H 2D-PRESTO-III heteronuclear correlation spectroscopy), which were corroborated by quantum chemical calculations with an embedded cluster method (EEIM) at the DFT level. From the combined data we conclude that only a small part of the provided Al is incorporated into the ZnO structure by substitution of Zn. The related (27)Al NMR signal undergoes a Knight shift when the material is subjected to a reductive treatment with forming gas. At higher (formal) doping levels Al forms insulating (Al, H and C containing) side-phases, which cover the surface of the ZnO:Al particles and increase the sheet resistivity of spin-coated material. Moreover, calculated (27)Al quadrupole coupling constants serve as a spectroscopic fingerprint by which previously suggested point-defects can be identified and in their great majority be ruled out.

  14. Magnetic structure of low-dimensional LiCu{sub 2}O{sub 2} multiferroic according to {sup 63,65}Cu and {sup 7}Li NMR studies

    SciTech Connect

    Sadykov, A. F. Gerashchenko, A. P.; Piskunov, Yu. V.; Ogloblichev, V. V.; Smol'nikov, A. G.; Verkhovskii, S. V.; Yakubovskii, A. Yu.; Tishchenko, E. A.; Bush, A. A.

    2012-10-15

    The complex NMR study of the magnetic structure of LiCu{sub 2}O{sub 2} multiferroic has been performed. It has been shown that the spin spirals in LiCu{sub 2}O{sub 2} are beyond the ab, bc, and ac crystallographic planes. The external magnetic field applied along the c axis of the crystal does not change the spatial orientation of spirals in Cu{sup 2+} chains. A magnetic field of H{sub 0} = 94 kOe applied along the a and b axes rotates the planes of spin spirals in chains, tending to orient the normal n of spirals along the external magnetic field. The rotation angle of the planes of the magnetic moments are maximal at H{sub 0} Double-Vertical-Line b.

  15. NMR-Metabolic Methodology in the Study of GM Foods

    PubMed Central

    Sobolev, Anatoly P.; Capitani, Donatella; Giannino, Donato; Nicolodi, Chiara; Testone, Giulio; Santoro, Flavio; Frugis, Giovanna; Iannelli, Maria A.; Mattoo, Autar K.; Brosio, Elvino; Gianferri, Raffaella; D’Amico, Irene; Mannina, Luisa

    2010-01-01

    The 1H-NMR methodology used in the study of genetically modified (GM) foods is discussed. Transgenic lettuce (Lactuca sativa cv "Luxor") over-expressing the ArabidopsisKNAT1 gene is presented as a case study. Twenty-two water-soluble metabolites (amino acids, organic acids, sugars) present in leaves of conventional and GM lettuce were monitored by NMR and quantified at two developmental stages. The NMR spectra did not reveal any difference in metabolite composition between the GM lettuce and the wild type counterpart. Statistical analyses of metabolite variables highlighted metabolism variation as a function of leaf development as well as the transgene. A main effect of the transgene was in altering sugar metabolism. PMID:22253988

  16. Structure vs. composition: A solid-state 1H and 29Si NMR study of quenched glasses along the Na 2O-SiO 2-H 2O join

    NASA Astrophysics Data System (ADS)

    Cody, George D.; Mysen, Bjorn O.; Lee, Sung Keun

    2005-05-01

    A suite of six hydrous (7 wt.% H 2O) sodium silicate glasses spanning sodium octasilicate to sodium disilicate in composition were analyzed using 29Si single pulse (SP) magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, 1H- 29Si cross polarization (CP) MAS NMR, and fast MAS 1H-NMR. From the 29Si SPMAS data it is observed that at low sodium compositions dissolved water significantly depolymerizes the silicate network. At higher sodium contents, however, dissolved H 2O does not affect a significant increase in depolymerization over that predicted based on the Na/Si ratio alone. The fast MAS 1H-NMR data reveal considerable complexity in proton environments in each of the glasses studied. The fast MAS 1H-NMR spectra of the highest sodium concentration glasses do not exhibit evidence of signficantly greater fractions of dissolved water as molecular H 2O than the lower sodium concentration glasses requiring that the decrease in polymerization at high sodium contents involves a change in sodium solution mechanism. Variable contact time 1H- 29Si cross polarization (CP) MAS NMR data reveal an increase in the rotating frame spin lattice relaxation rate constant ( T1ρ*) for various Q n species with increasing sodium content that correlates with a reduction in the average 1H- 29Si coupling strength. At the highest sodium concentration, however, T1ρ* drops significantly, consistent with a change in the Na 2O solution mechanism.

  17. N-H...F hydrogen bonds in fluorinated benzanilides: NMR and DFT study.

    PubMed

    Manjunatha Reddy, G N; Vasantha Kumar, M V; Guru Row, T N; Suryaprakash, N

    2010-10-28

    Using (19)F and (1)H-NMR (with (14)N decoupling) spectroscopic techniques together with density functional theoretical (DFT) calculations, we have investigated weak molecular interactions in isomeric fluorinated benzanilides. Simultaneous presence of through space nuclear spin-spin couplings ((1h)J(N-HF)) of diverse strengths and feeble structural fluctuations are detected as a function of site specific substitution of fluorine atoms within the basic identical molecular framework. The transfer of hydrogen bonding interaction energies through space is established by perturbing their strengths and monitoring the effect on NMR parameters. Multiple quantum (MQ) excitation, up to the highest possible MQ orders of coupled protons, is utilized as a tool for accurate (1)H assignments. Results of NMR studies and DFT calculations are compared with the relevant structural parameters taken from single crystal X-ray diffraction studies.

  18. Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.

    PubMed

    Shi, Chaowei; Fricke, Pascal; Lin, Lin; Chevelkov, Veniamin; Wegstroth, Melanie; Giller, Karin; Becker, Stefan; Thanbichler, Martin; Lange, Adam

    2015-12-01

    Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR-derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

  19. NMR relaxometry as a versatile tool to study Li ion dynamics in potential battery materials.

    PubMed

    Kuhn, A; Kunze, M; Sreeraj, P; Wiemhöfer, H D; Thangadurai, V; Wilkening, M; Heitjans, P

    2012-04-01

    NMR spin relaxometry is known to be a powerful tool for the investigation of Li(+) dynamics in (non-paramagnetic) crystalline and amorphous solids. As long as significant structural changes are absent in a relatively wide temperature range, with NMR spin-lattice (as well as spin-spin) relaxation measurements information on Li self-diffusion parameters such as jump rates and activation energies are accessible. Diffusion-induced NMR relaxation rates are governed by a motional correlation function describing the ion dynamics present. Besides the mean correlation rate of the dynamic process, the motional correlation function (i) reflects deviations from random motion (so-called correlation effects) and (ii) gives insights into the dimensionality of the hopping process. In favorable cases, i.e., when temperature- and frequency-dependent NMR relaxation rates are available over a large dynamic range, NMR spin relaxometry is able to provide a comprehensive picture of the relevant Li dynamic processes. In the present contribution, we exemplarily present two recent variable-temperature (7)Li NMR spin-lattice relaxation studies focussing on Li(+) dynamics in crystalline ion conductors which are of relevance for battery applications, viz. Li(7) La(3)Zr(2)O(12) and Li(12)Si(7).

  20. Indole-containing new types of dyes and their UV-vis and NMR spectra and electronic structures: Experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Kuzu, Burak; Menges, Nurettin

    2016-06-01

    Indole containing dyes were synthesized via a simple method with high yield. These molecules have different colors and UV-vis spectra of them were recorded. Impact of solvents on absorbances was investigated and it was observed that basic solvent such as DMF and pyridine have blue shift. TD-DFT calculations were done and results were compared with experimental data. NMR data of molecules were analyzed and tautomeric forms of colorants and their ratio were determined. It was find out that two tautomers might be formed in solution, called indole and indolenine form. HOMO-LUMO and energy gaps were calculated and plotted. Furthermore, molecular electrostatic potentials were simulated to find out electrophilic and nucleophilic regions.

  1. A study of structure and dynamics of poly(aspartic acid) sodium/poly(vinyl alcohol) blends by 13C CP/MAS NMR

    NASA Astrophysics Data System (ADS)

    Wang, P.; Ando, I.

    1999-09-01

    Solid state 13C CP/MAS NMR measurements have been carried out on poly(aspartic acid) sodium (PAANa)/poly(vinyl alcohol) (PVA) blends over a wide range of temperatures. From these experimental results, it is found that the main-chain conformations of PAANa in PAANa/PVA blends take the α-helix form over a wide range of blend ratios, and, in contrast, the conformation and dynamics of the side chains of PAANa are strongly influenced by the formation of an intermolecular hydrogen bond between the carboxyl group of the side chains and the hydroxyl group of PVA. The behavior of the proton spin-lattice relaxation times in the rotating frame ( T1 ρ(H)) and the laboratory frame ( T1(H)) indicates that when the blend ratio of PAANa and PVA is 1:1, they are miscible.

  2. Ionic motion and Disordered Structure in the Rotator Phase of Butylammonium Chloride Studied by Temperature Dependences of 35Cl and 2H NMR

    NASA Astrophysics Data System (ADS)

    Hattori, Mineyuki; Onoda, Yoshito; Erata, Tomoki; Smith, M. E.; Hattori, Masakazu; Ohki, Hiroshi; Ikeda, Ryuichi

    1994-02-01

    Temperature dependences of 35Cl and 2H quadrupole coupling constants and 35Cl NMR spin-lat­tice relaxation times in polycrystalline samples were measured in the rotator phase of the butylammonium chlorides C4H9NH3C1 and C4H9ND3C1, obtainable above the phase transition temperature of 241 K. A rapid decrease o f the quadrupole coupling constants of both nuclei upon heating is attributed to increasing dynamic disorder formed around the polar head. The presence of self-diffussion of Cl- ions was revealed from the spin-spin relaxation time and resonance line-width in single crystals, and confirmed by measuring the dc electrical conductivity.

  3. Structure and dynamics of retinal in rhodopsin elucidated by deuterium solid state NMR

    NASA Astrophysics Data System (ADS)

    Salgado, Gilmar Fernandes De Jesus

    Rhodopsin is a seven transmembrane helix GPCR found which mediates dim light vision, in which the binding pocket is occupied by the ligand 11- cis-retinal. A site-directed 2H-labeling approach utilizing solid-state 2H NMR spectroscopy was used to investigate the structure and dynamics of retinal within its binding pocket in the dark state of rhodopsin, and as well the MetaI and MetaII. 11-cis-[5-C 2H3]-, 11-cis-[9-C 2H3]-, and 11-cis-[13-C2H 3]-retinal were used to regenerate bleached rhodopsin. Recombinant membranes comprising purified rhodopsin and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were prepared (1:50 molar ratio). Solid-state 2H NMR spectra were obtained for the aligned rhodopsin/POPC recombinant membranes at temperatures below the order-disorder phase transition temperature of POPC. The solid-state NMR studies of aligned samples, give the orientations of the 2H nuclear coupling tensor relative to the membrane frame, which involve both the conformation and orientation of the bound retinal chromophore. Theoretical simulations of the experimental 2H NMR spectra employed a new lineshape treatment for a semi-random distribution due to static uniaxial disorder. The analysis gives the orientation of the 2H-labeled C-C2H3 methyl bond axes relative to the membrane plane as well as the extent of three-dimensional alignment disorder (mosaic spread). These results clearly demonstrate the applicability of site-directed 2H NMR methods for investigating conformational changes and dynamics of ligands bound to rhodopsin and other GPCRs in relation to their characteristic mechanisms of action.

  4. Structure and conformation of 2,3-diethoxycarbonyl-1-methylpyridinium iodide studied by NMR, FTIR, Raman, X-ray diffraction and DFT methods.

    PubMed

    Barczyński, P; Ratajczak-Sitarz, M; Nowaczyk, Ł; Katrusiak, A; Dega-Szafran, Z; Komasa, A; Szafran, M

    2013-11-01

    Computational and spectroscopic properties of 2,3-diethoxycarbonyl-1-methylpyridinium iodide, 1, were studied. The crystal structure of 1 was analyzed by X-ray diffraction. Molecular geometry of title compound has been calculated using the density functional theory (DFT) at B3LYP/6-311G(d,p) level of theory and was compared with the experimental data. Iodide anion interacts electrostatically with the positively charged pyridinium nitrogen atom and via weak CH⋯I(-) hydrogen bonds. In crystals the N-methyl and ethoxycarbonyl groups are disordered in two orientations. The structures of 2 (in vacuum), 3 (in CHCl3) and 4 (in DMSO) optimized by the B3LYP/6-311G(d,p) approach are different than that in crystal 1. The experimental (13)C and (1)H chemical shifts (δexp) of the investigated ester in CDCl3 and DMSO-d6 correlate linearly with GIAO/B3LYP/6-311G(d,p) magnetic isotropic shielding constants calculated according to the screening solvation model (COSMO), δexp=a+b σcalc. The FTIR and Raman spectra of the solid compound are consisted with the X-ray structure.

  5. A study of molecular structure, UV, IR, and 1H NMR spectra of a new dichroic dye on the basis of quinoline derivative

    NASA Astrophysics Data System (ADS)

    Shahab, Siyamak; Almodarresiyeh, Hora Alhosseini; Kumar, Rakesh; Darroudi, Mahdieh

    2015-05-01

    In this study, the structure and some molecular properties of a new substance sodium 4-[(4E)-4-[(2E)-2-(2-chloro-3-{(E)-2-[1-(4-sulfonatobutyl)quinolinium-4-yl]ethenyl}-2,3-dihydro-1H-inden-1-ylidene)ethylidene]quinolin-1(4H)-yl]butane-1-sulfonate (Q) with maximum absorption in near-IR region (λmax = 832 nm) was modeled using the Density Functional Theory method (DFT) and then synthesized. The electronic absorption spectrum of Q in dimethylformamide (DMF) solution was calculated. The UV, IR, and PMR spectra of Q were also presented.

  6. Novel Dodecaarylporphyrins: Synthesis and Variable Temperature NMR Studies

    SciTech Connect

    Cancilla, Mark; Lebrilla, Carlito; Ma, Jian-Guo; Medforth, Craig J.; Muzzi, Cinzia M.; Shelnutt, John A.; Smith, Kevin M.; Voss, Lisa

    1999-05-05

    An investigation of the synthesis of novel dodecaarylporphyrins using the Suzuki coupling reaction of arylboronic acids with octabromotetraarylporphyrins is reported. Studies of the dynamic properties of these new porphyrins using variable temperature (VT) 1H NMR spectroscopy and molecular mechanics provide interesting insights into their dynamic properties, including the first determination of {beta} aryl rotation in a porphyrin system.

  7. Solid-state NMR studies of form I of atorvastatin calcium.

    PubMed

    Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

    2012-03-22

    Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

  8. Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Kauten, R.J.

    1987-11-03

    The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by /sup 1/H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and /sup 1/H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only /sup 1/H NMR clearly distinguishes all three ferric isomers. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first /sup 1/H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albiet to a smaller extent.

  9. Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

    PubMed Central

    Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

    2013-01-01

    We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc. PMID:23180575

  10. An assignment of intrinsically disordered regions of proteins based on NMR structures.

    PubMed

    Ota, Motonori; Koike, Ryotaro; Amemiya, Takayuki; Tenno, Takeshi; Romero, Pedro R; Hiroaki, Hidekazu; Dunker, A Keith; Fukuchi, Satoshi

    2013-01-01

    Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as missing residues in protein structures determined by X-ray crystallography, no protocol has been developed to identify IDRs from structures obtained by Nuclear Magnetic Resonance (NMR). Here, we propose a computational method to assign IDRs based on NMR structures. We compared missing residues of X-ray structures with residue-wise deviations of NMR structures for identical proteins, and derived a threshold deviation that gives the best correlation of ordered and disordered regions of both structures. The obtained threshold of 3.2Å was applied to proteins whose structures were only determined by NMR, and the resulting IDRs were analyzed and compared to those of X-ray structures with no NMR counterpart in terms of sequence length, IDR fraction, protein function, cellular location, and amino acid composition, all of which suggest distinct characteristics. The structural knowledge of IDPs is still inadequate compared with that of structured proteins. Our method can collect and utilize IDRs from structures determined by NMR, potentially enhancing the understanding of IDPs.

  11. Solid-state NMR and ESR studies of activated carbons produced from pecan shells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Activated carbon from pecan shells has shown promise as an adsorbent in water treatment and sugar refining. However, the chemistry of the material is complex and not fully understood. We report here the application of solid state NMR and ESR to study the chemical structure, mobility, and pore volu...

  12. Studies of Transition Metal Complexes Using Dynamic NMR Techniques.

    NASA Astrophysics Data System (ADS)

    Coston, Timothy Peter John

    Available from UMI in association with The British Library. This Thesis is primarily concerned with the quantitative study of fluxional processes in, predominantly platinum(IV) complexes, with the ligands 1,1,2,2-tetrakis(methylthio)ethane (MeS)_2CHCH(SMe)_2 , and 1,1,2,2-tetrakis(methylthio)ethene (MeS) _2C=C(SMe)_2. Quantitative information relating to the energetics of these processes has been obtained by a combination of one- and two-dimensional NMR techniques. Chapter One provides an introduction to the background of fluxional processes in transition metal complexes together with data concerning the energetics of the processes that have already been studied by NMR techniques. Chapter Two provides a thorough grounding in NMR techniques, in particular those concerned with the quantitative measurement of rates involved in chemical exchange processes. A description of the use of 2D EXSY NMR spectroscopy in obtaining rate data is given. The properties of the magnetic isotope of platinum are given in Chapter Three. A general survey is also given of some additional compounds that have already been studied by platinum-195 spectroscopy. Chapter Four is concerned with the quantitative study of low temperature (<293 K) fluxionality (sulphur inversion) in the complexes (PtXMe_3 (MeS)_2CHCH(SMe) _2) (X = Cl, Br, I). These complexes were studied by dynamic nuclear magnetic resonance and the information regarding the rates of sulphur inversion was obtained by complete band-shape analysis. Chapter Five is concerned with high temperature (>333 K) fluxionality, of the previous complexes, as studied by a combination of one- and two -dimensional NMR techniques. Aside from obtaining thermodynamic parameters for all the processes, a new novel mechanism is proposed. Chapter Six is primarily concerned with the NMR investigation of the new dinuclear complexes ((PtXMe _3)_2(MeS) _2CHCH(SMe)_2) (X = Cl, Br, I). The solution properties have been established and thermo-dynamic parameters

  13. Diffusion NMR methods applied to xenon gas for materials study

    NASA Technical Reports Server (NTRS)

    Mair, R. W.; Rosen, M. S.; Wang, R.; Cory, D. G.; Walsworth, R. L.

    2002-01-01

    We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. c2002 John Wiley & Sons, Ltd.

  14. Solid state NMR: The essential technology for helical membrane protein structural characterization

    NASA Astrophysics Data System (ADS)

    Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

  15. Solid state NMR: The essential technology for helical membrane protein structural characterization.

    PubMed

    Cross, Timothy A; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

  16. NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline

    PubMed Central

    Page, Rebecca; Peti, Wolfgang; Wilson, Ian A.; Stevens, Raymond C.; Wüthrich, Kurt

    2005-01-01

    In the Joint Center for Structural Genomics, one-dimensional (1D) 1H NMR spectroscopy is routinely used to characterize the folded state of protein targets and, thus, serves to guide subsequent crystallization efforts and to identify proteins for NMR structure determination. Here, we describe 1D 1H NMR screening of a group of 79 mouse homologue proteins, which correlates the NMR data with the outcome of subsequent crystallization experiments and crystallographic structure determination. Based on the 1D 1H NMR spectra, the proteins are classified into four groups, “A” to “D.” A-type proteins are candidates for structure determination by NMR or crystallography; “B”-type are earmarked for crystallography; “C” indicates folded globular proteins with broadened line shapes; and “D” are nonglobular, “unfolded” polypeptides. The results obtained from coarse- and fine-screen crystallization trials imply that only A- and B-type proteins should be used for extensive crystallization trials in the future, with C and D proteins subjected only to coarse-screen crystallization trials. Of the presently studied 79 soluble protein targets, 63% yielded A- or B-quality 1D 1H NMR spectra. Although similar yields of crystallization hits were obtained for all four groups, A to D, crystals from A- and B-type proteins diffracted on average to significantly higher resolution than crystals produced from C- or D-type proteins. Furthermore, the output of refined crystal structures from this test set of proteins was 4-fold higher for A- and B-type than for C- and D-type proteins. PMID:15677718

  17. Fractional Order Analysis of Sephadex Gel Structures: NMR Measurements Reflecting Anomalous Diffusion.

    PubMed

    Magin, Richard L; Akpa, Belinda S; Neuberger, Thomas; Webb, Andrew G

    2011-12-01

    We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-(bD)(α)], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4,000 s-mm(-2)). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.

  18. Application of /sup 13/C NMR, fluorescence, and light-scattering techniques for structural studies of oil-in-water microemulsions

    SciTech Connect

    Tricot, Y.; Kiwi, J.; Niederberger, W.; Graetzel, M.

    1981-04-02

    The nature of the microdroplets present in oil-in-water microemulsions was examined by using the 4-component model system water-hexadecane-sodium hexadecyl sulfate-pentanol. Three compositions were selected corresponding to regions in the pahse diagram where the content of water, cosurfactant, and oil, respectively, approached the tolerable limit to yield clear isotropic solutions. In the water-side microemulsion, the radius of the droplets is 127A as determined from quasi-elastic light-scattering measurements. Fluorescence experiments showed that the core of the microspheres has a microviscosity similar to hexadecane at room temperature. /sup 13/C NMR shift analysis was applied to test the partitioning of cosurfactant between the surface and the interior of the droplet. For all three compositions significant fractions of the cosurfactant are present in the interior. This is corroborated by results obtained from T/sub 1/ relaxation-time analysis at different field strengths. The influence of the field strength on T/sub 1/ is explained in terms of a model based on a distribution of correlation times. In particular, the importance of taking into account slower rotational modes such as the tumbling of the whole microsphere is illustrated.

  19. Study of cultured fibroblasts in vivo using NMR

    SciTech Connect

    Karczmar, G.S.

    1984-01-01

    The goal of this thesis was to study the compartmentation of phosphorylated glycolytic intermediates in intact Chicken Embryo Fibroblasts (CEFs) using /sup 31/P NMR at 109 MHz. Because glycolysis is regulated differently in normal and virally transformed CEFs, NMR experiments were performed on both types of cells. A technique for maintaining functional cells at high densities in an NMR magnet is described. Signals were detected from cytoplasmic inorganic phosphate (P/sub i/), ATP, NAD, NADH, phosphorylcholine and phosphorylethanolamine. The effect of external glucose on cytoplasmic pools of phosphates was studied. However, experiments with /sup 32/P labelled P/sub i/ showed that as the concentration of glucose in the medium was increased, the amount of phosphate sequestered in the cells increased. They conclude that there is a pool of P/sub i/ which is not detected by high resolution of NMR and that the size of this pool increases as the rate of glycolysis increases. These effects were found only in cultured cells; the data for transformed and normal cells were similar. Longitudinal relaxation times of intracellular phosphates in normal, transformed, and primary CEFs were measured.

  20. Study of correlations in molecular motion by multiple quantum NMR

    SciTech Connect

    Tang, J.H.

    1981-11-01

    Nuclear magnetic resonance is a very useful tool for characterizing molecular configurations through the measurement of transition frequencies and dipolar couplings. The measurement of spectral lineshapes, spin-lattice relaxation times, and transverse relaxation times also provide us with valuable information about correlations in molecular motion. The new technique of multiple quantum nuclear magnetic resonance has numerous advantages over the conventional single quantum NMR techniques in obtaining information about static and dynamic interactions of coupled spin systems. In the first two chapters, the theoretical background of spin Hamiltonians and the density matrix formalism of multiple quantum NMR is discussed. The creation and detection of multiple quantum coherence by multiple pulse sequence are discussed. Prototype multiple quantum spectra of oriented benzene are presented. Redfield relaxation theory and the application of multiple quantum NMR to the study of correlations in fluctuations are presented. A specific example of an oriented methyl group relaxed by paramagnetic impurities is studied in detail. The study of possible correlated motion between two coupled methyl groups by multiple quantum NMR is presented. For a six spin system it is shown that the four-quantum spectrum is sensitive to two-body correlations, and serves a ready test of correlated motion. The study of the spin-lattice dynamics of orienting or tunneling methyl groups (CH/sub 3/ and CD/sub 3/) at low temperatures is presented. The anisotropic spin-lattice relaxation of deuterated hexamethylbenzene, caused by the sixfold reorientation of the molecules, is investigated, and the NMR spectrometers and other experimental details are discussed.

  1. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    PubMed

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  2. The PAW/GIPAW approach for computing NMR parameters: a new dimension added to NMR study of solids.

    PubMed

    Charpentier, Thibault

    2011-07-01

    In 2001, Mauri and Pickard introduced the gauge including projected augmented wave (GIPAW) method that enabled for the first time the calculation of all-electron NMR parameters in solids, i.e. accounting for periodic boundary conditions. The GIPAW method roots in the plane wave pseudopotential formalism of the density functional theory (DFT), and avoids the use of the cluster approximation. This method has undoubtedly revitalized the interest in quantum chemical calculations in the solid-state NMR community. It has quickly evolved and improved so that the calculation of the key components of NMR interactions, namely the shielding and electric field gradient tensors, has now become a routine for most of the common nuclei studied in NMR. Availability of reliable implementations in several software packages (CASTEP, Quantum Espresso, PARATEC) make its usage more and more increasingly popular, maybe indispensable in near future for all material NMR studies. The majority of nuclei of the periodic table have already been investigated by GIPAW, and because of its high accuracy it is quickly becoming an essential tool for interpreting and understanding experimental NMR spectra, providing reliable assignments of the observed resonances to crystallographic sites or enabling a priori prediction of NMR data. The continuous increase of computing power makes ever larger (and thus more realistic) systems amenable to first-principles analysis. In the near future perspectives, as the incorporation of dynamical effects and/or disorder are still at their early developments, these areas will certainly be the prime target.

  3. NMR Investigations of Structure and Dynamics in Polymers for Energy Storage Applications

    NASA Astrophysics Data System (ADS)

    Greenbaum, Steven

    Materials innovation is needed to realize major progress in energy storage capacity for lithium batteries and capacitors. Polymers hold considerable promise as ion conducting media in batteries and electrochemical capacitors and as dielectrics in thin film capacitors. Structural studies of materials utilized in lithium battery technology are hampered by the lack of long-range order found in well-defined crystalline phases. Powder x-ray diffraction yields structural parameters that have been averaged over hundreds of lattice sites, and is unable to provide structural information about amorphous phases. Our laboratory uses solid state nuclear magnetic resonance (NMR) methods to investigate structural and chemical aspects of lithium ion cathodes, anodes, electrolytes, interfaces and interphases. NMR is element- (nuclear-) specific and sensitive to small variations in the immediate environment of the ions being probed, for example Li+, and in most cases is a reliably quantitative spectroscopy in that the integrated intensity of a particular spectral component is directly proportional to the number of nuclei in the corresponding material phase. NMR is also a powerful tool for probing ionic and molecular motion in lithium battery electrolytes with a dynamic range spanning some ten orders of magnitude through spin-lattice relaxation and self-diffusion measurements. Broadband relaxometry based on Fast Field Cycling NMR (FFCNMR) methods can span three to four of these orders of magnitude in a single set of measurements. Results of several recent NMR investigations performed on our lab will be presented. We explore the ion transport mechanism in polyether-based and lithium polymer electrolytes and those based on other base polymers, in particular, the extent to which ionic motion is coupled to polymer segmental motion. Polycarbonates are being considered as a possible replacement for polypropylene in high power thin film capacitors due to their favorable dielectric

  4. Multinuclear NMR studies of gaseous and liquid sevoflurane

    NASA Astrophysics Data System (ADS)

    Macięga, E.; Makulski, W.; Jackowski, K.; Blicharska, B.

    2006-03-01

    For the first time, a small amount of sevoflurane ((CF 3) 2CHOCH 2F) in carbon dioxide and xenon as the gaseous solvents has been studied using 19F and 1H NMR spectra. Density-dependent 19F and 1H nuclear magnetic shielding was observed when the pressure of each solvent was increased. After extrapolation of the results to the zero-density limit it was possible to determine the appropriate shielding constants free from intermolecular interactions, σ0(F) and σ0(H). Similar procedure has also been applied for the investigation of fluorine-proton spin-spin couplings and the 2J 0(FH) and 3J 0(FH) constants of an isolated (CF 3) 2CHOCH 2F molecule were also obtained. Additionally, high-resolution 1H, 13C, 17O and 19F NMR spectra of pure liquid sevoflurane were also recorded and all the 1H- 13C, 1H- 19F and 19F- 13C spin-spin coupling constants and NMR chemical shifts were measured. It is shown that the experimental NMR parameters are suitable for comparison with the results of recent quantum-chemical calculations.

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

    PubMed Central

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

    2015-01-01

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in 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 [1H,1H]-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. PMID:26227870

  6. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

    PubMed

    Gottstein, Daniel; Kirchner, Donata K; Güntert, Peter

    2012-04-01

    A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative 'regmean structure' is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordinates than the alternatives while maintaining the same quality as individual conformers. The method is thus suitable to generate representative single structure representations of protein structure ensembles in torsion angle space. Since in the case of NMR structure calculations with CYANA the single structure is calculated in the same way as the individual conformers except that weak positional and torsion angle restraints are added, we propose to represent new NMR structures by a 'regmean bundle' consisting of the single representative structure as the first conformer and all but one original individual conformers (the original conformer with the highest target function value is discarded in order to keep the number of conformers in the

  7. An NMR Study of Enzyme Activity.

    ERIC Educational Resources Information Center

    Peterman, Keith E.; And Others

    1989-01-01

    A laboratory experiment designed as a model for studying enzyme activity with a basic spectrometer is presented. Included are background information, experimental procedures, and a discussion of probable results. Stressed is the value of the use of Nuclear Magnetic Resonance in biochemistry. (CW)

  8. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    PubMed

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

  9. NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen αC-Domain Fragment†

    PubMed Central

    Burton, Robert A.; Tsurupa, Galina; Hantgan, Roy R.; Tjandra, Nico; Medved, Leonid

    2008-01-01

    According to the current hypothesis, in fibrinogen, the COOH-terminal portions of two Aα chains are folded into compact αC-domains that interact intramolecularly with each other and with the central region of the molecule; in fibrin, the αC-domains switch to an intermolecular interaction resulting in αC polymers. In agreement, our recent NMR study identified within the bovine fibrinogen Aα374-538 αC-domain fragment an ordered compact structure including a β-hairpin restricted at the base by a 423–453 disulfide linkage. To establish the complete structure of the αC-domain and to further test the hypothesis, we expressed a shorter αC-fragment, Aα406-483, and performed detailed analysis of its structure, stability, and interactions. NMR experiments on the Aα406-483 fragment identified a second loose β-hairpin formed by residues 459–476, yielding a structure consisting of an intrinsically unstable mixed parallel/anti-parallel β-sheet. Size-exclusion chromatography and sedimentation velocity experiments revealed that the Aα406-483 fragment forms soluble oligomers whose fraction increases with increasing concentration. This was confirmed by sedimentation equilibrium analysis, which also revealed that the addition of each monomer to an assembling αC oligomer substantially increases its stabilizing free energy. In agreement, unfolding experiments monitored by CD established that oligomerization of Aα406-483 results in increased thermal stability. Altogether, these experiments establish the complete NMR solution structure of the Aα406-483 αC-domain fragment, provide direct evidence for the intra- and intermolecular interactions between the αC-domains, and confirm that these interactions are thermodynamically driven. PMID:17590019

  10. NMR studies and applications of perfluorocarbon gases

    NASA Astrophysics Data System (ADS)

    Chang, Yulin

    Hyperpolarized 3He has been very successful in magnetic resonance imaging (MRI) of the lungs. It provides ways to study the physiological properties of the lungs and lung function. However, the high costs of the polarizing apparatus and the complicated polarizing procedure are preventing this technique from being clinically used routinely. Recent developments have shown that several fluorinated gases have the potential to replace 3He in some of its applications. This thesis presents some preliminary results of human excised lung imaging using C2F6 and C3F8. These two fluorinated gases were able to yield images with good signal-to-noise ratio and reasonable resolutions in a 1.5 T magnet. Using diffusion MRI of these two gases can distinguish emphysematous lungs from healthy ones. An important application of these gases would be to determine local lung surface-to-volume (S/V) ratio in vivo, which requires the unrestricted (free) diffusivity in each pixel to be known. We present data in this thesis which allow free diffusivities to be calculated from the relaxation time T1. Samples of pure C 2F6 and C3F8 at different pressures and in mixtures with oxygen at different concentrations were made. Measurements were done at two different magnetic fields and temperature was regulated to study the temperature dependence over a small range. These two gases were also used in studies of carbon-block filters, where the strong adsorption of the gases to the high surface-area carbon is beneficial. A brief review of our work on mouse lung imaging using hyperpolarized 3He is presented in Appendix A; Appendix B is a study of the longitudinal spin magnetization in the presence of a strong magnetic field gradient; the construction of the pulsed field gradient waveform measurement coils and some experimental results using these coils are contained in Appendix C.

  11. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

    SciTech Connect

    Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

    2015-12-28

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

  12. NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins.

    PubMed

    Carbajo, Rodrigo J; Sanz, Libia; Perez, Alicia; Calvete, Juan J

    2015-01-01

    Extant disintegrins, as found in the venoms of Viperidae and Crotalidae snakes (vipers and rattlesnakes, represent a family of polypeptides that block the function of β1 and β3 integrin receptors, both potently and with a high degree of selectivity. This toxin family owes its origin to the neofunctionalization of the extracellular region of an ADAM (a disintegrin and metalloprotease) molecule recruited into the snake venom gland proteome in the Jurassic. The evolutionary structural diversification of the disintegrin scaffold, from the ancestral long disintegrins to the more recently evolved medium-sized, dimeric and short disintegrins, involved the stepwise loss of pairs of class-specific disulfide linkages and the processing of the N-terminal region. NMR and crystal structures of medium-sized, dimeric and short disintegrins have been solved. However, the structure of a long disintegrin remained unknown. The present study reports the NMR solution structures of two disulfide bond conformers of the long disintegrin bitistatin from the African puff adder Bitis arietans. The findings provide insight into how a structural domain of the extracellular region of an ADAM molecule, recruited into and selectively expressed in the snake venom gland proteome as a PIII metalloprotease in the Jurassic, has subsequently been tranformed into a family of integrin receptor antagonists.

  13. Elucidation of the structures of residual and dissolved pine kraft lignins using an HMQC NMR technique.

    PubMed

    Balakshin, Mikhail Yu; Capanema, Ewellyn A; Chen, Chen-Loung; Gracz, Hanna S

    2003-10-08

    Comparative studies on the structures of residual and dissolved lignins isolated from pine kraft pulp and pulping liquor have been undertaken using the (1)H-(13)C HMQC NMR technique, GPC, and sugar analysis to elucidate the reaction mechanisms in kraft pulping and the lignin reactivity. A modified procedure for the isolation of enzymatic residual lignins has resulted in an appreciable decrease in protein contaminants in the residual lignin preparations (N content < 0.2%). The very high dispersion of HMQC spectra allows identification of different lignin moieties, which signals appear overlapped in 1D (13)C NMR spectra. Elucidation of the role of condensation reactions indicates that an increase in the degree of lignin condensation during pulping results from accumulation of original condensed lignin moieties rather than from the formation of new alkyl-aryl structures. Among aryl-vinyl type moieties, only stilbene structures are accumulated in lignin in appreciable amounts. Benzyl ether lignin-carbohydrate bonds involving primary hydroxyl groups of carbohydrates have been detected in residual and dissolved lignin preparations. Structures of the alpha-hydroxyacid type have been postulated to be among the important lignin degradation products in kraft pulping. The effect of the isolation method on the lignin structure and differences between the residual and dissolved lignins are discussed.

  14. NMR study on small proteins from Helicobacter pylori for antibiotic target discovery: a review.

    PubMed

    Kang, Su-Jin; Kim, Do-Hee; Lee, Bong-Jin

    2013-10-30

    Due to the widespread and increasing appearance of antibiotic resistance, a new strategy is needed for developing novel antibiotics. Especially, there are no specific antibiotics for Helicobacter pylori (H. pylori). H. pylori are bacteria that live in the stomach and are related to many serious gastric problems such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. Because of its importance as a human pathogen, it's worth studying the structure and function of the proteins from H. pylori. After the sequencing of the H. pylori strain 26695 in 1997, more than 1,600 genes were identified from H. pylori. Until now, the structures of 334 proteins from H. pylori have been determined. Among them, 309 structures were determined by X-ray crystallography and 25 structures by Nuclear Magnetic Resonance (NMR), respectively. Overall, the structures of large proteins were determined by X-ray crystallography and those of small proteins by NMR. In our lab, we have studied the structural and functional characteristics of small proteins from H. pylori. In this review, 25 NMR structures of H. pylori proteins will be introduced and their structure-function relationships will be discussed.

  15. Multivalent ligand mimetics of LecA from P. aeruginosa: synthesis and NMR studies.

    PubMed

    Bini, Davide; Marchetti, Roberta; Russo, Laura; Molinaro, Antonio; Silipo, Alba; Cipolla, Laura

    2016-06-24

    Molecular recognition of glycans plays an important role in glycomic and glycobiology studies. For example, pathogens have a number of different types of lectin for targeting host sugars. In bacteria, lectins exist sometimes as domains of bacterial toxins and exploit adhesion to glycoconjugates as a means of entering host cells. Herein, we describe the synthesis of three glycodendrons with the aim to dissect the fine structural details involved in the multivalent carbohydrate-protein interactions. LecA, from the pathogen Pseudomonas aeruginosa, has been used to characterize galactose dendrons interaction using one of the most widespread NMR technique for the elucidation of receptor-ligand binding in solution, the saturation transfer difference (STD) NMR. Furthermore, the effective hydrodynamic radius of each dendrimer recognized by LecA was estimated from the diffusion coefficients determined by pulsed-field-gradient stimulated echo (PFG-STE) NMR experiments.

  16. Structure elucidation and NMR assignments of an unusual triterpene saponin derivative from Ilex kudincha.

    PubMed

    Zuo, Wenjian; Wang, Qinghu; Li, Wen; Sha, Yi; Li, Xian; Wang, Jinhui

    2012-04-01

    One unusual triterpenoid derivative, ilekudinchoside E (1), was isolated from the leaves of Ilex kudincha. The structure was established by various spectroscopic techniques, including one- and two-dimensional NMR, HRTOFMS and CD spectra.

  17. Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy.

    PubMed

    Lundborg, Magnus; Fontana, Carolina; Widmalm, Göran

    2011-11-14

    The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (-)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic (1)H and (13)C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and implemented herein. The method is additionally advantageous in that reference data only have to be prepared once and from a user's point of view only the unknown sample has to be derivatized for use in CASPER.

  18. Understanding the directed ortho lithiation of (R)-Ph₂P(=NCO₂Me)NHCH(Me)Ph. NMR spectroscopic and computational study of the structure of the N-lithiated species.

    PubMed

    Casimiro, M; García-López, J; Iglesias, M J; López-Ortiz, F

    2014-10-14

    A multinuclear magnetic resonance ((1)H, (7)Li, (13)C, (15)N, (31)P) and DFT computational study at the M06-2X(SMD,THF)/6-311+G(d,p)//B3LYP/6-31G(d) level of the structure of a N-lithiated phosphinimidic amide (R)-Ph2P(=NCO2Me)NHCH(Me)Ph 13 has been performed. In THF solution it exists as an equilibrium mixture of monomers and dimers. The monomers consist of a six-membered ring formed by coordination of the lithium atom with the deprotonated nitrogen and the oxygen atom of the carbonyl group. This coordination mode is in contrast to the standard N,N-chelation observed in N-lithiated N,N'-bis(trimethylsilyl)phosphinimidic amides. The calculations showed that the metallacycle adopts a twist-boat conformation and that the lithium atom is in a tetrahedral environment involving O,N-chelation by the ligand and coordination to two/one THF molecules in the monomer/dimer. Dimerization takes place through O-Li bridges. For all species two series of isomers have been identified, which originated by restricted rotation of the methoxy group and ring inversion. The twist-boat conformational interconversion seems to be operating for explaining the pattern of signals observed in the (7)Li and (31)P NMR spectra. The structure found for the most stable dimer is analogous to the molecular structure reported for a related C(α)-lithiated phosphazene 20. The structural study revealed that the chiral side-arm of the N-lithiated species is oriented to the outer face of the pro-S P-phenyl ring, which shows one ortho-proton very close to the nitrogen atom of the carbamate moiety. In this conformation, proton abstraction by a base is highly favoured, in agreement with the experimental results.

  19. β2-Adrenergic receptor solutions for structural biology analyzed with microscale NMR diffusion measurements.

    PubMed

    Horst, Reto; Stanczak, Pawel; Stevens, Raymond C; Wüthrich, Kurt

    2013-01-02

    Microcoil NMR measurements were performed to determine the final composition of solutions of the β(2)-adrenergic receptor (β(2)AR) reconstituted with a detergent and to study the hydrodynamic properties of the detergent micelles containing β(2)AR. Standards are established for the reproducible preparation of G-protein-coupled receptor solutions for crystallization trials and solution NMR studies.

  20. NMR study of non-structural proteins--part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).

    PubMed

    Melekis, Efstathios; Tsika, Aikaterini C; Lichière, Julie; Chasapis, Christos T; Margiolaki, Irene; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2015-04-01

    Macro domains are ADP-ribose-binding modules present in all eukaryotic organisms, bacteria and archaea. They are also found in non-structural proteins of several positive strand RNA viruses such as alphaviruses. Here, we report the high yield expression and preliminary structural analysis through solution NMR spectroscopy of the macro domain from New World Mayaro Alphavirus. The recombinant protein was well-folded and in a monomeric state. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure determined by TALOS+.

  1. 1H NMR, 13C NMR and mass spectral studies of some Schiff bases derived from 3-amino-1,2,4-triazole.

    PubMed

    Issa, Y M; Hassib, H B; Abdelaal, H E

    2009-11-01

    Heterocyclic Schiff bases derived from 3-amino-1,2,4-triazole and different substituted aromatic aldehydes are prepared and subjected to (1)H NMR, (13)C NMR and mass spectral analyses. (1)H NMR spectra in DMSO exhibit a sharp singlet within the 9.35-8.90ppm region which corresponds to the azomethine proton. The position of this signal is largely dependent on the nature of the substituents on the benzal moiety. It is observed that the shape, position and the integration value of the signal of the aromatic proton of the triazole ring ((5)C) are clearly affected by the rate of exchange, relaxation time, concentration of solution as well as the solvent used. (13)C NMR is taken as substantial support for the results reached from (1)H NMR studies. The mass spectral results are taken as a tool to confirm the structure of the investigated compounds. The base peak (100%), mostly the M-1 peak, indicates the facile loss of hydrogen radical. The fragmentation pattern of the unsubstituted Schiff base is taken as the general scheme. Differences in the other schemes result from the effect of the electronegativity of the substituents attached to the aromatic ring.

  2. Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

    PubMed

    Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

    2016-06-01

    NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html.

  3. An NMR Study of Biomimetic Fluorapatite - Gelatine Mesocrystals.

    PubMed

    Vyalikh, Anastasia; Simon, Paul; Rosseeva, Elena; Buder, Jana; Scheler, Ulrich; Kniep, Rüdiger

    2015-10-30

    The mesocrystal system fluoroapatite-gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO4(3-) groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers, and with experimental observations of an amorphous cover layer in biominerals.

  4. An NMR Study of Biomimetic Fluorapatite - Gelatine Mesocrystals

    NASA Astrophysics Data System (ADS)

    Vyalikh, Anastasia; Simon, Paul; Rosseeva, Elena; Buder, Jana; Scheler, Ulrich; Kniep, Rüdiger

    2015-10-01

    The mesocrystal system fluoroapatite—gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO43- groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers, and with experimental observations of an amorphous cover layer in biominerals.

  5. An NMR Study of Biomimetic Fluorapatite – Gelatine Mesocrystals

    PubMed Central

    Vyalikh, Anastasia; Simon, Paul; Rosseeva, Elena; Buder, Jana; Scheler, Ulrich; Kniep, Rüdiger

    2015-01-01

    The mesocrystal system fluoroapatite—gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO43− groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers, and with experimental observations of an amorphous cover layer in biominerals. PMID:26515127

  6. Design, pharmacology, and NMR structure of a minimized cystine knot with agouti-related protein activity.

    PubMed

    Jackson, Pilgrim J; McNulty, Joseph C; Yang, Ying-Kui; Thompson, Darren A; Chai, Biaoxin; Gantz, Ira; Barsh, Gregory S; Millhauser, Glenn L

    2002-06-18

    The agouti-related protein (AGRP) is an endogenous antagonist of the melanocortin receptors MC3R and MC4R found in the hypothalamus and exhibits potent orexigenic activity. The cysteine-rich C-terminal domain of this protein, corresponding to AGRP(87-132), exhibits receptor binding affinity and antagonism equivalent to that of the full-length protein. The NMR structure of this active domain was recently determined and suggested that melanocortin receptor contacts were made primarily by two loops presented by a well-structured cystine knot domain within AGRP(87-132) [McNulty et al. (2001) Biochemistry 40, 15520-15527]. This hypothesis is tested here with NMR structure and activity studies of a 34-residue AGRP analogue designed to contain only the cystine knot domain. The designed miniprotein folds to a homogeneous product, retains the desired cystine knot architecture, functions as an antagonist, and maintains the melanocortin receptor pharmacological profile of AGRP(87-132). The AGRP-like activity of this molecule supports the hypothesis that indeed the cystine knot region possesses the melanocortin receptor contact points. Moreover, this potent AGRP analogue is synthetically accessible, may serve in the development of therapeutics for the treatment of diseases related to energy balance. and may also find use as a new reagent for probing melanocortin receptor structure and function.

  7. [NMR structure and dynamics of the chimeric protein SH3-F2].

    PubMed

    Kutyshenko, V P; Gushchina, L V; Khristoforov, V S; Prokhorov, D A; Timchenko, M A; Kudrevatykh, Iu A; Fediukina, D V; Filimonov, V V

    2010-01-01

    For the further elucidation of structural and dynamic principles of protein self-organization and protein-ligand interactions the design of new chimeric protein SH3-F2 was made and genetically engineered construct was created. The SH3-F2 amino acid sequence consists of polyproline ligand mgAPPLPPYSA, GG linker and the sequence of spectrin SH3 domain circular permutant S19-P20s. Structural and dynamics properties of the protein were studied by high-resolution NMR. According to NMR data the tertiary structure of the chimeric protein SH3-F2 has the topology which is typical of SH3 domains in the complex with the ligand, forming polyproline type II helix, located in the conservative region of binding in the orientation II. The polyproline ligand closely adjoins with the protein globule and is stabilized by hydrophobic interactions. However the interaction of ligand and the part of globule relative to SH3 domain is not too large because the analysis of protein dynamic characteristics points to the low amplitude, high-frequency ligand tumbling in relation to the slow intramolecular motions of the main globule. The constructed chimera permits to carry out further structural and thermodynamic investigations of polyproline helix properties and its interaction with regulatory domains.

  8. NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.

    PubMed

    Espinosa, J F; Asensio, J L; García, J L; Laynez, J; Bruix, M; Wright, C; Siebert, H C; Gabius, H J; Cañada, F J; Jiménez-Barbero, J

    2000-07-01

    The specific interaction of the isolated B domain of wheat germ agglutinin (WGA-B) with N,N',N"-triacetylchitotriose has been analyzed by 1H-NMR spectroscopy. The association constants for the binding of WGA-B to this trisaccharide have been determined from both 1H-NMR titration experiments and microcalorimetry methods. Entropy and enthalpy of binding have been obtained. The driving force for the binding process is provided by a negative DeltaH which is partially compensated by negative DeltaS. These negative signs indicate that hydrogen bonding and van der Waals forces are the major interactions stabilizing the complex. NOESY NMR experiments in water solution provided 327 protein proton-proton distance constraints. All the experimental constraints were used in a refinement protocol including restrained molecular dynamics in order to determine the refined solution conformation of this protein/carbohydrate complex. With regard to the NMR structure of the free protein, no important changes in the protein NOEs were observed, indicating that carbohydrate-induced conformational changes are small. The average backbone rmsd of the 35 refined structures was 1.05 A, while the heavy atom rmsd was 2.10 A. Focusing on the bound ligand, two different orientations of the trisaccharide within WGA-B binding site are possible. It can be deduced that both hydrogen bonds and van der Waals contacts confer stability to both complexes. A comparison of the three-dimensional structure of WGA-B in solution to that reported in the solid state and to those deduced for hevein and pseudohevein in solution has also been performed.

  9. Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline.

    PubMed

    Pathak, S K; Srivastava, R; Sachan, A K; Prasad, O; Sinha, L; Asiri, A M; Karabacak, M

    2015-01-25

    Comprehensive investigation of geometrical and electronic structure in ground as well as the first excited state of 3,5-Difluoroaniline (C6H5NF2) was carried out. The experimentally observed spectral data (FT-TR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were measured by TD-DFT approach. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. Global and local reactivity descriptors were computed to predict reactivity and reactive sites on the molecule. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data obtained. Moreover, the thermodynamic properties were evaluated.

  10. 2H NMR studies of supercooled and glassy aspirin

    NASA Astrophysics Data System (ADS)

    Nath, R.; Nowaczyk, A.; Geil, B.; Bohmer, R.

    2007-11-01

    Acetyl salicylic acid, deuterated at the methyl group, was investigated using 2H-NMR in its supercooled and glassy states. Just above the glass transition temperature the molecular reorientations were studied using stimulated-echo spectroscopy and demonstrated a large degree of similarity with other glass formers. Deep in the glassy phase the NMR spectra look similar to those reported for the crystal [A. Detken, P. Focke, H. Zimmermann, U. Haeberlen, Z. Olejniczak, Z. T. Lalowicz, Z. Naturforsch. A 50 (1995) 95] and below 20 K they are indicative for rotational tunneling with a relatively large tunneling frequency. Measurements of the spin-lattice relaxation times for temperatures below 150 K reveal a broad distribution of correlation times in the glass. The dominant energy barrier characterizing the slow-down of the methyl group is significantly smaller than the well defined barrier in the crystal.

  11. A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

    ERIC Educational Resources Information Center

    Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

    2004-01-01

    An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

  12. Glass Structure by Scattering Methods and Spectroscopy — D. SOLID STATE NMR AS A STRUCTURAL TOOL IN GLASS SCIENCE

    NASA Astrophysics Data System (ADS)

    Eckert, Hellmut

    The following sections are included: * Introduction * Fundamentals of Solid State NMR * Nuclear magnetism and resonance * Spectroscopic technique * Internal interactions * Chemical shielding interaction * Direct magnetic dipole-dipole coupling * Nuclear electric quadrupolar interaction * Experimental separation strategies * Magic-angle spinning * Multi-dimensional NMR * Structural Issues in Non-crystalline Solids and Glasses * Short-Range Order in Oxide Glasses * Local coordination number and symmetry * Bond angle distribution functions * Spatial distribution of modifier cations and structural implications of the mixed-alkali effect * Short-Range Order in Non-Oxide Glasses * Chemical bond distribution and intermediate range order * Chemical equilibria and kinetics in glassforming liquids * Future Perspectives * Towards higher resolution for quadrupolar nuclei * Recovery of dipolar interactions in MAS-NMR: site connectivities * Double resonance NMR in heteronuclear systems * Zero- and double quantum NMR in homonuclear systems * Acknowledgments * References

  13. Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography

    PubMed Central

    Miyazaki, Yasuyuki; Irobalieva, Rossitza N.; Tolbert, Blanton; Smalls-Mantey, Adjoa; Iyalla, Kilali; Loeliger, Kelsey; D’Souza, Victoria; Khant, Htet; Schmid, Michael F.; Garcia, Eric; Telesnitsky, Alice; Chiu, Wah; Summers, Michael F.

    2010-01-01

    The 5′-untranslated regions (5′-UTRs) of all gammaretroviruses contain a conserved “double hairpin motif” (ΨCD) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming “kissing” interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney Murine Leukemia Virus (MoMuLV) ([ΨCD]2, 132-nucleotides, 42.8 kDaltons) using a 2H-edited NMR spectroscopy-based approach. This approach enabled the detection of 1H-1H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional 1H-1H correlated and 1H-13C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D’ and SLC’ to SL-D), and stack in an end-to-end manner (SL-C to SL-D and SL-C’ to SL-D’) that gives rise to an elongated overall shape (ca. 95 Å by 45 Å by 25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [ΨCD]2 simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [ΨCD]2 functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins. PMID:20933521

  14. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    SciTech Connect

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.

  15. Hyperpolarized 13C NMR lifetimes in the liquid-state: relating structures and T1 relaxation times

    NASA Astrophysics Data System (ADS)

    Parish, Christopher; Niedbalski, Peter; Hashami, Zohreh; Fidelino, Leila; Kovacs, Zoltan; Lumata, Lloyd

    Among the various attempts to solve the insensitivity problem in nuclear magnetic resonance (NMR), the physics-based technique dissolution dynamic nuclear polarization (DNP) is probably the most successful method of hyperpolarization or amplifying NMR signals. Using this technique, liquid-state NMR signal enhancements of several thousand-fold are expected for low-gamma nuclei such as carbon-13. The lifetimes of these hyperpolarized 13C NMR signals are directly related to their 13C spin-lattice relaxation times T1. Depending upon the 13C isotopic location, the lifetimes of hyperpolarized 13C compounds can range from a few seconds to minutes. In this study, we have investigated the hyperpolarized 13C NMR lifetimes of several 13C compounds with various chemical structures from glucose, acetate, citric acid, naphthalene to tetramethylallene and their deuterated analogs at 9.4 T and 25 deg C. Our results show that the 13C T1s of these compounds can range from a few seconds to more than 60 s at this field. Correlations between the chemical structures and T1 relaxation times will be discussed and corresponding implications of these results on 13C DNP experiments will be revealed. US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  16. Structure of an inclusive compound of bis(piperidinium-4-carboxylate)hydrogen semi-tartrate with water and methanol studied by X-ray diffraction, NMR, FTIR and DFT methods

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Fojud, Z.; Katrusiak, A.; Szafran, M.

    2009-06-01

    The complex consisting of two piperidine-4-carboxylic acid, L-tartaric acid, water and methanol molecules has been synthesized and characterized by X-ray diffraction, 1H, 13C NMR, 13C CP MAS NMR, FTIR spectra and DFT calculations. The title complex is composed of the following units: piperidinium-4-carboxylate (P4C), piperidinium-4-carboxylic acid (P4CH), semi-tartrate anion (TA), water and methanol; it crystallizes in orthorhombic space group P2 12 12 1. TA anions form infinite chains through the COOH···OOC hydrogen bond of 2.503(5) Å. The zwitterionic P4C molecules are linked by the N +H···OOC hydrogen bond of 2.780(5) Å into chains. The P4CH cation is a bridge between the TA and P4C chains. P4CH and P4C form a homoconjugated cation through the COOH···OOC hydrogen bonds of 2.559(5) Å. Water interacts with TA and P4CH, while methanol interacts only with water. In the optimized molecule of the (P4C) 2H·TA·H 2O·HOCH 3 complex, the components form a cyclic oligomer through four O-H···O and four N-H···O hydrogen bonds. The 1H and 13C NMR spectra elucidate the structure of the title complex in the aqueous solution. The 13C CP MAS NMR spectrum is consistent with the X-ray results. The FTIR spectrum confirms a very complex structure of the title compound.

  17. 7Li NMR study of normal human erythrocytes

    NASA Astrophysics Data System (ADS)

    Pettegrew, J. W.; Post, J. F. M.; Panchalingam, K.; Withers, G.; Woessner, D. E.

    The biological action of lithium is of great interest because of the therapeutic efficacy of the cation in manic-depressive illness. To investigate possible molecular interactions of lithium, 7Li NMR studies were conducted on normal human erythrocytes which had been incubated with lithium chloride. The uptake of lithium ions was followed by 7Li NMR, using a dysprosium, tripolyphosphate shift reagent. Lithium uptake followed single-exponential kinetics with a time constant of 14.7 h. The intracellular lithium relaxation times were T 1 ⋍ 5 s and T 2 ⋍ 0.15 s, which implies a lengthening of the lithium correlation time. It was found that lithium does not interact significantly with hemoglobin, the erythrocyte membrane, or artificial phospholipid membranes. Based on measurements of lithium T1 and T2 in concentrated agar gels, the large difference between T1 and T2 for intracellular lithium ions may be due to diffusion of the hydrated lithium ion through heterogeneous electrostatic field gradients created by the erythrocyte membrane-associated cytoskeletal network. Lithium binding to the membrane-associated cytoskeleton, however, cannot be ruled out. Because of the large differences between T1 and T2 of intracellular lithium ions, 1Li NMR may be a sensitive and promising noninvasive method to probe the intracellular environment.

  18. Watching protein structure at work in living cells using NMR spectroscopy.

    PubMed

    Tochio, Hidehito

    2012-12-01

    Isotope-assisted multi-dimensional NMR spectroscopy can now be applied to proteins inside living cells. The technique, called in-cell NMR, aims to investigate the structures, interactions and dynamics of proteins under their native conditions, ideally at an atomic resolution. The application has begun with bacterial cells but has now expanded to mammalian cultured cells, such as HeLa cells. The importance of the realization of such 'in-mammalian cell' NMR should be stressed, as these are the cells most often employed in cell biology. Hence, a substantially wide range of application would be possible in the near future once the technique has been well developed.

  19. Structure elucidation of a new isoflavone by exclusive use of ¹H NMR measurements.

    PubMed

    Ortega, Alfredo R; Toscano, Rubén A; Hernández-Barragán, Angelina; Alvarez-Cisneros, Celina; Joseph-Nathan, Pedro

    2015-10-01

    The leaves of Piscidia carthagenensis provided new 7,2',5'-trimethoxy-3',4'-methylenedioxyisoflavone (1), admixed with known 6,7-dimethoxy-3',4'-methylenedioxyisoflavone (2), and 5,4'-dihydroxy-7,2',5'-trimethoxyisoflavone (3), which were separated by extensive fractional solubillization. Selective irradiation of the H-5 "singlet" of 2 allowed distinction of the two methoxy group signals, whose chemical shift difference is only 0.004 ppm (1.2 Hz at 300 MHz). The (1)H and (13)C NMR data of 3 were assigned with the aid of HETCOR and gHMBC measurements. Although 1 looked inhomogeneous in the solid state, its solution structure followed from (1)H NMR measurements, where it looked homogeneous. To clarify the solid state aspect and confirm the structure of 1, two types of crystals were mechanically separated and subjected to single crystal X-ray diffraction measurements. This study revealed polymorphism because of the concomitant presence of orthorhombic and triclinic crystals, but showed no atropisomerism. The structure of 3 was also verified by X-ray diffraction crystallography.

  20. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR.

    PubMed

    Peti, Wolfgang; Page, Rebecca; Moy, Kin; O'Neil-Johnson, Mark; Wilson, Ian A; Stevens, Raymond C; Wüthrich, Kurt

    2005-12-01

    In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D 1H NMR spectra or 2D [1H,15N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D 1H NMR and/or 2D [1H,15N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the "macro-scale" Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.

  1. MRI and unilateral NMR study of reindeer skin tanning processes.

    PubMed

    Zhu, Lizheng; Del Federico, Eleonora; Ilott, Andrew J; Klokkernes, Torunn; Kehlet, Cindie; Jerschow, Alexej

    2015-04-07

    The study of arctic or subarctic indigenous skin clothing material, known for its design and ability to keep the body warm, provides information about the tanning materials and techniques. The study also provides clues about the culture that created it, since tanning processes are often specific to certain indigenous groups. Untreated skin samples and samples treated with willow (Salix sp) bark extract and cod liver oil are compared in this study using both MRI and unilateral NMR techniques. The two types of samples show different proton spatial distributions and different relaxation times, which may also provide information about the tanning technique and aging behavior.

  2. Determining the effects of microwave heating on the ordered structures of rice starch by NMR.

    PubMed

    Fan, Daming; Ma, Wenrui; Wang, Liyun; Huang, Jianlian; Zhang, Fengmin; Zhao, Jianxin; Zhang, Hao; Chen, Wei

    2013-02-15

    The effects of microwave heating on the double helices, single helix and amorphous structures and the relative crystallinity of rice starch were studied by (13)C CP/MAS NMR method, with rapid heating in an oil bath and conventional slow heating as controls. The results indicated that compared with rapid heating, microwave heating did not significantly change the ordered and disordered structures. All of the heating methods exhibited similar content changes to the double helices, V-type single helix and amorphous structures with rising temperature. The rapid heating effects caused by microwave and oil bath accelerated the destruction of the V-type single helix in the starch granules. The electromagnetic effect of microwave heating did not affect the decrease of the double helices or the amorphous content of the starch.

  3. Solution structure and dynamics of lanthanide complexes of the macrocyclic polyamino carboxylate DTPA-dien. NMR study and crystal structures of the lanthanum(III) and europium(III) complexes

    SciTech Connect

    Franklin, S.J.; Raymond, K.N.

    1994-12-07

    An 18-membered macrocyclic DTPA-bis(amide) ligand (DTPA = diethylenetriaminepentaacetic acid) containing a heteroatom in the amide link has been prepared via the condensation of DTPA-dianhydride and diethylenetriamine. The solution structures of the two isomeric pairs present in the Ln(III) complexes of DTPA-dien have been investigated by {sup 1}H NMR. The structures of the lanthanum(III) and europium(III) DTPA-dien complexes have been determined by X-ray analysis. [La(DTPA-dienH{sup +})H{sub 2}O]{sub 2}(CF{sub 3}SO{sub 3}{sup -}){sub 2}{center_dot}18H{sub 2}O (I) crystallizes as a carboxylate-bridged dimer about a center of inversion in the orthorhombic space group Pbca with a = 12.626(2) {angstrom}, b = 21.405(3) {angstrom}, c = 26.422(9) {angstrom}, and Z = 8. Each lanthanum ion is 11-coordinate with octadentate ligand coordination, an {eta}{sup 2} bridging carboxylate, and one water. [Eu(DTPA-dienH{sup +})]{sub 4}(CF{sub 3}SO{sub 3}{sup -}){sub 4}{center_dot}6NaCF{sub 3}SO{sub 3}{center_dot}20H{sub 2}O (II) crystallizes as a carboxylate-bridged tetramer with two crystallographically independent Eu(III) positions (Z = 8 for each) in the monoclinic space group C2/c: a = 30.94(1) {angstrom}, b = 23.456(3) {angstrom}, c = 22.611(4) {angstrom}, {beta} = 105.78(2){degrees}. The coordination geometries about Eu1 and Eu2 are nearly identical and are described as a nine-coordinate tricapped trigonal prism with octadentate ligand coordination plus an {eta}{sup 1} bridging carboxylate. The tendency to oligomerize is attributed to the constraints imposed by the macrocycle and the hydrogen bonding available with the link heteroatom. The structural differences between the two complexes are attributed to a difference in La(III) and Eu(III) ionic size.

  4. Structure elucidation and complete NMR spectral assignments of four new diterpenoids from Smallantus sonchifolius.

    PubMed

    Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Kang, Ting-Guo; Dong, Feng

    2008-08-01

    Four new diterpenoids, named smaditerpenic acid A-D, together with five known compounds, were isolated from the H(2)O extract of the leaves of Smallantus sonchifolius (yacon) cultivated in Liaoning, China and their structures were elucidated on the basis of one- and two-dimensional NMR (including (1)H, (13)C-NMR, (1)H-(1)H COSY, HSQC, TOCSY, HMBC, and ROESY), electrospray ionization mass spectrometry (ESI-MS), and chemical methods.

  5. Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies.

    PubMed

    Bayro, Marvin J; Tycko, Robert

    2016-07-13

    The HIV-1 capsid protein (CA) forms the capsid shell that encloses RNA within a mature HIV-1 virion. Previous studies by electron microscopy have shown that the capsid shell is primarily a triangular lattice of CA hexamers, with variable curvature that destroys the ideal symmetry of a planar lattice. The mature CA lattice depends on CA dimerization, which occurs through interactions between helix 9 segments of the C-terminal domain (CTD) of CA. Several high-resolution structures of the CTD-CTD dimerization interface have been reported, based on X-ray crystallography and multidimensional solution nuclear magnetic resonance (NMR), with significant differences in amino acid side chain conformations and helix 9-helix 9 orientations. In a structural model for tubular CA assemblies based on cryogenic electron microscopy (cryoEM) [Zhao et al. Nature, 2013, 497, 643-646], the dimerization interface is substantially disordered. The dimerization interface structure in noncrystalline CA assemblies and the extent to which this interface is structurally ordered within a curved lattice have therefore been unclear. Here we describe solid state NMR measurements on the dimerization interface in tubular CA assemblies, which contain the curved triangular lattice of a mature virion, including quantitative measurements of intermolecular and intramolecular distances using dipolar recoupling techniques, solid state NMR chemical shifts, and long-range side chain-side chain contacts. When combined with restraints on the distance and orientation between helix 9 segments from the cryoEM study, the solid state NMR data lead to a unique high-resolution structure for the dimerization interface in the noncrystalline lattice of CA tubes. These results demonstrate that CA lattice curvature is not dependent on disorder or variability in the dimerization interface. This work also demonstrates the feasibility of local structure determination within large noncrystalline assemblies formed by high

  6. The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution

    SciTech Connect

    Weber, C.; Wilder, G.; von Freyberg, B.; Braun, W.; Wuethrich, K. ); Traber, R.; Widmer, H. )

    1991-07-02

    Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform {sup 15}N- or {sup 13}C-labeling of cyclosporin A and heteronuclear spectral editing techniques. With an input of 108 intramolecular NOEs and four vicinal {sup 3}J{sub HN{alpha}} coupling constants, the three-dimensional structure of cyclosporin A bound to cyclophilin was calculated with the distance geometry program DISMAN, and the structures resulting from 181 converged calculations were energy refined with the program FANTOM. A group of 120 conformers was selected on the basis of the residual constraint violations and energy criteria to represent the solution structure. The average of the pairwise root-mean-square distances calculated for the backbone atoms of the 120 structures was 0.58 {angstrom}. The structure represents a novel conformation of cyclosporin A, for which the backbone conformation is significantly different from the previously reported structures in single crystals and in chloroform solution. The structure has all peptide bonds in the trans form, contains no elements of regular secondary structure and no intramolecular hydrogen bonds, and exposes nearly all polar groups to its environment. The root-mean-square distance between the backbone atoms of the crystal structure of cyclosporin A and the mean of the 120 conformers representing the NMR structure of cyclosporin A bound to cyclophilin is 2.5 {angstrom}.

  7. Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

    SciTech Connect

    Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

    2014-11-19

    Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

  8. A tabu search approach for the NMR protein structure-based assignment problem.

    PubMed

    Cavuşlar, Gizem; Çatay, Bülent; Apaydın, Mehmet Serkan

    2012-01-01

    Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this computationally challenging problem by using prior information about the protein obtained from a homologous structure. NVR-BIP used the Nuclear Vector Replacement (NVR) framework to model SBA as a binary integer programming problem. In this paper, we prove that this problem is NP-hard and propose a tabu search (TS) algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVR-TS uses a quadratic penalty relaxation of NVR-BIP where the violations in the Nuclear Overhauser Effect constraints are penalized in the objective function. Experimental results indicate that our algorithm finds the optimal solution on NVRBIP’s data set which consists of seven proteins with 25 templates (31 to 126 residues). Furthermore, it achieves relatively high assignment accuracies on two additional large proteins, MBP and EIN (348 and 243 residues, respectively), which NVR-BIP failed to solve. The executable and the input files are available for download at http://people.sabanciuniv.edu/catay/NVR-TS/NVR-TS.html.

  9. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  10. Solid-state and unilateral NMR study of deterioration of a Dead Sea Scroll fragment.

    PubMed

    Masic, A; Chierotti, M R; Gobetto, R; Martra, G; Rabin, I; Coluccia, S

    2012-02-01

    Unilateral and solid-state nuclear magnetic resonance (NMR) analyses were performed on a parchment fragment of the Dead Sea Scroll (DSS). The analyzed sample belongs to the collection of non-inscribed and nontreated fragments of known archaeological provenance from the John Rylands University Library in Manchester. Therefore, it can be considered as original DSS material free from any contamination related to the post-discovery period. Considering the paramount significance of the DSS, noninvasive approaches and portable in situ nondestructive methods are of fundamental importance for the determination of composition, structure, and chemical-physical properties of the materials under study. NMR studies reveal low amounts of water content associated with very short proton relaxation times, T(1), indicating a high level of deterioration of collagen molecules within scroll fragments. In addition, (13)C cross-polarization magic-angle-spinning (CPMAS) NMR spectroscopy shows characteristic peaks of lipids whose presence we attribute to the production technology that did not involve liming. Extraction with chloroform led to the reduction of both lipid and protein signals in the (13)C CPMAS spectrum indicating probable involvement of lipids in parchment degradation processes. NMR absorption and relaxation measurements provide nondestructive, discriminative, and sensitive tools for studying the deterioration effects on the organization and properties of water and collagen within ancient manuscripts.

  11. Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

    PubMed Central

    2015-01-01

    The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

  12. Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.

    PubMed Central

    Tejero, R.; Bassolino-Klimas, D.; Bruccoleri, R. E.; Montelione, G. T.

    1996-01-01

    The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF and 424 NMR-derived constraints for hTGF alpha were used in these energy-refinement calculations. Different weighting schemes and starting conformations were studied to check and/or improve the sampling of the low-energy conformational space that is consistent with all constraints. The results demonstrate that loosened (i.e., "relaxed") sets of the EGF and hTGF alpha internuclear distance constraints allow molecules to overcome local minima in the search for a global minimum with respect to both distance restraints and conformational energy. The resulting energy-refined structures of mEGF and hTGF alpha are compared with structures determined previously and with structures of homologous proteins determined by NMR and X-ray crystallography. PMID:8845748

  13. Determination of the Structural Basis of Antibody Diversity Using NMR

    DTIC Science & Technology

    1988-09-15

    1): 290. "Distances of tyruzsnc residues from a spin-label hapten in the combining site of a specific monoclonal antibody," Jacob Anglister, Tom Frey...anti-spin-label antibody," Tom Frey, Jacob Anglister and Harden M. McConnell, Biochemistry 23, 6470-6473 (1984). 298. "NMR technique for assessing...contributions of heavy and light chains to an antibody combining site," Jacob Anglister, Tom Frey and Harden M. McConnell, Nature 315, 65-67 (1985). 305

  14. Structural changes of lipoprotein lipids by 1H NMR

    NASA Astrophysics Data System (ADS)

    Ala-Korpela, M.; Oja, J.; Lounila, J.; Jokisaari, J.; Savolainen, M. J.; Kesäniemi, Y. A.

    1995-08-01

    A new procedure for detecting structural changes of lipoprotein lipids is introduced and applied to study native low (LDL) and high density lipoprotein (HDL) particles. The method involves lineshape fitting analyses of specific resonances in proton nuclear magnetic resonance spectra together with numerical derivation of the obtained intensity curves with respect to temperature. In addition to the well-known phase transition of the LDL core cholesterol esters, a novel structural change was revealed in the phospholipid monolayer of both native LDL and HDL particles. The attributes of this phenomenon are discussed.

  15. NMR structure of the N-terminal domain of the replication initiator protein DnaA

    SciTech Connect

    Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David E.

    2007-08-07

    DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

  16. NMR characterization of hydrocarbon adsorption on calcite surfaces: A first principles study

    SciTech Connect

    Bevilaqua, Rochele C. A.; Miranda, Caetano R.; Rigo, Vagner A.; Veríssimo-Alves, Marcos

    2014-11-28

    The electronic and coordination environment of minerals surfaces, as calcite, are very difficult to characterize experimentally. This is mainly due to the fact that there are relatively few spectroscopic techniques able to detect Ca{sup 2+}. Since calcite is a major constituent of sedimentary rocks in oil reservoir, a more detailed characterization of the interaction between hydrocarbon molecules and mineral surfaces is highly desirable. Here we perform a first principles study on the adsorption of hydrocarbon molecules on calcite surface (CaCO{sub 3} (101{sup ¯}4)). The simulations were based on Density Functional Theory with Solid State Nuclear Magnetic Resonance (SS-NMR) calculations. The Gauge-Including Projector Augmented Wave method was used to compute mainly SS-NMR parameters for {sup 43}Ca, {sup 13}C, and {sup 17}O in calcite surface. It was possible to assign the peaks in the theoretical NMR spectra for all structures studied. Besides showing different chemical shifts for atoms located on different environments (bulk and surface) for calcite, the results also display changes on the chemical shift, mainly for Ca sites, when the hydrocarbon molecules are present. Even though the interaction of the benzene molecule with the calcite surface is weak, there is a clearly distinguishable displacement of the signal of the Ca sites over which the hydrocarbon molecule is located. A similar effect is also observed for hexane adsorption. Through NMR spectroscopy, we show that aromatic and alkane hydrocarbon molecules adsorbed on carbonate surfaces can be differentiated.

  17. Heteronuclear NMR studies of cobalamins. 11. sup 15 N NMR studies of the axial nucleotide and amide side chains of cyanocobalamin and dicyanocobamides

    SciTech Connect

    Brown, K.; Brooks, H.B.; Xiang, Zou ); Victor, M.; Ray, A. ); Timkovich, R. )

    1990-11-28

    Spectroscopic and thermodynamic evidence for the structure of cobalamines and dicyanocobalamin (CN){sub 2}Cbl have been previously reported. The structure indicated the occurrence of the so-called tuck-in species. Further observations and characterization of the tuck-in species of (CN){sub 2}Cbl by {sup 15}N NMR spectroscopy are presented herein. These results represent the first observation of the {sup 15}N NMR spectrum of benzimidazole nucleotide of cobalamins. The first NMR observation of the amide protons of cobalamins and their connectivity to the amide nitrogens are also reported. 50 refs., 2 figs., 2 tabs.

  18. INSTRUMENTS AND METHODS OF INVESTIGATION: NMR potentials for studying physical processes in fossil coals

    NASA Astrophysics Data System (ADS)

    Alekseev, Anatolii D.; Ul'yanova, Ekaterina V.; Vasilenko, Tat'yana A.

    2005-11-01

    High-resolution, pulsed, and wide-line NMR studies of fossil coals are reviewed. Coal substance conversion due to outbursts is discussed. Results on water and methane interactions with coal substance, which provide insight into the dynamic characteristics of boundary water, the location of methane in coal structure, and water and methane's hazard implications for coal beds (gas- or geodynamic phenomena) are presented; these are shown to have potential for predicting and preventing life threatening situations.

  19. NMR study of CeTe at low temperatures

    NASA Astrophysics Data System (ADS)

    Hinderer, J.; Weyeneth, S. M.; Weller, M.; Gavilano, J. L.; Felder, E.; Hulliger, F.; Ott, H. R.

    2006-05-01

    We present 125Te NMR measurements on CeTe powder at temperatures between 1 and 150 K and in magnetic fields between 5 and 8 T. CeTe is a rocksalt-type intermetallic compound. It orders antiferromagnetically at TN≈2.2 K with a much reduced ordered moment [H.R. Ott, J.K. Kjems, F. Hulliger, Phys. Rev. Lett. 42 20 (1979) 1378]. From our low-temperature NMR spectra we infer the presence of at least three inequivalent Te sites at low temperatures. Considering the crystal structure this result is completely unexpected. The linewidths and the Knight shifts of the individual lines are significantly different and increase substantially with decreasing temperature. They follow the temperature dependence of the magnetic susceptibility above 20 K. Above TN, hyperfine fields of 1.6, 0.8 and 0.0 T at the three Te sites per Bohr magneton of Ce moment are deduced from Knight shift vs. magnetic susceptibility data. These values are typical for transferred hyperfine fields via conduction electrons.

  20. Solid state NMR study of SEI formation in lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Zhao, Dachun

    the SEI with temperature. In Chapter 5 we report on the use of NMR to study the effect of electrolyte/solvent and electrode structure on SEI formation. The intensity of the SEI in a cell containing LiBOB electrolyte with EC and DEC is greater than that in a cell with LiPF6 electrolyte with EC and DMC. This implies that the cell containing LiBOB electrolyte with EC and DEC is more stable. From the analysis of NMR of the cathode, it was found that it is easier to form SEI in layered structure cathode than in a spinel structure, suggesting that spinel structure materials may be better choices as cathode in lithium ion batteries. Evidently, then, the choice of electrolyte/solvent materials and electrode materials are key factors in determining the performance of lithium ion batteries.

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

    SciTech Connect

    Gronenborn, A.M.; Clore, G.M.

    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. A Unique Tool for Cellular Structural Biology: In-cell NMR*

    PubMed Central

    Luchinat, Enrico; Banci, Lucia

    2016-01-01

    Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When this is done, important structural and functional features of macromolecules, which depend on their native network of interactions within the cell, may be lost. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that allows macromolecules to be analyzed in living cells, at the atomic level. In-cell NMR can be applied to several cellular systems to obtain biologically relevant structural and functional information. Here we summarize the existing approaches and focus on the applications to protein folding, interactions, and post-translational modifications. PMID:26677229

  3. NMR study of a membrane protein in detergent-free aqueous solution.

    PubMed

    Zoonens, Manuela; Catoire, Laurent J; Giusti, Fabrice; Popot, Jean-Luc

    2005-06-21

    One of the major obstacles to membrane protein (MP) structural studies is the destabilizing effect of detergents. Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep MPs water-soluble under mild conditions. In the present work, we have explored the feasibility of studying the structure of APol-complexed MPs by NMR. As a test MP, we chose the 171-residue transmembrane domain of outer MP A from Escherichia coli (tOmpA), whose x-ray and NMR structures in detergent are known. 2H,15N-labeled tOmpA was produced as inclusion bodies, refolded in detergent solution, trapped with APol A8-35, and the detergent removed by adsorption onto polystyrene beads. The resolution of transverse relaxation-optimized spectroscopy-heteronuclear single-quantum correlation spectra of tOmpA/A8-35 complexes was found to be close to that of the best spectra obtained in detergent solutions. The dispersion of chemical shifts indicated that the protein had regained its native fold and retained it during the exchange of surfactants. MP-APol interactions were mapped by substituting hydrogenated for deuterated A8-35. The resulting dipolar broadening of amide proton linewidths was found to be limited to the beta-barrel region of tOmpA, indicating that A8-35 binds specifically to the hydrophobic transmembrane surface of the protein. The potential of this approach to MP studies by solution NMR is discussed.

  4. Structure determination of α-helical membrane proteins by solution-state NMR: emphasis on retinal proteins.

    PubMed

    Gautier, Antoine

    2014-05-01

    The biochemical processes of living cells involve a numerous series of reactions that work with exceptional specificity and efficiency. The tight control of this intricate reaction network stems from the architecture of the proteins that drive the chemical reactions and mediate protein-protein interactions. Indeed, the structure of these proteins will determine both their function and interaction partners. A detailed understanding of the proximity and orientation of pivotal functional groups can reveal the molecular mechanistic basis for the activity of a protein. Together with X-ray crystallography and electron microscopy, NMR spectroscopy plays an important role in solving three-dimensional structures of proteins at atomic resolution. In the challenging field of membrane proteins, retinal-binding proteins are often employed as model systems and prototypes to develop biophysical techniques for the study of structural and functional mechanistic aspects. The recent determination of two 3D structures of seven-helical trans-membrane retinal proteins by solution-state NMR spectroscopy highlights the potential of solution NMR techniques in contributing to our understanding of membrane proteins. This review summarizes the multiple strategies available for expression of isotopically labeled membrane proteins. Different environments for mimicking lipid bilayers will be presented, along with the most important NMR methods and labeling schemes used to generate high-quality NMR spectra. The article concludes with an overview of types of conformational restraints used for generation of high-resolution structures of membrane proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

  5. The NMR and X-ray study of L-arginine derived Schiff bases and its cadmium complexes

    NASA Astrophysics Data System (ADS)

    Kołodziej, B.; Grech, E.; Schilf, W.; Kamieński, B.; Pazio, A.; Woźniak, K.

    2014-04-01

    The structure study of five Schiff bases derived from L-arginine (L-Arg) and 2-hydroxy carbonyl compounds were performed in both solution and solid state using NMR and X-ray methods. Both analytical methods applied to the solid state sample of two Schiff bases showed a significant difference in molecular structures of unsubstituted and 7-CH3 substituted compounds. This effect was explained as a steric interaction of methyl group. Additionally the structure of two Cd2+ complexes with some Schiff bases were determined by NMR methods in DMSO solution and in the solid state. On the base of heteronuclear NMR measurement (13C, 15N and 113Cd) it was possible to define the complexation site on nitrogen atom. The large set of spectral parameters: chemical shifts, homo- and heteronuclear coupling constants, were used in structure study.

  6. Li NMR study of heavy-fermion LiV2O4 containing magnetic defects

    SciTech Connect

    Zong, X.; Das, S.; Borsa, F.; Vannette, M.; Prozorov, R.; Schmalian, J.; Johnston, D.

    2008-04-21

    We present a systematic study of the variations of the {sup 7}Li NMR properties versus magnetic defect concentration up to 0.83 mol% within the spinel structure of polycrystalline powder samples and a collection of small single crystals of LiV2O4 in the temperature range from 0.5 to 4.2 K. We also report static magnetization measurements and ac magnetic susceptibility measurements at 14 MHz on the samples at low temperatures. Both the NMR spectrum and nuclear spin-lattice relaxation rate are inhomogeneous in the presence of the magnetic defects. The NMR data for the powders are well explained by assuming that (i) there is a random distribution of magnetic point defects, (ii) the same heavy Fermi liquid is present in the samples containing the magnetic defects as in magnetically pure LiV2O4, and (iii) the influences of the magnetic defects and of the Fermi liquid on the magnetization and NMR properties are separable. In the single crystals, somewhat different behaviors are observed. Remarkably, the magnetic defects in the powder samples show evidence of spin freezing below T {approx} 1.0 K, whereas in the single crystals with similar magnetic defect concentration no spin freezing was found down to 0.5 K. Thus different types of magnetic defects and/or interactions between them appear to arise in the powders versus the crystals, possibly due to the substantially different synthesis conditions of the powders and crystals.

  7. {sup 1}H NMR spectroscopic studies establish that heparanase is a retaining glycosidase

    SciTech Connect

    Wilson, Jennifer C.; Laloo, Andrew Elohim; Singh, Sanjesh; Ferro, Vito

    2014-01-03

    Highlights: •{sup 1}H and {sup 13}C NMR chemical shifts of fondaparinux were fully assigned by 1D and 2D NMR techniques. •Hydrolysis of fondaparinux by heparanase was monitored by {sup 1}H NMR spectroscopy. •Heparanase is established to be a retaining glycosidase. -- Abstract: Heparanase is an endo-β-glucuronidase that cleaves heparan sulfate side chains of proteoglycans in basement membranes and the extracellular matrix (ECM). Heparanase is implicated in several diverse pathological processes associated with ECM degradation such as metastasis, inflammation and angiogenesis and is thus an important target for anti-cancer and anti-inflammatory drug discovery. Heparanase has been classed as belonging to the clan A glycoside hydrolase family 79 based on sequence analysis, secondary structure predictions and mutagenic analysis, and thus it has been inferred that it is a retaining glycosidase. However, there has been no direct experimental evidence to support this conclusion. Herein we describe {sup 1}H NMR spectroscopic studies of the hydrolysis of the pentasaccharide substrate fondaparinux by heparanase, and provide conclusive evidence that heparanase hydrolyses its substrate with retention of configuration and is thus established as a retaining glycosidase. Knowledge of the mechanism of hydrolysis may have implications for future design of inhibitors for this important drug target.

  8. Molecular ordering of mixed surfactants in mesoporous silicas: A solid-state NMR study

    SciTech Connect

    Kobayashi, Takeshi; Mao, Kanmi; Wang, Shy-Guey; Lin, Victor S.-Y.; Pruski, Marek

    2011-02-17

    The use of mixed surfactants in the synthesis of mesoporous silica nanoparticles (MSNs) is of importance in the context of adjusting pore structures, sizes and morphologies. In the present study, the arrangement of molecules in micelles produced from a mixture of two surfactants, cetyltrimethylammonium bromide (CTAB) and cetylpyridinium bromide (CPB) was detailed by solid-state NMR spectroscopy. Proximities of methyl protons in the trimethylammonium headgroup of CTAB and protons in the pyridinium headgroup of CPB were observed under fast magic angle spinning (MAS) by {sup 1}H-{sup 1}H double quantum (DQ) MAS NMR and NOESY. This result suggested that CTAB and CPB co-exist in the pores without forming significant monocomponent domain structures. {sup 1}H-{sup 29}Si heteronuclear correlation (HETCOR) NMR showed that protons in the headgroups of CTAB are in closer proximity to the silica surface than those in the CPB headgroups. The structural information obtained in this investigation leads to better understanding of the mechanisms of self-assembly and their role in determining the structure and morphology of mesoporous materials.

  9. 1H NMR spectroscopic and quantum chemical studies on a poly(ester amide) model compound: Nalpha-benzoyl-L-argininate ethyl ester chloride. Structural preferences for the isolated molecule and in solution.

    PubMed

    Fonseca, A C; Jarmelo, S; Carvalho, R A; Fausto, R; Gil, M H; Simões, P N

    2010-05-13

    The molecular structure of the L-arginine derivative, N(alpha)-benzoyl-L-argininate ethyl ester chloride (BAEEH(+).Cl(-)), was characterized by combining quantum chemical methods and (1)H NMR spectroscopy. A conformational search on the potential energy surfaces of the three lowest-energy tautomers of BAEEH(+) [A: R-N(+)H=(NH(2))(2); B: R-NH-C(=NH)N(+)H(3); C: R-N(+)H(2)-C(=NH)NH(2); R = C(6)H(5)C(=O)NH-CH(COOCH(2)CH(3))CH(2)CH(2)CH(2)-] was carried out using the semiempirical PM3 method. The lowest-energy conformations obtained using this method were then optimized at the DFT(B3LYP)/6-31++G(d,p) level of theory. For all tautomers, it was found that all low-energy conformers present folded structures, in which a H-bond interaction between the guanidinium group and the amide carbonyl oxygen atom appears to be the most relevant stabilizing factor. (1)H NMR spectra of BAEEH(+).Cl(-) in DMF-D(7) were acquired in the temperature range [-55 to 75 degrees C], providing information about the rotational motions in the guanidinium group and showing that the tautomeric form of BAEEH(+) that exists in solution is tautomer A. The interpretation of the experimental findings was supported by (1)H NMR chemical shifts obtained theoretically at the DFT(B3LYP)/6-31++G(d,p) level of approximation, using both the polarized continuum model and a BAEEH(+)-water complex model.

  10. A novel one-pot synthesis of heterocyclic compound (4-benzoyl-5-phenyl-2-(pyridin-2-yl)-3,3a-dihydropyrazolo[1,5-c]pyrimidin-7(6H)-one): Structural (X-ray and DFT) and spectroscopic (FT-IR, NMR, UV-Vis and Mass) characterization Studies

    NASA Astrophysics Data System (ADS)

    Özdemir, Mecit; Sönmez, Mehmet; Şen, Fatih; Dinçer, Muharrem; Özdemir, Namık

    2015-02-01

    In this study, the title compound named as 4-benzoyl-5-phenyl-2-(pyridin-2-yl)-3,3a-dihydropyrazolo[1,5-c]pyrimidin-7(6H)-one (C24H18N4O2) was both experimentally and theoretically investigated. The compound was synthesized and characterized by FT-IR, NMR (1H NMR, 13C NMR and HETCOR-NMR), Mass spectroscopies and single-crystal X-ray diffraction methods. The compound crystallizes in the monoclinic space group P21/n with a = 6.1402 (3) Å, b = 21.4470 (15) Å, c = 15.0049 (8) Å and β = 97.407 (4)°. The molecular geometry was obtained from the X-ray structure determination optimized using density functional theory (DFT/B3LYP) method with the 6-31+G(d, p) basis set in ground state. From the optimized structure, geometric parameters, vibrational wavenumbers and chemical shifts of molecule were obtained. Experimental measurements were compared with its corresponding the calculated data. An excellent harmony between the two data was ascertained. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs) and non-linear optical (NLO) properties of the title molecule were investigated by theoretical calculations at the B3LYP/6-31+G(d, p) level.

  11. Structure determination of a partially ordered layered silicate material with an NMR crystallography approach.

    PubMed

    Brouwer, Darren Henry; Cadars, Sylvian; Hotke, Kathryn; Van Huizen, Jared; Van Huizen, Nicholas

    2017-03-01

    Structure determination of layered materials can present challenges for conventional diffraction methods due to the fact that such materials often lack full three-dimensional periodicity since adjacent layers may not stack in an orderly and regular fashion. In such cases, NMR crystallography strategies involving a combination of solid-state NMR spectroscopy, powder X-ray diffraction, and computational chemistry methods can often reveal structural details that cannot be acquired from diffraction alone. We present here the structure determination of a surfactant-templated layered silicate material that lacks full three-dimensional crystallinity using such an NMR crystallography approach. Through a combination of powder X-ray diffraction and advanced (29)Si solid-state NMR spectroscopy, it is revealed that the structure of the silicate layer of this layered silicate material templated with cetyltrimethylammonium surfactant cations is isostructural with the silicate layer of a previously reported material referred to as ilerite, octosilicate, or RUB-18. High-field (1)H NMR spectroscopy reveals differences between the materials in terms of the ordering of silanol groups on the surfaces of the layers, as well as the contents of the inter-layer space.

  12. Polyoxomolybdate promoted hydrolysis of a DNA-model phosphoester studied by NMR and EXAFS spectroscopy.

    PubMed

    Absillis, Gregory; Van Deun, Rik; Parac-Vogt, Tatjana N

    2011-11-21

    Hydrolysis of (p-nitrophenyl)phosphate (NPP), a commonly used phosphatase model substrate, was examined in molybdate solutions by means of (1)H, (31)P, and (95)Mo NMR spectroscopy and Mo K-edge Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. At 50 °C and pD 5.1 the cleavage of the phosphoester bond in NPP proceeds with a rate constant of 2.73 × 10(-5) s(-1) representing an acceleration of nearly 3 orders of magnitude as compared to the hydrolysis measured in the absence of molybdate. The pD dependence of k(obs) exhibits a bell-shaped profile, with the fastest cleavage observed in solutions where [Mo(7)O(24)](6-) is the major species in solution. Mixing of NPP and [Mo(7)O(24)](6-) resulted in formation of these two intermediate complexes that were detected by (31)P NMR spectroscopy. Complex A was characterized by a (31)P NMR resonance at -4.27 ppm and complex B was characterized by a (31)P NMR resonance at -7.42 ppm. On the basis of the previous results from diffusion ordered NMR spectroscopy, performed with the hydrolytically inactive substrate phenylphosphonate (PhP), the structure of these two complexes was deduced to be (NPP)(2)Mo(5)O(21)(4-) (complex A) and (NPP)(2)Mo(12)O(36)(H(2)O)(6)(4-) (complex B). The pH studies point out that both complexes are hydrolytically active and lead to the hydrolysis of phosphoester bond in NPP. The NMR spectra did not show evidence of any paramagnetic species, excluding the possibility of Mo(VI) reduction to Mo(V), and indicating that the cleavage of the phosphomonoester bond is purely hydrolytic. The Mo K-edge XANES region also did not show any sign of Mo(VI) to Mo(V) reduction during the hydrolytic reaction. (95)Mo NMR and Mo K-edge EXAFS spectra measured during different stages of the hydrolytic reaction showed a gradual disappearance of [Mo(7)O(24)](6-) during the hydrolytic reaction and appearance of [P(2)Mo(5)O(23)](6-), which was the final complex observed at the end of hydrolytic reaction.

  13. Tricritical point in ferroelastic ammonium titanyl fluoride: NMR study

    SciTech Connect

    Kavun, V.Ya.; Kozlova, S.G.; Laptash, N.M; Tkachenko, I.A.; Gabuda, S.P

    2010-09-15

    Ionic mobility and phase transitions in ammonium titanyl pentafluoride (NH{sub 4}){sub 3}TiOF{sub 5} were studied using the {sup 19}F and {sup 1}H NMR data. The high-temperature phase (I) is characterized by spherically symmetric (isotropic) reorientation of [TiOF{sub 5}]{sup 3-} anions and by uniaxial reorientation of these anions in the ferroelastic phase II. A previously unknown second-order phase transition to the low-temperature modification (NH{sub 4}){sub 3}TiOF{sub 5}(III) was found at 205 K. The transition is accompanied by hindering of uniaxial rotations of [TiOF{sub 5}]{sup 3-} anions and by noticeable change of {sup 19}F magnetic shielding tensor associated with the influence of pseudo-Jahn-Teller effect. A pressure-induced tricritical point with coordinates p{sub TCR{approx}}2 kbar and T{sub TCR{approx}}170 K is estimated on the base of {sup 19}F NMR chemical shift data, and previously studied p-T diagram of (NH{sub 4}){sub 3}TiOF{sub 5}. - Graphical abstract: p-T phase diagram of (NH{sub 4}){sub 3}TiOF{sub 5}.

  14. Synthesis, crystal structure analysis, spectral IR, NMR UV-Vis investigations, NBO and NLO of 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide with use of X-ray diffractions studies along with DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Sarioğlu, Ahmet Oral; Güler, Semih; Dege, Necmi; Sönmez, Mehmet

    2016-08-01

    The title compound, 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide compound (C22H16NO3Cl) has been synthesized and characterized by X-ray diffraction, IR, 1H and 13C NMR and UV-Vis spectra. Optimized geometrical structure, harmonic vibrational frequencies and chemical shifts were computed using hybrid-DFT (B3LYP and B3PW91) methods and 6-311G(d,p) as the basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The calculated optimized geometries, vibrational frequencies and 1H NMR chemical shift values are in strong agreement with experimentally measured values. UV-Vis spectrum of the title compound, was also recorded and the electronic properties, such as calculated energies, excitation energies, oscillator strengths, dipole moments and frontier orbital energies and band gap energies were computed with TDDFT-B3LYP methodolgy and using 6-311G(d,p) as the basis set. Furthermore, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), natural bond orbital (NBO) and non linear optical (NLO) properties were performed by using B3LYP/6-311G(d,p) level for the title compound.

  15. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.

    PubMed

    Kassem, Maher M; Wang, Yong; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2016-06-07

    Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.

  16. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

    PubMed

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

    2010-12-08

    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

  17. Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

    PubMed

    Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

    2017-01-31

    Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level.

  18. Entangled Polymer Melt Dynamics Studied By Low-Field NMR

    NASA Astrophysics Data System (ADS)

    Vaca Chavez, Fabian; Huebsch, Patrick; Zirbs, Ronald; Binder, Wolfgang; Saalwaechter, Kay

    2009-03-01

    Proton Multiple-Quantum (MQ) NMR is a powerful technique to investigate polymer dynamics due to its sensitivity to molecular motions on very different timescales. Entangled melts exhibit dynamic processes that cover a wide range of timescales, starting from fast ps-scale segmental reorientation up to diffusive and cooperative motions on the ms-s-scale. In this work, we apply MQ NMR to linear poly(cis-1,4-isoprene) and poly(isobutylene) of different molecular weight above the glass transition over suitable ranges of temperature, in order to establish the dynamic regimes predicted by the tube model, and, for the first time, to extract actual time scale information. This directly complements many neutron scattering studies, which are restricted to the sub-μs-timescale. Measurements on PIB-grafted silica particles with different molecular weights and different chain densities on the surface of the particle are also shown. The data is analyzed by establishing scaling laws which can be directly associated with different dynamic regimes predicted by the tube/reptation model. Full analytical analyses based on a correlation function which explicitly includes segmental, Rouse, and reptation dynamics are discussed.

  19. 13C NMR study of halogen bonding of haloarenes: measurements of solvent effects and theoretical analysis.

    PubMed

    Glaser, Rainer; Chen, Naijun; Wu, Hong; Knotts, Nathan; Kaupp, Martin

    2004-04-07

    Solvent effects on the NMR spectra of symmetrical (X = F (1), X = Cl (2), X = Br (3), X = I (4), X = NO2 (5), X = CN (6)) and unsymmetrical (X = I, Y = MeO (7), Y = PhO (8)) para-disubstituted acetophenone azines X-C6H4-CMe=N-N=CMe-C6H4-Y and of models X-C6H4-CMe=N-Z (X = I, Z = H (9), Z = NH2 (10)), 4-iodoacetophenone (11), and iodobenzene (12) were measured in CDCl(3), DMSO, THF, pyridine, and benzene to address one intramolecular and one intermolecular issue. Solvent effects on the (13)C NMR spectra are generally small, and this finding firmly establishes that the azine bridge indeed functions as a "conjugation stopper," an important design concept in our polar materials research. Since intermolecular halogen bonding of haloarenes do occur in polar organic crystalline materials, the NMR solution data pose the question as to whether the absence of solvent shifts indicates the absence of strong halogen bonding in solution. This question was studied by the theoretical analysis of the DMSO complexes of iodoarenes 4, 9-12, and of iodoacetylene. DFT and MP2 computations show iodine bonding, and characteristic structural and electronic features are described. The nonrelativistic complexation shifts and the change in the spin-orbit induced heavy atom effect of iodine compensate each other, and iodine bonding thus has no apparent effect on Ci in the iodoarenes. For iodides, complexation by DMSO occurs and may or may not manifest itself in the NMR spectra. The absence of complexation shifts in the NMR spectra of halides does not exclude the occurrence of halogen bonding in solution.

  20. Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization.

    PubMed

    Tong, Yan; Ji, Chang G; Mei, Ye; Zhang, John Z H

    2009-06-24

    Molecular dynamics simulations of NMR backbone relaxation order parameters have been carried out to investigate the polarization effect on the protein's local structure and dynamics for five benchmark proteins (bovine pancreatic trypsin inhibitor, immunoglobulin-binding domain (B1) of streptococcal protein G, bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and hen egg white lysozyme). In order to isolate the polarization effect from other interaction effects, our study employed both the standard AMBER force field (AMBER03) and polarized protein-specific charges (PPCs) in the MD simulations. The simulated order parameters, employing both the standard nonpolarizable and polarized force fields, are directly compared with experimental data. Our results show that residue-specific order parameters at some specific loop and turn regions are significantly underestimated by the MD simulations using the standard AMBER force field, indicating hyperflexibility of these local structures. Detailed analysis of the structures and dynamic motions of individual residues reveals that the hyperflexibility of these local structures is largely related to the breaking or weakening of relevant hydrogen bonds. In contrast, the agreement with the experimental results is significantly improved and more stable local structures are observed in the MD simulations using the polarized force field. The comparison between theory and experiment provides convincing evidence that intraprotein hydrogen bonds in these regions are stabilized by electronic polarization, which is critical to the dynamical stability of these local structures in proteins.

  1. NMR-based structural modeling of graphite oxide using multidimensional 13C solid-state NMR and ab initio chemical shift calculations.

    PubMed

    Casabianca, Leah B; Shaibat, Medhat A; Cai, Weiwei W; Park, Sungjin; Piner, Richard; Ruoff, Rodney S; Ishii, Yoshitaka

    2010-04-28

    Chemically modified graphenes and other graphite-based materials have attracted growing interest for their unique potential as lightweight electronic and structural nanomaterials. It is an important challenge to construct structural models of noncrystalline graphite-based materials on the basis of NMR or other spectroscopic data. To address this challenge, a solid-state NMR (SSNMR)-based structural modeling approach is presented on graphite oxide (GO), which is a prominent precursor and interesting benchmark system of modified graphene. An experimental 2D (13)C double-quantum/single-quantum correlation SSNMR spectrum of (13)C-labeled GO was compared with spectra simulated for different structural models using ab initio geometry optimization and chemical shift calculations. The results show that the spectral features of the GO sample are best reproduced by a geometry-optimized structural model that is based on the Lerf-Klinowski model (Lerf, A. et al. Phys. Chem. B 1998, 102, 4477); this model is composed of interconnected sp(2), 1,2-epoxide, and COH carbons. This study also convincingly excludes the possibility of other previously proposed models, including the highly oxidized structures involving 1,3-epoxide carbons (Szabo, I. et al. Chem. Mater. 2006, 18, 2740). (13)C chemical shift anisotropy (CSA) patterns measured by a 2D (13)C CSA/isotropic shift correlation SSNMR were well reproduced by the chemical shift tensor obtained by the ab initio calculation for the former model. The approach presented here is likely to be applicable to other chemically modified graphenes and graphite-based systems.

  2. Pulsed NMR study of the curing process of epoxy resin.

    PubMed

    Kimoto, Hiroki; Tanaka, Chikako; Yaginuma, Michiko; Shinohara, Emi; Asano, Atsushi; Kurotsu, Takuzo

    2008-07-01

    To analyze a curing process of epoxy resin in terms of molecular motion, we adapted a pulsed NMR method. Three kinds of (1)H spin-spin relaxation times (T(2L) (long), T(2S) (short) and T(2M) (intermediate)) were estimated from observed solid echo train signals as the curing process proceeded. A short T(2S) value below 20 micros suggests the existence of a motion-restricted chain, that is, cured elements of resin, and its fraction, P(S), sigmoidally increased with the curing time. On the other hand, the fraction of T(2L), P(L), decreased with the reaction time reciprocally against P(S), suggesting the disappearance of highly mobile molecules raised from pre-cured resin. The spin-lattice relaxation time, T(1), was also measured to check another aspect of molecular motion in the process. T(1) of the mixed epoxy resin and curing agent gradually increased just after mixing both of them. This corresponds to an increment of a less-mobile fraction, of which the correction time is more than 10(-6) s, and also means that the occurrence of a network structure whose mobility is strongly restricted by chemically bonded bridges between the epoxy resin and curing agent. The time courses of these parameters coincided with those of IR peaks pertinent to the curing reaction. Therefore, pulsed NMR is a useful tool to monitor the hardening process of epoxy resin in real time non-distractively in terms of the molecular motion of protons.

  3. High-resolution (19)F MAS NMR spectroscopy: structural disorder and unusual J couplings in a fluorinated hydroxy-silicate.

    PubMed

    Griffin, John M; Yates, Jonathan R; Berry, Andrew J; Wimperis, Stephen; Ashbrook, Sharon E

    2010-11-10

    High-resolution (19)F magic angle spinning (MAS) NMR spectroscopy is used to study disorder and bonding in a crystalline solid. (19)F MAS NMR reveals four distinct F sites in a 50% fluorine-substituted deuterated hydrous magnesium silicate (clinohumite, 4Mg(2)SiO(4)·Mg(OD(1-x)F(x))(2) with x = 0.5), indicating extensive structural disorder. The four (19)F peaks can be assigned using density functional theory (DFT) calculations of NMR parameters for a number of structural models with a range of possible local F environments generated by F(-)/OH(-) substitution. These assignments are supported by two-dimensional (19)F double-quantum MAS NMR experiments that correlate F sites based on either spatial proximity (via dipolar couplings) or through-bond connectivity (via scalar, or J, couplings). The observation of (19)F-(19)F J couplings is unexpected as the fluorines coordinate Mg atoms and the Mg-F interaction is normally considered to be ionic in character (i.e., there is no formal F-Mg-F covalent bonding arrangement). However, DFT calculations predict significant (19)F-(19)F J couplings, and these are in good agreement with the splittings observed in a (19)F J-resolved MAS NMR experiment. The existence of these J couplings is discussed in relation to both the nature of bonding in the solid state and the occurrence of so-called "through-space" (19)F-(19)F J couplings in solution. Finally, we note that we have found similar structural disorder and spin-spin interactions in both synthetic and naturally occurring clinohumite samples.

  4. Cu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR.

    PubMed

    Seebald, Leah M; DeMott, Christopher M; Ranganathan, Srivathsan; Asare Okai, Papa Nii; Glazunova, Anastasia; Chen, Alan; Shekhtman, Alexander; Royzen, Maksim

    2017-04-03

    Paramagnetic NMR techniques allow for studying three-dimensional structures of RNA-protein complexes. In particular, paramagnetic relaxation enhancement (PRE) data can provide valuable information about long-range distances between different structural components. For PRE NMR experiments, oligonucleotides are typically spin-labeled using nitroxide reagents. The current work describes an alternative approach involving a Cu(II) cyclen-based probe that can be covalently attached to an RNA strand in the vicinity of the protein's binding site using "click" chemistry. The approach has been applied to study binding of HIV-1 nucleocapsid protein 7 (NCp7) to a model RNA pentanucleotide, 5'-ACGCU-3'. Coordination of the paramagnetic metal to glutamic acid residue of NCp7 reduced flexibility of the probe, thus simplifying interpretation of the PRE data. NMR experiments showed attenuation of signal intensities from protein residues localized in proximity to the paramagnetic probe as the result of RNA-protein interactions. The extent of the attenuation was related to the probe's proximity allowing us to construct the protein's contact surface map.

  5. Cd(II) and Zn(II) complexes of two new hexadentate Schiff base ligands derived from different aldehydes and ethanol amine; X-ray crystal structure, IR and NMR spectroscopy studies

    NASA Astrophysics Data System (ADS)

    Golbedaghi, Reza; Rezaeivala, Majid; Albeheshti, Leila

    2014-11-01

    Four new [Cd(H2L1)(NO3)]ClO4 (1), [Zn(H2L1)](ClO4)2 (2), [Cd(H2L2)(NO3)]ClO4 (3), and [Zn(H2L2)](ClO4)2 (4), complexes were prepared by the reaction of two new Schiff base ligands and Cd(II) and Zn(II) metal ions in equimolar ratios. The ligands H2L1 and H2L2 were synthesized by reaction of 2-[2-(2-formyl phenoxy)ethoxy]benzaldehyde and/or 2-[2-(3-formyl phenoxy)propoxy]benzaldehyde and ethanol amine and characterized by IR, 1H and 13C NMR spectroscopy. All complexes were characterized by IR, 1H and 13C NMR, COSY, and elemental analysis. Also, the complex 1 was characterized by X-ray in addition to the above methods. The X-ray crystal structure of compound 1 showed that all nitrogen and oxygen atoms of ligand (N2O4) and a molecule of nitrate with two donor oxygen atom have been coordinated to the metal ion and the Cd(II) ion is in an eight-coordinate environment that is best described as a distorted dodecahedron geometry.

  6. Synthesis, characterization and spectroscopy studying of some metal complexes of a new Schiff base ligand; X-ray crystal structure, NMR and IR investigation of a new dodecahedron Cd(II) complex

    NASA Astrophysics Data System (ADS)

    Golbedaghi, Reza; Rezaeivala, Majid; Khalili, Maryam; Notash, Behrouz; Karimi, Javad

    2016-12-01

    Some new [Cd(H2L1)(NO3)]ClO4 (1), [Mn(H2L1)](ClO4)2 (2), [Ni(H2L1)](ClO4)2 (3) and [Cu(H2L1)](ClO4)2 (4) complexes were prepared by the reaction of a Schiff base ligand and M (II) metal ions in equimolar ratios (M = Cd, Mn, Ni and Cu). The ligand H2L1 was synthesized by reaction of 2-[2-(3-formyl phenoxy)propoxy]benzaldehyde and ethanol amine and characterized by IR, 1H,13C NMR spectroscopy and elemental analysis. The synthesized complexes were characterized with IR and elemental analysis in all cases and 1H, 13C NMR, and X-ray in the case of Cd(II) complex. The X-ray crystal structure of compound 1 showed that all nitrogen and oxygen atoms of Schiff base ligand (N2O4) and a molecule of nitrate with two donor oxygen atom have been coordinated to the metal ion and the Cd(II) ion is in an eight-coordinate environment that is best described as a distorted dodecahedron geometry.

  7. NMR Studies on the Aqueous Phase Photochemical Degradation of TNT

    SciTech Connect

    Thorn, Kevin A.; Cox, Larry G.

    2008-04-06

    Aqueous phase photochemical degradation of 2,4,6-trinitrotoluene (TNT) is an important pathway in several environments, including washout lagoon soils, impact craters from partially detonated munitions that fill with rain or groundwater, and shallow marine environments containing unexploded munitions that have corroded. Knowledge of the degradation products is necessary for compliance issues on military firing ranges and formerly used defense sites. Previous laboratory studies have indicated that UV irradiation of aqueous TNT solutions results in a multicomponent product mixture, including polymerization compounds, that has been only partially resolved by mass spectrometric analyses. This study illustrates how a combination of solid and liquid state 1H, 13C, and 15N NMR spectroscopy, including two dimensional analyses, provides complementary information on the total product mixture from aqueous photolysis of TNT, and the effect of reaction conditions. Among the degradation products detected were amine, amide, azoxy, azo, and carboxylic acid compounds.

  8. Unilateral NMR study of a XVI century wall painted

    NASA Astrophysics Data System (ADS)

    Proietti, N.; Capitani, D.; Rossi, E.; Cozzolino, S.; Segre, A. L.

    2007-06-01

    Wall paintings in the XVI century Serra Chapel in the "Chiesa di Nostra Signora del Sacro Cuore" Rome, have been studied using unilateral NMR. In order to map the distribution of moisture content in the wall painted, a large number of Hahn echo measurements, covering large areas of the wall painting were performed. Because the intensity of the Hahn echo is proportional to the amount of moisture in the area under study, the experimental data were transformed into 2D gradient colour maps which allowed an easy visualization of the moisture content of the wall. The state of conservation of the wall painting was monitored using T2 measurements specially with regards to outcropping salt.

  9. Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

    PubMed Central

    Horst, Reto; Wider, Gerhard; Fiaux, Jocelyne; Bertelsen, Eric B.; Horwich, Arthur L.; Wüthrich, Kurt

    2006-01-01

    The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution. PMID:17032756

  10. Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

    NASA Astrophysics Data System (ADS)

    Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

    2016-06-01

    In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

  11. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  12. Solid state NMR and IR characterization of wood polymer structure in relation to tree provenance.

    PubMed

    Santoni, Ilaria; Callone, Emanuela; Sandak, Anna; Sandak, Jakub; Dirè, Sandra

    2015-03-06

    (13)C nuclear magnetic resonance and mid-infrared spectroscopies were used for characterizing changes in the chemical structure of wood polymers (cellulose, hemicellulose and lignin) in relation to the tree growth location. Samples of three provenances in Europe (Finland, Poland and Italy) were selected for studies. The requirement was to use untreated solid wood samples to minimize any manipulation to the nanostructure of native wood. The results confirm that the chemical and physical properties of samples belonging to the same wood species (Picea abies Karst.) differ due to the origin. Both FT-IR and dynamic NMR spectroscopies were able to correctly discriminate samples originating from three different provenances in Europe. Such methods might be very useful for both, research and understanding of wood microstructure and its variability due to the growth conditions.

  13. Investigation of Local Structures in Layered Niobates by Solid-state NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Ting

    Research on ion-exchangeable layered niobates has attracted great attention due to their unique structures and corresponding variations in properties and applications, such as ion conductors, solid acids, and water splitting catalysts. Families of layered niobates include double-layered or triple-layered Dion-Jacobson type perovskites (ALaNb2O7, A = Cs, Rb, K, H; AM2Nb3O10, A = Rb, K, H; M = Sr, Ca), layered niobates with both edge and corner sharing of NbO6 octahedra (KNb3O8, HNb3O6, Nb 6O17 and H4Nb6O17) and many others. Lately, more developments in the layered niobates through a variety of topochemical manipulations have been achieved. The topochemical reactions include ion exchange, exfoliation, substitution, and etc. As a result, many new materials have been successfully prepared, for example, solid solutions (ALa2NbTi2O10, ACaLaNb2TiO 10 and ACa2Nb3-xTaxO10, etc.), nanosheets (HNb3O8, H4Nb6O17, HLaNb2O7, HCa2Nb3O10, etc., to intercalate with organic molecules such as tetrabutylammonium hydroxide or n-butylamines), and nanoscrolls (from H2K2Nb 6O17). While these structural modifications often induce improvements in properties, the fundamental mechanisms of improvements in properties upon the modifications, especially local structural arrangements are poorly understood, which is often limited by structural characterizations. Particularly, the characterizations of the exfoliated nanosheets can be difficult by conventional X-ray diffraction (XRD) method due to disordered structures. Alternatively, solid-state nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study local structures in solids. The structural information can be extracted by examining intrinsic interactions, such as quadrupolar, chemical shielding, and dipolar interactions, which are all associated with local environments surrounding a specific nucleus, 1H or 93Nb in layered niobates. The ultimate goal of this dissertation is to understand the relationships between local structures of

  14. /sup 13/C NMR studies of the molecular flexibility of antidepressants

    SciTech Connect

    Munro, S.L.; Andrews, P.R.; Craik, D.J.; Gale, D.J.

    1986-02-01

    The solution dynamics of a series of clinically potent antidepressants have been investigated by measuring /sup 13/C NMR relaxation parameters. Correlation times and internal motional rates were calculated from spin-lattice relaxation times and nuclear Overhauser effects for the protonated carbons in mianserin, imipramine-like antidepressants, and amitriptyline-like antidepressants. These data were interpreted in terms of overall molecular tumbling, internal rotations, and inherent flexibility of these structures. Of particular interest was the conformational variability of the tricyclic nucleus of the tricyclic antidepressants, where the data indicated a fivefold difference in mobility of the dimethylene bridge of imipramine-like antidepressants relative to amitriptyline-like compounds. The implications of such a difference in internal motions is discussed in relation to previous NMR studies and to the reported differences in pharmacological activity of these antidepressants.

  15. Synthesis of 24-phenyl-24-oxo steroids derived from bile acids by palladium-catalyzed cross coupling with phenylboronic acid. NMR characterization and X-ray structures.

    PubMed

    Mayorquín-Torres, Martha C; Romero-Ávila, Margarita; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

    2013-11-01

    Palladium-catalyzed cross coupling of phenyboronic acid with acetylated bile acids in which the carboxyl functions have been activated by formation of a mixed anhydride with pivalic anhydride afforded moderate to good yield of 24-phenyl-24-oxo-steroids. Unambiguous assignments of the NMR signals were made with the aid of combined 1D and 2D NMR techniques. X-ray diffraction studies confirmed the obtained structures.

  16. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    PubMed

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  17. NMR Solution Structure of a Cyanovirin Homolog from Wheat Head Blight Fungus

    PubMed Central

    Matei, Elena; Louis, John M.; Jee, JunGoo; Gronenborn, Angela M.

    2011-01-01

    Members of the cyanovirin-N homolog (CVNH) lectin family are found in bacteria, fungi and plants. As part of our ongoing work on CVNH structure-function studies, we determined the high-resolution NMR solution structure of the homolog from the wheat head blight disease causing ascomycetous fungus Gibberella zeae (or Fusarium graminearum), hereafter called GzCVNH. Like cyanovirin-N (CV-N), GzCVNH comprises two tandem sequence repeats and the protein sequence exhibits 30% identity with CV-N. The overall structure is similar to those of other members of the CVNH family, with the conserved pseudo-symmetric halves of the structure, domains A and B, closely resembling recently determined structures of Tuber borchii, Neurospora crassa and Ceratopteris richardii CVNH proteins. Although GzCVNH exhibits a similar glycan recognition profile to CV-N and specifically binds to Manα(1–2)Manα, its weak carbohydrate binding affinity to only one binding site is insufficient for conferring anti-HIV activity. PMID:21365681

  18. Ion transport in porous media studied by NMR.

    PubMed

    Pel, L; Huinink, H P; Kopinga, K; Rijniers, L A; Kaasschieter, E F

    2001-01-01

    Moisture and salt transport in masonry can give rise to damages. Therefore a detailed knowledge of the moisture and salt transport is essential for understanding the durability of masonry. A special NMR apparatus has been made allowing quasi-simultaneous measurements of both moisture and Na profiles in porous building materials. Using this apparatus both the absorption of a 4 M NaCl solution in a calcium silicate brick and the drying of a 3 M NaCl capillary saturated fired-clay brick have been studied. It was found that during the absorption process the Na ions clearly stay behind, which this is caused by adsorption of these ions to the pore surface. For the drying it was found that at the beginning of the drying process the ions accumulate near the surface. As the drying rate decreases, diffusion becomes dominant and the ion profile levels off again.

  19. ¹H NMR and hyperpolarized ¹³C NMR assays of pyruvate-lactate: a comparative study.

    PubMed

    Hill, Deborah K; Jamin, Yann; Orton, Matthew R; Tardif, Nicolas; Parkes, Harold G; Robinson, Simon P; Leach, Martin O; Chung, Yuen-Li; Eykyn, Thomas R

    2013-10-01

    Pyruvate-lactate exchange is mediated by the enzyme lactate dehydrogenase (LDH) and is central to the altered energy metabolism in cancer cells. The measurement of exchange kinetics using hyperpolarized (13) C NMR has provided a biomarker of response to novel therapeutics. However, the observable signal is restricted to the exchanging hyperpolarized (13) C pools and the endogenous pools of (12) C-labelled metabolites are invisible in these measurements. In this study, we investigated an alternative in vitro (1) H NMR assay, using [3-(13) C]pyruvate, and compared the measured kinetics with a hyperpolarized (13) C NMR assay, using [1-(13) C]pyruvate, under the same conditions in human colorectal carcinoma SW1222 cells. The apparent forward reaction rate constants (kPL ) derived from the two assays showed no significant difference, and both assays had similar reproducibility (kPL  = 0.506 ± 0.054 and kPL  = 0.441 ± 0.090 nmol/s/10(6) cells; mean ± standard deviation; n = 3); (1) H, (13) C assays, respectively). The apparent backward reaction rate constant (kLP ) could only be measured with good reproducibility using the (1) H NMR assay (kLP  = 0.376 ± 0.091 nmol/s/10(6) cells; mean ± standard deviation; n = 3). The (1) H NMR assay has adequate sensitivity to measure real-time pyruvate-lactate exchange kinetics in vitro, offering a complementary and accessible assay of apparent LDH activity.

  20. Structural Isomer Identification via NMR: A Nuclear Magnetic Resonance Experiment for Organic, Analytical, or Physical Chemistry.

    ERIC Educational Resources Information Center

    Szafran, Zvi

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment that examines the ability of nuclear magnetic resonance (NMR) to distinguish between structural isomers via resonance multiplicities and chemical shifts. Reasons for incorporating the experiment into organic, analytical, or physical chemistry…

  1. Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

    PubMed

    Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

    2015-10-06

    Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure.

  2. Structure elucidation and NMR assignments of two unusual monoterpene indole alkaloids from Psychotria stachyoides.

    PubMed

    Pimenta, Antonia Torres Avila; Braz-Filho, Raimundo; Delprete, Piero Giuseppe; de Souza, Elnatan Bezerra; Silveira, Edilberto Rocha; Lima, Mary Anne Sousa

    2010-09-01

    Two unusual monoterpene indole alkaloids, stachyoside (1) and nor-methyl-23-oxo-correantoside (2), have been isolated from the aerial parts of Psychotria stachyoides. The structural elucidation of both compounds was performed by the aid of HRESIMS, FT-IR, and 1D- and 2D-NMR techniques including COSY, HSQC, HMBC, and NOESY.

  3. Ultra-broadband NMR probe: numerical and experimental study of transmission line NMR probe.

    PubMed

    Kubo, Atsushi; Ichikawa, Shinji

    2003-06-01

    We have reinvestigated a transmission line NMR probe first published by Lowe and co-workers in 1970s [Rev. Sci. Instrum. 45 (1974) 631; 48 (1977) 268] numerically and experimentally. The probe is expected to be ultra-broadband, thus might enable new types of solid-state NMR experiments. The NMR probe consists of a coil and capacitors which are connected to the coil at regular intervals. The circuit is the same as a cascaded LC low-pass filter, except there are nonzero mutual inductances between different coil sections. We evaluated the mutual inductances by Neumann's formula and calculated the electrical characteristics of the probe as a function of a carrier frequency. We found that they were almost the same as those of a cascaded LC low-pass filter, when the inductance L of a section was estimated from the inductance of the whole coil divided by the number of the sections, and if C was set to the capacitance in a section. For example, the characteristic impedance of a transmission line coil is given by Z=(L/C)(1/2). We also calculated the magnitude and the distribution of RF magnetic field inside the probe. The magnitude of RF field decreases when the carrier frequency is increased because the phase delay between neighboring sections is proportional to the carrier frequency. For cylindrical coils, the RF field is proportional to (pinu/2nu(d))(1/2)exp(-nu/nu(d)), where the decay frequency nu(d) is determined by the dimensions of the coil. The observed carrier frequency thus must be much smaller than the decay frequency. This condition restricts the size of transmission line coils. We made a cylindrical coil for a 1H NMR probe operating below 400 MHz. It had a diameter 2.3mm and a pitch 1.2mm. Five capacitors of 6pF were connected at every three turns. The RF field strength was 40 and 60 kHz at the input RF power 100 W by a calculation and by experiments, respectively. The calculations showed that the RF field inhomogeneity along the coil axis was caused by a

  4. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  5. The NMR Structure of Human Obestatin in Membrane-Like Environments: Insights into the Structure-Bioactivity Relationship of Obestatin

    PubMed Central

    Gurriarán-Rodríguez, Uxía; Mosteiro, Carlos S.; Álvarez-Pérez, Juan C.; Otero-Alén, María; Camiña, Jesús P.; Gallego, Rosalía; García-Caballero, Tomás; Martín-Pastor, Manuel; Casanueva, Felipe F.; Jiménez-Barbero, Jesús; Pazos, Yolanda

    2012-01-01

    The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1). Other analogues, including human non-amidated obestatin (2) and the fragment peptides (6–23)-obestatin (3), (11–23)-obestatin (4), and (16–23)-obestatin (5) have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS). Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation). Our findings emphasize the importance of both the primary structure (composition and size) and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively) at both the structural and bioactivity levels. PMID:23056203

  6. 4F-PBP (4'-fluoro-α-pyrrolidinobutyrophenone), a new substance of abuse: Structural characterization and purity NMR profiling.

    PubMed

    Gaspar, Helena; Bronze, Soraia; Ciríaco, Sara; Queirós, Cláudio Rafael; Matias, Ana; Rodrigues, João; Oliveira, Cristina; Cordeiro, Carlos; Santos, Susana

    2015-07-01

    The rapidly growing problem of new psychoactive substances (NPS) makes the time management for international control a real challenge, with the traditional detection methods becoming increasingly inadequate. NPS screening technologies, such as NMR, which allows multiple substances to be detected, characterized and quantified simultaneously from a single sample, offers a rapid solution to this problem. This study describes the application of NMR to the simultaneous detection, characterization and quantification of samples of white powders seized by the Portuguese Police. 4F-PBP (4'-fluoro-α-pyrolidinobutyrophenone) a new synthetic psychoactive cathinone cut with myo-inositol was found in two seized products. The structural characterization of 4F-PBP was elucidated in the mixture, and confirmed after isolation from the matrix by (1)H, (13)C, (19)F NMR and MS. Myo-inositol was found for the first time as a cutting agent of cathinones. Furthermore another seized product was characterized as being MDPBP, with a high degree of purity, and its spectroscopic elucidation enabled the correction of (13)C NMR literature assignments.

  7. Solid-state structure and solution conformation of the nootropic agent N[2-( N,N-Diisopropylamino)ethyl]-2-oxo-1-pyrrolidinacetamide sulphate. X-ray and homonuclear two-dimensional 1H NMR studies

    NASA Astrophysics Data System (ADS)

    Bandoli, Giuliano; Nicolini, Marino; Pappalardo, Giuseppe C.; Grassi, Antonio; Perly, Bruno

    1987-04-01

    The crystal and molecular structure of the nootropic agent N-[2-( N,N-diisopropyl-amino)ethyl]-2-oxo-1-pyrrolidinacetamide sulphate was determined by X-ray analysis. The conformational properties in the solution state were deduced from the 1H-NMR spectrum run in 2H 2O at 500 MHz. Spectral assignments were made with the aid of the COSY 45 shift correlation experiment. Crystals were triclinic with unit cell dimensions a = 13.410(10), b = 11.382(8), c = 6.697(4) », α = 83.80(3), β = 88.61(3)and γ = 72.25(6)° ; space group Poverline1. The structure was determined from 1047 three-dimensional counter data and refined to a value of 7.5% for the conventional discrepancy factor R. One molecule of the solvent acetonitrile is incorporated per two of the (C 14H 28N 3O 2) +-(HSO 4) -. The five-membered heterocyclic ring is in an envelope ( Cs) conformation and the "flap" atom deviates by 0.31 » from the plane of the other four. This plane forms a dihedral angle of 71.4° with the amide group, with the CO fragment directed toward the ring. All bond angles and distances are in good agreement with expected standard values. A strong OH⋯O intermolecular bond (2.61 ») links the cation of the hydrogen-sulphate anion, while the loosely held MeCN molecule is trapped in the polar pockets. The molecular conformation in the solid was compared with results from 1H NMR spectral analysis which showed that in solution wide torsional oscillations can occur about the bonds of the chain bonded to the N(1) atom.

  8. NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

    PubMed

    Harris, Kimberly A; Bobay, Benjamin G; Sarachan, Kathryn L; Sims, Alexis F; Bilbille, Yann; Deutsch, Christopher; Iwata-Reuyl, Dirk; Agris, Paul F

    2015-08-14

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in the biosynthesis of t(6)A37, the details of the enzymatic mechanism remain unsolved. Therefore, the solution structure of Escherichia coli TsaC was characterized by NMR to further study the interactions with ATP and L-threonine, both substrates of TsaC in the biosynthesis of L-threonylcarbamoyl-AMP. Several conserved amino acids were identified that create a hydrophobic binding pocket for the adenine of ATP. Additionally, two residues were found to interact with L-threonine. Both binding sites are located in a deep cavity at the center of the protein. Models derived from the NMR data and molecular modeling reveal several sites with considerable conformational flexibility in TsaC that may be important for L-threonine recognition, ATP activation, and/or protein/protein interactions. These observations further the understanding of the enzymatic reaction catalyzed by TsaC, a threonylcarbamoyl-AMP synthase, and provide structure-based insight into the mechanism of t(6)A37 biosynthesis.

  9. Structure and dynamics of bacteriophage IKe major coat protein in MPG micelles by solution NMR.

    PubMed

    Williams, K A; Farrow, N A; Deber, C M; Kay, L E

    1996-04-23

    The structure and dynamics of the 53-residue filamentous bacteriophage IKe major coat protein in fully protonated myristoyllysophosphatidylglycerol (MPG) micelles were characterized using multinuclear solution NMR spectroscopy. Detergent-solubilized coat protein [sequence: see text] mimics the membrane-bound "assembly intermediate" form of the coat protein which occurs during part of the phage life cycle. NMR studies of the IKe coat protein show that the coat protein is largely alpha-helical, exhibiting a long amphipathic surface. helix (Asn 4 to Ser 26) and a shorter "micelle-spanning" C-terminal helix which begins at TRP 29 and continues at least to Phe 48. Pro 30 likely occurs in the first turn of the C-terminal helix, where it is ideally situated given the hydrogen bonding and steric restrictions imposed by this residue. The similarity of 15N relaxation values (T1, T2, and NOE and 500 MHz and T2 at 600 MHz) among much of the N-terminal helix and all of the TM helix indicates that the N-terminal helix is as closely associated with the micelle as the TM helix. The description of the protein in the micelle is supported by the observation of NOEs between lysolipid protons and protein amide protons between asn 8 and Ser 50. The N-terminal and TM helices exhibit substantial mobility on the microsecond to second time scale, which likely reflects changes in the orientation between the two helices. The overall findings serve to clarify the role of individual residues in the context of a TM alpha-helix and provide an understanding of the secondary structure, dynamics, and aqueous and micellar environments of the coat protein.

  10. A 29Si MAS-NMR study of transition metal site occupancy in forsterite

    NASA Astrophysics Data System (ADS)

    Mccarty, R. J.; Palke, A.; Stebbins, J. F.; Hartman, S.

    2012-12-01

    In this study, we address the problem of transition metal site occupancy in Mg-rich olivine using solid-state magic-angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. Transition metal substitution in olivine can occur in either of the two crystallographically unique octahedral sites: the smaller, more symmetric M1 site or the larger, more distorted M2 site. Site occupancy of the transition metal is expected to correlate with ionic radius and d-orbital structure. In NMR spectroscopy the presence of paramagnetic ions, such as transition metal ions, can produce accessory peaks referred to as "contact shifts," due to the interaction between unpaired electrons on the paramagnetic ion locally associated with the resonating nucleus. The position and intensity of the contact shifts are dependent on the geometrical association such as bond distances and bond angles between the paramagnetic ion and the resonating nucleus. 29Si MAS-NMR spectra collected on synthetic forsterite (Mg2SiO4) doped with minor amounts (0.2-5%) of individual, divalent, paramagnetic, transition metal cations (Mn, Co, Ni, or Cu) substituting for Mg in the octahedral sites, reveals multiple contact shifts. An interpretation of the number of such contact shifts and their relative intensities correlated with structural information of possible 29Si-M1 and 29Si-M2 configurations, potentially allows for the assignment of specific transition metals to individual M1 or M2 sites. An analysis of the MAS-NMR data will potentially bring a new level of confidence to transition metal site occupancy in forsterite.

  11. NMR Studies of Thermo-responsive Behavior of an Amphiphilic Poly(asparagine) Derivative in Water.

    PubMed

    Watanabe, Eiji; Boutis, Gregory S; Sato, Hiroko; Sekine, Sokei; Asakura, Tetsuo

    2014-01-14

    The thermo-responsive behavior of a unique biocompatible polymer, poly(N-substituted α/β-asparagine) derivative (PAD), has been studied with several NMR methods. The (1)H and (13)C solution NMR measurements of the PAD in DMSO-d6 were used to investigate the isolated polymer and perform spectral assignments. By systematic addition of D2O we have tracked structural changes due to aggregation and observed contraction of hydrophilic side chains. Solution and cross polarization / magic angle spinning (CP/MAS) (13)C NMR approaches were implemented to investigate the aggregates of the PAD aqueous solution during the liquid to gel transition as the temperature was increased. At temperatures near 20 °C, all of the peaks from the PAD were observed in the (13)C CP/MAS and (13)C solution NMR spectra, indicating the presence of polymer chain nodes. Increasing the temperature to 40 °C resulted in a partial disentanglement of the nodes due to thermal agitation and further heating resulted in little to no additional structural changes. Deuterium T1-T2 and T2-T2 two-dimensional relaxation spectroscopies using an inverse Laplace transform, were also implemented to monitor the water-PAD interaction during the phase transition. At temperatures near 20 °C the dynamical characteristics of water were manifested into one peak in the deuterium T1-T2 map. Increasing the temperature to 40 °C resulted in several distinguishable reservoirs of water with different dynamical characteristics. The observation of several reservoirs of water at the temperature of gel formation at 40 °C is consistent with a physical picture of a gel involving a network of interconnected polymer chains trapping a fluid. Further increase in temperature to 70 °C resulted in two non-exchanging water reservoirs probed by deuterium T2-T2 measurements.

  12. NMR structure of hypothetical protein MG354 from Mycoplasmagenitalium

    SciTech Connect

    Pelton, Jeffrey G.; Shi, Jianxia; Yokotoa, Hisao; Kim, Rosalind; Wemmer, David E.

    2005-04-12

    Mycoplasma genitalium (Mg) and M. pneumoniae (Mp) are human pathogens with two of the smallest genomes sequenced to date ({approx} 480 and 680 genes, respectively). The Berkeley Structural Genomics Center is determining representative structures for gene products in these organisms, helping to understand the set of protein folds needed to sustain this minimal organism. The protein coded by gene MG354 (gi3844938) from M. genitalium has a relatively unique sequence, related only to MPN530 from M. pneumoniae (68% identity, coverage 99%) and MGA{_}0870 from the avian pathogen M. gallisepticum (23% identity, coverage 94%), has no homologue with a determined structure, and no functional annotations.

  13. Isolation and structure elucidation of tetrameric procyanidins from unripe apples (Malus pumila cv. Fuji) by NMR spectroscopy.

    PubMed

    Nakashima, Shohei; Oda, Chihiro; Masuda, Susumu; Tagashira, Motoyuki; Kanda, Tomomasa

    2012-11-01

    Procyanidins are plant secondary metabolites widely consumed and known to have various physiological functions, but their bioavailability and mechanism of action are still unclear especially for larger oligomers. One of the reasons is scarce information about the detailed structure of oligomeric procyanidins. As for apple, structures of procyanidin components larger than trimers are scarcely known. In this study, 11 tetrameric procyanidins including two known compounds were isolated from unripe apples (Malus pumila cv. Fuji) and identified by NMR spectroscopic analysis and phloroglucinol degradation. As a result, the detailed structural diversity of tetrameric procyanidins in apple was established.

  14. SPINS: a laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations.

    PubMed

    Baran, Michael C; Moseley, Hunter N B; Aramini, James M; Bayro, Marvin J; Monleon, Daniel; Locke, Jessica Y; Montelione, Gaetano T

    2006-03-01

    Recent technological advances and experimental techniques have contributed to an increasing number and size of NMR datasets. In order to scale up productivity, laboratory information management systems for handling these extensive data need to be designed and implemented. The SPINS (Standardized ProteIn Nmr Storage) Laboratory Information Management System (LIMS) addresses these needs by providing an interface for archival of complete protein NMR structure determinations, together with functionality for depositing these data to the public BioMagResBank (BMRB). The software tracks intermediate files during each step of an NMR structure-determination process, including: data collection, data processing, resonance assignments, resonance assignment validation, structure calculation, and structure validation. The underlying SPINS data dictionary allows for the integration of various third party NMR data processing and analysis software, enabling users to launch programs they are accustomed to using for each step of the structure determination process directly out of the SPINS user interface.

  15. NMR structure analysis of uniformly 13C-labeled carbohydrates.

    PubMed

    Fontana, Carolina; Kovacs, Helena; Widmalm, Göran

    2014-06-01

    In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.

  16. Low-temperature NMR studies of Zn tautomerism and hindered rotations in solid zincocene derivatives.

    PubMed

    Lopez del Amo, Juan Miguel; Buntkowsky, Gerd; Limbach, Hans-Heinrich; Resa, Irene; Fernandez, Rafael; Carmona, Ernesto

    2008-04-24

    Using a combination of NMR methods we have detected and studied fluxional motions in the slip-sandwich structure of solid decamethylzincocene (I, [(eta5-C5Me5)Zn(eta1-C5Me5)]). For comparison, we have also studied the solid iminoacyl derivative [(eta5-C5Me5)Zn(eta1-C(NXyl)C5Me5)] (II). The variable temperature 13C CPMAS NMR spectra of I indicate fast rotations of both Cp* rings in the molecule down to 156 K as well as the presence of an order-disorder phase transition around 210 K. The disorder is shown to be dynamic arising from a fast combined Zn tautomerism and eta1/eta5 reorganization of the Cp* rings between two degenerate states A and B related by a molecular inversion. In the ordered phase, the degeneracy of A and B is lifted; that is, the two rings X and Y are inequivalent, where X exhibits a larger fraction of time in the eta5 state than Y. However, the interconversion is still fast and characterized by a reaction enthalpy of DeltaH = 2.4 kJ mol-1 and a reaction entropy of DeltaS = 4.9 J K-1 mol-1. In order to obtain quantitative kinetic information, variable temperature 2H NMR experiments were performed on static samples of I-d6 and II-d6 between 300 and 100 K, where in each ring one CH3 is replaced by one CD3 group. For II-d6, the 2H NMR line shapes indicate fast CD3 group rotations and a fast "eta5 rotation", corresponding to 72 degrees rotational jumps of the eta5 coordinated Cp* ring. The latter motion becomes slow around 130 K. By line shape analysis, an activation energy of the eta5 rotation of about 21 kJ mol-1 was obtained. 2H NMR line shapes analysis of I-d6 indicates fast CD3 group rotations at all temperatures. Moreover, between 100 and 150 K, a transition from the slow to the fast exchange regime is observed for the 5-fold rotational jumps of both Cp* rings, exhibiting an activation energy of 18 kJ mol-1. This value was corroborated by 2H NMR relaxometry from which additionally the activation energies 6.3 kJ mol-1 and 11.2 kJ mol-1 for the CD3

  17. Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data.

    PubMed

    Toukach, F V; Shashkov, A S

    2001-09-28

    A computer-assisted approach to the prediction of the primary structures of regular glycopolymers is described. The analysis is based on comparing the calculated 13C NMR spectra of all the possible structures of the repeating unit (for the given monomeric composition) to an experimental 13C NMR spectrum. The spectra generation is based on the spectral database containing information on the 13C chemical shifts of monomers, di- and trimeric fragments. If the required data are missing from this database, the special database for average glycosylation effects is used. The analysis reveals those structures with the calculated 13C NMR spectrum most close to observed. The structures of repeating units of any topology containing up to six residues linked by glycosidic, amidic or phospho-diester bridges can be predicted. Unambiguous selection of the proper structure from the output list of possible structures may require additional experimental data. Testing the created program and databases on bacterial polysaccharides and their derivatives containing up to three non-sugar residues (alditols, amino acids, phosphate groups etc.) per repeating unit revealed the good convergence of prediction with independently obtained structural data.

  18. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    PubMed

    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.

  19. Studies of 27Al NMR in SrAl4

    NASA Astrophysics Data System (ADS)

    Niki, Haruo; Higa, Nonoka; Kuroshima, Hiroko; Toji, Tatsuki; Morishima, Mach; Minei, Motofumi; Yogi, Mamoru; Nakamura, Ai; Hedo, Masato; Nakama, Takao; Ōnuki, Yoshichika; Harima, Hisatomo

    A charge density wave (CDW) transition at TCDW = 243 K and a structural phase (SP) transition at approximately 100 K occur in SrAl4 with the BaAl4-type body center tetragonal structure, which is the divalent and non-4f electron reference compound of EuAl4. To understand the behaviors of the CDW and SP transitions, the 27Al NMR measurements using a single crystal and a powder sample of SrAl4 have been carried out. The line width below TCDW is modulated by an electrical quadruple interaction between 27Al nucleus and CDW charge modulation. The incommensurate CDW state below TCDW changes into a different structure below TSP. The temperature dependences of Knight shifts of 27Al(I) and 27Al(II) show the different behaviors. The temperature variation of 27Al(I) Knight shift shows anomalies at the CDW and SP transition temperatures, revealing the shift to negative side below TCDW, which is attributable to the core polarization of the d-electrons. However, 27Al(II) Knight shift keeps almost constant except for the small shift due to the SP transition. The 1/T1T of 27Al(I) indicates the obvious changes due to the CDW and SP transitions, while that of 27Al(II) takes a constant value. The density of state at the Fermi level at Al(I) site below 60 K would be about 0.9 times less than that above TCDW.

  20. Solid-state NMR/NQR and first-principles study of two niobium halide cluster compounds.

    PubMed

    Perić, Berislav; Gautier, Régis; Pickard, Chris J; Bosiočić, Marko; Grbić, Mihael S; Požek, Miroslav

    2014-01-01

    Two hexanuclear niobium halide cluster compounds with a [Nb6X12](2+) (X=Cl, Br) diamagnetic cluster core, have been studied by a combination of experimental solid-state NMR/NQR techniques and PAW/GIPAW calculations. For niobium sites the NMR parameters were determined by using variable Bo field static broadband NMR measurements and additional NQR measurements. It was found that they possess large positive chemical shifts, contrary to majority of niobium compounds studied so far by solid-state NMR, but in accordance with chemical shifts of (95)Mo nuclei in structurally related compounds containing [Mo6Br8](4+) cluster cores. Experimentally determined δiso((93)Nb) values are in the range from 2,400 to 3,000 ppm. A detailed analysis of geometrical relations between computed electric field gradient (EFG) and chemical shift (CS) tensors with respect to structural features of cluster units was carried out. These tensors on niobium sites are almost axially symmetric with parallel orientation of the largest EFG and the smallest CS principal axes (Vzz and δ33) coinciding with the molecular four-fold axis of the [Nb6X12](2+) unit. Bridging halogen sites are characterized by large asymmetry of EFG and CS tensors, the largest EFG principal axis (Vzz) is perpendicular to the X-Nb bonds, while intermediate EFG principal axis (Vyy) and the largest CS principal axis (δ11) are oriented in the radial direction with respect to the center of the cluster unit. For more symmetrical bromide compound the PAW predictions for EFG parameters are in better correspondence with the NMR/NQR measurements than in the less symmetrical chlorine compound. Theoretically predicted NMR parameters of bridging halogen sites were checked by (79/81)Br NQR and (35)Cl solid-state NMR measurements.

  1. Structure and Dynamics of the Aβ21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations

    PubMed Central

    Fawzi, Nicolas L.; Phillips, Aaron H.; Ruscio, Jory Z.; Doucleff, Michaeleen; Wemmer, David E.; Head-Gordon, Teresa

    2012-01-01

    We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Aβ21–30 peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer’s disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants (3JHNHα), chemical-shift values, 13C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Aβ21–30. We find robust prediction of the 13C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Aβ21–30 peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Aβ21–30 conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Aβ21–30 peptide involves a majority population (~60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a β-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Aβ1–40 and Aβ1–42, for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high

  2. The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.

    PubMed

    Bonneau, Eric; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

    2015-09-01

    As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg(2+)-binding sites within this structure using Mn(2+)-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg(2+) ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg(2+) ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme.

  3. The NMR structure of the II–III–VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure

    PubMed Central

    Bonneau, Eric; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

    2015-01-01

    As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III–IV–V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II–III–VI three-way junction and its adjoining stems. In addition, we localize Mg2+-binding sites within this structure using Mn2+-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg2+ ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge–bulge interaction and Mg2+ ions are critical for the stable folding of the II–III–VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II–III–VI junction that does not contain the II–VI bulge–bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme. PMID:26124200

  4. The DNA sequence at echinomycin binding sites determines the structural changes induced by drug binding: NMR studies of echinomycin binding to (d(ACGTACGT)) sub 2 and (d(TCGATCGA)) sub 2

    SciTech Connect

    Gilbert, D.E.; Feigon, J. )

    1991-03-05

    The complexes formed between the cyclic octadepsipeptide antibiotic echinomycin and the two DNA octamers (d(ACGTACGT)){sub 2} and (d(TCGATCGA)){sub 2} have been investigated by using one- and two-dimensional proton NMR spectroscopy techniques. The results obtained for the two complexes are compared to each other, to the crystal structures of related DNA-echinomycin complexes, and to enzymatic ad chemical footprinting results. In the saturated complexes, two echinomycin molecules bind to each octamer by bisintercalation of the quinoxaline moieties on either side of each CpG step. Binding of echinomycin to the octamer (d(ACGTACGT)){sub 2} is cooperative so that only the two-drug complex is observed at lower drug-DNA ratios, but binding to (d(TCGATCGA)){sub 2} is not cooperative. Thus, the structure and stability of the DNA in echinomycin-DNA complexes depends on the sequence at and adjacent to the binding site. While the authors conclude that no single structural change in the DNA can explain all of the footprinting results, unwinding of the DNA helix in the drug-DNA complexes appears to be an important factor while Hoogsteen base pair formation does not.

  5. Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

    PubMed

    Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

    2015-02-01

    We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924.

  6. Novel electrolytes for use in new and improved batteries: An NMR study

    NASA Astrophysics Data System (ADS)

    Berman, Marc B.

    This thesis focuses on the use of nuclear magnetic resonance (NMR) spectroscopy in order to study materials for use as electrolytes in batteries. The details of four projects are described in this thesis as well as a brief theoretical background of NMR. Structural and dynamics properties were determined using several NMR techniques such as static, MAS, PFG diffusion, and relaxation to understand microscopic and macroscopic properties of the materials described within. Nuclei investigate were 1H, 2H, 7Li, 13C, 19F, 23Na, and 27Al. The first project focuses on an exciting new material to be used as a solid electrolyte membrane. T. The second project focuses on the dynamics of ionic liquid-solvent mixtures and their comparison to molecular dynamics computer simulations. The third project involves a solvent-free film containing NaTFSI salt mixed in to PEO for use in sodium-ion batteries. This final project focuses on a composite electrolyte consisting of a ceramic and solid: LiI:PEO:LiAlO2.

  7. NMR structural determination of unique invertebrate glycosaminoglycans endowed with medical properties.

    PubMed

    Pomin, Vitor H

    2015-09-02

    Glycosaminoglycans (GAGs) are sulfated polysaccharides of complex structure endowed with numerous biomedical functions. Although ubiquitously distributed in vertebrates, GAGs can also occur in certain terrestrial or marine invertebrates. Solution nuclear magnetic resonance (NMR) spectroscopy has been the analytical technique mostly employed in structural characterization of GAGs from any source. This review aims at illustrating the application of NMR in structural determination of few representative invertebrate GAG examples of unique structures and endowed with therapeutic actions. They are the holothurian fucosylated chondroitin sulfate, the acharan sulfate isolated from the snail Achatina fulica, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei. These invertebrate GAGs exhibit distinct structures when compared to those extracted from mammalian GAGs. The distinct structures of the invertebrate GAGs lead also to different mechanisms of actions as compared to the mammalian GAG standards. Invertebrate GAGs comprise promising therapeutic candidates in fights against diseases. Solution NMR has been playing a pivotal role in this carbohydrate-based drug research, discovery and development.

  8. Structural investigations of borosilicate glasses containing MoO 3 by MAS NMR and Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Caurant, D.; Majérus, O.; Fadel, E.; Quintas, A.; Gervais, C.; Charpentier, T.; Neuville, D.

    2010-01-01

    High molybdenum concentration in glass compositions may lead to alkali and alkaline-earth molybdates crystallization during melt cooling that must be controlled particularly during the preparation of highly radioactive nuclear glassy waste forms. To understand the effect of molybdenum addition on the structure of a simplified nuclear glass and to know how composition changes can affect molybdates crystallization tendency, the structure of two glass series belonging to the SiO 2-B 2O 3-Na 2O-CaO-MoO 3 system was studied by 29Si, 11B, 23Na MAS NMR and Raman spectroscopies by increasing MoO 3 or B 2O 3 concentrations. Increasing MoO 3 amount induced an increase of the silicate network reticulation but no significant effect was observed on the proportion of BO4- units and on the distribution of Na + cations in glass structure. By increasing B 2O 3 concentration, a strong evolution of the distribution of Na + cations was observed that could explain the evolution of the nature of molybdate crystals (CaMoO 4 or Na 2MoO 4) formed during melt cooling.

  9. Dynamic Nuclear Polarization Enhanced MAS NMR for Structural Analysis of HIV-1 Protein Assemblies

    PubMed Central

    Gupta, Rupal; Lu, Manman; Hou, Guangjin; Caporini, Marc A.; Rosay, Melanie; Maas, Werner; Struppe, Jochem; Suiter, Christopher; Ahn, Jinwoo; Byeon, In-Ja L.; Franks, W. Trent; Orwick-Rydmark, Marcella; Bertarello, Andrea; Oschkinat, Hartmut; Lesage, Anne; Pintacuda, Guido; Gronenborn, Angela M.; Polenova, Tatyana

    2016-01-01

    Mature infectious HIV-1 virions contain conical capsids comprised of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20 – 64 fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4 – 18.8 T) and temperature (109 – 180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine sidechain conformers, unique intermolecular correlations across two CA molecules, and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR as an excellent tool for characterization of HIV-1 assemblies. PMID:26709853

  10. Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies.

    PubMed

    Gupta, Rupal; Lu, Manman; Hou, Guangjin; Caporini, Marc A; Rosay, Melanie; Maas, Werner; Struppe, Jochem; Suiter, Christopher; Ahn, Jinwoo; Byeon, In-Ja L; Franks, W Trent; Orwick-Rydmark, Marcella; Bertarello, Andrea; Oschkinat, Hartmut; Lesage, Anne; Pintacuda, Guido; Gronenborn, Angela M; Polenova, Tatyana

    2016-01-21

    Mature infectious HIV-1 virions contain conical capsids composed of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20-64-fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar-based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4-18.8 T) and temperature (109-180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of the temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine side-chain conformers; unique intermolecular correlations across two CA molecules; and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR spectroscopy as an excellent tool for the characterization of HIV-1 assemblies.

  11. Combined high resolution NMR and 1H and 17O relaxometric study sheds light on the solution structure and dynamics of the lanthanide(III) complexes of HPDO3A.

    PubMed

    Delli Castelli, Daniela; Caligara, Maria C; Botta, Mauro; Terreno, Enzo; Aime, Silvio

    2013-06-17

    GdHPDO3A is one of the most used MRI contrast agents (CAs) for clinical use. However, unlike most of the other commercially available Gd-based CAs, only limited information is available on its solution structure and dynamics. 600 MHz high resolution (1)H NMR spectra of nine LnHPDO3A complexes (Ln = Pr, Nd, Eu, Tb, Dy, Ho, Er, Tm, and Yb) have been recorded at 298 K and neutral pH. Because of the low symmetry of the Ln-chelates, each proton gives rise to a different peak. Despite the very crowded spectra, it is possible to detect the presence of two sets of resonances associated with different isomers in solution in slow exchange in the NMR time scale. In principle, the LnHPDO3A complexes may be present in solution as eight isomeric forms (four enantiomeric pairs) differing in the layout of the acetate arms (Δ or Λ), in the conformation of the macrocyclic ring (δδδδ or λλλλ) and in the configuration of the chiral center (R or S). 1D- and 2D proton NMR spectra were measured as a function of temperature across the Lanthanide series. The data allow identifying the nature of the most abundant isomeric species in solution (e.g., Λ(λλλλ)-R/Λ(δδδδ)-R and their enantiomeric forms Δ(δδδδ)-S/Δ(λλλλ)-S) and their interconversion process. Analysis of the data led us to identify the presence in solution of a third isomeric species, lacking the coordinated water molecule (q = 0), whose population becomes more relevant for the heavier lanthanides (Ln = Er-Lu). Moreover, we have introduced an innovative way of modeling the thermodynamic equilibrium between the various isomeric forms of LnHPDO3A that can be extended to a number of other systems. This analysis enabled us to calculate the molar fractions of the two isomeric forms for GdHPDO3A (χ = 0.7 and 0.30, for SAP and TSAP, respectively). This information has allowed interpreting the slightly anomalous relaxometric properties of GdHPDO3A. In particular, we observed that the temperature dependence of

  12. NMR study of a membrane protein in detergent-free aqueous solution

    PubMed Central

    Zoonens, Manuela; Catoire, Laurent J.; Giusti, Fabrice; Popot, Jean-Luc

    2005-01-01

    One of the major obstacles to membrane protein (MP) structural studies is the destabilizing effect of detergents. Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep MPs water-soluble under mild conditions. In the present work, we have explored the feasibility of studying the structure of APol-complexed MPs by NMR. As a test MP, we chose the 171-residue transmembrane domain of outer MP A from Escherichia coli (tOmpA), whose x-ray and NMR structures in detergent are known. 2H,15N-labeled tOmpA was produced as inclusion bodies, refolded in detergent solution, trapped with APol A8-35, and the detergent removed by adsorption onto polystyrene beads. The resolution of transverse relaxation-optimized spectroscopy–heteronuclear single-quantum correlation spectra of tOmpA/A8-35 complexes was found to be close to that of the best spectra obtained in detergent solutions. The dispersion of chemical shifts indicated that the protein had regained its native fold and retained it during the exchange of surfactants. MP–APol interactions were mapped by substituting hydrogenated for deuterated A8-35. The resulting dipolar broadening of amide proton linewidths was found to be limited to the β-barrel region of tOmpA, indicating that A8-35 binds specifically to the hydrophobic transmembrane surface of the protein. The potential of this approach to MP studies by solution NMR is discussed. PMID:15956183

  13. Structural analysis of complex saponins of Balanites aegyptiaca by 800 MHz 1H NMR spectroscopy.

    PubMed

    Staerk, Dan; Chapagain, Bishnu P; Lindin, Therese; Wiesman, Zeev; Jaroszewski, Jerzy W

    2006-10-01

    The main saponin (1) present in the mesocarp of Balanites aegyptiaca fruit is a mixture of 22R and 22S epimers of 26-(O-beta-D-glucopyranosyl)-3-beta-[4-O-(beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyloxy]-22,26-dihydroxyfurost-5-ene. This structure differs from a previously reported saponin isolated from this source by the site of attachment of the rhamnosyl residue, and presumably represents a structural revision of the latter. The main saponin (2) present in the kernel is a xylopyranosyl derivative of 1. The use of high-field NMR enabled the practically complete assignment of 1H and 13C chemical shifts of these complex saponins, existing as a mixture of C-22 epimers. Moreover, the work represents a new approach to structural elucidation of saponins: direct preparative-scale HPLC-RID of crude extracts followed by high-field NMR investigations supported by ESI-MSn.

  14. Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

    PubMed Central

    Schanda, Paul; Ernst, Matthias

    2016-01-01

    Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution. PMID:27110043

  15. NMR structure of d(CGCA3T3GCG)2:tren-microgonotropen-b:Zn(II) complex and solution studies of metal ion complexes of tren-microgonotropen-b interacting with DNA.

    PubMed

    Blaskó, A; Browne, K A; Bruice, T C

    1995-06-01

    The solution structure of a 1:1 complex of zinc tren-microgonotropen-b [6b:Zn(II)] with d(CGCAAATTTGCG)2 has been determined by 2D nuclear Overhauser effect 1H NMR spectroscopy and restrained molecular modeling. The exchangeable and nonexchangeable proton resonances of d(CGCA3T3GCG)2:6b:Zn(II) indicate that the Zn(II) is interacting in the A+T-rich region of the dsDNA and the tren region of 6b, while 31P NMR shows interaction of the Zn(II) with the phosphate backbone. Proton chemical shift differences between d(CGCA3T3GCG)2:6b:Zn(II) and d(CGCA3T3GCG)2:6b are in agreement with the polyamino substituent of 6b [-(CH2)4N(CH2CH2)N-(CH2CH2NH2)2] forming a four-coordinated Zn(II) complex similar to that found in the X-ray structure of 'tren-chloride':Zn(II). The P9 and P10 phosphate oxygens that are held by hydrogen bonding to the tren substituent of 6b in the DNA:6b complex become ligands to the tren-complexed Zn(II) in DNA:6b:Zn(II). To do so there is a 2 A decrease in the adjacent phosphate-to-phosphate distance at the Zn(II) binding site. This motion brings about an increased bend of 14.6 degrees in the helical axis of d(CGCA3T3GCG)2:6b:Zn(II) compared to that found in d(CGCA3T3GCG)2:6b. Single stranded cleavage of linear DNA fragments was not observed in the presence of 6b and Fe(II), Co(II), Ni(II), Cu(II), Zn(II), La(III) or Ce(III); this is likely due to the metal ion being sequestered as in the structure of d(CGCA3T3GCG)2:6b:Zn(II) complex. Supercoiled DNA was susceptible to cleavage by 6b:Cu(II) in the presence of O2 and a reducing agent.

  16. Temperature and pressure based NMR studies of detergent micelle phase equilibria.

    PubMed

    Alvares, Rohan; Gupta, Shaan; Macdonald, Peter M; Prosser, R Scott

    2014-05-29

    Bulk thermodynamic and volumetric parameters (ΔGmic°, ΔHmic°, ΔSmic°, ΔCp,mic°, ΔVmic°, and Δκmic°) associated with the monomer–micelle equilibrium, were directly determined for a variety of common detergents [sodium n-dodecyl sulfate (SDS), n-dodecyl phosphocholine (DPC), n-dodecyl-β-d-maltoside (DDM), and 7-cyclohexyl-1-heptyl phosphocholine (CyF)] via 1H NMR spectroscopy. For each temperature and pressure point, the critical micelle concentration (cmc) was obtained from a single 1H NMR spectrum at a single intermediate concentration by referencing the observed chemical shift to those of pure monomer and pure micellar phases. This permitted rapid measurements of the cmc over a range of temperatures and pressures. In all cases, micelle formation was strongly entropically favored, while enthalpy changes were all positive, with the exception of SDS, which exhibited a modestly negative enthalpy of micellization. Heat capacity changes were also characteristically negative, while partial molar volume changes were uniformly positive, as expected for an aggregation process dictated by hydrophobic effects. Isothermal compressibility changes were found to be consistent with previous measurements using other techniques. Thermodynamic measurements were also related to spectroscopic studies of topology and micelle structure. For example, paramagnetic effects resulting from the addition of dioxygen provided microscopic topological details concerning the hydrophobicity gradient along the detergent chains within their respective micelles as detected by 1H NMR. In a second example, combined 13C and 1H NMR chemical shift changes arising from application of high pressure, or upon micellization, of CyF provided site-specific details regarding micelle topology. In this fashion, bulk thermodynamics could be related to microscopic topological details within the detergent micelle.

  17. Determination of the Structural Basis of Antibody Diversity Using NMR

    DTIC Science & Technology

    1990-12-14

    22. Perkins, S.J. and Dwek, R.A. (1980). Comparison of Ring-Current Shifts Calculated from the Crystal Structure of Egg White Lysozyme 27 of Hen with...the first and second kind with modulus k = 2 J (4) + p) 2 + z 2 Values for the parameters a and i are giver, in Table I. The separation of the current...the sp 2 plane of the two doublely bonded nuclei. The current loops were separated from this plane by 0.638 A. Each ring was given one electron. The

  18. Combined experimental (FT-IR, UV-visible spectra, NMR) and theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of Phomarin

    NASA Astrophysics Data System (ADS)

    Kumar, Abhishek; Srivastava, Ambrish Kumar; Gangwar, Shashi; Misra, Neeraj; Mondal, Avijit; Brahmachari, Goutam

    2015-09-01

    Phomarin is an important natural product belonging to anthraquinone series of compounds. The equilibrium geometry of phomarin has been determined and analyzed at DFT method employing B3LYP/6-311++G(d,p) level of computation. The reactivity of molecule using various descriptors such as Fukui functions, local softness, electrophilicity, electronegativity, Hardness, HOMO-LUMO gap are calculated and discussed. The infrared and UV-vis spectra of phomarin are calculated and compared with the experimentally observed ones. Moreover, 1H and 13C NMR spectra have been calculated by using the gauge independent atomic orbital method. We also notice that phomarin shows remarkable biological activities against malaria parasite. The study suggests further investigation on phomarin for their pharmacological importance.

  19. Structural analysis of N,N-diacyl-1,4-dihydropyrazine by variable-temperature NMR and DFT calculation

    NASA Astrophysics Data System (ADS)

    Song, Xiu-qing; Tan, Hong-bo; Yan, Hong; Chang, Yu

    2017-04-01

    N,N-diacyl-1,4-dihydropyrazine derivatives (1) were prepared via an efficient microwave-assisted synthesis. 1 was isolated and unambiguously confirmed by NMR spectra and high-resolution mass spectrometry. The NMR spectra of 1 showed complicated rather than conventional spectroscopy. Variable-temperature experiments and DFT calculation (PES) were used to investigate this phenomenon. DFT calculations confirmed that the structures of the two rotamers of 1 correspond to those determined by NMR in solution, and gave the syn-anti interconversion barriers of rotamers. The results showed that two isomers exist in solution (deuterated solvent) at room temperature, resulting in complicated NMR spectra.

  20. Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters.

    PubMed

    Mali, Gregor

    2017-03-01

    Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS2, exhibiting a modified rocksalt structure, in which S(2-) anions were replaced by S2(2-) dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, (25)Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined (25)Mg NMR parameters of magnesium sulfide species.

  1. APSY-NMR for protein backbone assignment in high-throughput structural biology

    PubMed Central

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael; Pedrini, Bill; Herrmann, Torsten; Wüthrich, Kurt

    2014-01-01

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90% of the residues. For most proteins the APSY data acquisition was completed in less than 30 hours. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. PMID:25428764

  2. [1H-NMR studies of the ACTH-like immunoregulatory peptides].

    PubMed

    Khristoforov, V S; Kutyshenko, V P; Abramov, V M; Zav'ialov, V P

    1997-01-01

    A comparative study of the conformational and dynamics properties of the ACTH-like linear peptides, sequences of which correspond to amino acid residues 11-20 of the heavy chain of human immunoglobulin G1 Eu, residues 78-85 of human pro-interleukin-1 alpha and site 10-18 of human ACTH, was performed in aqueous solution and dimethylsulfoxide by 1H-NMR spectroscopy at 400 MHz. The peptides were shown to possess an unordered unfolded flexible conformation in aqueous solution. The revealed structural and dynamic features of the peptides are discussed together with biological activity of this class of compounds.

  3. NMR study on iridium(III) complexes for identifying disulfonate substituted bathophenanthroline regio-isomers.

    PubMed

    Liu, Chenchen; Yu, Linpo; Liu, Yang; Li, Fang; Zhou, Ming

    2011-12-01

    A series of novel biscyclometalated iridium (III) complexes with an ancillary disulfonated bathophenanthroline (DSBP(2-)) ligand, Ir(L)(2)DSBPNa, L = 2-phenylpyridine (ppy), 2,4-difluorophenylpyridine (fppy), and 1-phenylisoquinoline (piq) were found to have two isomeric forms. The chemical structures of the isomers were determined by the one- and two-dimensional (1)H and (13)C NMR studies. The isomeric state was proved to have originated from the disulfonate-related regio-isomer of the DSBP(2-) ligand.

  4. Fundamental studies of supported bimetallic catalysts by NMR spectroscopy

    SciTech Connect

    Savargaonkar, Nilesh

    1996-10-17

    Various hydrogenation reactions on transition metals are important commercially whereas certain hydrogenolysis reactions are useful from fundamental point of view. Understanding the hydrogen mobility and kinetics of adsorption-desorption of hydrogen is important in understanding the mechanisms of such reactions involving hydrogen. The kinetics of hydrogen chemisorption was studied by means of selective excitation NMR on silica supported Pt, Rh and Pt-Rh catalysts. The activation energy of hydrogen desorption was found to be lower on silica supported Pt catalysts as compared to Rh and Pt-Rh catalysts. It was found that the rates of hydrogen adsorption and desorption on Pt-Rh catalyst were similar to those on Rh catalyst and much higher as compared to Pt catalyst. The Ru-Ag bimetallic system is much simpler to study than the Pt-Rh system and serves as a model system to characterize more complicated systems such as the K/Ru system. Ag was found to decrease the amounts of adsorbed hydrogen and the hydrogen-to-ruthenium stoichiometry. Ag reduced the populations of states with low and intermediate binding energies of hydrogen on silica supported Ru catalyst. The rates of hydrogen adsorption and desorption were also lower on silica supported Ru-Ag catalyst as compared to Ru catalyst. This report contains introductory information, the literature review, general conclusions, and four appendices. An additional four chapters and one appendix have been processed separately for inclusion on the data base.

  5. NMR solution structure of Ole e 6, a major allergen from olive tree pollen.

    PubMed

    Treviño, Miguel Angel; García-Mayoral, María Flor; Barral, Patricia; Villalba, Mayte; Santoro, Jorge; Rico, Manuel; Rodríguez, Rosalía; Bruix, Marta

    2004-09-10

    Ole e 6 is a pollen protein from the olive tree (Olea europaea) that exhibits allergenic activity with a high prevalence among olive-allergic individuals. The three-dimensional structure of Ole e 6 has been determined in solution by NMR methods. This is the first experimentally determined structure of an olive tree pollen allergen. The structure of this 50-residue protein is based on 486 upper limit distance constraints derived from nuclear Overhauser effects and 24 torsion angle restraints. The global fold of Ole e 6 consists of two nearly antiparallel alpha-helices, spanning residues 3-19 and 23-33, that are connected by a short loop and followed by a long, unstructured C-terminal tail. Viewed edge-on, the structured N terminus has a dumbbell-like shape with the two helices on the outside and with the hydrophobic core, mainly composed of 3 aromatic and 6 cysteine residues, on the inside. All the aromatic rings lie on top of and pack against the three disulfide bonds. The lack of thermal unfolding, even at 85 degrees C, indicates a high conformational stability. Based on the analysis of the molecular surface, we propose five plausible epitopes for IgE recognition. The results presented here provide the structural foundation for future experiments to verify the antigenicity of the proposed epitopes, as well as to design novel hypoallergenic forms of the protein suitable for diagnosis and treatment of type-I allergies. In addition, three-dimensional structure features of Ole e 6 are discussed to provide a basis for future functional studies.

  6. Probing Structure Property Relationships in Complex Engineering Silicones by 1H NMR

    SciTech Connect

    Chinn, S C; Gjersing, E L; Maxwell, R S; Eastwood, E; Bowen, D; Stephens, T

    2006-07-14

    It is generally accepted that the properties of polymeric materials are controlled by the network structure and the reactions by which they have been constructed. These properties include the bulk moduli at creation, but also the properties as a function of age during use. In order to interpret mechanical properties and predict the time dependent changes in these properties, detailed knowledge of the effect of structural changes must be obtained. The degree and type of crosslinking, the molecular weight between crosslinks, the number of elastically ineffective chains (loops, dangling chain ends, sol-fraction) must be characterized. A number of theoretical and experimental efforts have been reported in the last few years on model networks prepared by endlinking reactions and the relationships of those structures with the ultimate mechanical properties. A range of experimental methods have been used to investigate structure including rheometric, scattering, infrared, {sup 29}Si MAS and CPMAS, {sup 1}H relaxation measurements, and recently {sup 1}H multiple quantum methods. Characterization of the growth of multiple quantum coherences have recently been shown to provide detailed insight into silicone network structure by the ability to selective probe the individual components of the polymer network, such as the polymer-filler interface or network chains. We have employed recently developed MQ methods to investigate the structure-property relationships in a series of complex, endlinked filled-PDMS blends. Here, a systematic study of the relationship between the molecular formulation, as dictated by the amount and type of crosslinks present and by the remaining network chains, and the segmental dynamics as observed by MQ NMR was performed.

  7. Effects of temperature on the structures of silicate liquids: 29Si NMR results

    NASA Astrophysics Data System (ADS)

    Brandriss, Mark E.; Stebbins, Jonathan F.

    1988-11-01

    The effect of temperature on the structures of three silicate liquids has been studied by 29Si NMR spectroscopy on glass samples prepared with different glass transition temperatures. The compositions studied are (Na 2O) .34(SiO 2) .66 and (CaO) .10(Na 2O) .15(SiO 2) .75 and (CaO) .25(MgO) .25(SiO 2) .50. In the first two, the abundance of SiO 4 tetrahedra with four bridging oxygens ( Q 4) increases significantly with temperature. This change results from the disproportionation reaction 2Q 3ái Q 2 + Q 4 ( Q n is a SiO 4 tetrahedron with n bridging oxygens), with the observed increase in disproportionation at higher temperatures implying increased randomization of the anionic structure. In the (Na 2O) .34(SiO 2) .66 composition, the temperature dependence of Q 4 abundance enables us to estimate ΔH 0 for this reaction to be 30 ± 15 kJ per mole of Si. Although this reaction thus makes only a minor contribution to the conngurational heat capacity of each liquid, it probably has a major influence on the thermodynamic activity of SiO 2. Widening of the (CaO) .25(MgO) .25(SiO 2) .50 spectral peak with increasing temperature likewise implies increasing randomization of the anionic structure, although specific structural contributions to this widening are not identified. Models of melt structures at liquidus temperatures will be limited in accuracy if they assume that the speciation observed in glasses is unaffected by temperature change.

  8. Studies of Molecular Dynamics by Solid State Deuterium NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhao, Baiyi

    The rotational dynamics of molecules in a number of solid systems were followed by variable temperature deuterium (^2H), nuclear magnetic resonance (NMR) spectroscopy via changes in the spectral lineshapes and spin-lattice relaxation times (T _1). First the pure solid trimethylamine-borane adduct, (CH_3)_3NBH_3, was studied. For a methyl deuterated sample, T _1 measurements yielded two T_1 minima, 6.9 ms and 4.3 ms corresponding to the slowing of methyl and trimethyl rotation, respectively, with decreasing temperature. Activation energies for methyl and trimethyl rotation, obtained from fitting the T _1 curve as a function of temperature, were 32.8 and 15.0 kJ/mol, respectively; simulations of the spectral lineshapes gave 26.6 and 18.9 kT/mol, respectively. Fitting of the ^2H T_1 curve for the borane deuterated sample gave a BH _3 rotation activation energy of 14.1 kT/mol and a ^2H quadrupolar coupling constant, chi, of 101 kHz. The activation energy for BH_3 rotation obtained from the spectral lineshape simulations gave 12.6 kT/mol. A series of deuterated organic chalcogen cations: (CH_3)_3S^+, (CH_3)_3Se^+ and (CH_3)_3Te^+, were ion exchanged into the cavities of sodium Mordenite LZ-M5 and the dynamics of these guests within the hydrated zeolite were followed by ^2H NMR. All three undergo isotropic motion above about -80 to -90^circC. Below this temperature two superimposed ^2H powder spectra appear; the broad lineshape is consistent with only methyl rotation in a hindered, coordinated site, and the other narrow lineshape is due to both methyl and trimethyl rotation in a less hindered, uncoordinated site. As the temperature is lowered the population of the lower energy coordinated site increases. Relative peak areas yield adsorption enthalpies of 6.7, 7.8 and 10.0 kJ/mol for (CH_3)_3S^+, (CH_3)_3Se^+ and (CH_3)_3Te^+, respectively. The series of methyl deuterated ammonium and phosphonium cations: (CH_3)NH_3^+ , (CH_3)_2NH^+ , (CH_3)_3NH^+ and (CH_3)_4P^+ , were

  9. A systematic study of (25)Mg NMR in paramagnetic transition metal oxides: applications to Mg-ion battery materials.

    PubMed

    Lee, Jeongjae; Seymour, Ieuan D; Pell, Andrew J; Dutton, Siân E; Grey, Clare P

    2016-12-21

    Rechargeable battery systems based on Mg-ion chemistries are generating significant interest as potential alternatives to Li-ion batteries. Despite the wealth of local structural information that could potentially be gained from Nuclear Magnetic Resonance (NMR) experiments of Mg-ion battery materials, systematic (25)Mg solid-state NMR studies have been scarce due to the low natural abundance, low gyromagnetic ratio, and significant quadrupole moment of (25)Mg (I = 5/2). This work reports a combined experimental (25)Mg NMR and first principles density functional theory (DFT) study of paramagnetic Mg transition metal oxide systems Mg6MnO8 and MgCr2O4 that serve as model systems for Mg-ion battery cathode materials. Magnetic parameters, hyperfine shifts and quadrupolar parameters were calculated ab initio using hybrid DFT and compared to the experimental values obtained from NMR and magnetic measurements. We show that the rotor assisted population transfer (RAPT) pulse sequence can be used to enhance the signal-to-noise ratio in paramagnetic (25)Mg spectra without distortions in the spinning sideband manifold. In addition, the value of the predicted quadrupolar coupling constant of Mg6MnO8 was confirmed using the RAPT pulse sequence. We further apply the same methodology to study the NMR spectra of spinel compounds MgV2O4 and MgMn2O4, candidate cathode materials for Mg-ion batteries.

  10. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  11. Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins.

    PubMed

    Liu, Jing; Liu, Chang; Fan, Ying; Munro, Rachel A; Ladizhansky, Vladimir; Brown, Leonid S; Wang, Shenlin

    2016-05-01

    We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the expression medium. This strategy improves the spectral resolution by 1.5 fold, displays site-specific labelling patterns, and has advantages for collecting long-range distance restraints for structure determination of large eukaryotic membrane proteins by solid-state NMR.

  12. High resolution deuterium NMR studies of bacterial metabolism

    SciTech Connect

    Aguayo, J.B.; Gamcsik, M.P.; Dick, J.D.

    1988-12-25

    High resolution deuterium NMR spectra were obtained from suspensions of five bacterial strains: Escherichia coli, Clostridium perfringens, Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus aureus. Deuterium-labeled D-glucose at C-1, C-2, and C-6 was used to monitor dynamically anaerobic metabolism. The flux of glucose through the various bacterial metabolic pathways could be determined by following the disappearance of glucose and the appearance of the major end products in the 2H NMR spectrum. The presence of both labeled and unlabeled metabolites could be detected using 1H NMR spectroscopy since the proton resonances in the labeled species are shifted upfield due to an isotopic chemical shift effect. The 1H-1H scalar coupling observed in both the 2H and 1H NMR spectra was used to assign definitively the resonances of labeled species. An increase in the intensity of natural abundance deuterium signal of water can be used to monitor pathways in which a deuteron is lost from the labeled metabolite. The steps in which label loss can occur are outlined, and the influence these processes have on the ability of 2H NMR spectroscopy to monitor metabolism are assessed.

  13. A Deuterium NMR Study of Bent-Core Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Dingemans, Theo J.; Madsen, Louis A.; Samulski, Edward T.

    2002-10-01

    We have synthesized two deuterated boomerang-shaped liquid crystals based on 2,5-bis(4-hydroxyphenyl)-1,3,4-oxadiazole (ODBP). Deuterium was introduced in the rigid 2,5-diphenyl-1,3,4-oxadiazole core and in the aromatic ring of the terminal 4-dodecyloxyphenyl moiety using standard acid catalyzed deuterium exchange conditions. Both compounds, (4,4'(1,3,4-oxadiazole-2,5-diyl-d4) di-4-dodecyloxybenzoate: ODBP-d4-Ph-O-C12) and (4,4'(1,3,4-oxadiazole-2,5-diyl) di-4-dodecyloxy-benzoate-d4; ODBP-Ph-d4-O-C12) were investigated by nuclear magnetic resonance, optical microscopy and differential scanning calorimetry. The optical textures and thermal behavior of both compounds were found to be identical to the non-deuterated analog 4,4(1,3,4-oxadiazole-2,5-diyl) di-4-dodecyloxybenzoate (ODBP-Ph-O-C12) which we reported earlier. These compounds exhibit behavior indicative of a biaxial nematic liquid crystal phase, which we hope to confirm using deuterium NMR spectroscopy in the next phase of this study.

  14. Vibrational and NMR probe studies of S Az-1 montmorillonite

    SciTech Connect

    Johnston, C.T.; Erickson, C.; Earl, W.L.

    1992-09-01

    This paper reports a study of the interactions of exchangeable metal cations with mineral surfaces using a combined spectroscopic/macroscopic approach. Objectives were to examine the use of water molecules and metal cations as molecular probes of smectite water interactions. The {nu}{sub 2} mode of water is used as a diagnostic vibrational band. An FTIR-gravimetric cell is used to examine the FTIR spectra of water on homoionic smectites. The {sup 23}Na NMR resonance is used to probe metal-water interactions on the surface. Results show that there are strong changes in both position and absorption coefficient of the H-O-H bending mode of water sorbed on SAz-1 montmorillonite as a function of water content. These changes are attributed to strong electrostatic forces and mobility changes that occur when the water in the interlammelar space is associated with the metal ion. The clay surface is viewed as having at least two distinct sites to which a hydrated Na{sup +} can bind. 32 refs, 5 figs. (DLC)

  15. Vibrational and NMR probe studies of S Az-1 montmorillonite

    SciTech Connect

    Johnston, C.T.; Erickson, C. . Dept. of Soil Science); Earl, W.L. )

    1992-01-01

    This paper reports a study of the interactions of exchangeable metal cations with mineral surfaces using a combined spectroscopic/macroscopic approach. Objectives were to examine the use of water molecules and metal cations as molecular probes of smectite water interactions. The {nu}{sub 2} mode of water is used as a diagnostic vibrational band. An FTIR-gravimetric cell is used to examine the FTIR spectra of water on homoionic smectites. The {sup 23}Na NMR resonance is used to probe metal-water interactions on the surface. Results show that there are strong changes in both position and absorption coefficient of the H-O-H bending mode of water sorbed on SAz-1 montmorillonite as a function of water content. These changes are attributed to strong electrostatic forces and mobility changes that occur when the water in the interlammelar space is associated with the metal ion. The clay surface is viewed as having at least two distinct sites to which a hydrated Na{sup +} can bind. 32 refs, 5 figs. (DLC)

  16. NMR studies of the conformational interconversion of butaclamol in solution.

    PubMed

    Casarotto, M G; Craik, D J; Lloyd, E J

    1991-07-01

    1H NMR experiments at 300 MHz have been carried out to determine the identity and study the interconversion of two conformations of butaclamol in solution. The hydrochloride salt in DMSO exists as an equilibrium mixture of two conformations, which differ in their stereochemistry about the ring junction that contains the single nitrogen atom in butaclamol. The trans form has a relative population of 80% and the cis I form 20%. In CDCl3 only the trans form is observed, while in CDCl3-DMSO mixtures, both forms are detected in a ratio (trans:cis I) that decreases as the percentage of CDCl3 decreases. For the free base in either CD2Cl2 or DMSO, only a single set of resonances is observed at room temperature, but as temperature is lowered, peaks from methine protons H4a and H13b near the ring junction broaden and (for samples in CD2Cl2) eventually split into two resonances corresponding to the cis and trans forms. It is suggested that nitrogen inversion is the dynamic process responsible for the interconversion of the two forms. Line shape analysis as a function of temperature yielded an energy barrier of 9.6 +/- 0.5 kcal/mol for the interconversion, in good agreement with values obtained from saturation transfer experiments. In the hydrochloride salt, the barrier in DMSO was somewhat higher, i.e., 17.3 +/- 0.9 kcal/mol, as determined by saturation transfer and variable-temperature measurements.

  17. Protein secondary structure of Green Lynx spider dragline silk investigated by solid-state NMR and X-ray diffraction

    PubMed Central

    Xu, Dian; Shi, Xiangyan; Thompson, Forrest; Weber, Warner S.; Mou, Qiushi; Yarger, Jeffery L

    2016-01-01

    In this study, the secondary structure of the major ampullate silk from Peucetia viridans (Green Lynx) spiders is characterized by X-ray diffraction and solid-state NMR spectroscopy. From X-ray diffraction measurement, β-sheet nanocrystallites were observed and found to be highly oriented along the fiber axis, with an orientational order, fc ≈ 0.98. The size of the nanocrystallites was determined to be on average 2.5 nm × 3.3 nm × 3.8 nm. Besides a prominent nanocrystalline region, a partially oriented amorphous region was also observed with an fa ≈ 0.89. Two-dimensional 13C–13C through-space and through-bond solid-state NMR experiments were employed to elucidate structure details of P. viridans silk proteins. It reveals that β-sheet nanocrystallites constitutes 40.0 ± 1.2% of the protein and are dominated by alanine-rich repetitive motifs. Furthermore, based upon the NMR data, 18 ± 1% of alanine, 60 ± 2% glycine and 54 ± 2% serine are incorporated into helical conformations. PMID:26226457

  18. Stereospecific assignment of 1H resonances through chemical shift calculation and their use in structure determination by NMR

    NASA Astrophysics Data System (ADS)

    Harvey, Timothy S.; van Gunsteren, Wilfred F.; Ikura, Mitsuhiko

    1995-04-01

    Understanding of the factors which influence proton chemical shifts in nuclear magnetic resonance (NMR) spectra of proteins has advanced steadily as the number of proteins, for which assignments in conjunction with high resolution structures have been obtained, has increased. Progress has been made in both the calculation of chemical shifts from given coordinates, both empirically for 1H (Williamson & Asakura J. Magn. Reson. (1991) 94, 557) and using ab initio approaches for calculation of 13C (De Dios et al. Science (1993) 260, 1491). Concomitantly Wishart et al. (J. Mol. Biol. (1992) 222, 311), using statistical methods have clarified the relationship between Hα chemical shift and regular secondary structure in proteins to a high degree of accuracy. We recently demonstrated the significant amount of structural information present in the Hα chemical shift through the use of chemical shift restrained molecular dynamics simulations (Harvey & van Gunsteren Techniques in Protein Chemistry IV (1993) 615, Academic Press). Here we apply a similar methodology to the stereospecific assignment of methylene and methyl proton resonances in proteins. Stereospecific assignment of such 1H resonances dramatically increases the degree of precision of ensembles of structures derived from NMR data. However, this is often a cumbersome process, requiring detailed analysis of large amounts of data. Furthermore, experimental considerations such as poor signal-to-noise ratios, spectral overlap and spin diffusion combine to make this process somewhat unreliable. We present calculations of the chemical shifts for the known structures of bovine pancreatic trypsin inhibitor (Mw 6.5 kDa) and the α-amylase inhibitor tendamistat (Mw 8 kDa), for which stereospecific assignments and high resolution structures from both NMR and crystallographic studies are available. The methods described are also applied to the ensemble of structures obtained for protein S (Mw 19 kDa) for both structure

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

    PubMed Central

    Kucharska, Iga; Edrington, Thomas C.; Liang, Binyong

    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. PMID:25869397

  20. Unique molecular dynamics of structural elements in an asymmetric Janus bisamide supramolecule characterized by solid-state NMR.

    PubMed

    Chen, Wei; Sun, Hao-Jan; Miyoshi, Toshikazu

    2013-10-31

    An asymmetric tapered Janus bisamide supramolecule consisting of 1,4-bis[3,4,5-tris(alkan-1-yloxy)benzamido]benzene bisamide (abbreviated as C22PhBAEO3) can possess three-dimensional (3D) long-range order under mild thermal treatment conditions. To understand its structural formation and unique phase-transition processes, the locally detailed structure and molecular dynamics of its structural elements in disordered and ordered phases of C22PhBAEO3 were investigated using various solid-state (SS) NMR techniques at the atomic level. On the basis of the determined conformations and packing structures of the alkyl chains in ordered and disordered crystalline phases, along with the geometry and kinetic parameters of the structural elements' dynamics, this study addresses the self-assembly, the phase-transition mechanisms, and the relationship between the structure and dynamics of these asymmetric Janus bisamide supramolecules.

  1. NMR study of black-phase in SmS

    NASA Astrophysics Data System (ADS)

    Koyama, T.; Yamada, H.; Ueda, K.; Mito, T.; Haga, Y.

    2015-03-01

    We report the result of the 33S nuclear magnetic resonance (NMR) measurement on the nonmagnetic semiconductor SmS at ambient pressure. For this measurement, the 33S isotope enriched powder sample of SmS was prepared to increase the 33S NMR intensity. We have attempted 33S NMR measurement on SmS and successfully observed the signal of it. With decreasing temperature, the spectrum measured at the constant magnetic field shifted to lower frequency and became weakly temperature dependent below 50 K. The presence of the energy gap was microscopically established by the rapid decrease in the nuclear spin-lattice relaxation rate 1/T1. The activation energy was deduced to be 625 K from an Arrhenius plot of T1.

  2. High-temperature, high-pressure hydrothermal synthesis, crystal structure, and solid-state NMR spectroscopy of Cs2(UO2)(Si2O6) and variable-temperature powder X-ray diffraction study of the hydrate phase Cs2(UO2)(Si2O6) x 0.5H2O.

    PubMed

    Chen, Chih-Shan; Chiang, Ray-Kuang; Kao, Hsien-Ming; Lii, Kwang-Hwa

    2005-05-30

    A new uranium(VI) silicate, Cs2(UO2)(Si2O6), has been synthesized by a high-temperature, high-pressure hydrothermal method and characterized by single-crystal X-ray diffraction and solid-state NMR spectroscopy. It crystallizes in the orthorhombic space group Ibca (No. 73) with a = 15.137(1) A, b = 15.295(1) A, c = 16.401(1) A, and Z = 16. Its structure consists of corrugated achter single chains of silicate tetrahedra extending along the c axis linked together via corner-sharing by UO6 tetragonal bipyramids to form a 3-D framework which delimits 8- and 6-ring channels. The Cs+ cations are located in the channels or at sites between channels. The 29Si and 133Cs MAS NMR spectra are consistent with the crystal structure as determined from X-ray diffraction, and the resonances in the spectra are assigned. Variable-temperature in situ powder X-ray diffraction study of the hydrate Cs2(UO2)(Si2O6) x 0.5H2O indicates that the framework structure is stable up to 800 degrees C and transforms to the structure of the title compound at 900 degrees C. A comparison of related uranyl silicate structures is made.

  3. Probing membrane protein structure using water polarization transfer solid-state NMR

    NASA Astrophysics Data System (ADS)

    Williams, Jonathan K.; Hong, Mei

    2014-10-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected 1H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins.

  4. Probing membrane protein structure using water polarization transfer solid-state NMR.

    PubMed

    Williams, Jonathan K; Hong, Mei

    2014-10-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins.

  5. NMR studies of osmoregulation in methanogenic archaebacteria. [NMR (nuclear magnetic resonance)

    SciTech Connect

    Robertson, D.E.

    1991-01-01

    Methanogens are strict anaerobic archaebacteria whose metabolism centers around the reduction of CO[sub 2] to CH[sub 4]. Their environments are often extreme (high temperatures, high salt, few nutrients, etc.) and they may have evolved unique ways to handle these stresses. It is proposed that methanogenic archaebacteria respond to osmotic stress by accumulating a series of organic solutes. In two strains of marine methanogens, Methanogenium cariaci and Methanococcus thermolithotrophicus, four key organic solutes are observed: L-[alpha]-glutamate, [beta]-glutamate, N[sup e]-acetyl-[beta]-lysine, and glycine betaine. The first three of these are synthesized de novo; glycine betaine is transported into the Mg. cariaci cells from the medium. In the absence of betaine, Mg. cariaci synthesizes N[sup e]-acetyl-[beta]-lysine as the dominant osmolyte. Mc. thermolithotrophicus also synthesizes N[sup e]-acetyl-[beta]-lysine but only at salt concentrations greater than 1 M. In Mc. thermolithotrophicus intracellular potassium ion concentrations, determined by [sup 39]K NMR spectroscopy, are balanced by the total concentration of anionic amino acid species, [alpha]-glutamate and [beta]-glutamate. Turnover of the organic solutes has been monitored using [sup 13]C-pulse/[sup 12]C-chase, and [sup 15]N-pulse/[sup 14]N-chase experiments. The [beta]-amino acids exhibit slower turnover rates compared to L-[alpha]-glutamate or aspartate, consistent with their role as compatible solutes. Biosynthetic information for the [beta]-amino acids was provided by [sup 13]C-label incorporation and steady state labeling experiments. [beta]-glutamate shows a lag in [sup 13]C uptake from [sup 13]CO[sub 2], indicative of its biosynthesis from a precursor not in equilibrium with the soluble L-[alpha]-glutamate pool, probably a macromolecule. A novel biosynthetic pathway is proposed for N[sup e]-acetyl-[beta]-lysine from the diaminopimelate pathway.

  6. Well-defined azazirconacyclopropane complexes supported on silica structurally determined by 2D NMR comparative elucidation.

    PubMed

    El Eter, Mohamad; Hamzaoui, Bilel; Abou-Hamad, Edy; Pelletier, Jérémie D A; Basset, Jean-Marie

    2013-05-21

    Grafting of Zr(NMe2)4 on mesoporous silica SBA-15 afforded selectively well-defined surface species [triple bond, length as m-dash]SiOZr(NMe2)(η2NMeCH2). 2D solid-state NMR ((1)H-(13)C HETCOR, Multiple Quantum) experiments have shown a unique structural rearrangement occurring on the immobilised zirconium bis methylamido ligand.

  7. Structural variation in ethylenediamine and -diphosphine adducts of (2,6-Me2C6H3S)2Pb: a single crystal X-ray diffraction and 207Pb solid-state NMR spectroscopy study.

    PubMed

    Rossini, Aaron J; Macgregor, Alan W; Smith, Anita S; Schatte, Gabriele; Schurko, Robert W; Briand, Glen G

    2013-07-14

    Coordination complexes of (2,6-Me2C6H3S)2Pb (1) with flexible bidentate ligands have been prepared to explore new bonding environments for Pb(II) thiolates. The reaction of 1 with a series of ethylenediamine and ethylenediphosphine ligands resulted in isolation of the adducts [(2,6-Me2C6H3S)2Pb]2(tmeda) (9), [(2,6-Me2C6H3S)2Pb]3(dmpe) (10) and [(2,6-Me2C6H3S)2Pb]2(dppe) (11) [tmeda = N,N,N',N'-tetramethylethylenediamine; dmpe = bis(dimethylphosphino)ethane; dppe = bis(diphenylphosphino)ethane]. The X-ray crystal structure of 9 shows a dinuclear species in which tmeda is chelating a ψ-trigonal bipyramidal S2N2 Pb centre via axial and equatorial sites. The structure of 10 displays a trinuclear structural unit in which dmpe is chelating a ψ-trigonal bipyramidal S2P2 Pb centre via equatorial sites. Compounds 9 and 10 also contain a second unique metal centre with ψ-tetrahedral S3Pb bonding motifs. The structure of 11 shows the dppe ligand bridging two Pb ψ-tetrahedral S2P metal bonding environments. Static (207)Pb solid-state NMR (SSNMR) spectra of 9-11 and [Ph4As][(PhS)3Pb] (12) were acquired with cross polarization (CP)-CPMG and frequency swept pulse (WURST)-CPMG pulse sequences, and the efficiencies of these pulse sequences are compared. The (207)Pb SSNMR spectra reveal that the lead chemical shift anisotropies (CSA) vary greatly between the different Pb sites, and are generally large in magnitude. DFT calculations are utilized to relate the orientations of the (207)Pb nuclear magnetic shielding tensors to the molecular structures, and to aid in spectral assignment where multiple Pb centres are present. The combination of X-ray diffraction, (207)Pb SSNMR and DFT is shown to be invaluable for the structural characterization of these important structural motifs, and should find wide-ranging application to numerous lead coordination compounds.

  8. Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.

    PubMed

    Mareuil, Fabien; Malliavin, Thérèse E; Nilges, Michael; Bardiaux, Benjamin

    2015-08-01

    In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD-NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD-NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.

  9. Dynamics of Reassembled Thioredoxin Studied by Magic Angle Spinning NMR: Snapshots from Different Timescales

    PubMed Central

    Yang, Jun; Tasayco, Maria Luisa; Polenova, Tatyana

    2014-01-01

    Solid-state NMR spectroscopy can be used to probe internal protein dynamics in the absence of the overall molecular tumbling. In this study, we report 15N backbone dynamics in differentially enriched 1-73(U-13C, 15N)/74-108(U-15N) reassembled thioredoxin on multiple timescales using a series of 2D and 3D MAS NMR experiments probing the backbone amide 15N longitudinal relaxation, 1H-15N dipolar order parameters, 15N chemical shift anisotropy (CSA), and signal intensities in the temperature-dependent and 1H T2′ -filtered NCA experiments. The spin-lattice relaxation rates R1(R1 = 1/T1) were observed in the range from 0.012 to 0.64 s-1 indicating large site-to-site variations in dynamics on pico- to nanosecond time scales. The 1H-15N dipolar order parameters, , and 15N CSA anisotropies, δσ reveal the backbone mobilities in reassembled thioredoxin, as reflected in the average = 0.89 ± 0.06 and δσ = 92.3 ± 5.2 ppm, respectively. From the aggregate of experimental data from different dynamics methods, some degree of correlation between the motions on the different time scales has been suggested. Analysis of the dynamics parameters derived from these solid-state NMR experiments indicates higher mobilities for the residues constituting irregular secondary structure elements than for those located in the α-helic