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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. NMR structural studies on antifreeze proteins.

    PubMed

    Sönnichsen, F D; Davies, P L; Sykes, B D

    1998-01-01

    Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of approximately 1 degree C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice.

  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 focused on variable temperature spin lattice relaxation measurements for several of the Argonne coals. 5 figs.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

    PubMed Central

    Konrat, Robert

    2014-01-01

    Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. NMR studies of molecular structure in fruit cuticle polyesters.

    PubMed

    Fang, X; Qiu, F; Yan, B; Wang, H; Mort, A J; Stark, R E

    2001-07-01

    The cuticle of higher plants functions primarily as a protective barrier for the leaves and fruits, controlling microbial attack as well as the diffusion of water and chemicals from the outside environment. Its major chemical constituents are waxes (for waterproofing) and cutin (a structural support polymer). However, the insolubility of cutin has hampered investigations of its covalent structure and domain architecture, which are viewed as essential for the design of crop protection strategies and the development of improved synthetic waterproofing materials. Recently developed strategies designed to meet these investigative challenges include partial depolymerization using enzymatic or chemical reagents and spectroscopic examination of the intact polyesters in a solvent-swelled form. The soluble oligomers from degradative treatments of lime fruit cutin are composed primarily of the expected 10,16-dihydroxyhexadecanoic and 16-hydroxy-10-oxo-hexadecanoic acids; low-temperature HF treatments also reveal sugar units that are covalently attached to the hydroxyfatty acids. Parallel investigations of solvent-swollen cutin using 2D NMR spectroscopy assisted by magic-angle spinning yield well-resolved spectra that permit detailed comparisons to be made among chemical moieties present in the intact biopolymer, the soluble degradation products, and the unreacted solid residue.

  1. Investigation of structural information for boron-rich solids and aluminates via NMR and NQR studies

    SciTech Connect

    Lee, D.

    1991-01-01

    Along with NMR, Nuclear Quadrupole Resonance (NQR) has become important recently for obtaining structural information from oxide glasses. The NQR studies prove in this thesis that they provide more accurate structural information than the NMR studies have done. This study presents boron and aluminum NMR, and NQR studies for some borate glasses and compounds, icosahedral boron-rich solids, some crystalline aluminosilicates. Various borates were employed to acquire structural information as well as to determine the quadrupole parameters (the quadrupole coupling constant Qcc and the asymmetry parameter {eta}) using NQR under a guidance of NMR or vice versa. By NQR a previously unknown boron site was observed for vitreous Li{sub 2}O{center dot}B{sub 2}O{sub 3}. The NMR and NQR studies were performed on some icosachedral boron-rich solids: {alpha}-rhombohedral boron (B{sub 12}), {beta}-boron (B{sub 105}) and boron carbide (B{sub 12}C{sub 3}). Three different forms of crystalline aluminosilicate (Al{sub 2}SiO{sub 5}) were studied by NQR. The NQR study yielded more accurate values of the quadrupole parameters for {sup 27}Al than the previous NMR single crystal study did.

  2. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding.

    PubMed

    Tugarinov, Vitali

    2014-02-01

    A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. 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.

  4. Studies on solution NMR structure of brazzein : Secondary structure and molecular scaffold.

    PubMed

    Gao, G; Dai, J; Ding, M; Hellekant, G; Wang, J; Wang, D

    1999-08-01

    Brazzein is a sweet-tasting protein isolated from the fruit of West African plantPentadiplandra brazzeana Baillon. It is the smallest and the most water-soluble sweet protein discovered so far and is highly thermostable. The proton NMR study of brazzein at 600 MHz (pH 3.5, 300 K) is presented. The complete sequence specific assignments of the individual backbone and sidechain proton resonances were achieved using through-bond and through-space connectivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one alpha-helix (residues 21-29), one short 3(10)-helix (residues 14-17), two strands of antiparallel beta-sheet (residues 34-39, 44-50) and probably a third strand (residues 5-7) near the N-terminus. A comparative analysis found that brazzein shares a so-called 'cysteine-stabilized alpha-beta' (CSalphabeta) motif with scorpion neurotoxins, insect defensins and plant gamma - thionins. The significance of this multi-function motif, the possible active sites and the structural basis of themostability were discussed.

  5. Crystal structure and dynamic NMR studies of octaacetyl-tetra(propyl)calix[4]resorcinarene

    NASA Astrophysics Data System (ADS)

    Velásquez-Silva, Astrid; Cortés, Brian; Rivera-Monroy, Zuly J.; Pérez-Redondo, Adrián; Maldonado, Mauricio

    2017-06-01

    The reaction between C-tetra(propyl)calix[4]resorcinarene (1) and acetic anhydride in pyridine results in the formation of octaacetyl-tetra(propyl)calix[4]resorcinarene (2). The structure was determined using FT-IR, 1H-NMR and 13C-NMR. The dynamic 1H-NMR of acetylated resorcinarene was studied by means of variable temperature in a CDCl3 solution and revealed that two conformers are formed in the solution. Boat conformations for acetylated resorcinarene exhibited a rapid interconversion at low temperatures, and the activation barrier for the pseudorotation was determined (54.72 kJmol-1). The acetylated resorcinarene 2 was also characterized by an X-ray crystal structure determination. This analysis indicated a boat configuration for the macrocycle skeleton in the solid state. Csbnd H⋯O hydrogen bonding interactions were observed in the packing of compound.

  6. 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.

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

    SciTech Connect

    Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; Gan, Zhehong; Kelly, Jeffery W.; Wright, Peter E.; Wemmer, David E.

    2016-09-20

    © 2016 American Chemical Society. Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectively 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.

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

    DOE PAGES

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

    2016-09-20

    © 2016 American Chemical Society. Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlationmore » MAS spectra obtained with selectively 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

  9. Preparation of Protein Samples for NMR Structure, Function, and Small Molecule Screening Studies

    PubMed Central

    Acton, Thomas B.; Xiao, Rong; Anderson, Stephen; Aramini, James; Buchwald, William A.; Ciccosanti, Colleen; Conover, Ken; Everett, John; Hamilton, Keith; Huang, Yuanpeng Janet; Janjua, Haleema; Kornhaber, Gregory; Lau, Jessica; Lee, Dong Yup; Liu, Gaohua; Maglaqui, Melissa; Ma, Lichung; Mao, Lei; Patel, Dayaban; Rossi, Paolo; Sahdev, Seema; Shastry, Ritu; Swapna, G.V.T.; Tang, Yeufeng; Tong, Saichiu; Wang, Dongyan; Wang, Huang; Zhao, Li; Montelione, Gaetano T.

    2014-01-01

    In this chapter, we concentrate on the production of high quality protein samples for NMR studies. In particular, we provide an in-depth description of recent advances in the production of NMR samples and their synergistic use with recent advancements in NMR hardware. We describe the protein production platform of the Northeast Structural Genomics Consortium, and outline our high-throughput strategies for producing high quality protein samples for nuclear magnetic resonance (NMR) studies. Our strategy is based on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems and isotope enrichment in minimal media. We describe 96-well ligation-independent cloning and analytical expression systems, parallel preparative scale fermentation, and high-throughput purification protocols. The 6X-His affinity tag allows for a similar two-step purification procedure implemented in a parallel high-throughput fashion that routinely results in purity levels sufficient for NMR studies (> 97% homogeneity). Using this platform, the protein open reading frames of over 17,500 different targeted proteins (or domains) have been cloned as over 28,000 constructs. Nearly 5,000 of these proteins have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html), resulting in more than 950 new protein structures, including more than 400 NMR structures, deposited in the Protein Data Bank. The Northeast Structural Genomics Consortium pipeline has been effective in producing protein samples of both prokaryotic and eukaryotic origin. Although this paper describes our entire pipeline for producing isotope-enriched protein samples, it focuses on the major updates introduced during the last 5 years (Phase 2 of the National Institute of General Medical Sciences Protein Structure Initiative). Our advanced automated and/or parallel cloning, expression, purification, and biophysical screening

  10. 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

  11. 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.

  12. A high-resolution solid-state NMR approach for the structural studies of bicelles.

    PubMed

    Dvinskikh, Sergey; Dürr, Ulrich; Yamamoto, Kazutoshi; Ramamoorthy, Ayyalusamy

    2006-05-17

    Bicelles are increasingly being used as membrane mimicking systems in NMR experiments to investigate the structure of membrane proteins. In this study, we demonstrate the effectiveness of a 2D solid-state NMR approach that can be used to measure the structural constraints, such as heteronuclear dipolar couplings between 1H, 13C, and 31P nuclei, in bicelles without the need for isotopic enrichment. This method does not require a high radio frequency power unlike the presently used rotating-frame separated-local-field (SLF) techniques, such as PISEMA. In addition, multiple dipolar couplings can be measured accurately, and the presence of a strong dipolar coupling does not suppress the weak couplings. High-resolution spectra obtained from magnetically aligned DMPC:DHPC bicelles even in the presence of peptides suggest that this approach will be useful in understanding lipid-protein interactions that play a vital role in shaping up the function of membrane proteins.

  13. A High Resolution Solid State NMR Approach for the Structural Studies of Bicelles

    PubMed Central

    Dvinskikh, Sergey; Dürr, Ulrich; Yamamoto, Kazutoshi; Ramamoorthy, Ayyalusamy

    2008-01-01

    Bicelles are increasingly being used as membrane mimicking systems in NMR experiments to investigate the structure of membrane proteins. In this study, we demonstrate the effectiveness of a 2D solid-state NMR approach that can be used to measure the structural constraints such as heteronuclear dipolar couplings between 1H, 13C and 31P nuclei in bicelles without the need for isotopic enrichment. This method does not require a high radio frequency power unlike the presently used rotating-frame separated-local-field (SLF) techniques like PISEMA. In addition, multiple dipolar couplings can be measured accurately and the presence of a strong dipolar coupling does not suppress the weak couplings. High resolution spectra obtained from magnetically aligned DMPC:DHPC bicelles even in the presence of peptides suggest that this approach will be useful in understanding lipid-protein interactions that play a vital role in shaping up the function of membrane proteins. PMID:16683791

  14. (1)H NMR Study of the solution structure of sarafotoxin-S6b.

    PubMed

    Aumelas, A; Chiche, L; Mahe, E; Le-Nguyen, D; Sizun, P; Berthault, P; Perly, B

    1991-01-01

    Sarafotoxin-S6b has been synthesized and studied by (1)H NMR in 50 50 acetonitrile/water mixture. All spin systems were identified and assigned with the aid of 2D experiments. On the basis of these data, a 3D structure of sarafotoxin is proposed and compared to that of [Nle(7)]endothelin obtained in the same conditions. From this study, it appeared that sarafotoxin-S6b and [Nle(7)]endothelin roughly share the same 3D structure, the main differences being located in the 4-7 loop bearing the sequence variation.

  15. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy

    PubMed Central

    Jaroniec, Christopher P.

    2015-01-01

    Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ~20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags. PMID:25797004

  16. Structure-activity study of thiazides by magnetic resonance methods (NQR, NMR, EPR) and DFT calculations.

    PubMed

    Latosińska, J N

    2005-01-01

    The paper presents a comprehensive analysis of the relationship between the electronic structure of thiazides and their biological activity. The compounds of interest were studied in solid state by the resonance methods nuclear quadrupole resonance (NQR), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) and quantum chemistry (ab inito and DFT) methods. Detailed parallel analysis of the spectroscopic parameters such as quadrupole coupling constant (QCC) NQR chemical shift (delta), chemical shift anisotropy (CSA), asymmetry parameter (eta), NMR and hyperfine coupling constant (A), EPR was performed and the electronic effects (polarisation and delocalisation) were revealed and compared. Biological activity of thiazides has been found to depend on many factors, but mainly on the physico-chemical properties whose assessment was possible on the basis of electron density determination in the molecules performed by experimental and theoretical methods.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. NMR studies of protein structure and dynamics - a look backwards and forwards.

    PubMed

    Kay, Lewis E

    2011-12-01

    NMR spectroscopy has evolved to become one of the most powerful tools for the study of protein structure and dynamics. Advances over the past decade have greatly extended the methodology to studies of molecules of ever increasing complexity. Herein I provide a short perspective relating the circumstances that led to some of the contributions from my laboratory in this area and highlight how these original experiments, summarized in a Journal of Magnetic Resonance article in 2005 (JMR, 173 193–207), have influenced the current focus of my research. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Solid-state NMR studies of the dynamics and structure of mouse keratin intermediate filaments

    SciTech Connect

    Mack, J.W.; Torchia, D.A.; Steinert, P.M.

    1988-07-26

    The molecular dynamics and structural organization of mouse epidermal keratin intermediate filaments (IF) have been studied via solid-state nuclear magnetic resonance (NMR) experiments performed on IF labeled both in vivo and in vitro with isotopically enriched amino acids. As a probe of the organization of the peripheral glycine-rich end domains of the IF, carbon-13 NMR experiments have been performed on subfilamentous forms (prekeratin) and on IF reassembled in vitro that had been labeled with either (1-/sup 13/C)glycine or (2-/sup 13/C)glycine, as more than 90% of the glycines of the keratins are located in the end domains. Measurements of carbon relaxation times, nuclear Overhauser enhancements, and signal intensities show that the motions of the peptide backbone in the end domains are effectively isotropic. These results indicate that the end domains of IF are remarkably flexible and have little or no structural order. To probe the structural organization of the coiled-coil rod domains of the IF, separate samples of native keratin IF, raised in primary tissue culture, were labeled with L-(1-/sup 13/C)leucine, L-(/sup 2/H/sub 10/)leucine, or L-(2,3,3-/sup 2/H/sub 3/)leucine, as greater than 90% of the leucyl residues of the keratin IF types studied are located in the coiled coils which form the central core of IF. Deuterium NMR experiments performed on IF labeled with deuteriated leucines indeed reveal a marked degree of peptide backbone rigidity within the coiled coils, confirming the initial conclusions of the carbon-13 data. These data, demonstrating relative peptide backbone rigidity yet side-chain flexibility, are interpreted to mean that the coiled coils of these keratin IF are not tightly packed together but rather form a somewhat looser structure which permits a significant degree of side-chain mobility.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Improving NMR Structures of RNA

    PubMed Central

    Bermejo, Guillermo A.; Clore, G. Marius; Schwieters, Charles D.

    2016-01-01

    SUMMARY Here, we show that modern solution NMR structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA. PMID:27066747

  11. NMR study of lanthanide(III) nitrate-CMPO extraction system (I) structure of extracted chemical species

    SciTech Connect

    Nakamura, Takashi; Miyake, Chie )

    1994-10-01

    NMR measurements carried out to study the coordination structure of lanthanide(III)-CMPO complexes indicate that the CMPO molecule is located in the equatorial region with respect to the principal magnetic Z axis. NMR longitudinal relaxation time measurements suggest that CMPO coordinates to the central Ce[sup 3+] ion in a bidentate manner with the phosphoryl and carbonyl groups. Further, it was observed that a rapid intramolecular interconversion occurs at a higher temperature region. 14 refs., 10 figs., 3 tabs.

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  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. Two dimensional NMR and NMR relaxation studies of coal structure. Progress report, April 1, 1992--June 30, 1992

    SciTech Connect

    Zilm, K.W.

    1992-09-01

    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.

  20. Structural studies of. cap alpha. -bungarotoxin. 1. Sequence-specific /sub 1/H NMR resonance assignments

    SciTech Connect

    Basus, V.J.; Billeter, M.; Love, R.A.; Stroud, R.M.; Kuntz, I.D.

    1988-04-19

    The authors report the complete sequence-specific assignment of the backbone resonances and most of the side-chain resonances in the /sup 1/H NMR spectrum of ..cap alpha..-bungarotoxin by two-dimensional NMR. Problems with resonance overlap were resolved with the assistance of the HRNOESY experiment described in an accompanying paper. Significant differences exist between the solution structure described here and the crystal structure of ..cap alpha..-bungarotoxin, on the basis of the proton to proton distances obtained by nuclear Overhauser enhancement spectroscopy (NOESY) and the corresponding distances from the X-ray crystal structure. These differences include a larger ..beta..-sheet in solution and a different orientation of the invariant tryptophan, Trp-28, making the solution structure more consistent with the crystal structure of the homologous neurotoxin ..cap alpha..-cobratoxin. Four errors in the order of the amino acids in the primary sequence were indicated by the NMR data. These errors were confirmed by chemical means, as described in an accompanying paper.

  1. 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.

  2. NMR study of vacancy and structure-induced changes in Cu2-xTe

    NASA Astrophysics Data System (ADS)

    Sirusi, Ali A.; Page, Alexander; Uher, Ctirad; Ross, Joseph H.

    2017-07-01

    We report Cu and Te NMR measurements on Cu2-xTe with x between 0.13 and 0.22. Aided by powder x-ray analysis and computed NMR quadrupole shifts, a structure change near x=0.20 was found consistent with structures reported by Baranova, with best fits to the β-I structure for x=0.22 and β-III for smaller x. NMR T1 and Hall effect results demonstrate p-type electronic behavior with filling of simple hole pockets induced by increased numbers of vacancies for both phases. Furthermore the Cu and Te chemical shifts are large and negative, as observed in topologically inverted semiconductors, with a splitting into two distinct local environments for both Cu and Te sites in the x=0.22 structure. Cu T1 results show a rapid decrease of the energy barrier for initiation of Cu ion hopping to 0.12 eV for x=0.22, considerably smaller than observed at higher temperatures, indicating a tail of relatively mobile Cu ions which may be of significance for potential device applications.

  3. High-resolution /sup 1/H NMR study of the solution structure of delta-hemolysin

    SciTech Connect

    Tappin, M.J.; Pastore, A.; Norton, R.S.; Freer, J.H.; Campbell, I.D.

    1988-03-08

    The 26-residue toxin from Staphylococcus aureus delta-hemolysin, is thought to act by traversing the plasma membrane. The structure of this peptide, in methanol solution, has been investigated by using high-resolution NMR in combination with molecular dynamics calculations. The /sup 1/H NMR spectrum has been completely assigned, and it is shown that residues 2-20 form a relatively stable helix while the residues at the C-terminal end appear to be more flexible. The structures were calculated only from nuclear Overhauser effect data and standard bond lengths. It is shown that the results are consistent with /sup 3/J/sub NH-..cap alpha..CH/ coupling constants and amide hydrogen exchange rates.

  4. Structure and dynamics of aqueous 2-propanol: a THz-TDS, NMR and neutron diffraction study.

    PubMed

    McGregor, James; Li, Ruoyu; Zeitler, J Axel; D'Agostino, Carmine; Collins, James H P; Mantle, Mick D; Manyar, Haresh; Holbrey, John D; Falkowska, Marta; Youngs, Tristan G A; Hardacre, Christopher; Stitt, E Hugh; Gladden, Lynn F

    2015-11-11

    Aqueous liquid mixtures, in particular, those involving amphiphilic species, play an important role in many physical, chemical and biological processes. Of particular interest are alcohol/water mixtures; however, the structural dynamics of such systems are still not fully understood. Herein, a combination of terahertz time-domain spectroscopy (THz-TDS) and NMR relaxation time analysis has been applied to investigate 2-propanol/water mixtures across the entire composition range; while neutron diffraction studies have been carried out at two specific concentrations. Excellent agreement is seen between the techniques with a maximum in both the relative absorption coefficient and the activation energy to molecular motion occurring at ∼90 mol% H2O. Furthermore, this is the same value at which well-established excess thermodynamic functions exhibit a maximum/minimum. Additionally, both neutron diffraction and THz-TDS have been used to provide estimates of the size of the hydration shell around 2-propanol in solution. Both methods determine that between 4 and 5 H2O molecules per 2-propanol are found in the 2-propanol/water clusters at 90 mol% H2O. Based on the acquired data, a description of the structure of 2-propanol/water across the composition range is presented.

  5. 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.

  6. 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

  7. 224} studied by NMR

    SciTech Connect

    Furukawa, Y; Fang, X; Kögerler, P

    2014-05-14

    7Li nuclear magnetic resonance (NMR) studies have been performed to investigate magnetic properties and spin dynamics of Mn3+ (S = 2) spins in the giant polyoxometalate molecule {Mn40W224}. The 7Li-NMR line width is proportional to the external magnetic field H as expected in a paramagnetic state above 3 K. Below this temperature the line width shows a sudden increase and is almost independent of H, which indicates freezing of the local Mn3+ spins. The temperature dependence of T1 for both 1H and 7Li reveals slow spin dynamics at low temperatures, consistent with spin freezing. The slow spin dynamics is also evidenced by the observation of a peak of 1/T2 around 3 K, where the fluctuation frequency of spins is of the order of ~200 kHz. An explicit form of the temperature dependence of the fluctuation frequency of Mn3+ spins is derived from the nuclear relaxation data.

  8. 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. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. NMR solution structure study of one saturated sulphur-containing amides from Glycosmis lucida.

    PubMed

    Geng, Zhu-Feng; Yang, Kai; Li, Yin-Ping; Guo, Shan-Shan; You, Chun-Xue; Zhang, Wen-Juan; Zhang, Zhe; Du, Shu-Shan

    2017-04-01

    One sulphur-containing amide (N-[2-(4-Hydroxyphenyl)-ethyl]-3-methanesulfonyl-N-methyl-propionamide) which was isolated from Glycosmis lucida Wall ex Huang had a different NMR profile with this kind of compounds' normal case. Based on the information obtained by nuclear magnetic resonance pectroscopy (NMR) and mass spectrometry (MS), its configurations in solution were investigated. The results indicated that the compound would have two stable configurations in solution as the double bond switched between C-N and C-O in an appropriate rate. This phenomenon was clearly exposed by the one dimension selective NOE (1D-NOE) experiments. This conclusion would play an active role in the structure analysis work of this kind of compounds.

  11. 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.

  12. The Three Dimensional Structure and Interaction Studies of HCV p7 in DHPC by Solution NMR

    PubMed Central

    Cook, Gabriel A.; Dawson, Lindsay A.; Tian, Ye; Opella, Stanley J.

    2013-01-01

    Hepatitis C Virus (HCV) protein p7 plays an important role in the assembly and release of mature virus particles. This small 63-residue membrane protein has been shown to induce channel activity, which may contribute to its functions. p7 is highly conserved throughout the entire range of HCV genotypes, which contributes to making p7 a potential target for anti-viral drugs. The secondary structure of p7 from the J4 genotype and the tilt angles of the helices within bilayers have been previously characterized by NMR. Here we describe the three-dimensional structure of p7 in short chain phospholipid (DHPC) micelles, which provide a reasonably effective membrane-mimicking environment that is compatible with solution NMR experiments. Using a combination of chemical shifts and residual dipolar couplings we determined the structure of p7 using an implicit membrane potential combining both CS-Rosetta decoys and Xplor-NIH refinement. The final set of structures has a backbone RMSD of 2.18 Å. Molecular dynamic simulations in NAMD indicate that several side chain interactions might be taking place, and that these could affect the dynamics of the protein. In addition to probing the dynamics of p7, several drug-protein and protein-protein interactions were evaluated. Established channel-blocking compounds such as amantadine, hexamethylene amiloride (HMA), and long alkyl-chain iminosugar derivatives inhibit the ion channel activity of p7. It has also been shown that the protein interacts with the HCV non-structural protein 2 (NS2) at the endoplasmic reticulum, and that this interaction may be important for the infectivity of the virus. Changes in the chemical shift frequencies of solution NMR spectra identify the residues taking part in these interactions. PMID:23841474

  13. 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.

  14. NMR study of oligonucleotides containing base pair mismatches and a human growth hormone peptide for the determination of solution structures

    SciTech Connect

    Roongta, V.A.

    1989-01-01

    Formation of unusual basepairs in DNA for random mutations in DNA was proposed in the sixties. These mismatches arise due to errors in replication, and from deamination of the 5-methylcytosine. The author's interest in studying mismatches and other oligonucleotides has been two fold. One is related to {sup 31}P chemical shifts and the backbone structure of oligonucleotides. He wanted to find out the significance of the dispersion of {sup 31}p chemical shifts in oligonucleotides. He wished to address whether this dispersion in {sup 31}P chemical shifts is related to global structural parameters of oligonucleotides like helix twist and whether he can prove the relationship between {sup 31}P chemical shifts and the backbone torsional angles epsilon and zeta. How does a mismatch affect {sup 31}P chemical shifts and the backbone torsional angle The second interest is related to solving the three dimensional structure of these biopolymers by using NMR data (NOESY distances) and computer simulations. His major study of these mismatches has been in the assignments of the protons resonances and the phosphorus resonances by 2D NMR. He has also tried to answer the question about the relationships between {sup 31}P chemical shifts and global parameters for DNA such as the helix twist. He has made substantial progress in determination of J(H3{prime}-P) coupling constants by 2D NMR and also in determining the relationship between the SIP chemical shifts and the backbone torsional angles by using the mismatch dodecamer sequences and the tetradecamer sequences. The 2D NMR data for the GG and GT mismatch have been used to determine three dimensional structures by using distance restrained molecular dynamics. The second project involved studying a 28 residue synthetic peptide by NMR.

  15. Structural study of the membrane protein MscL using cell-free expression and solid-state NMR.

    PubMed

    Abdine, Alaa; Verhoeven, Michiel A; Park, Kyu-Ho; Ghazi, Alexandre; Guittet, Eric; Berrier, Catherine; Van Heijenoort, Carine; Warschawski, Dror E

    2010-05-01

    High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75kDa pentameric alpha-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR. Copyright 2010 Elsevier Inc. All rights reserved.

  16. Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

    PubMed Central

    Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

    2010-01-01

    The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

  17. 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

  18. 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.

  19. NMR structural studies of the antibiotic lipopeptide daptomycin in DHPC micelles.

    PubMed

    Scott, Walter R P; Baek, Seung-Bin; Jung, David; Hancock, Robert E W; Straus, Suzana K

    2007-12-01

    Daptomycin is a cyclic anionic lipopeptide that exerts its rapid bactericidal effect by perturbing the bacterial cell membrane, a mode of action different from most other currently commercially available antibiotics (except e.g. polymyxin and gramicidin). Recent work has shown that daptomycin requires calcium in the form of Ca2+ to form a micellar structure in solution and to bind to bacterial model membranes. This evidence sheds light on the initial steps in the mechanism of action of this novel antibiotic. To understand how daptomycin goes on to perturb bacterial membranes, its three-dimensional structure has been determined in the presence of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles. NMR spectra of daptomycin in DHPC were obtained under two conditions, namely in the presence of Ca2+ as used by Jung et al. [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57] to solve the calcium-conjugated structure of daptomycin in solution and in a phosphate buffer as used by Rotondi and Gierasch [K.S. Rotondi, L.M. Gierasch, A well-defined amphipathic conformation for the calcium-free cyclic lipopeptide antibiotic, daptomycin, in aqueous solution, Biopolymers 80 (2005) 374-85] to solve the structure of apo-daptomycin. The structures were calculated using molecular dynamics time-averaged refinement. The different sample conditions used to obtain the NMR spectra are discussed in light of fluorescence data, lipid flip-flop and calcein release assays in PC liposomes, in the presence and absence of Ca2+ [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57]. The implications of these results for the membrane perturbation mechanism of daptomycin are discussed.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. The chemical structure of highly aromatic humic acids in three volcanic ash soils as determined by dipolar dephasing NMR studies

    USGS Publications Warehouse

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

    1989-01-01

    Dipolar dephasing 13C NMR studies of three highly aromatic humic acids, one from a modern soil and two from paleosols, have permitted the determination of the degree of aromatic substitution. From these data and the normal solid-state 13C NMR data we have been able to develop a model for the average chemical structure of these humic acids that generally correlates well with permanganate oxidation data. The models depict these humic acids as benzene di- and tricarboxylic acids interconnected by biphenyl linkages. An increasing degree of substitution is observed with increasing geologic age. These structures may be characteristic of the resistant aromatic part of the "core" of humic substances that survives degradation. ?? 1989.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Structural transitions in short-chain lipid assemblies studied by (31)P-NMR spectroscopy.

    PubMed

    Kleinschmidt, Jörg H; Tamm, Lukas K

    2002-08-01

    The self-assembled supramolecular structures of diacylphosphatidylcholine (diC(n)PC), diacylphosphatidylethanolamine (diC(n)PE), diacylphosphatidyglycerol (diC(n)PG), and diacylphosphatidylserine (diC(n)PS) were investigated by (31)P nuclear magnetic resonance (NMR) spectroscopy as a function of the hydrophobic acyl chain length. Short-chain homologs of these lipids formed micelles, and longer-chain homologs formed bilayers. The shortest acyl chain lengths that supported bilayer structures depended on the headgroup of the lipids. They increased in the order PE (C(6)) < PC (C(9)) < or = PS (C(9) or C(10)) < PG (C(11) or C(12)). This order correlated with the effective headgroup area, which is a function of the physical size, charge, hydration, and hydrogen-bonding capacity of the four headgroups. Electrostatic screening of the headgroup charge with NaCl reduced the effective headgroup area of PS and PG and thereby decreased the micelle-to-bilayer transition of these lipid classes to shorter chain lengths. The experimentally determined supramolecular structures were compared to the assembly states predicted by packing constraints that were calculated from the hydrocarbon-chain volume and effective headgroup area of each lipid. The model accurately predicted the chain-length threshold for bilayer formation if the relative displacement of the acyl chains of the phospholipid were taken into account. The model also predicted cylindrical rather than spherical micelles for all four diacylphospholipid classes and the (31)P-NMR spectra provided evidence for a tubular network that appeared as an intermediate phase at the micelle-to-bilayer transition. The free energy of micellization per methylene group was independent of the structure of the supramolecular assembly, but was -0.95 kJ/mol (-0.23 kcal/mol) for the PGs compared to -2.5 kJ/mol (-0.60 kcal/mol) for the PCs. The integral membrane protein OmpA did not change the bilayer structure of thin (diC(10)PC) bilayers.

  12. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.

    PubMed

    Faraggi, Eshel; Dunker, A Keith; Sussman, Joel L; Kloczkowski, Andrzej

    2017-08-08

    Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure. We find a close statistical correspondence between NMR and X-ray structures if fluctuations inherent to the NMR protocol are taken into account. Intuitively this tends to lend support to the validity of both NMR and X-ray protocols in deriving biomolecular models that correspond to in vivo conditions. We then establish Lindemann-like parameters for NMR derived structures and examine what order/disorder cutoffs for these parameters are most consistent with X-ray data and how consistent are they. Finally, we find critical value of [Formula: see text] for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value [Formula: see text] if a balance between false positive and false negative prediction is sought. We examine a few non-conforming cases, and examine the origin of the structure derived in X-ray. This study could help in assigning meaningful disorder from NMR experiments.

  13. 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.

  14. Integrated NMR and computational study of push-pull NLO probes: interplay of solvent and structural effects.

    PubMed

    Marini, Alberto; Macchi, Sara; Jurinovich, Sandro; Catalano, Donata; Mennucci, Benedetta

    2011-09-08

    In this study we combined QM calculations and NMR measurements to understand at a detailed level the complex interplay of structural/electronic properties with the effects of the solvent in the NLO activity of push-pull systems, quantified in terms of variations of the static hyperpolarizability. Different parameters (bond lengths and bond length alternation, vibrational frequencies, electronic charge distribution) are introduced and tested to rationalize both the solvent sensitivity of three molecular systems (namely, p-nitroaniline, ethyl 4-ammino benzoate, and 5-nitro-1H-indole) and the differences among them. This analysis has finally allowed us to establish a clear correlation between the charge transfer behavior of the systems, their NLO properties, and NMR parameters also validating simplified but effective chemical analyses based on resonance limit forms.

  15. 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.

  16. 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.

  17. 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.

  18. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher expression and solubility.

    PubMed

    Kobayashi, Hiroshi; Swapna, G V T; Wu, Kuen-Phon; Afinogenova, Yuliya; Conover, Kenith; Mao, Binchen; Montelione, Gaetano T; Inouye, Masayori

    2012-04-01

    A common obstacle to NMR studies of proteins is sample preparation. In many cases, proteins targeted for NMR studies are poorly expressed and/or expressed in insoluble forms. Here, we describe a novel approach to overcome these problems. In the protein S tag-intein (PSTI) technology, two tandem 92-residue N-terminal domains of protein S (PrS(2)) from Myxococcus xanthus is fused at the N-terminal end of a protein to enhance its expression and solubility. Using intein technology, the isotope-labeled PrS(2)-tag is replaced with non-isotope labeled PrS(2)-tag, silencing the NMR signals from PrS(2)-tag in isotope-filtered (1)H-detected NMR experiments. This method was applied to the E. coli ribosome binding factor A (RbfA), which aggregates and precipitates in the absence of a solubilization tag unless the C-terminal 25-residue segment is deleted (RbfAΔ25). Using the PrS(2)-tag, full-length well-behaved RbfA samples could be successfully prepared for NMR studies. PrS(2) (non-labeled)-tagged RbfA (isotope-labeled) was produced with the use of the intein approach. The well-resolved TROSY-HSQC spectrum of full-length PrS(2)-tagged RbfA superimposes with the TROSY-HSQC spectrum of RbfAΔ25, indicating that PrS(2)-tag does not affect the structure of the protein to which it is fused. Using a smaller PrS-tag, consisting of a single N-terminal domain of protein S, triple resonance experiments were performed, and most of the backbone (1)H, (15)N and (13)C resonance assignments for full-length E. coli RbfA were determined. Analysis of these chemical shift data with the Chemical Shift Index and heteronuclear (1)H-(15)N NOE measurements reveal the dynamic nature of the C-terminal segment of the full-length RbfA protein, which could not be inferred using the truncated RbfAΔ25 construct. CS-Rosetta calculations also demonstrate that the core structure of full-length RbfA is similar to that of the RbfAΔ25 construct.

  19. On the structure of amorphous calcium carbonate--a detailed study by solid-state NMR spectroscopy.

    PubMed

    Nebel, Holger; Neumann, Markus; Mayer, Christian; Epple, Matthias

    2008-09-01

    The calcium carbonate phases calcite, aragonite, vaterite, monohydrocalcite (calcium carbonate monohydrate), and ikaite (calcium carbonate hexahydrate) were studied by solid-state NMR spectroscopy ( (1)H and (13)C). Further model compounds were sodium hydrogencarbonate, potassium hydrogencarbonate, and calcium hydroxide. With the help of these data, the structure of synthetically prepared additive-free amorphous calcium carbonate (ACC) was analyzed. ACC contains molecular water (as H 2O), a small amount of mobile hydroxide, and no hydrogencarbonate. This supports the concept of ACC as a transient precursor in the formation of calcium carbonate biominerals.

  20. 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

  1. 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.

  2. An improved 13C-tracer method for the study of lignin structure and reactions : differential 13C-NMR

    Treesearch

    Noritsugu Terashima; Dmitry Evtuguin; Carlos Pascoal Neto; Jim Parkas; Magnus Paulsson; Ulla Westermark; Sally Ralph; John Ralph

    2003-01-01

    The technique of selective 13C-enrichment of specific carbons in lignin combined with 13C-NMR differential spectrometry between spectra of 13C-enriched and unenriched lignins (Ä13C-NMR) provides definitive information on the structure of the lignin macromolecule. Improvements were made on, (1) specific 13C-enrichment of almost all carbons involved in inter-unit bonds...

  3. 1 H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    NASA Astrophysics Data System (ADS)

    Schmid, M.; Goze-Bac, C.; Bouhrara, M.; Saih, Y.; Mehring, M.; Abou-Hamad, E.

    2011-09-01

    Structural and dynamical properties of the THF solvent in single-walled carbon nanotubes intercalated with lithium are investigated by NMR. 1H NMR experiments reveal the existence of two types of inequivalent THF solvent molecules with different chemical environments and dynamical behavior. At low temperatures THF molecules perpendicularly arranged in between adjacent SWNT presumably exhibit a restricted rotation around their dipolar axis. At higher temperatures THF molecules are isotropically rotating and diffusing along the interstitial channels of the SWNT bundles.

  4. 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.

  5. 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.

  6. Structure and pharmaceutical formulation development of a new long-acting recombinant human insulin analog studied by NMR and MS.

    PubMed

    Bednarek, Elżbieta; Sitkowski, Jerzy; Bocian, Wojciech; Borowicz, Piotr; Płucienniczak, Grażyna; Stadnik, Dorota; Surmacz-Chwedoruk, Weronika; Jaworska, Beata; Kozerski, Lech

    2017-02-20

    A monomer structure of a novel human insulin analog A22(S)-B3(K)-B31(R) (SK3R) has been characterized by NMR in water/acetonitrile solution and compared with the structure of human insulin (HIS) established in the same medium. The composition of the oligomer ensemble for neat insulins in water was qualitatively assessed by monitoring, derived from NMR experiment, translational diffusion coefficient Dix10(-10)m(2)s(-1), whose value is a population averaged of individual coefficients for species in oligomeric ensemble. Nanospray ESI/MS experiment was used to establish the masses of oligomers in pharmaceutical formulation of the SK3R insulin. The pharmacodynamic data were established and compared to insulin glargine characterized by the same profile of action in diabetics. The oligomerization process of insulin during development of pharmaceutical formulation with routinely used excipients has been studied using translation diffusion coefficient Dix10(-10)m(2)s(-1) established in water solution. These properties were compared with those of human insulin (HIS) which is a standard reference for novel recombinant insulins. Copyright © 2016. Published by Elsevier B.V.

  7. Solid-state NMR and SAXS studies provide a structural basis for the activation of αB-crystallin oligomers

    PubMed Central

    Jehle, Stefan; Rajagopal, Ponni; Bardiaux, Benjamin; Markovic, Stefan; Kühne, Ronald; Stout, Joseph R; Higman, Victoria A; Klevit, Rachel E; van Rossum, Barth-Jan; Oschkinat, Hartmut

    2010-01-01

    The small heat shock protein αB-crystallin (αB) contributes to cellular protection against stress. For decades, high-resolution structural studies on oligomeric αB have been confounded by its polydisperse nature. Here, we present a structural basis of oligomer assembly and activation of the chaperone using solid-state NMR and small-angle X-ray scattering (SAXS). The basic building block is a curved dimer, with an angle of ~121° between the planes of the β-sandwich formed by α-crystallin domains. The highly conserved IXI motif covers a substrate binding site at pH 7.5. We observe a pH-dependent modulation of the interaction of the IXI motif with β4 and β8, consistent with a pH-dependent regulation of the chaperone function. N-terminal region residues Ser59-Trp60-Phe61 are involved in intermolecular interaction with β3. Intermolecular restraints from NMR and volumetric restraints from SAXS were combined to calculate a model of a 24-subunit αB oligomer with tetrahedral symmetry. PMID:20802487

  8. Solid-state NMR and SAXS studies provide a structural basis for the activation of alphaB-crystallin oligomers.

    PubMed

    Jehle, Stefan; Rajagopal, Ponni; Bardiaux, Benjamin; Markovic, Stefan; Kühne, Ronald; Stout, Joseph R; Higman, Victoria A; Klevit, Rachel E; van Rossum, Barth-Jan; Oschkinat, Hartmut

    2010-09-01

    The small heat shock protein alphaB-crystallin (alphaB) contributes to cellular protection against stress. For decades, high-resolution structural studies on oligomeric alphaB have been confounded by its polydisperse nature. Here, we present a structural basis of oligomer assembly and activation of the chaperone using solid-state NMR and small-angle X-ray scattering (SAXS). The basic building block is a curved dimer, with an angle of approximately 121 degrees between the planes of the beta-sandwich formed by alpha-crystallin domains. The highly conserved IXI motif covers a substrate binding site at pH 7.5. We observe a pH-dependent modulation of the interaction of the IXI motif with beta4 and beta8, consistent with a pH-dependent regulation of the chaperone function. N-terminal region residues Ser59-Trp60-Phe61 are involved in intermolecular interaction with beta3. Intermolecular restraints from NMR and volumetric restraints from SAXS were combined to calculate a model of a 24-subunit alphaB oligomer with tetrahedral symmetry.

  9. 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.

  10. 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.

  11. The structure of tellurite glass: A combined NMR, neutron diffraction, and x-ray diffraction study

    SciTech Connect

    McLaughlin, J. C.; Tagg, S. L.; Zwanzier, J. W.; Shastri, S. D.; Haeffner, D. R.

    2000-04-04

    Models are presented of sodium tellurite glasses in the composition range (Na{sub 2}0){sub x}-(TeO{sub 2}){sub 1{minus}x}. 0.1 < x < 0.3. The models combine self-consistently data from three different and complementary sources: sodium-23 nuclear magnetic resonance (NMR), neutron diffraction, and x-ray diffraction. The models were generated using the Reverse Monte Carlo algorithm, modified to include NMR data in addition to diffraction data. The presence in the models of all five tellurite polyhedra consistent with the Te{sup +4} oxidation state were found to be necessary to achieve agreement with the data. The distribution of polyhedra among these types varied from a predominance of highly bridged species at low sodium content, to polyhedra with one or zero bridging oxygen at high sodium content. The models indicate that the sodium cations themselves form sodium oxide clusters particularly at the x = 0.2 composition.

  12. 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.

  13. Structural features of the protophorphyrin-apomyoglobin complex. A proton NMR spectroscopy study

    SciTech Connect

    Lecomte, J.T.J.; Cocco, M.J. )

    1990-12-01

    The structural properties of the complex formed by apomyoglobin and protoporphyrin IX (des-iron myoglobin) were studied to probe the influence of iron-to-histidine coordination on the native myoglobin fold and the heme binding site geometry. Standard two-dimensional proton nuclear magnetic resonance spectroscopy methods were applied to identify porphyrin and protein signals. A pronounced spectral resemblance between carbonmonoxymyoglobin and des-iron myogobin was noticed that could be exploited to assign a number of resonances by nuclear Overhauser spectroscopy. Protoporphyrin IX was determined to bind in the same orientation as the heme. Most residues in contact with the prosthetic group were found in the holomyoglobin conformation. Several tertiary structure features were also characterized near the protein termini. It was concluded that the protoporphyrin-apomyoglobin interactions are capable of organizing the binding site and the unfolded region of the apoprotein into the native holoprotein structure.

  14. 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.

  15. 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.

  16. 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.

  17. 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).

  18. Lamellar structures formed by stratum corneum lipids in vitro: a deuterium nuclear magnetic resonance (NMR) study.

    PubMed

    Abraham, W; Downing, D T

    1992-11-01

    Hydrated lipid mixtures consisting of stratum corneum ceramides, cholesterol, specifically deuterated palmitic acid, and cholesteryl sulfate were investigated by solid-state 2H NMR spectroscopy at different temperatures. The mole ratio of cholesterol to ceramides was varied from 1 to 0. 2H NMR spectra from these mixtures showed powder patterns with quadrupolar splittings smaller than those obtained from control mixtures containing dipalmitoylphosphatidylcholine (DPPC) instead of the ceramides. This result is attributed to the rigid amide group of the ceramides, with a planar configuration, which could prevent close packing of the alpha-methylenes of the acyl chains. There was a gradual loss of symmetry in the powder pattern as the amount of cholesterol was decreased and the amount of ceramides (or DPPC) was increased concomitantly. The loss was more pronounced in the ceramide-containing samples. This phenomenon is interpreted as a decrease in the axial reorientation rate of the alpha-deuterated palmitic acid in the bilayers, presumably caused by the increased hydrogen bonding resulting from the high amount of hydroxyl-bearing ceramides. Spectra obtained at temperatures above 60 degrees C indicated the formation of a hexagonal phase (HII) by the ceramide-containing mixtures. Spectra of the omega-deuterated palmitic acid in the mixture containing 76 mol% ceramides and no cholesterol indicated phase separation into a more rigid phase and a more mobile phase in the temperature range of 25 to 60 degrees C. The bilayer configuration of lipids at 25 degrees C was confirmed by thin-section electron microscopy.

  19. 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.

  20. 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.

  1. Photoprotein Aequorin Structure Determination by NMR Spectroscopy

    DTIC Science & Technology

    1993-07-09

    AD-A267 066 July 9, 1993 Final Rept. 15 Apr. 1992-31 Dec. 1992 Photoprotein Aequorin Structure Determination by NMR Spectroscopy Grant # N00014-92-J...specific assignments of proteins using homo- and heteronuclear 2D-NMR. Assignments were made for approximately 95% of the 1H and 15N atoms of Bacillus... structure of r-aequorin is included. 028 93-1584993 7 . -,I m!,,•slil Aequorin, bioluminescence, nuclear magnetic reburndie, 3D structure . Unclassified

  2. 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.

  3. Partial 13C isotopic enrichment of nucleoside monophosphates: useful reporters for NMR structural studies.

    PubMed

    Kishore, Anita I; Mayer, Michael R; Prestegard, James H

    2005-10-27

    Analysis of the 13C isotopic labeling patterns of nucleoside monophosphates (NMPs) extracted from Escherichia coli grown in a mixture of C-1 and C-2 glucose is presented. By comparing our results to previous observations on amino acids grown in similar media, we have been able to rationalize the labeling pattern based on the well-known biochemistry of nucleotide biosynthesis. Except for a few notable absences of label (C4 in purines and C3' in ribose) and one highly enriched site (C1' in ribose), most carbons are randomly enriched at a low level (an average of 13%). These sparsely labeled NMPs give less complex NMR spectra than their fully isotopically labeled analogs due to the elimination of most 13C-13C scalar couplings. The spectral simplicity is particularly advantageous when working in ordered systems, as illustrated with guanosine diphosphate (GDP) bound to ADP ribosylation factor 1 (ARF1) aligned in a liquid crystalline medium. In this system, the absence of scalar couplings and additional long-range dipolar couplings significantly enhances signal to noise and resolution.

  4. Partial 13C isotopic enrichment of nucleoside monophosphates: useful reporters for NMR structural studies

    PubMed Central

    Kishore, Anita I.; Mayer, Michael R.; Prestegard, James H.

    2005-01-01

    Analysis of the 13C isotopic labeling patterns of nucleoside monophosphates (NMPs) extracted from Escherichia coli grown in a mixture of C-1 and C-2 glucose is presented. By comparing our results to previous observations on amino acids grown in similar media, we have been able to rationalize the labeling pattern based on the well-known biochemistry of nucleotide biosynthesis. Except for a few notable absences of label (C4 in purines and C3′ in ribose) and one highly enriched site (C1′ in ribose), most carbons are randomly enriched at a low level (an average of 13%). These sparsely labeled NMPs give less complex NMR spectra than their fully isotopically labeled analogs due to the elimination of most 13C–13C scalar couplings. The spectral simplicity is particularly advantageous when working in ordered systems, as illustrated with guanosine diphosphate (GDP) bound to ADP ribosylation factor 1 (ARF1) aligned in a liquid crystalline medium. In this system, the absence of scalar couplings and additional long-range dipolar couplings significantly enhances signal to noise and resolution. PMID:16254075

  5. 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.

  6. 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.

  7. Molecular mobility and microscopic structure changes in κ-carrageenan solutions studied by gradient NMR.

    PubMed

    Zhao, Qiuhua; Brenner, Tom; Matsukawa, Shingo

    2013-06-05

    Changes in the molecular mobility of κ-carrageenan were observed by the pulsed field gradient stimulated echo (PGSTE) and Carr-Purcell-Meiboom-Gill (CPMG) methods for elucidating the molecular aspect of the sol-to-gel transition. The echo signal intensity of κ-carrageenan without a gradient, Ikap(0), decreased steeply near the sol-to-gel temperature (Tsg), suggesting that κ-carrageenan chains formed aggregates and a network structure. Below Tsg, the spin-spin relaxation time T2 and the diffusion coefficient of κ-carrageenan (Dkap) increased with decreasing temperature, indicating that the solute κ-carrageenan chains have a lower molecular weight Mw than chains involved in the aggregation. The diffusion coefficient of pullulan (Dpul) added as a probe molecule in κ-carrageenan solutions was measured, and the characteristic hydrodynamic screening length, ξ, was then estimated from the degree of diffusion restriction. Below a certain temperature, Dkap reached a higher value than that of Dpul, suggesting that the Mw of solute κ-carrageenan became lower than that of pullulan. GPC measurements confirmed the presence of κ-carrageenan chains with a lower Mw than that of pullulan. A simple physical model of the structural change in κ-carrageenan solution was proposed with a bimodal distribution of κ-carrageenan with higher and lower Mw than the pullulan probe. The higher Mw chains form the gel network restricting the probe's diffusion, and the lower Mw chains increase the effective viscosity. The concentration of the high Mw solute κ-carrageenan chains in 1%, 2% and 4% κ-carrageenan solutions was estimated from Ikap(0) and the total κ-carrageenan concentration, and the relation with pullulan diffusion was studied. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. 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.

  9. 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.

  10. 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.

  11. An NMR Study of Microvoids in Polymers

    NASA Technical Reports Server (NTRS)

    Toy, James; Mattrix, Larry

    1996-01-01

    An understanding of polymer defect structures, like microvoids in polymeric matrices, is most crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally not be found naturally in polymer or in NMR probe materials. There are two NMR active Xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb and Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe-129-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts in Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of Xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A series of spectra were obtained interspersed with applications of vacuum and heating to drive out the adsorbed Xe and determine the role of Xe-Xe interactions in the observed chemical shift.

  12. 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…

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 1H NMR study of the effect of variable ligand on heme oxygenase electronic and molecular structure

    PubMed Central

    Ma, Li-Hua; Liu, Yangzhong; Zhang, Xuhong; Yoshida, Tadashi; La Mar, Gerd N.

    2009-01-01

    Heme oxygenase carries out stereospecific catabolism of protohemin to yield iron, CO and biliverdin. Instability of the physiological oxy complex has necessitated the use of model ligands, of which cyanide and azide are amenable to solution NMR characterization. Since cyanide and azide are contrasting models for bound oxygen, it is of interest to characterize differences in their molecular and/or electronic structures. We report on detailed 2D NMR comparison of the azide and cyanide substrate complexes of heme oxygenase from Neisseria meningitidis, which reveals significant and widespread differences in chemical shifts between the two complexes. To differentiate molecular from electronic structural changes between the two complexes, the anisotropy and orientation of the paramagnetic susceptibility tensor were determined for the azide complex for comparison with those for the cyanide complex. Comparison of the predicted and observed dipolar shifts reveals that shift differences are strongly dominated by differences in electronic structure and do not provide any evidence for detectable differences in molecular structure or hydrogen bonding except in the immediate vicinity of the distal ligand. The readily cleaved C-terminus interacts with the active site and saturation-transfer allows difficult heme assignments in the high-spin aquo complex. PMID:18976815

  5. 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.

  6. 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.

  7. Structure and ionic interactions of organic-inorganic composite polymer electrolytes studied by solid-state NMR and Raman spectroscopy.

    PubMed

    Joo, Chan Gyu; Bronstein, Lyudmila M; Karlinsey, Robert L; Zwanziger, Josef W

    2002-01-01

    Solid-state NMR studies of composite polymer electrolytes are reported. The materials consist of polyethylene oxide and an organic inorganic composite, together with a lithium salt, and are candidates for electrolytes in solid-state lithium ion batteries. Silicon and aluminum MAS and multiple quantum MAS are used to characterize the network character of the organic-inorganic composite, and spin diffusion measurements are used to determine the nanostructure of the polymer/composite blending. Multiple quantum spin counting is used to measure the ion aggregation. The NMR results are supported by Raman spectra, calorimetry, and impedance spectroscopy. From these experiments it is concluded that the composite suppresses polymer crystallization without suppressing its local mobility, and also suppresses the tendency for the ions to aggregate. This polymer composite thus appears very promising for application in lithium ion batteries.

  8. 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.

  9. 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.

  10. An NMR study of microvoids in polymers

    NASA Technical Reports Server (NTRS)

    Toy, James; Mattix, Larry

    1995-01-01

    An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the

  11. Dermostatin A and B: chromatography, structural and configurational studies using HPLC, CCD, 13C (125 MHz) and 1H (500 MHz) NMR spectroscopy.

    PubMed

    Swamy, M B; Sastry, M K; Nanda, R K

    1994-01-01

    HPLC of crude Dermostatin indicated presence of three pairs of components. Hence, attempts were made to purify Dermostatin. Purification of crude Dermostatin has been carried out using column chromatography and counter current distribution methods. Each of these fractions were tested for activity. The major fraction which showed greater activity was taken for the preparation of Dermostatin nona-acetate. Structural characterisation of Dermostatin nona-acetate has been carried out using UV-visible spectroscopy in different solvents to obtain the characteristic spectrum of a carbonyl conjugated hexaene at room temperature. Structural and configurational studies of Dermostatin nona-acetate using 500 MHz 1H NMR and 125 MHz 13C NMR has been used in the assignment of various functional groups in Dermostatin A and B as well as to provide corroboration to the earlier structural elucidation.

  12. 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.

  13. Towards understanding cellular structure biology: In-cell NMR.

    PubMed

    Rahman, Safikur; Byun, Younhwa; Hassan, Md Imtaiyaz; Kim, Jihoe; Kumar, Vijay

    2017-05-01

    To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. 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.

  15. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes.

    PubMed

    Mahalakshmi, Radhakrishnan; Franzin, Carla M; Choi, Jungyuen; Marassi, Francesca M

    2007-12-01

    The beta-barrels found in the outer membranes of prokaryotic and eukaryotic organisms constitute an important functional class of proteins. Here we present solid-state NMR spectra of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. We show that OmpX is folded in both glass-supported oriented lipid bilayers and in lipid bicelles that can be magnetically oriented with the membrane plane parallel or perpendicular to the direction of the magnetic field. The presence of resolved peaks in these spectra demonstrates that OmpX undergoes rotational diffusion around an axis perpendicular to the membrane surface. A tightly hydrogen-bonded domain of OmpX resists exchange with D2O for days and is assigned to the transmembrane beta-barrel, while peaks at isotropic resonance frequencies that disappear rapidly in D2O are assigned to the extracellular and periplasmic loops. The two-dimensional 1H/15N separated local field spectra of OmpX have several resolved peaks, and agree well with the spectra calculated from the crystal structure of OmpX rotated with the barrel axis nearly parallel (5 degrees tilt) to the direction of the magnetic field. The data indicate that it will be possible to obtain site-specific resonance assignments and to determine the structure, tilt, and rotation of OmpX in membranes using the solid-state NMR methods that are currently being applied to alpha-helical membrane proteins.

  16. 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.

  17. 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.

  18. [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.

  19. 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.

  20. 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.

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

    PubMed

    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, (1)H NMR and (13)C 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 (1)H NMR peaks are 0.87 and 0.17 ppm and for those of (13)C NMR are 5.6 and 5.3 ppm, respectively for naltrexone and oxycodone. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. 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

  3. 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

  4. 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. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. On the structural diversity of [K(18-crown-6)EPh3] complexes (E = C, Si, Ge, Sn, Pb): synthesis, crystal structures and NOESY NMR study.

    PubMed

    Kleeberg, Christian

    2013-06-21

    A series of homologous potassium triphenylelement complexes [K(18-crown-6)EPh3] 6a-e of group 14 elements (E = C, Si, Ge, Sn, Pb) was synthesised by alkoxide induced heterolytic cleavage of boron-element compounds. The complexes 6a-e are isolated as storable solids possibly useful as sources of nucleophilic [EPh3](-) moieties. The solid state structures of 6a-e were established by X-ray crystal structure determination. Whilst all structures can be described as polymeric chains consisting of alternating [K(18-crown-6)](+) and [EPh3](-) units, the interaction within each chain varies systematically with the coordination properties of E. For Si and Ge, classical E-K coordination along with secondary phenyl-K interactions are characteristic, whilst for Sn and Pb, potassium coordination via the phenyl π-system is observed due to inefficient coordination by the free electron pair localised in an 'inert' s-orbital. The carbon derivative is exceptional as the central sp(2)-hybridised carbon atom gives rise to extensive charge delocalisation and coordination via these partially charged π-systems. A (1)H-(1)H NOESY NMR spectroscopic study in THF-d8 suggests appreciable anion/cation interactions for Si to Pb and hence the presence of contact ion pairs.

  6. 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

  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. [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.

  10. 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

  11. 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.

  12. 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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO2(L)(H2O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H2L) and MoO2(acac)2. The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, 1H NMR and 13C 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, 1H NMR and 13C 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 1H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental 1H NMR spectra. However, the 13C 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 13C 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.

  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. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. 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.

  15. 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.

  16. 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.

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

    PubMed Central

    2014-01-01

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

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

    PubMed

    Jang, Richard; Wang, Yan; Xue, Zhidong; Zhang, Yang

    2015-08-01

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

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

    PubMed Central

    Jang, Richard; Wang, Yan

    2015-01-01

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement. PMID:25737244

  20. 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.

  1. 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.

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

    SciTech Connect

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

    1988-11-01

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

  3. Structural studies in the BaO-B 2O 3-TiO 2 system by XAS and 11B-NMR

    NASA Astrophysics Data System (ADS)

    Maia, L. J. Q.; Mastelaro, V. R.; Schneider, J. F.; Parent, P.; Laffon, C.

    2005-05-01

    The structure of barium-titanium-metaborate xBaO- xB 2O 3- yTiO 2 ( y=0%, 4%, 8%, 16% and x=50- y/2) amorphous and crystallized powders, obtained using a polymeric precursor method, was investigated by Ti and B K-edge X-ray absorption spectroscopy (XAS) and 11B-NMR high-resolution techniques. XANES study of amorphous samples shows that Ti 4+ ions exist as [4]Ti species associated to [6]Ti and [5]Ti species in a practically equivalent amount. After crystallization, titanium environment is predominately composed by [6]Ti species. According to XANES results obtained at the B K-edge, the fraction of boron in tetrahedral sites ( [4]B) reduces as the amount of TiO 2 is increased from x=0% to 4%, with a consequent increase of boron in trigonal sites ( [3]B). By a combination of 11B-NMR spin-echo and triple quantum magic angle spinning (3Q-MAS) techniques, the detailed borate speciation was determined as consisting in [4]B and two kind of trigonal sites, [3]B A and [3]B B, corresponding, respectively, to borates sharing three and two O atoms with other boron units. NMR results reveal not only the reduction in boron coordination also seen by XANES but also the simultaneous reduction in the condensation degree of trigonal units, when the Ti content is increased in the glass. In crystallized samples, β-BaB 2O 4 and BaTi(BO 3) 2 phases were identified and quantified by 11B-NMR.

  4. NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

    PubMed

    Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

    2016-02-15

    Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. 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.

  6. Structural study, 31P NMR and europium photoluminescence properties of a new synthetic fillowite-type phosphate: Na3SrMg11(PO4)9

    NASA Astrophysics Data System (ADS)

    Boukhris, Amal; Ben Hamed, Teycir; Glorieux, Benoit; Ben Amara, Mongi

    2017-05-01

    A new phosphate compound, Na3SrMg11(PO4)9 was synthesized as single crystals by flux method and as powdered sample by Pechini technique and investigated by X-ray diffraction, 31P NMR and photoluminescence spectroscopies. This compound crystallizes in the rhombohedral space group R 3 bar and its equivalent hexagonal cell has the following parameters: a = 14.941(1) Ǻ, c = 42.478(2) Ǻ and Z = 12. The structure consisted of MgOx (x = 5,6), NaOx (x = 6,7) and (Na,Sr)Ox (x = 8,9) polyhedra which are linked either directly through common corners, edges and faces and by means of the PO4 tetrahedra via common corners and edges, giving rise to a three-dimensional framework, similar to that of the fillowite-like structure. 31P NMR spectroscopy confirmed the presence of six distinct phosphors sites in the structure. Finally, strontium was partially substitute by divalent europium in order to examine whether this material could be used in optical applications. Optical studies were performed on the Na3Sr0.98Eu2+0.02Mg11(PO4)9 compound. The photoluminescence are consistent with the crystal structural and show various properties as a function of the excitation wavelength.

  7. 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.

  8. NMR study of magnetism and superparamagnetism

    NASA Astrophysics Data System (ADS)

    Yuan, Shaojie

    The research described in this dissertation is concerned with two different types of magnetic materials. Both types of systems involve competing interactions between transition metal ions. New approaches involving magnetic resonance in the large hyperfine fields at nuclear sites have been developed. The interactions responsible for the properties that have been investigated in the materials studied are geometric frustration in an insulator and ferromagnetic and antiferromagnetic interactions in a metal alloy. Further details are given below. The extended kagome frustrated system YBaCo4O7 has 2D kagome and triangular lattices of Co ions stacked along the c-axis. Antiferromagnetic (AF) ordering accompanied by a structural transition has been reported in the literature. From a zero field (ZF) NMR single crystal rotation experiment, we have obtained the Co spin configurations for both the kagome and triangular layers. A 'spin-flop' configuration between the spins on the kagome layer and the spins on the triangular layer is indicated by our results. Our NMR findings are compared with neutron scattering results for this intriguing frustrated AF spin system. The non-stoichiometric oxygenated sister compound YBaCo4O7.1 has application potential for oxygen storage. While, its' magnetic properties are quite different from those of the stoichiometric compound, in spite of their similar structures of alternating kagome and triangular Co layers. Various techniques, including ZF NMR have been used to investigate the spin dynamics and spin configuration in a single crystal of YBaCo4O7.1. A magnetic transition at 80 K is observed, which is interpreted as the freezing out of spins in the triangular layers. At low temperatures (below 50 K), the spin dynamics persists and a fraction of spins in the kagome layers form a viscous spin liquid. Below 10 K, a glass-like spin structure forms and a large distribution of spin correlation times are suggested by nuclear spin lattice relaxation

  9. 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

  10. A low-temperature NMR study of the structure of the ionic complexes of phosphoryl compounds with a hydrogen bond

    SciTech Connect

    Golubov, N.S.; Denisov, G.S.; Matrosov, E.I.; Kabachnik, M.I.

    1982-04-01

    In the present work, low-temperature /sup 1/H NMR spectroscopy was used to study two types of complexes in which the phosphoryl group is part of either the acid or basic part of the molecule. Ionic complexes of trifluoromethylsulfonic acid with phosphoryl bases: (C/sub 8/H/sub 17/)/sub 3/P=O (1), (C/sub 2/H/sub 5/)/sub 2/PON(C/sub 2/H/sub 5/)/sub 2/ (2), and the dioxide (C/sub 2/H/sub 5/)/sub 2/P(O)CH/sub 2/CH/sub 2/P(O)(C/sub 2/H/sub 5/)/sub 2/ (3), and complexes of diethylphosphoric acid with dimethylformamide (4), dimethylsulfoxide (5), THF (6), and other ionic complexes of the type (C/sub 2/H/sub 5/O/sub 2/PO/sub 2/)/sub 2//sup -/HX/sup +/ with a homoconjugated anion, where X = N(C/sub 4/H/sub 9/) or (CD/sub 3/)/sub 3/ /sup 15/NH were studied.

  11. 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.

  12. 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

  13. Synthetic analogues of the histidine-chlorophyll complex: a NMR study to mimic structural features of the photosynthetic reaction center and the light-harvesting complex.

    PubMed

    van Gammeren, Adriaan J; Hulsbergen, Frans B; Erkelens, Cornelis; De Groot, Huub J M

    2004-01-01

    Mg(II)-porphyrin-ligand and (bacterio)chlorophyl-ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. (1)H, (13)C and (15)N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9-5.2 ppm (1)H, 0.2-5.5 ppm (13)C and 2.1-27.2 ppm (15)N coordination shifts were measured for selectively labeled [1,3-(15)N]-Im, [1,3-(15)N,2-(13)C]-Im and [1,3-(15)N,1,2-(13)C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the (1)H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a-histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex.

  14. Solvent effects on chemical exchange in a push-pull ethylene as studied by NMR and electronic structure calculations.

    PubMed

    Ababneh-Khasawneh, Maysoon; Fortier-McGill, Blythe E; Occhionorelli, Marzia E; Bain, Alex D

    2011-07-07

    NMR measurements of chemical exchange in a push-pull ethylene, dissolved in a number of different solvents, are presented. These are complemented by high-level electronic structure calculations, using both gas-phase conditions and those which simulate solvents. The results show that it is essential to include entropy effects in order to understand the observed trends. For instance, the equilibrium state in this case represents the state with lowest Gibbs free energy, as it must, but not the lowest enthalpy. The particular molecule is methyl 3-dimethylamino-2-cyanocrotonate (MDACC). The geometry at the carbon-carbon double bond can be either E or Z with roughly equal populations at ambient temperature. We have measured the equilibrium constant and the rates for the exchange between these states in a number of solvents: methanol, chloroform, acetonitrile, toluene, dichloromethane, acetone, and tetrahydrofuran. Furthermore, the N,N-dimethylamino group attached to the double bond also shows restricted rotation, and this has been measured in both the E and Z conformations. The equilibrium constant and the three rotational barriers provide excellent probes of the solvent effects. Electronic structure calculations with a number of basis sets up to the 6-311++G(2df,2p) level, using both Hartree-Fock and density functional (B3LYP) methods were used to predict the E and Z ground states, and the three transition states. The calculations were done for an isolated molecule and also for solvent models representing toluene, acetone, and ethanol. The E conformation is more stable in solution, is the structure in the crystal, and is also the prediction for the gas phase from the calculations. However, the dependence of the equilibrium constant on temperature shows that the Z conformation actually has lower enthalpy. The stability of the E conformation in solution must be due to entropic effects. Similarly, the solvent effect on the E-Z barrier is primarily due to entropy. The

  15. 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.

  16. Solid-state NMR structures of integral membrane proteins.

    PubMed

    Patching, Simon G

    2015-01-01

    Solid-state NMR is unique for its ability to obtain three-dimensional structures and to measure atomic-resolution structural and dynamic information for membrane proteins in native lipid bilayers. An increasing number and complexity of integral membrane protein structures have been determined by solid-state NMR using two main methods. Oriented sample solid-state NMR uses macroscopically aligned lipid bilayers to obtain orientational restraints that define secondary structure and global fold of embedded peptides and proteins and their orientation and topology in lipid bilayers. Magic angle spinning (MAS) solid-state NMR uses unoriented rapidly spinning samples to obtain distance and torsion angle restraints that define tertiary structure and helix packing arrangements. Details of all current protein structures are described, highlighting developments in experimental strategy and other technological advancements. Some structures originate from combining solid- and solution-state NMR information and some have used solid-state NMR to refine X-ray crystal structures. Solid-state NMR has also validated the structures of proteins determined in different membrane mimetics by solution-state NMR and X-ray crystallography and is therefore complementary to other structural biology techniques. By continuing efforts in identifying membrane protein targets and developing expression, isotope labelling and sample preparation strategies, probe technology, NMR experiments, calculation and modelling methods and combination with other techniques, it should be feasible to determine the structures of many more membrane proteins of biological and biomedical importance using solid-state NMR. This will provide three-dimensional structures and atomic-resolution structural information for characterising ligand and drug interactions, dynamics and molecular mechanisms of membrane proteins under physiological lipid bilayer conditions.

  17. 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

  18. 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

  19. 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).

  20. 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

  1. 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.

  2. DNA hairpin structures in solution: 500-MHz two-dimensional /sup 1/H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

    SciTech Connect

    Gupta, G.; Sarma, M.H.; Sarma, R.H.

    1987-12-01

    A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz /sup 1/H NMR studies in H/sub 2/O and D/sub 2/O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

  3. 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.

  4. 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.

  5. Design, synthesis, biological evaluation, NMR and DFT studies of structurally simplified trimethoxy benzamides as selective P-glycoprotein inhibitors: the role of molecular flatness.

    PubMed

    Stefanachi, Angela; Mangiatordi, Giuseppe Felice; Tardia, Piero; Alberga, Domenico; Leonetti, Francesco; Niso, Mauro; Colabufo, Nicola Antonio; Adamo, Carlo; Nicolotti, Orazio; Cellamare, Saverio

    2016-12-01

    In a recent investigation carried out on a panel of trimethoxybenzanilides, we showed that the formation of an intramolecular hydrogen bond is a key element for tuning P-gp inhibitory activity. In this study, we designed new structurally simplified trimethoxy benzamides (5-17, Table ) with the aim to uncover the minimal molecular requirements needed for P-gp inhibition. The new prepared smaller-sized compounds exhibited IC50 in the low micromolar range. The combined use of NMR and DFT studies suggested that molecular flatness is causatively related to the P-gp inhibition. Our results clearly pointed out that concerted theoretical and experimental approaches herein presented might be very helpful in addressing the design of structurally simplified and highly efficient compounds biasing P-gp protein. © 2016 John Wiley & Sons A/S.

  6. 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.

  7. 2-Methoxypyridine as Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability and NMR Structural Studies.

    PubMed

    Novosjolova, Irina; Kennedy, Scott D; Rozners, Eriks

    2017-08-31

    Development of nucleic acid base pair analogues that use new modes of molecular recognition is important for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme could enhance the thermal stability of DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability by ~10 ºC in DNA-DNA duplexes and ~20 ºC in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A

    PubMed Central

    Kitahara, Ryo; Simorellis, Alana K.; Hata, Kazumi; Maeno, Akihiro; Yokoyama, Shigeyuki; Koide, Shohei; Akasaka, Kazuyuki

    2012-01-01

    Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer β-sheet connecting the N- and C-terminal domains with τ << ms, which may give the two domains certain independence in mobility and thermodynamic stability. Furthermore, we found that folded, native OspA is in equilibrium (τ >> ms) with a minor conformer I, which is almost fully disordered and hydrated for the entire C-terminal part of the polypeptide chain from β8 to the C-terminus. Conformer I is characterized with ΔG0 = 32 ± 9 kJ/mol and ΔV0 = −140 ± 40 mL/mol, populating only ∼0.001% at 40°C at 0.1 MPa, pH 5.9. Because in the folded conformer the receptor binding epitope of OspA is buried in the C-terminal domain, its transition into conformer I under in vivo conditions may be critical for the infection of B. burgdorferi. The formation and stability of the peculiar conformer I are apparently supported by a large packing defect or cavity located in the C-terminal domain. PMID:22385863

  9. NMR Methods to Study Dynamic Allostery.

    PubMed

    Grutsch, Sarina; Brüschweiler, Sven; Tollinger, Martin

    2016-03-01

    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.

  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. 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

  12. Protein folding on the ribosome studied using NMR spectroscopy

    PubMed Central

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

    2013-01-01

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

  13. 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

  14. Synthesis, NMR spectral and structural studies on mixed ligand complexes of Pd(II) dithiocarbamates: First structural report on palladium(II) dithiocarbamate with SCN-ligand

    NASA Astrophysics Data System (ADS)

    Prakasam, Balasubramaniam Arul; Lahtinen, Manu; Peuronen, Anssi; Muruganandham, Manickavachagam; Kolehmainen, Erkki; Haapaniemi, Esa; Sillanpää, Mika

    2016-03-01

    Three new mixed ligand complexes of palladium(II) dithiocarbamates; [Pd(4-dpmpzdtc)(PPh3)(SCN)] (1), [Pd(4-dpmpzdtc)(PPh3)Cl] (2) and [Pd(bzbudtc)(PPh3)Cl] (3), (where, 4-dpmpzdtc = 4-(diphenylmethyl)piperazinecarbodithioato anion, bzbudtc = N-benzyl-N-butyldithiocarbamato anion and PPh3 = triphenylphosphine) have been synthesized from their respective parent dithiocarbamates by ligand exchange reactions and characterized by IR and NMR (1H, 13C and 31P) spectroscopy. IR and NMR spectral data support the isobidentate coordination of the dithiocarbamate ligands in all complexes (1-3) in solid and in solution, respectively. Single crystal diffraction analysis of complexes 1-3 evidences that all three complexes are exhibiting distorted square planar geometry. The Pd-S distances in 1-3 vary in accordance with the differences in trans influences of PPh3, SCN- and Cl- and it is in the order of PPh3 > SCN- > and Cl-. Interchange of the anionic auxiliary ligand (SCN- to Cl-) induces asymmetry to the dithiocarbamate-metal bonds. Thioureide C-N bond distances are short in 1-3, supporting a contribution of thioureide form to the structures. The observed distortions in the square planar geometry for 1-3, are in the order of 1 > 2 > 3.

  15. Structural and dynamic aspects of binding of prototype lexitropsin to the decadeoxyribonucleotide d(CGCAATTGCC)/sub 2/ deduced from high-resolution /sup 1/H NMR studies

    SciTech Connect

    Lee, M.; Chang, D.K.; Hartley, J.A.; Pon, R.T.; Krowicki, K.; Lown, J.W.

    1988-01-12

    Structural and dynamic properties of the self-complementary decadeoxyribonucleotide d-(CGCAATTGCC)/sub 2/ and the interaction between a prototype lexitropsin, or information-reading oligopeptide, and the decadeoxyribonucleotide and are deduced by using high-resolution /sup 1/H NMR techniques. The nonexchangeable and imino proton resonances of d(CGCAATTGCG)/sub 2/ have been completely assigned by two-dimensional NMR studies. The decadeoxyribonucleotide exists as a right-handed B-DNA. In the /sup 1/H NMR spectrum of the l:1 complex, the selective chemical shifts and removal of degeneracy of AH2(4), AH2(5), T-CH/sub 3/(6), and T-CH/sub 3/(7) due to the anisotropy effects of the heterocyclic moieties of the ligand, and with lesser effects at the flanking base sites C(3) and G(8), locate the drug centrally in the decadeoxyribonucleotide. This conclusion is supported by plots of individual chemical shift changes across the decadeoxyribonucleotide. Strong nuclear Overhauser effects (NOEs) between pyrrol H5 and AH2(5), and weaker NOEs to AH1'(5), TH3'(6), and AH2'(5), firmly locate the ligand in the minor groove. Intraligand NOEs between the adjacent heterocyclic moieties indicate that the lexitropsin is subject to propeller twisting about the N6-C9 bond in both the bound and free forms. Nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy (COSY) experiments also indicate that the removal of degeneracy of the C16 methylene protons upon complexation may arise from restricted rotation about the C15-N9, C15-C16, and C16-C17 bonds. NOE measurements on the decadeoxyribonucleotide in the 1:1 complex confirm it exists as a right-handed helix and belongs to the B family. Alternative mechanisms for this exchange process are considered.

  16. sup 139 La NMR and NQR study of the temperature dependent structure of La sub 2 CuO sub 4+. delta

    SciTech Connect

    Hammel, P.C.; Ahrens, E.T.; Reyes, A.P.; Heffner, R.H.; Canfield, P.C.; Cheong, S-W; Fisk, Z. ); Schirber, J.E. )

    1991-01-01

    NMR and NQR reveal substantial structural changes in the metallic phase of LA{sub 2}CuO{sub 4+}{delta} which occur below 220 K. The oxygen octahedra in the metallic phase are not tilted at phase separation; upon cooling to 40 K considerable tilt has developed. The low temperature structure is highly disordered. 4 refs., 2 figs.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. (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.

  2. 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.

  3. 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.

  4. 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.

  5. High temperature NMR study of the local structure of molten LaF3-AF (A = Li, Na, K and Rb) mixtures.

    PubMed

    Rollet, Anne-Laure; Godier, Stéphanie; Bessada, Catherine

    2008-06-14

    The local structures of molten lanthanum alkali fluoride binaries have been studied using HT NMR technique. The chemical shifts of (19)F, (23)Na and (139)La in solid and in liquid have been compared for AF (A = alkali) and LaF(3). In pure molten alkali fluorides, the polarisability of anion-cation pairs appears to be a key parameter to depict the observed evolution of (19)F chemical shifts. The influence of the composition has also been studied by measuring the chemical shifts in molten LaF(3)-AF as a function of LaF(3) concentration. A strong influence of the alkali influence is observed. The coordination number of lanthanum is decreased versus AF amount all the more since the alkali atomic number is high. Moreover, the more polarisable the alkali, the less bridging fluorines between the LaF(x) units.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Structural Determinants in the Binding of BB2 Receptor Ligands: In Silico, X-Ray and NMR Studies in PD176252 Analogues.

    PubMed

    Carrieri, Antonio; Lacivita, Enza; Belviso, Benny Danilo; Caliandro, Rocco; Mastrorilli, Piero; Gallo, Vito; Niso, Mauro; Leopoldo, Marcello

    2017-01-01

    The mammalian bombesin receptor family comprises three G proteincoupled receptors: the neuromedin B receptor, the gastrin-releasing peptide receptor (BB2), and the bombesin receptor subtype 3. BB2 receptor plays a role in gastrointestinal functions; however, at present the role of this subtype in physiological and pathological conditions is unknown due to the lack of specific binders for all subclasses of bombesin receptors. Here, we present a study focused on the properties of the peptoid bombesin antagonist called PD176252, and other structural analogues with the aim to elucidate causes of their different affinity towards the BB2 receptor. By means of computational techniques, based on QSAR, docking and homology building, supported by experimental data (X-ray diffraction and NMR spectroscopy) fresh insights on binding modes of this class of biological targets were achieved. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. 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.

  14. ' q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Son, Woo Sung; Park, Sang Ho; Nothnagel, Henry J.; Lu, George J.; Wang, Yan; Zhang, Hua; Cook, Gabriel A.; Howell, Stanley C.; Opella, Stanley J.

    2012-01-01

    ' q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly 15N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios ( q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers ( q > 2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (˜10 5 Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features

  15. Residual dipolar couplings: synergy between NMR and structural genomics.

    PubMed

    Al-Hashimi, Hashim M; Patel, Dinshaw J

    2002-01-01

    Structural genomics is on a quest for the structure and function of a significant fraction of gene products. Current efforts are focusing on structure determination of single-domain proteins, which can readily be targeted by X-ray crystallography, NMR spectroscopy and computational homology modeling. However, comprehensive association of gene products with functions also requires systematic determination of more complex protein structures and other biomolecules participating in cellular processes such as nucleic acids, and characterization of biomolecular interactions and dynamics relevant to function. Such NMR investigations are becoming more feasible, not only due to recent advances in NMR methodology, but also because structural genomics is providing valuable structural information and new experimental and computational tools. The measurement of residual dipolar couplings in partially oriented systems and other new NMR methods will play an important role in this synergistic relationship between NMR and structural genomics. Both an expansion in the domain of NMR application, and important contributions to future structural genomics efforts can be anticipated.

  16. 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.

  17. Databases of Conformations and NMR Structures of Glycan Determinants.

    PubMed

    Sarkar, Anita; Drouillard, Sophie; Rivet, Alain; Perez, Serge

    2015-12-01

    The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. 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.

  19. Structure and dynamics in the methylated exopyridine anthracene rotaxane: 13C, 1H and 19F solid-state NMR studies

    NASA Astrophysics Data System (ADS)

    Bourdon, X.; Leupold, J.; Mehring, M.; Thies, J.; Kidd, T.; Loontjens, T.

    2000-11-01

    We report on the structural and dynamic characterization by solid state NMR of a new rotaxane consisting of a thread molecule enclosed by a macrocycle, which can eventually shuttle or rotate along/around the thread. Different kinds of slow and fast motions are detected in the methylated exopyridine anthracene rotaxane by 1H, 13C and 19F relaxation time versus temperature measurements. Analysis of the proton decoupled and temperature dependent 19F NMR spectra gives some indications of the possible motions of the macrocycle and breaking of the hydrogen bond in the solid-state at temperatures above 360 K.

  20. 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.

  1. 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.

  2. 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

  3. Structural, spectroscopic (FT-IR, NMR, UV-visible), nonlinear optical (NLO), cytotoxic and molecular docking studies of 4-nitro-isonitrosoacetophenone (ninapH) by DFT method

    NASA Astrophysics Data System (ADS)

    Kucuk, Ilhan; Kaya, Yunus; Kaya, A. Asli

    2017-07-01

    (4-Nitro-phenyl)-oxo-acetaldehyde oxime (ninapH) is a type of oxime, which has a oxime and α-carbonyl groups. This molecule has been synthesized from literature procedure. The structural properties and conformational behaviors were examined using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, the most stable conformer was determined, and then this molecule was optimized with the same basis set. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR, NMR and UV-vis spectrometry. The calculated HOMO and LUMO energies show that charge transfer within the molecule. The first order hyperpolarizability and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the ninapH have been calculated at different temperatures, 100-1000 K. In addition, the molecular docking studies have been performed with DNA and protein structures (downloaded from Protein Data Bank).

  4. 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.

  5. 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.

  6. 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.

  7. Solution structures of Alzheimer's amyloid Aβ13-23 peptide: NMR studies in solution and in SDS

    NASA Astrophysics Data System (ADS)

    Usachev, K. S.; Filippov, A. V.; Filippova, E. A.; Antzutkin, O. N.; Klochkov, V. V.

    2013-10-01

    To be believed that interaction of amyloid peptides with the cellular membrane is one of the mechanisms for the neurotoxicity of Aβ. Therefore, structural studies of beta-amyloid in solution and in a "peptide-bio-membrane" complex are of intense interest. The aim of this study was to acquire a better understanding of the mechanism of "Aβ peptide-micelle surface" complex formation. Previous studies of Aβ peptides binding on the micelle surface show the presence of helical region between 15-24 residues and that fragment between 11-28 residues have a tendency to exit the hydrophobic environment of the micelle core and to bind to the micelle surface. In present paper we considered the fragment of Aβ from 13 to 23 residues and found that L17, F19 and F20 residues region play a great role in the process of binding of Aβ to the micelle surface.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    DOE PAGES

    Perras, Frederic A.

    2015-12-15

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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Solution NMR Spectroscopy for the Study of Enzyme Allostery

    PubMed Central

    Lisi, George P.; Loria, J. Patrick

    2016-01-01

    Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery. PMID:26734986

  18. 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.

  19. 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.

  20. Structural characteristics for phase transitions of [N(CH3)4]2CuCl4 by (13)C CP/MAS NMR and (14)N NMR.

    PubMed

    Hee Kim, Nam; Lim, Ae Ran

    2015-09-01

    Structure geometry changes in [N(CH3)4]2CuCl4 near the phase transition temperature were studied by (13)C CP/MAS NMR and (14)N NMR spectrum. We distinguished the two chemically inequivalent N(1)(CH3)4 and N(2)(CH3)4 groups by (13)C CP/MAS NMR and (14)N NMR spectrum. The abrupt changes in chemical shifts and the split of the NMR signals near the phase transition temperatures for (13)C and (14)N are explained by a structural phase transition, implying that the structural geometry depends on the temperature. The mechanism behind this phase transition is based on ferroelasticity, and is also mainly related to the (14)N ions in N(CH3)4 ions. Furthermore, both phases III and IV exhibit ferroelastic properties with identical orientational domains. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. 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.

  2. 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

  3. 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.

  4. Relaxation dispersion NMR spectroscopy for the study of protein allostery.

    PubMed

    Farber, Patrick J; Mittermaier, Anthony

    2015-06-01

    Allosteric transmission of information between distant sites in biological macromolecules often involves collective transitions between active and inactive conformations. Nuclear magnetic resonance (NMR) spectroscopy can yield detailed information on these dynamics. In particular, relaxation dispersion techniques provide structural, dynamic, and mechanistic information on conformational transitions occurring on the millisecond to microsecond timescales. In this review, we provide an overview of the theory and analysis of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments and briefly describe their application to the study of allosteric dynamics in the homeodomain from the PBX transcription factor (PBX-HD). CPMG NMR data show that local folding (helix/coil) transitions in one part of PBX-HD help to communicate information between two distant binding sites. Furthermore, the combination of CPMG and other spin relaxation data show that this region can also undergo local misfolding, reminiscent of conformational ensemble models of allostery.

  5. 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.

  6. The structure and dynamics of the non-network forming elements sodium and magnesium in glassy and molten silicates: A high temperature NMR study

    NASA Astrophysics Data System (ADS)

    George, Anna Melissa

    Properties of silicate glasses and melts like diffusivities, partitioning of elements, and ionic conductivity are thought to depend on the structure and motional behavior of non-network elements like Na and Mg; however, little is directly known about the roles of these elements in the structure. Solid-state NMR spectroscopy is an element-specific technique which can yield information about the local structure of an element through chemical shift measurements and its dynamics, from spin-lattice relaxation times. This dissertation covers recent sp{23}Na and sp{25}Mg in situ high temperature NMR spectroscopy of silicates from room temperature to 1500sp°C. sp{23}Na chemical shifts vary linearly with bond length in crystalline materials, as shown by a MAS study of sodium chemical shifts in albite (NaAlSisb3Osb8) from 25sp°-350sp°C. This correlation of decreasing frequency with increasing bond length is used to interpret the differences in silicate glass and melt signals as a function of temperature and composition. sp{23}Na spin-lattice relaxation times are related to local cation hopping and ionic conductivity; the effect of adding Al to silicates on sodium mobility is discussed in this context. A discussion of the difficulties in interpreting data from quadrupolar nuclides like sp{23}Na is also included. sp{23}Na chemical shifts were also shown to follow a trend of decreasing frequency with increasing average bond length in crystalline sodium borates and germanates, and glass and melt spectra were interpreted from this correlation. The trends with size of sodium site in silicates, borates, and germanates are discussed in terms of being due to a decreased contribution from the paramagnetic shielding as the bonds become longer and more ionic. sp{25}Mg measurements show that the oxygen coordination number of Mg in the melts is between five and six and that the size of the Mg site varies with field strength of other cations present. Relaxation times indicate that the

  7. Multi-responsive cellulose nanocrystal-rhodamine conjugates: an advanced structure study by solid-state dynamic nuclear polarization (DNP) NMR.

    PubMed

    Zhao, Li; Li, Wei; Plog, Andreas; Xu, Yeping; Buntkowsky, Gerd; Gutmann, Torsten; Zhang, Kai

    2014-12-21

    Multi-stimuli responsive materials based on cellulose nanocrystals (CNCs), especially using non-conventional stimuli including light, still need more explorations, to fulfill the requirements of complicated application environments. The structure determination of functional groups on the CNC surface constitutes a significant challenge, partially due to their low amounts. In this study, rhodamine spiroamide groups are immobilized onto the surface of CNCs leading to a hybrid compound being responsive to pH-values, heat and UV light. After the treatment with external stimuli, the fluorescent and correlated optical color change can be induced, which refers to a ring opening and closing process. Amine and amide groups in rhodamine spiroamide play the critical role in this switching process. Solid-state NMR spectroscopy coupled with sensitivity-enhanced dynamic nuclear polarization (DNP) was used to measure (13)C and (15)N in natural abundance, allowing the determination of structural changes during the switching process. It is shown that a temporary bond through an electrostatic interaction could be formed within the confined environment on the CNC surface during the heat treatment. The carboxyl groups on the CNC surface play a pivotal role in stabilizing the open status of rhodamine spiroamide groups.

  8. 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.

  9. Ab initio structure search and in situ 7Li NMR studies of discharge products in the Li–S battery system

    DOE PAGES

    See, Kimberly A.; Leskes, Michal; Griffin, John M.; ...

    2014-11-10

    The high theoretical gravimetric capacity of the Li–S battery system makes it an attractive candidate for numerous energy storage applications. In practice, cell performance is plagued by low practical capacity and poor cycling. In an effort to explore the mechanism of the discharge with the goal of better understanding performance, we examine the Li–S phase diagram using computational techniques and complement this with an in situ 7Li NMR study of the cell during discharge. Both the computational and experimental studies are consistent with the suggestion that the only solid product formed in the cell is Li2S, formed soon after cellmore » discharge is initiated. In situ NMR spectroscopy also allows the direct observation of soluble Li+-species during cell discharge; species that are known to be highly detrimental to capacity retention. We suggest that during the first discharge plateau, S is reduced to soluble polysulfide species concurrently with the formation of a solid component (Li2S) which forms near the beginning of the first plateau, in the cell configuration studied here. The NMR data suggest that the second plateau is defined by the reduction of the residual soluble species to solid product (Li2S). Lastly, a ternary diagram is presented to rationalize the phases observed with NMR during the discharge pathway and provide thermodynamic underpinnings for the shape of the discharge profile as a function of cell composition.« less

  10. 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

  11. Structure determination of membrane proteins by NMR spectroscopy

    PubMed Central

    Opella, S.J.; Nevzorov, A.; Mesleh, M.F.; Marassi, F.M.

    2012-01-01

    Current strategies for determining the structures of membrane proteins in lipid environments by NMR spectroscopy rely on the anisotropy of nuclear spin interactions, which are experimentally accessible through experiments performed on weakly and completely aligned samples. Importantly, the anisotropy of nuclear spin interactions results in a mapping of structure to the resonance frequencies and splittings observed in NMR spectra. Distinctive wheel-like patterns are observed in two-dimensional 1H–15N heteronuclear dipolar/15N chemical shift PISEMA (polarization inversion spin-exchange at the magic angle) spectra of helical membrane proteins in highly aligned lipid bilayer samples. One-dimensional dipolar waves are an extension of two-dimensional PISA (polarity index slant angle) wheels that map protein structures in NMR spectra of both weakly and completely aligned samples. Dipolar waves describe the periodic wave-like variations of the magnitudes of the heteronuclear dipolar couplings as a function of residue number in the absence of chemical shift effects. Since weakly aligned samples of proteins display these same effects, primarily as residual dipolar couplings, in solution NMR spectra, this represents a convergence of solid-state and solution NMR approaches to structure determination. PMID:12440700

  12. Myowater dynamics and protein secondary structural changes as affected by heating rate in three pork qualities: a combined FT-IR microspectroscopic and 1H NMR relaxometry study.

    PubMed

    Wu, Zhiyun; Bertram, Hanne Christine; Böcker, Ulrike; Ofstad, Ragni; Kohler, Achim

    2007-05-16

    The objective of this study was to investigate the influence of heating rate on myowater dynamics and protein secondary structures in three pork qualities by proton NMR T2 relaxation and Fourier transform infrared (FT-IR) microspectroscopy measurements. Two oven temperatures at 100 degrees C and 200 degrees C corresponding to slow and fast heating rates were applied on three pork qualities (DFD, PSE, and normal) to an internal center temperature of 65 degrees C. The fast heating induced a higher cooking loss, particularly for PSE meat. The water proton T21 distribution representing water entrapped within the myofibrillar network was influenced by heating rate and meat quality. Fast heating broadened the T21 distribution and decreased the relaxation times of the T21 peak position for three meat qualities. The changes in T21 relaxation times in meat can be interpreted in terms of chemical and diffusive exchange. FT-IR showed that fast heating caused a higher gain of random structures and aggregated beta-sheets at the expense of native alpha-helixes, and these changes dominate the fast-heating-induced broadening of T21 distribution and reduction in T21 times. Furthermore, of the three meat qualities, PSE meat had the broadest T21 distribution and the lowest T21 times for both heating rates, reflecting that the protein aggregation of PSE caused by heating is more extensive than those of DFD and normal, which is consistent with the IR data. The present study demonstrated that the changes in T2 relaxation times of water protons affected by heating rate and raw meat quality are well related to the protein secondary structural changes as probed by FT-IR microspectroscopy.

  13. Determination of the structure of [Nle7]-endothelin by 1H NMR.

    PubMed

    Aumelas, A; Chiche, L; Mahe, E; Le-Nguyen, D; Sizun, P; Berthault, P; Perly, B

    1991-04-01

    [Nle7]-endothelin was synthesized and studied by 1H NMR and distance geometry calculations. The NMR study was performed first in DMSO-d6 and then in 50% acetonitrile/water since this peptide aggregates in pure water. In both cases, all spin systems were identified and assigned with the aid of two-dimensional spectroscopy (2D): COSY (for scalar couplings) and NOESY (for dipolar couplings). On the basis of the acetonitrile/water NMR parameters, and using the DISGEO program, a three-dimensional structure of [Nle7]-endothelin is proposed and discussed.

  14. 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.

  15. 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.

  16. 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.

  17. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. 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.

  19. Dilute Bicellar Solutions for Structural NMR Work

    NASA Astrophysics Data System (ADS)

    Struppe, Jochem; Vold, Regitze R.

    1998-12-01

    Deuterium NMR spectroscopy has been employed to characterize the concentration dependence of orientational order in DMPC/DHPC bicellar solutions with molar ratiosq= [DMPC]/[DHPC] = 3.3, 2.7, and 2.3. The stability of a discotic nematic phase can, in general, be predicted from a simple Onsager picture involving the size and concentration of the mesogenic unit, but for the bicellar solutions this model is not adequate. Specifically, macroscopic alignment is observed at total lipid concentrations well below that, 1-10% (w/w) predicted by Onsager's model. Thus the discotic nematic phase is stable to ≈3-5% (w/w) forq= 3.3-2.3, and the bicellar order is highest just before phase separation occurs at the minimum total phospholipid concentration. This implies the presence of a DHPCbic⇄ DHPCsolequilibrium in establishing bicellar size, thereby extending the range of concentrations for which alignment occurs. Bicellar morphology has been verified for a wide range of concentrations, temperatures, andq-values, but as viscosity measurements demonstrate, major morphological changes take place as the temperature is reduced below 30°C.

  20. Polymeric proanthocyanidins 13C NMR studies of procyanidins

    Treesearch

    Lawrence J. Porter; Roger H. Newman; Lai Yeap Foo; Herbert Wong; Richard W. Hemingway

    1982-01-01

    Proanthocyanidin polymers have been shown to consist entirely of flavan-3-ol units by a combination of techniques including 13C n.m.r. spectroscopy. The 13C n.m.r. spectra of the polymers and related molecules are now considered in more detail. Prior to this study UC n.m.r. data has been published of procyanidins and...

  1. 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

  2. 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.

  3. 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.

  4. HPLC & NMR-based forced degradation studies of ifosfamide: The potential of NMR in stability studies.

    PubMed

    Salman, D; Peron, J-M R; Goronga, T; Barton, S; Swinden, J; Nabhani-Gebara, S

    2016-03-01

    The aim of this study is to conduct a forced degradation study on ifosfamide under several stress conditions to investigate the robustness of the developed HPLC method. It also aims to provide further insight into the stability of ifosfamide and its degradation profile using both HPLC and NMR. Ifosfamide solutions (20mg/mL; n=15, 20mL) were stressed in triplicate by heating (70°C), under acidic (pH 1 & 4) and alkaline (pH 10 & 12) conditions. Samples were analysed periodically using HPLC and FT-NMR. Ifosfamide was most stable under weakly acidic conditions (pH 4). NMR results suggested that the mechanism of ifosfamide degradation involves the cleavage of the PN bond. For all stress conditions, HPLC was not able to detect ifosfamide degradation products that were detected by NMR. These results suggest that the developed HPLC method for ifosfamide did not detect the degradation products shown by NMR. It is possible that degradation products co-elute with ifosfamide, do not elute altogether or are not amenable to the detection method employed. Therefore, investigation of ifosfamide stability requires additional techniques that do not suffer from the aforementioned shortcomings. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

  5. Blind testing of routine, fully automated determination of protein structures from NMR data

    PubMed Central

    Rosato, Antonio; Aramini, James M.; Arrowsmith, Cheryl; Bagaria, Anurag; Baker, David; Cavalli, Andrea; Doreleijers, Jurgen F.; Eletsky, Alexander; Giachetti, Andrea; Guerry, Paul; Gutmanas, Aleksandras; Güntert, Peter; He, Yunfen; Herrmann, Torsten; Huang, Yuanpeng J.; Jaravine, Victor; Jonker, Hendrik R.A.; Kennedy, Michael A.; Lange, Oliver F.; Liu, Gaohua; Malliavin, Thérèse E.; Mani, Rajeswari; Mao, Binchen; Montelione, Gaetano T.; Nilges, Michael; Rossi, Paolo; van der Schot, Gijs; Schwalbe, Harald; Szyperski, Thomas A.; Vendruscolo, Michele; Vernon, Robert; Vranken, Wim F.; de Vries, Sjoerd; Vuister, Geerten W.; Wu, Bin; Yang, Yunhuang; Bonvin, Alexandre M.J.J.

    2012-01-01

    SUMMARY The protocols currently used for protein structure determination by NMR depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered ten experimental datasets with unassigned NOESY peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent “blind” assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR. PMID:22325772

  6. Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data.

    PubMed Central

    Mattinen, Maija-Liisa; Pääkkönen, Kimmo; Ikonen, Teemu; Craven, Jeremy; Drakenberg, Torbjörn; Serimaa, Ritva; Waltho, Jonathan; Annila, Arto

    2002-01-01

    A new principle in constructing molecular complexes from the known high-resolution domain structures joining data from NMR and small-angle x-ray scattering (SAXS) measurements is described. Structure of calmodulin in complex with trifluoperazine was built from N- and C-terminal domains oriented based on residual dipolar couplings measured by NMR in a dilute liquid crystal, and the overall shape of the complex was derived from SAXS data. The residual dipolar coupling data serves to reduce angular degrees of freedom, and the small-angle scattering data serves to confine the translational degrees of freedom. The complex built by this method was found to be consistent with the known crystal structure. The study demonstrates how approximate tertiary structures of modular proteins or quaternary structures composed of subunits can be assembled from high-resolution structures of domains or subunits using mutually complementary NMR and SAXS data. PMID:12124297

  7. 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.

  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. 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.

  10. Multinuclear NMR study of silica fiberglass modified with zirconia.

    PubMed

    Lapina, O B; Khabibulin, D F; Terskikh, V V

    2011-01-01

    Silica fiberglass textiles are emerging as uniquely suited supports in catalysis, which offer unprecedented flexibility in designing advanced catalytic systems for chemical and auto industries. During manufacturing fiberglass materials are often modified with additives of various nature to improve glass properties. Glass network formers, such as zirconia and alumina, are known to provide the glass fibers with higher strength and to slow down undesirable devitrification processes. In this work multinuclear (1)H, (23)Na, (29)Si, and (91)Zr NMR spectroscopy was used to characterize the effect of zirconia on the molecular-level fiberglass structure. (29)Si NMR results help in understanding why zirconia-modified fiberglass is more stable towards devitrification comparing with pure silica glass. Internal void spaces formed in zirconia-silica glass fibers after acidic leaching correlate with sodium and water distributions in the starting bulk glass as probed by (23)Na and (1)H NMR. These voids spaces are important for stabilization of catalytically active species in the supported catalysts. Potentials of high-field (91)Zr NMR spectroscopy to study zirconia-containing glasses and similarly disordered systems are illustrated. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. 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.

  12. 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.

  13. 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.

  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. 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. © 2015 The Protein Society.

  17. Comparison of the NMR solution structures of cyclosporin A determined by different techniques

    NASA Astrophysics Data System (ADS)

    Pachter, Ruth; Altman, Russ B.; Czaplicki, Jerzy; Jardetzky, Oleg

    An evaluation and comparison of the NMR solution structures of Cyclosporin A are presented in this study. A new structure has been calculated by the probability filtered estimate (PROFILE) technique using new NMR data, in addition to the previously reported data. The mean structure, along with explicit estimates of uncertainty in the position of each atom, satisfies the NMR constraints but does not imply a unique structure. A comparison of this structural calculation with models obtained with other computational methods shows large variations in the Ramachandran angles (φ, ψ). These differences are explained on the basis of both the calculated uncertainty in backbone atomic coordinates and the cooperative motion of the backbone dihedral angles.

  18. Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

    PubMed

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-05

    Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2017-09-01

    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.

  20. 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.

  1. NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure.

    PubMed

    Cox, M; Dekker, N; Boelens, R; Verrijzer, C P; van der Vliet, P C; Kaptein, R

    1993-06-15

    The 1H and 15N resonances of the POU-specific DNA-binding domain of transcription factor Oct-1 have been assigned sequentially using two-dimensional homo- and heteronuclear NMR techniques, as well as three-dimensional heteronuclear NMR techniques, including TOCSY, 2D NOE, and NOESY-HMQC experiments. A number of typical short- and medium-range NOE contacts, as well as amide proton exchange data, gave evidence for the presence of four alpha-helices, in the peptide segments 1-19, 23-34, 40-49, and 54-71, which are connected by short loops of irregular structure. Interestingly, the second helix contains three glycine residues and the fourth helix a proline in the middle of the helix. Although the regular pattern of hydrogen bonds in the fourth helix is interrupted, due to the absence of an amide proton in proline, the helix is remarkably stable. All four helices are amphipathic, which suggests a packing of the apolar sides of the helices in the folded structure of the protein.

  2. 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.

  3. Overcoming the Solubility Limit with Solubility-Enhancement Tags: Successful Applications in Biomolecular NMR Studies

    PubMed Central

    Zhou, Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs. PMID:19731047

  4. Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II.

    PubMed

    Asakura, Tetsuo; Suita, Kohei; Kameda, Tsunenori; Afonin, Sergii; Ulrich, Anne S

    2004-02-01

    The influence of the bulky and H-bonding Tyr side-chain on its Ala- and Gly-rich environment in Bombyx mori silk fibroin was examined by (13)C cross-polarization magic angle spinning (CP/MAS), static (2)H and (19)F NMR and molecular mechanics calculations. Model peptides of the type (AG)(15) were synthesized with Tyr in a number of different positions, precipitated under conditions favoring either of the two characteristic protein conformations, and the resulting structures were assigned from their (13)C chemical shifts. Dialysis of native fibroin or the simple (AG)(15) peptide from a 9 M LiBr solution against water produces silk I (the structure of silk before spinning), whereas drying from formic acid yields silk II (fibrous structure after spinning). We found that the introduction one or more Tyr into (AG)(15) can have a dramatic effect not only on the local backbone conformation but also on the long-range intermolecular chain packing in the samples. The antiparallel beta-sheet conformation of silk II is able readily to accommodate a single Tyr residue. Interestingly, the beta-turn conformation of silk I only remains stable when Tyr is positioned near the chain terminus in (AG)(12)YG(AG)(2), but the conformation is driven towards silk II when Tyr is located in the central region of (AG)(7)YG(AG)(7). The role of H-bonding was tested by replacing Tyr with Phe or 4F-Phe, which are no longer compatible with silk I and fully induced a silk II conformation. In the presence of several Tyr residues a mixture of distorted beta-sheet and beta-turn conformations was obtained, regardless of the precipitation conditions. Static (2)H NMR of ring-deuterated [3',5'-(2)H(2)]Tyr located in the central region of (AG)(7)YG(AG)(7) showed that the side-chain is immobilized in both silk I and II, which was also observed by static (19)F NMR of the 4F-Phe analogue. To visualize the local packing around the Tyr side-chain, molecular mechanics calculations were performed on a mixture of

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. Application of lanthanide-induced shifts in solution NMR studies of coordinated extractants. [Dibutylbutylphosphonate; butyldibutylphosphinate

    SciTech Connect

    Kalina, D.G.; Horwitz, E.P.

    1983-01-01

    A NMR study was conducted to study the coordination of monofunctional extractants (TBP, dibutylbutylphosphonate, and butyldibutylphosphinate) and bifunctional extractants (DHDECMP). Pr, Eu, and Yb ions were used as solution structural probes. (DLC)

  11. 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.

  12. DNA Nanotubes for NMR Structure Determination of Membrane Proteins

    PubMed Central

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

    2013-01-01

    Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

  13. 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.

  14. 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.

  15. A 3D structural and conformational study of procyanidin dimers in water and hydro-alcoholic media as viewed by NMR and molecular modeling.

    PubMed

    Tarascou, Isabelle; Barathieu, Karine; Simon, Cécile; Ducasse, Marie-Agnès; André, Yann; Fouquet, Eric; Dufourc, Erick J; de Freitas, Victor; Laguerre, Michel; Pianet, Isabelle

    2006-09-01

    The three-dimensional structures of 5 procyanidin dimers have been determined in a hydro-alcoholic medium and in water using 2D NMR and molecular mechanics. They are made from monomers of catechin (CAT) and epicatechin (EPI)-B1: EPI-CAT, B2: EPI-EPI, B3: CAT-CAT, B4: CAT-EPI and B2g: EPI-EPI-3-O-gallate. These tannins exist in two conformations that are in slow exchange in the NMR timescale (s), one is compact and the other extended. The compact form is found to dominate (76-98%) when the dimer is made of at least one CAT monomer (B1, B3, B4). Both forms are found in even proportions only in the case of procyanidin B2. The latter tannin can be converted into a dominant compact form when the lower EPI unit is galloylated. The finding of a predominant compact form for procyanidin dimers is discussed in relation with tannin-saliva protein interactions that are of importance for the wine-tasting/making processes. Copyright (c) 2006 John Wiley & Sons, Ltd.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. sup 15 N and sup 13 C NMR studies of ligands bound to the 280,000-dalton protein porphobilinogen synthase elucidate the structures of enzyme-bound product and a Schiff base intermediate

    SciTech Connect

    Jaffe, E.K.; Rajagopalan, J.S. ); Markham, G.D. )

    1990-09-11

    Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation of two molecules of 5-aminolevulinic acid (ALA). Despite the 280,000-dalton size of PBGS, much can be learned about the reaction mechanism through {sup 13}C and {sup 15}N NMR. The authors knowledge, these studies represent the largest protein complex for which individual nuclei have been characterized by {sup 13}C or {sup 15}N NMR. Here they extend their {sup 13}C NMR studies to PBGS complexes with (3,3-{sup 2}H{sub 2},3-{sup 13}C)ALA and report {sup 15}N NMR studies of ({sup 15}N)ALA bound to PBGS. As in their previous {sup 13}C NMR studies, observation of enzyme-bound {sup 15}N-labeled species was facilitated by deuteration at nitrogens that are attached to slowly exchanging hydrogens. For holo-PBGS at neutral pH, the NMR spectra reflect the structure of the enzyme-bound product porphobilinogen (PBG), whose chemical shifts are uniformly consistent with deprotonation of the amino group whose solution pK{sub a} is 11. Despite this local environment, the protons of the amino group are in rapid exchange with solvent. For methyl methanethiosulfonate (MMTS) modified PBGS, the NMR spectra reflect the chemistry of an enzyme-bound Schiff base intermediate that is formed between C{sub 4} of ALA and an active-site lysine. The {sup 13}C chemical shift of (3,3-{sup 2}H{sub 2},3-{sup 13}C)ALA confirms that the Schiff base is an imine of E stereochemistry. By comparison to model imines formed between ({sup 15}N)ALA and hydrazine or hydroxylamine, the {sup 15}N chemical shift of the enzyme-bound Schiff base suggests that the free amino group is an environment resembling partial deprotonation. Deprotonation of the amino group would facilitate formation of a Schiff base between the amino group of the enzyme-bound Schiff base and C{sub 4} of the second ALA substrate. This is the first evidence supporting carbon-nitrogen bond formation as the initial site of interaction between the two substrate molecules.

  3. 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.

  4. 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.

  5. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  6. 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.

  7. 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

  8. 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

  9. 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).

  10. 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.

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

    SciTech Connect

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

    1988-03-08

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

  12. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  14. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. 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.

  17. 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.

  18. 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.

  19. Comprehensive multiphase NMR: a promising technology to study plants in their native state.

    PubMed

    Wheeler, Heather L; Soong, Ronald; Courtier-Murias, Denis; Botana, Adolfo; Fortier-Mcgill, Blythe; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Campbell, Malcolm M; Simpson, Andre

    2015-09-01

    Nuclear magnetic resonance (NMR) spectroscopy is arguably one the most powerful tools to study the interactions and molecular structure within plants. Traditionally, however, NMR has developed as two separate fields, one dealing with liquids and the other dealing with solids. Plants in their native state contain components that are soluble, swollen, and true solids. Here, a new form of NMR spectroscopy, developed in 2012, termed comprehensive multiphase (CMP)-NMR is applied for plant analysis. The technology composes all aspects of solution, gel, and solid-state NMR into a single NMR probe such that all components in all phases in native unaltered samples can be studied and differentiated in situ. The technology is evaluated using wild-type Arabidopsis thaliana and the cellulose-deficient mutant ectopic lignification1 (eli1) as examples. Using CMP-NMR to study intact samples eliminated the bias introduced by extraction methods and enabled the acquisition of a more complete structural and metabolic profile; thus, CMP-NMR revealed molecular differences between wild type (WT) and eli1 that could be overlooked by conventional methods. Methanol, fatty acids and/or lipids, glutamine, phenylalanine, starch, and nucleic acids were more abundant in eli1 than in WT. Pentaglycine was present in A. thaliana seedlings and more abundant in eli1 than in WT. Copyright © 2015 John Wiley & Sons, Ltd.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. /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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Sensitivity enhanced NMR reveals alterations in protein structure by cellular milieus

    PubMed Central

    Frederick, Kendra K.; Michaelis, Vladimir K.; Corzilius, Björn; Ong, Ta-Chung; Jacavone, Angela C.; Griffin, Robert G.; Lindquist, Susan

    2015-01-01

    Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of NMR spectroscopy and enable structural studies in biologically complex environments. Here we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an instrinsically disordered region, the yeast prion protein Sup35. We added an exogenously-prepared isotopically-labeled protein to deuterated lysates, rendering the biological environment “invisible” and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible and such contexts can influence protein structure. PMID:26456111

  11. Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus.

    PubMed

    Frederick, Kendra K; Michaelis, Vladimir K; Corzilius, Björn; Ong, Ta-Chung; Jacavone, Angela C; Griffin, Robert G; Lindquist, Susan

    2015-10-22

    Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and enable structural studies in biologically complex environments. Here, we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an intrinsically disordered region, the yeast prion protein Sup35. We added an exogenously prepared isotopically labeled protein to deuterated lysates, rendering the biological environment "invisible" and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible, and such contexts can influence protein structure. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. Solid-state (79/81)Br NMR and gauge-including projector-augmented wave study of structure, symmetry, and hydration state in alkaline earth metal bromides.

    PubMed

    Widdifield, Cory M; Bryce, David L

    2010-02-11

    Bromine-79/81 solid-state NMR (SSNMR) spectroscopy is established as a tool to characterize the local structure and symmetry about bromide ions in inorganic systems. Benchmark experimental (79/81)Br SSNMR data are acquired for CaBr(2), SrBr(2), BaBr(2), MgBr(2).6H(2)O, SrBr(2).6H(2)O, BaBr(2).2H(2)O, and CaBr(2).xH(2)O using the Solomon echo and/or QCPMG pulse sequences in magnetic fields of 11.75 and 21.1 T. Analytical line-shape analysis provides (79/81)Br electric field gradient (EFG) tensor parameters (including (79)Br quadrupolar coupling constants, C(Q)((79)Br), of up to 75.1(5) MHz in CaBr(2)), chemical shift tensor parameters (including the largest reported anisotropy), and the relative orientation of the tensor principal axis systems. These data are interpreted in terms of structure and symmetry. Our results indicate that ionic bromide systems should be generally accessible to characterization by (79/81)Br SSNMR despite sizable quadrupolar interactions. The resolving capabilities of (79/81)Br SSNMR spectroscopy are illustrated, using samples which possess up to four magnetically inequivalent sites, and through a rare example of (79)Br magic-angle spinning NMR for a Br in a noncubic lattice. Bromine-79/81 SSNMR spectroscopy is demonstrated to be sensitive to the presence of hydrates (i.e., pseudopolymorphism), via drastic changes in C(Q) and delta(iso). The changes are diagnostic to an extent that the composition of the mixture CaBr(2).xH(2)O is determined for the first time. This technique should therefore be applicable to characterize other unknown mixtures or polymorphs. Important instances where (79)Br nuclear quadrupole resonance data were found to be deficient are noted and corrected. GIPAW DFT computations are shown to be generally in very good agreement with the experimental (79/81)Br SSNMR observations. Finally, it is demonstrated that the origin of the EFG at the Br nuclei cannot be described quantitatively using a point charge model, even after

  18. 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…

  19. 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…

  20. 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

  1. 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.

  2. Structure determination of the seven-helical transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy

    PubMed Central

    Gautier, Antoine; Mott, Helen R.; Bostock, Mark J.; Kirkpatrick, John P.; Nietlispach, Daniel

    2010-01-01

    Seven-helical membrane proteins represent a challenge for structural biology. Here, we report the first NMR structure determination of a detergent-solubilized seven-helical transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is extremely good (backbone root mean squared deviation of 0.48 Å) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins including members of the family of G protein-coupled receptors (GPCRs). PMID:20512150

  3. 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

  4. 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

  5. In-Situ Studies of Structure Transformation and Al Coordination of KAl(MoO₄)₂ during Heating by High Temperature Raman and (27)Al NMR Spectroscopies.

    PubMed

    Wang, Min; You, Jinglin; Sobol, Alexander; Lu, Liming; Wang, Jian; Xie, Yingfang

    2017-03-17

    Recent interest in optimizing composition and synthesis conditions of functional crystals, and the further exploration of new possible candidates for tunable solid-state lasers, has led to significant research on compounds in this family M(I)M(III)(M(VI)O₄)₂ (M(I) = alkali metal, M(III) = Al, In, Sc, Fe, Bi, lanthanide; M(VI) = Mo, W). The vibrational modes, structure transformation, and Al coordination of crystalline, glassy, and molten states of KAl(MoO₄)₂ have been investigated by in-situ high temperature Raman scattering and (27)Al magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, together with first principles density functional simulation of room temperature Raman spectrum. The results showed that, under the present fast quenching conditions, Al is present predominantly in [AlO₆] octahedra in both KAl(MoO₄)₂ glass and melt, with the tetrahedrally coordinated Al being minor at approximately 2.7%. The effect of K⁺, from ordered arrangement in the crystal to random distribution in the melt, on the local chemical environment of Al, was also revealed. The distribution and quantitative analysis of different Al coordination subspecies are final discussed and found to be dependent on the thermal history of the glass samples.

  6. 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.

  7. In situ solid-state NMR and XRD studies of the ADOR process and the unusual structure of zeolite IPC-6

    NASA Astrophysics Data System (ADS)

    Morris, Samuel A.; Bignami, Giulia P. M.; Tian, Yuyang; Navarro, Marta; Firth, Daniel S.; Čejka, Jiří; Wheatley, Paul S.; Dawson, Daniel M.; Slawinski, Wojciech A.; Wragg, David S.; Morris, Russell E.; Ashbrook, Sharon E.

    2017-10-01

    The assembly-disassembly-organization-reassembly (ADOR) mechanism is a recent method for preparing inorganic framework materials and, in particular, zeolites. This flexible approach has enabled the synthesis of isoreticular families of zeolites with unprecedented continuous control over porosity, and the design and preparation of materials that would have been difficult—or even impossible—to obtain using traditional hydrothermal techniques. Applying the ADOR process to a parent zeolite with the UTL framework topology, for example, has led to six previously unknown zeolites (named IPC-n, where n = 2, 4, 6, 7, 9 and 10). To realize the full potential of the ADOR method, however, a further understanding of the complex mechanism at play is needed. Here, we probe the disassembly, organization and reassembly steps of the ADOR process through a combination of in situ solid-state NMR spectroscopy and powder X-ray diffraction experiments. We further use the insight gained to explain the formation of the unusual structure of zeolite IPC-6.

  8. 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

  9. Solid-state NMR relaxation studies of Australian spider silks.

    PubMed

    Kishore, A I; Herberstein, M E; Craig, C L; Separovic, F

    Solid-state NMR techniques were used to study two different types of spider silk from two Australian orb-web spider species, Nephila edulis and Argiope keyserlingi. A comparison of (13)C-T(1) and (1)H-T(1rho) solid-state NMR relaxation data of the Ala Calpha, Ala Cbeta, Gly Calpha, and carbonyl resonances revealed subtle differences between dragline and cocoon silk. (13)C-T(1rho) and (1)H-T(1) relaxation experiments showed significant differences between silks of the two species with possible structural variations. Comparison of our data to previous (13)C-T(1) relaxation studies of silk from Nephila clavipes (A. Simmons et al., Macromolecules, 1994, Vol. 27, pp. 5235-5237) also supports the finding that differences in molecular mobility of dragline silk exist between species. Interspecies differences in silk structure may be due to different functional properties. Relaxation studies performed on wet (supercontracted) and dry silks showed that the degree of hydration affects relaxation properties, and hence changes in molecular mobility are correlated with functional properties of silk. Copyright 2002 Wiley Periodicals, Inc.

  10. 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

  11. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR.

    PubMed

    Rogawski, Rivkah; McDermott, Ann E

    2017-08-15

    Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments. Copyright © 2017. Published by Elsevier Inc.

  12. Studies of organic paint binders by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Spyros, A.; Anglos, D.

    2006-06-01

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

  13. Distinguishing Phosphate Structural Defects From Inclusions in Calcite and Aragonite by NMR Spectroscopy (Invited)

    NASA Astrophysics Data System (ADS)

    Phillips, B. L.; Mason, H. E.

    2010-12-01

    Variations in the concentration of minor and trace elements are being studied extensively for potential use as proxies to infer environmental conditions at the time of mineral deposition. Such proxies rely fundamentally on a relationship between the activities in the solution and in the solid that would seem to be simple only in the case that the species substitutes into the mineral structure. Other incorporation mechanisms are possible, including inclusions (both mineral and fluid) and occlusion of surface adsorbate complexes, that might be sensitive to other factors, such as crystallization kinetics, and difficult to distinguish analytically. For example, it is known from mineral adsorption studies that surface precipitates can be nanoscopic, and might not be apparent at resolutions typical of microchemical analysis. Techniques by which a structural relationship between the substituting element and the host mineral structure are needed to provide a sound basis for geochemical proxies. NMR spectroscopy offers methods for probing such spatial relationship. We are using solid-state NMR spectroscopy to investigate phosphate incorporation in calcium carbonate minerals, including calcite speleothems and coral skeletal aragonite, at concentrations of the order 100 μg P g -1. In 31P NMR spectra of most samples, narrow peaks arising from crystalline inclusions can be resolved, including apatite in coral aragonite and an unidentified phase in calcite. All samples studied yield also a broad 31P signal, centered near chemical shifts of +3 to +4 ppm, that could be assigned to phosphate defects in the host mineral and from which the fraction of P occurring in the carbonate mineral structure can be determined. To test this assignment we applied rotational-echo double-resonance (REDOR) NMR techniques that probe the molecular-scale proximity of carbonate groups to the phosphate responsible for the broad 31P peak. This method measures dipole-dipole coupling between 31P of

  14. 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

  15. 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.

  16. Surface Binding of TOTAPOL Assists Structural Investigations of Amyloid Fibrils by Dynamic Nuclear Polarization NMR Spectroscopy.

    PubMed

    Nagaraj, Madhu; Franks, Trent W; Saeidpour, Siavash; Schubeis, Tobias; Oschkinat, Hartmut; Ritter, Christiane; van Rossum, Barth-Jan

    2016-07-15

    Dynamic nuclear polarization (DNP) NMR can enhance sensitivity but often comes at the price of a substantial loss of resolution. Two major factors affect spectral quality: low-temperature heterogeneous line broadening and paramagnetic relaxation enhancement (PRE) effects. Investigations by NMR spectroscopy, isothermal titration calorimetry (ITC), and EPR revealed a new substantial affinity of TOTAPOL to amyloid surfaces, very similar to that shown by the fluorescent dye thioflavin-T (ThT). As a consequence, DNP spectra with remarkably good resolution and still reasonable enhancement could be obtained at very low TOTAPOL concentrations, typically 400 times lower than commonly employed. These spectra yielded several long-range constraints that were difficult to obtain without DNP. Our findings open up new strategies for structural studies with DNP NMR spectroscopy on amyloids that can bind the biradical with affinity similar to that shown towards ThT. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. 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.

  18. 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.

  19. 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.

  20. Influence of aging and salting on protein secondary structures and water distribution in uncooked and cooked pork. A combined FT-IR microspectroscopy and 1H NMR relaxometry study.

    PubMed

    Wu, Zhiyun; Bertram, Hanne Christine; Kohler, Achim; Böcker, Ulrike; Ofstad, Ragni; Andersen, Henrik J

    2006-11-01

    Fourier transform infrared (FT-IR) microspectroscopy and low-field (LF) proton NMR transverse relaxation measurements were used to study the changes in protein secondary structure and water distribution as a consequence of aging (1 day and 14 days) followed by salting (3%, 6%, and 9% NaCl) and cooking (65 degrees C). An enhanced water uptake and increased proton NMR relaxation times after salting were observed in aged meat (14 days) compared with nonaged meat (1 day). FT-IR bands revealed that salting induced an increase in native beta-sheet structure while aging triggered an increase in native alpha-helical structure before cooking, which could explain the effects of aging and salting on water distribution and water uptake. Moreover, the decrease in T2 relaxation times and loss of water upon cooking were attributed to an increase in aggregated beta-sheet structures and a simultaneous decrease in native protein structures. Finally, aging increased the cooking loss and subsequently decreased the final yield, which corresponded to a further decrease in T2 relaxation times in aged meat upon cooking. However, salting weakened the effect of aging on the final yield, which is consistent with the increased T2 relaxation times upon salting for aged meat after cooking and the weaker effect of aging on protein secondary structural changes for samples treated with high salt concentration. The present study reveals that changes in water distribution during aging, salting, and cooking are not only due to the accepted causal connection, i.e., proteolytic degradation of myofibrillar structures, change in electrostatic repulsion, and dissolution and denaturation of proteins, but also dynamic changes in specific protein secondary structures.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  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. 2D 1H- 31P solid-state NMR studies of the dependence of inter-bilayer water dynamics on lipid headgroup structure and membrane peptides

    NASA Astrophysics Data System (ADS)

    Doherty, Tim; Hong, Mei

    2009-01-01

    The dynamics of hydration-water in several phospholipid membranes of different compositions is studied by 2D 1H- 31P heteronuclear correlation NMR under magic-angle spinning. By using a 1H T2 filter before and a 1H mixing-time after the evolution period and 31P detection, inter-bilayer water is selectively detected without resonance overlap from bulk water outside the multilamellar vesicles. Moreover the 1H T2 relaxation time of the inter-bilayer water is measured. Lipid membranes with labile protons either in the lipid headgroup or in sterols exhibit water- 31P correlation peaks while membranes free of exchangeable protons do not, indicating that the mechanism for water-lipid correlation is chemical exchange followed by relayed magnetization transfer to 31P. In the absence of membrane proteins, the inter-bilayer water 1H T2's are several tens of milliseconds. Incorporation of charged membrane peptides shortened this inter-bilayer water T2 significantly. This T2 reduction is attributed to the peptides' exchangeable protons, molecular motion and intermolecular hydrogen bonding, which affect the water dynamics and the chemically relayed magnetization transfer process.

  8. The interaction between ketamine and some crown ethers in common organic solvents studied by NMR: The effect of donating atoms and ligand structure

    NASA Astrophysics Data System (ADS)

    Chekin, Fereshteh; Bordbar, Maryam; Fathollahi, Yaghoub; Alizadeh, Naader

    2006-02-01

    1H NMR spectroscopy was used to investigate the stoichiometry and stability of the drug ketamine cation complexes with some crown ethers, such as 15-crown-5 (15C5), aza-15-crown-5 (A15C5), 18-crown-6 (18C6), aza-18-crown-6 (A18C6), diaza-18-crown-6 (DA18C6), dibenzyl-diaza-18-crown-6 (DBzDA18C6) and cryptant [2,2,2] (C222) in acetonitrile (AN), dimethylsulfoxide (DMSO) and methanol (MeOH) at 27 °C. In order to evaluate the formation constants of the ketamine cation complexes, the CH 3 protons chemical shift (on the nitrogen atom of ketamine) was measured as function of ligand/ketamine mole ratio. The formation constant of resulting complexes were calculated by the computer fitting of chemical shift versus mole ratio data to appropriate equations. A significant chemical shift variation was not observed for 15C5 and 18C6. The stoichiometry of the mono aza and diaza ligands are 1:1 and 1:2 (ligand/ketamine), respectively. In all of the solvents studied, DA18C6 formed more stable complexes than other ligands. The solvent effect on the stability of these complexes is discussed.

  9. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25805858

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Study of molecular interactions with 13C DNP-NMR

    NASA Astrophysics Data System (ADS)

    Lerche, Mathilde H.; Meier, Sebastian; Jensen, Pernille R.; Baumann, Herbert; Petersen, Bent O.; Karlsson, Magnus; Duus, Jens Ø.; Ardenkjær-Larsen, Jan H.

    2010-03-01

    NMR spectroscopy is an established, versatile technique for the detection of molecular interactions, even when these interactions are weak. Signal enhancement by several orders of magnitude through dynamic nuclear polarization alleviates several practical limitations of NMR-based interaction studies. This enhanced non-equilibrium polarization contributes sensitivity for the detection of molecular interactions in a single NMR transient. We show that direct 13C NMR ligand binding studies at natural isotopic abundance of 13C gets feasible in this way. Resultant screens are easy to interpret and can be performed at 13C concentrations below μM. In addition to such ligand-detected studies of molecular interaction, ligand binding can be assessed and quantified with enzymatic assays that employ hyperpolarized substrates at varying enzyme inhibitor concentrations. The physical labeling of nuclear spins by hyperpolarization thus provides the opportunity to devise fast novel in vitro experiments with low material requirement and without the need for synthetic modifications of target or ligands.

  17. 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.

  18. 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.

  19. Synthesis of [F3S(triple bond)NXeF][AsF6] and structural study by multi-NMR and Raman spectroscopy, electronic structure calculations, and X-ray crystallography.

    PubMed

    Smith, Gregory L; Mercier, Hélène P A; Schrobilgen, Gary J

    2007-02-19

    The salt, [F3S(triple bond)NXeF][AsF6], has been synthesized by the reaction of [XeF][AsF6] with liquid N(triple bond)SF3 at -20 degrees C. The Xe-N bonded cation provides a rare example of xenon bound to an inorganic nitrogen base in which nitrogen is formally sp-hybridized. The F3S(triple bond)NXeF+ cation was characterized by Raman spectroscopy at -150 degrees C and by 129Xe, 19F, and 14N NMR spectroscopy in HF solution at -20 degrees C and in BrF5 solution at -60 degrees C. Colorless [F3S(triple bond)NXeF][AsF6] was crystallized from HF solvent at -45 degrees C, and its low-temperature X-ray crystal structure was determined. The Xe-N bond is among the longest Xe-N bonds known (2.236(4) A), whereas the Xe-F bond length (1.938(3) A) is significantly shorter than that of XeF2 but longer than in XeF+ salts. The Xe-F and Xe-N bond lengths are similar to those of HC(triple bond)NXeF+, placing it among the most ionic Xe-N bonds known. The nonlinear Xe-N-S angle (142.6(3)o) contrasts with the linear angle predicted by electronic structure calculations and is attributed to close N...F contacts within the crystallographic unit cell. Electronic structure calculations at the MP2 and DFT levels of theory were used to calculate the gas-phase geometries, charges, bond orders, and valencies of F3S(triple bond)NXeF+ and to assign vibrational frequencies. The calculated small energy difference (7.9 kJ mol-1) between bent and linear Xe-N-S angles also indicates that the bent geometry is likely the result of crystal packing. The structural studies, natural bond orbital analyses, and calculated gas-phase dissociation enthalpies reveal that F3S(triple bond)NXeF+ is among the weakest donor-acceptor adducts of XeF+ with an Xe-N donor-acceptor interaction that is very similar to that of HC(triple bond)NXeF+, but considerably stronger than that of F3S(triple bond)NAsF5. Despite the low dissociation enthalpy of the donor-acceptor bond in F3S(triple bond)NXeF+, 129Xe, 19F, and 14N NMR

  20. 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.

  1. 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.

  2. Interfaces in polymer nanocomposites – An NMR study

    SciTech Connect

    Böhme, Ute; Scheler, Ulrich

    2016-03-09

    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. {sup 1}H relaxation NMR gives insight on the polymer dynamics over a wide range of correlation times. For the polymer chain dynamics the transverse relaxation time T{sub 2} is most suited. In this presentation we report on two applications of T{sub 2} 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Tang, J. H.

    1981-11-01

    The theoretical background of spin Hamiltonians, the density matrix formalism of multiple quantum NMR are discussed as well as creation and detection of multiple quantum coherence by multiple pulse sequence. 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 considered. An oriented methyl group relaxed by paramagnetic impurities is examined and possible correlated motion between two coupled methyl groups is investigated by multiple quantum NMR. 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 spin lattice dynamics of orienting or tunneling methyl groups (CH3 and CD3) at low temperatures and the anisotropic spin lattice relaxation of deuterated hexamethylbenzene, caused by the sixfold reorientation of the molecules are described as well as NMR spectrometers.

  8. 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.

  9. NMR Studies of Some Plasma Proteins.

    NASA Astrophysics Data System (ADS)

    Lawrence, Mark P.

    Available from UMI in association with The British Library. Requires signed TDF. The work reported in this thesis consists of a study of the solution structure of a domain of protein structure found in some of the enzymes involved in blood coagulation. These domains, known as kringles, are of between 78 and 82 residues and contain three conserved disulphide bridges in their primary sequence. The study attempts to elucidate the nature of the lysine-binding site of the fourth kringle of human plasminogen to probe its physiological action, and a theory is developed to explain the overall fold of the protein in terms of its physiological role. The protein structure is found to contain only one small region of secondary structure, an antiparallel beta-sheet of about 8 residues, which provides the support for the binding site. The binding site itself consists of a hydrophobic channel provided by the aromatic residues at positions 61, 63, 71 and 73 in the beta-sheet and a negatively charged site at one end of this channel provided by the aspartic acid residues at positions 54 and 56. The beta-sheet appears to become more tightly defined on binding the kringle with alpha,omega -amino acids which are analogues of lysine and exhibit known anti-fibrinolytic properties. The rest of the solution structure appears to be less clearly defined and relies mainly on the three disulphide bridges and some rather isolated hydrogen bonding for maintenance of the fold. An explanation for this structure with a rigid binding site and a more flexible region for the remainder of the domain is proposed. Shorter studies are reported on the second kringle of bovine prothrombin and the first of human plasminogen which suggest strongly that the kringle fold is conserved.

  10. 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.

  11. NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

    PubMed

    Lykouras, Michail V; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2017-09-05

    Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain from CHIKV and its preliminary structural analysis via solution NMR spectroscopy. The macro domain seems to be folded in solution and an almost complete backbone assignment was achieved. In addition, the α/β/α sandwich topology with 4 α-helices and 6 β-strands was predicted by TALOS+.

  12. 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

  13. Structural studies of. cap alpha. -bungarotoxin. 2. /sub 1/H NMR assignments via an improved relayed coherence transfer nuclear Overhauser enhancement experiment

    SciTech Connect

    Basus, V.J.; Scheek, R.M.

    1988-04-19

    Complete sequence-specific assignments of the /sup 1/H NMR spectrum of bungarotoxin were reported in a previous paper. The assignment was significantly aided by the use of the homonuclear Hartman-Hahn relayed coherence transfer nuclear Overhauser enhancement spectroscopy experiment (HRNOESY) which we present here, as a modification of relayed coherence transfer nuclear Overhauser enhancement spectroscopy (relayed NOESY). As shown here, HRNOESY resolves problems of proton resonance overlap especially in extended chain conformations as found in ..beta..-sheets.

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

    PubMed Central

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

    2008-01-01

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

  15. Quadrupole coupling parameters and structural aspects of crystalline and amorphous solids by NMR and NQR

    SciTech Connect

    Mao, Degen.

    1991-01-01

    NMR and NQR techniques were combined to obtain the quadrupole coupling constant (Qcc) and asymmetry parameter ({eta}) and extract structural information for several borate, gallate, and metavanadate compounds and glasses. {sup 71}Ga and {sup 69}Ga NMR was used to study crystalline {beta}-Ga{sub 2}O{sub 3} and several gallate glasses. Quadrupole parameters were acquired for GaO{sub 6} and GaO{sub 4} units in {beta}-Ga{sub 2}O{sub 3} by the computer simulation of the NMR powder patterns. A sensitive CW NQR spectrometer was built to detect NQR resonances below 2 MHz. The spectrometer includes a modified Robinson oscillator-detector, a new bi-symmetric square wave Zeeman modulator and a computerized data acquisition system. {sup 51}V (I = 7/2) NQR resonances below 850 kHz were detected for several metavanadates at both room temperature and liquid nitrogen temperature. Two methods, Zeeman perturbed NQR powder pattern and {sup 10}B NQR, can be employed to obtain both Qcc and {eta}. With a double coil tank circuit design, pure {sup 11}B NQR was used to determine the fraction of borons in BO{sub 3} and BO{sub 4} configurations in hydrated zinc borates. {sup 11}B NMR and NQR were also used to study lead borate glasses.

  16. NMR studies on an oligodeoxynucleotide containing 2-aminopurine opposite adenine

    SciTech Connect

    Fazakerley, G.V.; Sowers, L.C.; Eritja, R.; Kaplan, B.E.; Goodman, M.F.

    1987-09-08

    A heteroduplex containing the mismatch 2-aminopurine (AP)-adenine has been synthesized and studied by proton NMR. The mismatch was incorporated into the sequence d(CGG(AP)GGC) x d-(GCCACCG). One-dimensional nuclear Overhauser effect measurements in H/sub 2/O and two-dimensional nuclear Overhauser effect spectra in D/sub 2/O show AP x A base pairs in a wobble structure in which both bases are in the anti conformation. The adenine is stacked well in the helix, but the helix twist between the adenine and neighboring cytosine in the 3' direction is unusually small. As a result, the aminopurine on the opposite strand is somewhat pushed out of the helix. From the measurements of the imino proton line widths, the two adjacent G x C base pairs are not found to be significantly destabilized by the presence of the purine-purine wobble pair.

  17. 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.

  18. 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.

  19. NMR structural studies of intramolecular (Y+) sub n ter dot (R+) sub n (Y minus ) sub n DNA triplexes in solution: Imino and amino proton and nitrogen markers of Gter dot TA base triple formation

    SciTech Connect

    Radhakrishnan, I.; de los Santos, C.; Patel, D.J. ); Gao, Xiaolian ); Live, D. )

    1991-09-17

    The authors reported previously on NMR studies of (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n}DNA triple helices containing one oligopurine strand (R){sub n} and two oligopyrimidine strands (Y){sub n} stabilized by T{center dot}AT and C{sup +}{center dot}GC base triples. Recently, it has been established that guanosine can recognize a thymidine{center dot}adenosine base pair to form a G{center dot}TA triple in an otherwise (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triple-helix motif. The present study extends the NMR research to the characterization of structural features of a 31-mer deoxyoligonucleotide that folds intramolecularly into a 7-mer (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triplex with the strands linked through two T{sub 5} loops and that contains a central G{center dot}TA triple flanked by T{center dot}AT triples. The NMR data are consistent with the proposed pairing alignment for the G{center dot}TA triple where the guanosine in an anti orientation pairs through a single hydrogen bond from one of its 2-amino protons to the 4-carbonyl group of thymidine in the Watson-Crick TA pair. They detect a set of NOEs between adjacent triples that establishes that the G{center dot}TA triple stacks between flanking T{center dot}AT triples in the G{center dot}TA triplex. These results demonstrate the capabilities of the NMR approach in monitoring individual base triples and their pairing alignments, as well as establishing that the G{center dot}TA triple can be readily accommodated in an otherwise intramolecular (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triple helix in solution.

  20. 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

    NASA Astrophysics Data System (ADS)

    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 13C 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.

  1. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. NMR solution structures of adducts derived from the binding of polycyclic aromatic diol epoxides to DNA

    SciTech Connect

    Cosman, M.; Patel, D.J.; Hingerty, B.E.; Amin, S.; Broyde, S.; Geacintov, N.E.

    1995-12-31

    Site-specifically modified oligonucleotides were derived from the reactions of stereoisomeric polycyclic aromatic diol epoxide metabolite model compounds with oligonucleotides of defined base composition and sequence. The NMR solution structures of ten different adducts studied so far are briefly described, and it is shown that stereochemical factors and the nature of the oligonucleotide context of the complementary strands, exert a powerful influence on the conformational features of these adducts.

  3. Structural elucidation of a novel transglycosylated compound α-glucosyl rhoifolin and of α-glucosyl rutin by NMR spectroscopy.

    PubMed

    Aoki, Chisa; Takeuchi, Yoshihiro; Higashi, Kenjirou; Okamoto, Yuta; Nakanishi, Akihito; Tandia, Mahamadou; Uzawa, Jun; Ueda, Keisuke; Moribe, Kunikazu

    2017-04-18

    We report the full assignment of (1)H and (13)C NMR signals belonging to α-glucosyl rhoifolin (Rhf-G), a novel transglycosylated compound synthesized from a flavone glycoside, rhoifolin, as well as its chemical structure. Furthermore, we report the complete NMR signal assignment for another transglycosylated compound, α-glucosyl rutin (Rutin-G), as the signals corresponding to its sugar moieties had not been identified. Electrospray ionization-mass spectrometry along with multiple NMR methods revealed that Rhf-G possesses three sugar moieties in its chemical structure. The additional glucose was bound directly via a transglycosylation to rhoifolin at position 3a of the sugar moiety. Interestingly, intramolecular hydrogen bonds in the basic Rhf-G and Rutin-G skeletons were confirmed by HMBC experiments. These findings will be helpful for comprehensive NMR studies on transglycosylated compounds in food, cosmetic, and pharmaceutical fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

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

    2013-04-21

    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.

  12. 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.

  13. 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.

  14. 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

  15. Structural investigation of Lisinopril by powder X-ray diffraction and solid-state NMR

    NASA Astrophysics Data System (ADS)

    Filip, Xenia; Tripon, Carmen; Borodi, Gheorghe; Oprean, Luminiţa; Filip, Claudiu

    2009-08-01

    Structural studies on polycrystalline Lisinopril (N-N-[(s)-1-carboxy-3-phenylpropyl]-L-lysil-L-proline) are performed by combined powder X-Ray diffraction and 13C solid-state nuclear magnetic resonance (NMR). The crystal structure of this drug, used primarily for the treatment of hypertension, has not yet been determined due to the impossibility of synthesizing single crystals of sufficient quality. It is shown here that valuable insights into the crystal and molecular structure of Lisinopril can be obtained on polycrystalline powder based on the complementary character of the information provided by the two techniques.

  16. 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.

  17. 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.

  18. 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.

  19. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

    Song, Xia; Mo, Wei; Liu, Xingang; Zhu, Lina; Yan, Xiaomin; Song, Houyan . E-mail: hysong@shmu.edu.cn; Dai, Linsen . E-mail: lsdai@fudan.edu.cn

    2007-08-17

    The solution structure of a new recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, was determined by {sup 1}H nuclear magnetic resonance spectroscopy and compared with the conformations of recombinant wild-type hirudin and hirudin (variant 2, Lys47) of the hirudin thrombin complex. On the basis of total 1284 distance and dihedral angle constraints derived from a series of NMR spectra, 20 conformers were computed with ARIA/CNS programs. The structure of residues 3-30 and 37-48 form a molecular core with two antiparallel {beta}-sheets as the other two hirudins. However, significant differences were found in the surface electrostatic charge distributions among the three hirudins, especially in the RGD segment of recombinant RGD-hirudin. This difference may be greatly beneficial to its additional function of anti-platelet aggregation. The difference in extended C-terminal makes its both ionic and hydrophobic interactions with the fibrinogen recognition exosite of thrombin more effective.

  20. Structure and dynamics of paramagnetic transients by pulsed EPR and NMR detection of nuclear resonance. [Pulse radiolysis of methanol in D/sub 2/O

    SciTech Connect

    Trifunac, A.D.

    1981-01-01

    Structure and dynamics of transient radicals in pulse radiolysis can be studied by time resolved EPR and NMR techniques. EPR study of kinetics and relaxation is illustrated. The NMR detection of nuclear resonance in transient radicals is a new method which allows the study of hyperfine coupling, population dynamics, radical kinetics, and reaction mechanism. 9 figures.

  1. Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations.

    PubMed

    Brown, David M L; Cho, Herman; de Jong, Wibe A

    2016-01-01

    The testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashion would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists. An implementation of an automated workflow has been developed for the integrated analysis of data from nuclear magnetic resonance (NMR) experiments and electronic structure calculations. Kepler (Altintas et al. 2004) open source software was used to coordinate the processing and transfer of data at each step of the workflow. This workflow incorporated several open source software components, including electronic structure code to compute NMR parameters, a program to simulate NMR signals, NMR data processing programs, and others. The Kepler software was found to be sufficiently flexible to address several minor implementation challenges without recourse to other software solutions. The automated workflow was demonstrated with data from a [Formula: see text] NMR study of uranyl salts described previously (Cho et al. in J Chem Phys 132:084501, 2010). The functional implementation of an automated process linking NMR data with electronic structure predictions demonstrates that modern software

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. TC and H NMR studies of PQQ and selected derivatives. [Pyrroloquinoline quinone

    SciTech Connect

    Houck, D.R.; Unkefer, C.J.

    1988-01-01

    The ortho-quinone structure of pyrroloquinoline quinone (PQQ) is famous for its reactivity with nucleophilic species of carbon, nitrogen, and oxygen(Duine et. al. 1987). In fact, the crystal structure of PQQ was solved in the form of the C-5 acetone adduct(Salisbury et. al 1979). The propensity of the ortho-quinone to accept nucleophiles is the chemical basis of the function of PQQ at enzyme active sites. The present study focuses on the NMR of PQQ and various derivatives formed with oxygen and nitrogen nucleophiles. Our goals are to assign the H, TC, and VN NMR spectra and to rigorously confirm the structures of the adducts. Once the NMR data of the relevant adducts are well defined, we will use TC and VN labeled substrates to probe the active sites of PQQ containing enzymes. 7 refs., 2 figs., 1 tab.

  7. 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.

  8. 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.

  9. 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.

  10. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.

    PubMed

    Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H; Ragan, Timothy J; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H; Kennedy, Michael; Acton, Thomas B; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T; Vuister, Geerten W

    2015-08-01

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  11. X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase.

    PubMed

    Demo, Gabriel; Papoušková, Veronika; Komárek, Jan; Kadeřávek, Pavel; Otrusinová, Olga; Srb, Pavel; Rabatinová, Alžbeta; Krásný, Libor; Zídek, Lukáš; Sklenář, Vladimír; Wimmerová, Michaela

    2014-08-01

    The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. NMR and NQR study of the electronic and structural properties of Al-Cu-Fe and Al-Cu-Ru quasicrystals

    SciTech Connect

    Shastri, A.; Borsa, F.; Torgeson, D.R.; Shield, J.E.; Goldman, A.I. )

    1994-12-01

    [sup 27]Al and [sup 63,65]Cu NMR is reported for powdered stable Al-Cu-Fe and Al-Cu-Ru icosahedral quasicrystals and crystalline approximants, and for an Al-Pd-Mn single-grain quasicrystal. [sup 27]Al NQR spectra at 4.2 K were observed in Al-Cu-Fe and Al-Cu-Ru samples. From quadrupole-perturbed NMR spectra at different magnetic fields, and from zero-field NQR spectra, a wide distribution of local electric-field gradient (EFG) tensor components and principal-axis-system orientations was found at the Al site. A model EFG calculation based on a 1/1 Al-Cu-Fe approximant successfully explained the observed NQR spectra. The average local gradient is largely determined by the [ital p]-electron wave function at the Al site, while the width of the distribution is due to EFG lattice contribution. Comparison of [sup 63]Cu and [sup 27]Al NMR shows the EFG distribution at the two sites is similar, but the electronic contribution to the EFG is considerably smaller at the Cu site, in agreement with a more [ital s]-type wave function of the conduction electrons. Overall spread of EFG values is well reproduced by calculation based on the approximant. However, the experimental spectra indicate a much larger number of nonequivalent sites when compared with the simulated NQR spectra based on the 1/1 approximant. The short-range, local chemical order is well represented by the approximant, but differences in coordination must be included at intermediate range in the quasicrystal. Measured [sup 27]Al Knight shift, magnetic susceptibility, and nuclear spin-lattice relaxation time as a function of temperature indicate reduced density of states at the Fermi level by a factor of 7 or 8 from the value in Al metal, consistent with the notion of a pseudogap for these quasicrystals. No differences in measured parameters were detected as a function of composition of the quasicrystalline alloys.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  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. 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).

  19. 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

  20. 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. © 2015 Giambaşu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  1. 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.

  2. 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.

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

    PubMed Central

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

    2016-01-01

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

  4. 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.

  5. NMR characterisation of a highly conserved secondary structural RNA motif of Halobacterium halobium 23S rRNA.

    PubMed

    King, John; Shammas, Christos; Nareen, Misbah; Lelli, Moreno; Ramesh, Vasudevan

    2013-05-28

    The highly conserved 29-mer RNA motif corresponding to the peptidyl transferase central circle region of the domain V of Halobacterium halobium 23S rRNA has been characterised by multidimensional NMR spectroscopy. The NMR structure has a good all atom average RMSD of 1.28 Å and a stable A-form helical conformation. The NMR structure differs from the X-ray crystal structure of an analogous motif, contained within the Escherichia coli ribosome, as none of the bases are flipped out and a number of non-canonical base pairs are formed in the solution structure. Thus in the observed NMR structure, the predicted A7 to U30 base pair is not seen and a non-canonical U6 to U30 base pair was formed in its place. Similarly the predicted A9 to U26 base pair was also not observed and another non-canonical A9 to A27 base pair was formed. It was also seen from the conformational analysis that the steps near the bulges had the greatest deviation from the canonical Watson-Crick base pair step parameters. Despite these differences, the 29-mer structure provides a working model of the RNA within the ribosome in a more natural solution state than that observed in the intact ribosome crystal structures, particularly around the A27 residue. The NMR structure determination of the 29-mer RNA motif provides a solid foundation for determining the NMR structure of the RNA-amicetin complex in the next step. To extend the above study, a fully (13)C and (15)N isotopically labelled 37-mer RNA version of the Halobacterium halobium RNA sample has been characterised using ultra high field 1 GHz spectroscopy. The results have been used to demonstrate the advantages conferred by the use of a 1 GHz spectrometer frequency over 800 MHz in terms of superior sensitivity and greater spectral dispersion achieved in the spectrum of the RNA.

  6. Identification of benzenoid and quinonoid structures by through-space NMR shieldings (TSNMRS).

    PubMed

    Kleinpeter, Erich; Koch, Andreas

    2010-05-13

    The spatial magnetic properties (through-space NMR shieldings (TSNMRS)) of benzenoid and quinonoid structures (hydroquinone/p-benzoquinone, p-phenylendiamine/p-phenylendiimine, pentacene, and N-containing heteropentacenes) have been calculated by the GIAO perturbation method employing the nucleus-independent chemical shift (NICS) concept of Paul von Rague Schleyer and visualized as isochemical shielding surfaces (ICSS) of various size and direction. The TSNMRS values, thus obtained, can be successfully employed to quantify and visualize the (anti)aromaticity of the compounds studied and to identify readily the existence of benzenoid and quinonoid structures, respectively. As an alternative, computed (as compared with experimental) (1)H chemical shifts can be employed.

  7. NMR STUDY OF MOLECULAR REFORIENTATION UNDER FIVEFOLD SYMMETRY SOLID PERMETHYLFERROCENE

    SciTech Connect

    Wemmer, D.E.; Ruben, D.J.; Pines, A.

    1980-08-01

    The ring reorientation in permethylferrocene has been studied using high resolution solid state {sup 13}C NMR. The constraints which symmetry places upon the number and types of motional parameters which may be determined from the NMR spectrum are discussed. From comparison of the experimental lineshapes in the slow reorientation temperatures range with theoretical models for random rotations and symmetry related jumps, it is concluded that the reorientation occurs as jumps between symmetry related orientations with jumps of 2{pi}/5 highly favored over 4{pi}/5. The activation energy derived for the jump process is 13.5 kjoules/mole.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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).

  14. {sup 57}Fe NMR study of multiferroic BiFeO{sub 3}

    SciTech Connect

    Pokatilov, V. S. Sigov, A. S.

    2010-03-15

    The effects of the {sup 57}Fe isotope content and high-frequency magnetic field amplitude h{sub 1} on the shape of the NMR spectrum of multiferroic BiFeO{sub 3} at T = 4.2 K are studied by pulsed nuclear magnetic resonance. The NMR spectrum shape and transverse relaxation time T{sub 2} are found to depend strongly on the {sup 57}Fe isotope content and h{sub 1} in multiferroic BiFeO{sub 3} in the presence of a spatial spin-modulated structure of a cycloid type. In a sample with a high {sup 57}Fe isotope content, the Suhl-Nakamura interaction contributes substantially to T{sub 2}. When these dynamic effects are taken into account for analysis of the NMR spectrum shape, an undisturbed (without an anharmonicity effect) spatial spin-modulated structure of a cycloid type is shown to exist in BiFeO{sub 3}.

  15. NMR crystallography: structure and properties of materials from solid-state nuclear magnetic resonance observables.

    PubMed

    Bryce, David L

    2017-07-01

    This topical review provides a brief overview of recent developments in NMR crystallography and related NMR approaches to studying the properties of molecular and ionic solids. Areas of complementarity with diffraction-based methods are underscored. These include the study of disordered systems, of dynamic systems, and other selected examples where NMR can provide unique insights. Highlights from the literature as well as recent work from my own group are discussed.