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Sample records for nmr structural investigation

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

    Science.gov (United States)

    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.

  2. NMR methods for the investigation of structure and transport

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, Edme H. [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Mechanische Verfahrenstechnik und Mechanik

    2012-07-01

    Extensive derivations of required fundamental relations for readers with engineering background New applications based on MRI, PGSE-NMR, and low-field NMR New concepts in quantitative data evaluation and image analysis Methods of nuclear magnetic resonance (NMR) are increasingly applied in engineering sciences. The book summarizes research in the field of chemical and process engineering performed at the Karlsruhe Institute of Technology (KIT). Fundamentals of the methods are exposed for readers with an engineering background. Applications cover the fields of mechanical process engineering (filtration, solid-liquid separation, powder mixing, rheometry), chemical process engineering (trickle-bed reactor, ceramic sponges), bioprocess engineering (biofilm growth), and food process engineering (microwave heating, emulsions). Magnetic Resonance Imaging (MRI) as well as low-field NMR are covered with notes on hardware. Emphasis is placed on quantitative data analysis and image processing. (orig.)

  3. Structural investigation of proapoptotic peptide by CD and NMR spectroscopy.

    Science.gov (United States)

    Pulsinelli, Emy; Vasile, Francesca; Vergani, Laura; Parodi, Silvio; Nicolini, Claudio

    2003-12-01

    We have performed a systematic investigation of the structural features of the peptides Int (a sequence able to cross cell membranes) and Int-H1(S6A,F8A) (which shows interesting antitumoral properties). After screening in aqueous solution at different ionic strength and pH values, we analyzed the structures of the peptides in different water/trifluoroethanol mixtures by Circular Dichroism and Nuclear Magnetic Resonance techniques.

  4. NMR methods for the investigation of structure and transport

    CERN Document Server

    Hardy, Edme H

    2011-01-01

    Methods of nuclear magnetic resonance (NMR) are increasingly applied in engineering sciences. The book summarizes research in the field of chemical and process engineering performed at the Karlsruhe Institute of Technology (KIT). Fundamentals of the methods are exposed for readers with an engineering background. Applications cover the fields of mechanical process engineering (filtration, solid-liquid separation, powder mixing, rheometry), chemical process engineering (trickle-bed reactor, ceramic sponges), bioprocess engineering (biofilm growth), and food process engineering (microwave heating

  5. Crystal structure, NMR and theoretical investigations on 2-( o-hydroxy-anilino)-1,4-napthoquinone

    Science.gov (United States)

    Feizi, Nourollah; Pinjari, Rahul V.; Gejji, Shridhar P.; Sayyed, Fareed B.; Gonnade, Rajesh; Rane, Sandhya Y.

    2010-03-01

    Crystal structure, 1H NMR and cyclic voltammetric investigations of 2-( o-hydroxy-anilino)-1,4-napthoquinone (HAN), resulting from coupling of aminophenol with 2-hydroxy-1,4-napthoquinone, have been carried out. X-ray structure reveals that the HAN ligand crystallizes in orthorhombic space group Pca2 1 with Z = 4, forming a chain via inter-molecular O2⋯H1A sbnd O1 and C15 sbnd H15⋯O3 interactions. Both 1H NMR and cyclic voltammetry experiments suggest the titled ligand is associated and exists as dimer in d6-DMSO while the monomer has been predicted in CDCl 3 solution. Density functional calculations can be utilized to gauge the strength of hydrogen-bonded interactions from the 1H chemical shifts in the NMR spectra. Self-consistent reaction field (SCRF) calculations further support the inferences drawn from cyclic voltammetry experiments.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Greenbaum, Steven

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

  8. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  9. HPLC-SPE-NMR for combinatorial biosynthetic investigations – Expanding the landscape of diterpene structural diversity

    DEFF Research Database (Denmark)

    Kongstad, Kenneth Thermann; Andersen-Ranberg, Johan; Hamberger, Björn Robert;

    In this work, the analytical technique, HPLC-HRMS-SPE-NMR was used for the first time in combination with combinatorial biosynthetic investigations in N. benthamiana. This efficient setup allowed for identification of several diterpene synthase (diTPS) combinations responsible for stereospecific...

  10. Structural Investigations of Portland Cement Components, Hydration, and Effects of Admixtures by Solid-State NMR Spectroscopy

    DEFF Research Database (Denmark)

    Skibsted, Jørgen Bengaard; Andersen, Morten D.; Jakobsen, Hans Jørgen

    2006-01-01

    Solid-state, magic-angle spinning (MAS) NMR spectroscopy represents a valuable tool for structural investigations on the nanoscale of the most important phases in anhydrous and hydrated Portland cements and of various admixtures. This is primarily due to the fact that the method reflects the first...... in the cement phases. The role of flouride ions is of special interest for mineralized Portland cements and it demonstrated that the location of these anions in anhydrous and hydrated Portland cements can be clarified using 19F MAS or 29Si{19F} CP/MAS NMR despite these cements contain only about 0.2 wt...

  11. The structure of polycaprolactone-clay nanocomposites investigated by 1H NMR relaxometry.

    Science.gov (United States)

    Monteiro, Mariana S S B; Rodrigues, Claudia Lopes; Neto, Roberto P C; Tavares, Maria Inês Bruno

    2012-09-01

    Nanocomposites based on polycaprolactone (PCL), containing concentrations of 1, 3 and 5 wt% of sodium montmorillonite (NT-25) and organo-modified montmorillonite clay, with three different salts (Viscogel B7, Viscogel S4 and Viscogel B8), were prepared employing the solution intercalation method using chloroform. The PCL nanocomposites were characterized by relaxometry, through determination of the hydrogen spin-lattice relaxation times using low-field nuclear magnetic resonance (NMR). Conventional X-ray diffraction (XDR) was also used to measure the basal space of the nanoclay. The proton spin-lattice relaxation parameters showed that hybrid nanocomposites were formed, containing different parts of intercalated and exfoliated organoclay. The proton T1rhoH also indicated changes in the microstructure, organization and the molecular mobility of the hybrid materials. NMR relaxometry is a good way to evaluate nanomaterials because it provides complementary information, since it is measured in a different time scale. Furthermore, differential scanning calorimetry and thermogravimetric analysis were also used to investigate the crystallization and thermal behavior of the nanocomposites, respectively. All materials had low crystallization temperature (Tc) and the melting temperature (Tm) were very close to that of the PCL matrix, but the degree of crystallinity of the nanocomposites decreased. TGA analysis demonstrated that montmorillonite accelerates PCL's decomposition while unmodified montmorillonite has the opposite effect.

  12. Tautomerism in o-hydroxyanilino-1,4-naphthoquinone derivatives: Structure, NMR, HPLC and density functional theoretic investigations

    Science.gov (United States)

    Bhand, Sujit; Patil, Rishikesh; Shinde, Yogesh; Lande, Dipali N.; Rao, Soniya S.; Kathawate, Laxmi; Gejji, Shridhar P.; Weyhermüller, Thomas; Salunke-Gawali, Sunita

    2016-11-01

    Structure and spectral characteristics of 'Ortho' ((E)-4-hydroxy-2-(2‧-(4‧-R)-hydroxyphenyl)-imino)-naphthalen-1(2H)-one) and 'para' (2-(2‧-(4‧-R)-hydroxyphenyl)-amino)-1,4-naphthoquinone) tautomers of o-hydroxyanilino-1,4-naphthoquinone derivatives (Rdbnd H, 1A; sbnd CH3, 2A; and -Cl, 3A) are investigated using the 1H, 13C, DEPT, gDQCOSY, gHSQCAD NMR, HPLC, cyclic voltammetry techniques combined with the density functional theory. The compound 2A crystallizes in monoclinic space group P21/c. wherein the polymer chain is facilitated via Osbnd H⋯O and Csbnd H⋯O intermolecular hydrogen bonding. Marginal variations in bond distances in quinonoid and aminophenol moieties render structural flexibility to these compounds those in solution exist as exist in 'ortho - para' tautomers. 1H and 13C NMR spectra in DMSO-d6 showed two sets of peaks in all compounds; whereas only the para tautomer of for 1A and 2A, the para tautomer is predominant in CD3CN solution. Further the ortho-para interconversion is accompanied by a large up-field signals for C(3)sbnd H(3) in their 1H and 13C NMR spectra. These inferences are corroborated by the density functional theoretic calculations.

  13. Structural Investigations of Portland Cement Components, Hydration, and Effects of Admixtures by Solid-State NMR Spectroscopy

    DEFF Research Database (Denmark)

    Skibsted, Jørgen Bengaard; Andersen, Morten D.; Jakobsen, Hans Jørgen

    2006-01-01

    Solid-state, magic-angle spinning (MAS) NMR spectroscopy represents a valuable tool for structural investigations on the nanoscale of the most important phases in anhydrous and hydrated Portland cements and of various admixtures. This is primarily due to the fact that the method reflects the firs.......% flourine. Finally, the detection and quantification of strätlingite (2CaO·Al2O3·SiO2·8H2O) in Portland cement mixtures containing metakaolin will be demonstrated....

  14. Investigations of the structure and "interfacial" surface chemistry of Bioglass (RTM) materials by solid-state multinuclear NMR spectroscopy

    Science.gov (United States)

    Sarkar, Gautam

    formation of surface silica species and follow the formation of phosphate species, respectively, while cross-polarization magic-angle spinning (CP/MAS) 29Si and 31P NMR have provided information about low intensity NMR peaks due to various silicon- and phosphorus-species present in the vicinity of associated protons on the surface of in vitro reacted BioglassRTM materials. The solid-state NMR investigations of the "interfacial" surface reactions of BioglassRTM materials are discussed in the context of the structure of these materials and the influence of this structure on the kinetics and the mechanism of their "interfacial" surface chemistry. (Abstract shortened by UMI.) BioglassRTM, trademark, University of Florida, Gainesville, FL, 32611.

  15. Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa

    Energy Technology Data Exchange (ETDEWEB)

    Jepkorir, Grace; Rodrguez, Juan Carlos; Rui, Huan; Im, Wonpil; Lovell, Scott; Battaile, Kevin P.; Alontaga, Aileen Y.; Yukl, Erik T.; Monne-Loccoz, Pierre; Rivera, Mario (Oregon State U.); (Kansas); (Hauptman)

    2010-08-16

    When challenged by low-iron conditions several Gram-negative pathogens secrete a hemophore (HasA) to scavenge hemin from its host and deliver it to a receptor (HasR) on their outer membrane for internalization. Here we report results from studies aimed at probing the structural and dynamic processes at play in the loading of the apo-hemophore secreted by P. aeruginosa (apo-HasAp) with hemin. The structure of apo-HasAp shows a large conformational change in the loop harboring axial ligand His32 relative to the structure of holo-HasAp, whereas the loop bearing the other axial ligand, Tyr75, remains intact. To investigate the role played by the axial ligand-bearing loops in the process of hemin capture we investigated the H32A mutant, which was found to exist as a monomer in its apo-form and as a mixture of monomers and dimers in its holo-form. We obtained an X-ray structure of dimeric H32A holo-HasAp, which revealed that the two subunits are linked by cofacial interactions of two hemin molecules and that the conformation of the Ala32 loop in the dimer is identical to that exhibited by the His32 loop in wild type apo-HasAp. Additional data suggest that the conformation of the Ala32 loop in the dimer is mainly a consequence of dimerization. Hence, to investigate the effect of hemin loading on the topology of the His32 loop we also obtained the crystal structure of monomeric H32A holo-HasAp coordinated by imidazole (H32A-imidazole) and investigated the monomeric H32A HasAp and H32A-imidazole species in solution by NMR spectroscopy. The structure of H32A-imidazole revealed that the Ala32 loop attains a 'closed' conformation nearly identical to that observed in wild type holo-HasAp, and the NMR investigations indicated that this conformation is maintained in solution. The NMR studies also highlighted conformational heterogeneity at the H32 loop hinges and in other key sections of the structure. Targeted molecular dynamics simulations allowed us to propose a

  16. Structural Basis for Asymmetric Conductance of the Influenza M2 Proton Channel Investigated by Solid-State NMR Spectroscopy.

    Science.gov (United States)

    Mandala, Venkata S; Liao, Shu-Yu; Kwon, Byungsu; Hong, Mei

    2017-07-07

    The influenza M2 protein forms an acid-activated proton channel that is essential for virus replication. The transmembrane H37 selects for protons under low external pH while W41 ensures proton conduction only from the N terminus to the C terminus and prevents reverse current under low internal pH. Here, we address the molecular basis for this asymmetric conduction by investigating the structure and dynamics of a mutant channel, W41F, which permits reverse current under low internal pH. Solid-state NMR experiments show that W41F M2 retains the pH-dependent α-helical conformations and tetrameric structure of the wild-type (WT) channel but has significantly altered protonation and tautomeric equilibria at H37. At high pH, the H37 structure is shifted toward the π tautomer and less cationic tetrads, consistent with faster forward deprotonation to the C terminus. At low pH, the mutant channel contains more cationic tetrads than the WT channel, consistent with faster reverse protonation from the C terminus. (15)N NMR spectra allow the extraction of four H37 pKas and show that the pKas are more clustered in the mutant channel compared to WT M2. Moreover, binding of the antiviral drug, amantadine, at the N-terminal pore at low pH did not convert all histidines to the neutral state, as seen in WT M2, but left half of all histidines cationic, unambiguously demonstrating C-terminal protonation of H37 in the mutant. These results indicate that asymmetric conduction in WT M2 is due to W41 inhibition of C-terminal acid activation by H37. When Trp is replaced by Phe, protons can be transferred to H37 bidirectionally with distinct rate constants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

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

  18. HPLC-SPE-NMR for combinatorial biosynthetic investigations – expanding the landscape of diterpene structural diversity

    DEFF Research Database (Denmark)

    Kongstad, Kenneth Thermann; Andersen-Ranberg, Johan; Hamberger, Björn Robert

    In this work, the analytical technique, HPLC-HRMS-SPE-NMR was used for the first time in combination with combinatorial biosynthetic investigations in N. benthamiana. This efficient setup allowed for identification of several diterpene synthase (diTPS) combinations responsible for stereospecific ......In this work, the analytical technique, HPLC-HRMS-SPE-NMR was used for the first time in combination with combinatorial biosynthetic investigations in N. benthamiana. This efficient setup allowed for identification of several diterpene synthase (diTPS) combinations responsible for...

  19. Structural Investigation of the Interaction between LolA and LolB Using NMR

    OpenAIRE

    Nakada, Shingo; Sakakura, Masayoshi; Takahashi, Hideo; Okuda, Suguru; Tokuda, Hajime; Shimada, Ichio

    2009-01-01

    Lipoproteins that play critical roles in various cellular functions of Gram-negative bacteria are localized in the cells inner and outer membranes. Lol proteins (LolA, LolB, LolC, LolD, and LolE) are involved in the transportation of outer membrane-directed lipoproteins from the inner to the outer membrane. LolA is a periplasmic chaperone that transports lipoproteins, and LolB is an outer membrane receptor that accepts lipoproteins. To clarify the structural basis for the lipoprotein transfer...

  20. 1H NMR and FT-IR dataset based structural investigation of poly(amic acids and polyimides from 4,4′-diaminostilbene

    Directory of Open Access Journals (Sweden)

    Amit Kumar

    2016-06-01

    Full Text Available Structural investigation of polymers by various available analytical methods is important in order to correlate the structure with polymer properties for which understanding of polymer structure is very important factor. The data presented here in this article shows the 1H NMR spectra used for the characterization of prepared poly(amic acids (PAAs. It is often difficult to assigns the peak in NMR of polymers due to its complexity. Data presented here helps in assigning the proton peak in complex NMR of PAAs prepared from aromatic diamines. Further functionality in polymer chains can be confirmed by FT-IR spectra. Change in functionality during some reaction or process can be monitored by disappearance or appearance of peaks in FT-IR. The complete imidization of PAAs to Polyimides (PIs is difficult to analyze because of the chemical stability i.e. insolubility of PIs in most of the solvent therefore the completion of imidization process was confirmed using FTIR.

  1. Chemical and nanometer-scale structure of kerogen and its change during thermal maturation investigated by advanced solid-state 13C NMR spectroscopy

    Science.gov (United States)

    Mao, J.; Fang, X.; Lan, Y.; Schimmelmann, A.; Mastalerz, Maria; Xu, L.; Schmidt-Rohr, K.

    2010-01-01

    We have used advanced and quantitative solid-state nuclear magnetic resonance (NMR) techniques to investigate structural changes in a series of type II kerogen samples from the New Albany Shale across a range of maturity (vitrinite reflectance R0 from 0.29% to 1.27%). Specific functional groups such as CH3, CH2, alkyl CH, aromatic CH, aromatic C-O, and other nonprotonated aromatics, as well as "oil prone" and "gas prone" carbons, have been quantified by 13C NMR; atomic H/C and O/C ratios calculated from the NMR data agree with elemental analysis. Relationships between NMR structural parameters and vitrinite reflectance, a proxy for thermal maturity, were evaluated. The aromatic cluster size is probed in terms of the fraction of aromatic carbons that are protonated (???30%) and the average distance of aromatic C from the nearest protons in long-range H-C dephasing, both of which do not increase much with maturation, in spite of a great increase in aromaticity. The aromatic clusters in the most mature sample consist of ???30 carbons, and of ???20 carbons in the least mature samples. Proof of many links between alkyl chains and aromatic rings is provided by short-range and long-range 1H-13C correlation NMR. The alkyl segments provide most H in the samples; even at a carbon aromaticity of 83%, the fraction of aromatic H is only 38%. While aromaticity increases with thermal maturity, most other NMR structural parameters, including the aromatic C-O fractions, decrease. Aromaticity is confirmed as an excellent NMR structural parameter for assessing thermal maturity. In this series of samples, thermal maturation mostly increases aromaticity by reducing the length of the alkyl chains attached to the aromatic cores, not by pronounced growth of the size of the fused aromatic ring clusters. ?? 2010 Elsevier Ltd. All rights reserved.

  2. Structural determination of Zn and Cd-DTPA complexes: MS, infrared, (13)C NMR and theoretical investigation.

    Science.gov (United States)

    Silva, Vanézia L; Carvalho, Ruy; Freitas, Matheus P; Tormena, Cláudio F; Melo, Walclée C

    2007-12-31

    The joint application of MS, infrared and (13)C NMR techniques for the determination of metal-DTPA structures (metal=Zn and Cd; DTPA=diethylenetriaminepentacetic acid) is reported. Mass spectrometry allowed determining the 1:1 stoichiometry of the complexes, while infrared analysis suggested that both nitrogen and carboxyl groups are sites for complexation. The (13)C NMR spectrum for the cadmium-containing complex evidenced the existence of free and complexed carboxyl groups, due to a straight singlet at 179.0 ppm (free carboxylic (13)C) and to two broad singlets or a broad doublet at 178.3 ppm (complexed carboxylic (13)C, (2)J(Cd-C(=O))=45.2 Hz). A similar interpretation might be given for the zinc derivative and, with the aid of DFT calculations, structures for both complexes were then proposed.

  3. Protein secondary structure of Green Lynx spider dragline silk investigated by solid-state NMR and X-ray diffraction.

    Science.gov (United States)

    Xu, Dian; Shi, Xiangyan; Thompson, Forrest; Weber, Warner S; Mou, Qiushi; Yarger, Jeffery L

    2015-11-01

    In this study, the secondary structure of the major ampullate silk from Peucetia viridans (Green Lynx) spiders is characterized by X-ray diffraction and solid-state NMR spectroscopy. From X-ray diffraction measurement, β-sheet nanocrystallites were observed and found to be highly oriented along the fiber axis, with an orientational order, fc≈0.98. The size of the nanocrystallites was determined to be on average 2.5nm×3.3nm×3.8nm. Besides a prominent nanocrystalline region, a partially oriented amorphous region was also observed with an fa≈0.89. Two-dimensional (13)C-(13)C through-space and through-bond solid-state NMR experiments were employed to elucidate structure details of P. viridans silk proteins. It reveals that β-sheet nanocrystallites constitutes 40.0±1.2% of the protein and are dominated by alanine-rich repetitive motifs. Furthermore, based upon the NMR data, 18±1% of alanine, 60±2% glycine and 54±2% serine are incorporated into helical conformations. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Theoretical NMR correlations based Structure Discussion

    Directory of Open Access Journals (Sweden)

    Junker Jochen

    2011-07-01

    Full Text Available Abstract The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction.

  5. A 125Te and 23Na NMR investigation of the structure and crystallisation of sodium tellurite glasses.

    Science.gov (United States)

    Holland, D; Bailey, J; Ward, G; Turner, B; Tierney, P; Dupree, R

    2005-01-01

    125Te static nuclear magnetic resonance (NMR) and 23Na and 125Te magic angle spinning (MAS) NMR have been used, in conjunction with X-ray diffraction, to examine the structure and crystallisation behaviour of glasses of composition xNa2O.(1-x)TeO2 (0.075 x 0.4). The MAS NMR 23Na spectra from the glasses are broad and featureless but shift by approximately +5 ppm with increased x, i.e. as the system becomes more ionic. The static 125Te NMR spectra show an increase in axial symmetry with increasing x, indicating a shift from predominantly [TeO4] to [TeO3] structural units. The 23Na and 125Te spectra from the crystallised samples have been fitted to obtain information on the sites in the metastable crystal phases, which are the first to form on heating and which are therefore more closely related to the glass structure than thermodynamically stable crystal phases. New sodium tellurite phases are reported, including a sodium stabilised, face centred cubic phase related to delta-TeO2; a metastable form of Na2Te4O9 containing 3 sodium and 4 tellurium sites; and a metastable form of Na2Te2O5 containing 2 sodium sites. There is evidence of oxidation of TeIV to TeVI occurring in glasses with high values of x and, at x=0.40 and 0.50 (outside the glass forming range), some sodium metatellurate (Na2TeO4) is formed at the same time as sodium metatellurite (Na2TeO3). The 125Te shift is very sensitive to environment within the sodium tellurite system, covering more than 320 ppm, with anisotropies varying from 640 to 1540 ppm. The lack of features in the 125Te spectra of the glass phases, combined with the large shift range and high but variable anisotropy, means than it is not possible to obtain a unique fit to any presumed species present. Furthermore, the chemical shift anisotropy parameters for three of the four Te sites in the Na2Te4O9 phase are found to lie outside the range used for previous simulations of glass spectra.

  6. Structural, vibrational and NMR spectroscopic investigations of newly synthesized 3-((ethylthio)(4-nitrophenyl)methyl)-1H-indole

    Science.gov (United States)

    Bhat, Sheeraz Ahmad; Dar, Ajaz A.; Ahmad, Shabbir; Khan, Abu T.

    2017-10-01

    The compound 3-((ethylthio)(4-nitrophenyl)methyl)-1H-indole was synthesized at room temperature through one-pot three-component reaction from 1H-indole, 4-nitrobenzaldehyde, and ethanethiol using hydrated ferric sulfate as a Lewis acid catalyst. The structure was characterised by single crystal XRD, FTIR (4000-400 cm-1), FT-Raman (4000-50 cm-1) and 1H and 13C NMR analysis. The compound crystallizes in the monoclinic with volume 3238.3(9) Å3. The experimental vibrational data find the theoretical support through anharmonic frequency calculations using DFT/B3LYP level of theory in combination with 6-31G(d,p) basis set. It is observed that the predicted geometry well reproduces the XRD structural parameters. The experimental 1H and 13C NMR spectra in CDCl3 solvent and the simulated spectra predicted using gauge independent atomic orbital (GIAO) approach are also found in agreement with each other. HOMO-LUMO, MEP, atomic charges and various other thermodynamic and NLO properties of the title molecule are also reported in this paper.

  7. Crystal structure, magnetism, {sup 89}Y solid state NMR, and {sup 121}Sb Moessbauer spectroscopic investigations of YIrSb

    Energy Technology Data Exchange (ETDEWEB)

    Benndorf, Christopher [Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Heletta, Lukas; Block, Theresa; Poettgen, Rainer [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Eckert, Hellmut [Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Institute of Physics in Sao Carlos, University of Sao Paulo, Sao Carlos (Brazil)

    2017-02-15

    The ternary antimonide YIrSb was synthesized from the binary precursor YIr and elemental antimony by a diffusion controlled solid-state reaction. Single crystals were obtained by a flux technique with elemental bismuth as an inert solvent. The YIrSb structure (TiNiSi type, space group Pnma) was refined from single-crystal X-ray diffractometer data: a = 711.06(9), b = 447.74(5), c = 784.20(8) pm, wR{sub 2} = 0.0455, 535 F{sup 2} values, 20 variables. {sup 89}Y solid state MAS NMR and {sup 121}Sb Moessbauer spectra show single resonance lines in agreement with single-crystal X-ray data. YIrSb is a Pauli paramagnet. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  8. αB-Crystallin. A Hybrid Solid-State/Solution-State NMR Investigation Reveals Structural Aspects of the Heterogeneous Oligomer

    Energy Technology Data Exchange (ETDEWEB)

    Jehle, Stefan [Freie Univ., Berlin (Germany); Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); van Rossum, Barth [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Stout, Joseph R. [Univ. of Washington, Seattle, WA (United States); Noguchi, Satoshi M. [Univ. of Washington, Seattle, WA (United States); Falber, Katja [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Rehbein, Kristina [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Oschkinat, Hartmut [Freie Univ., Berlin (Germany); Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Klevit, Rachel E. [Univ. of Washington, Seattle, WA (United States); Rajagopal, Ponni [Univ. of Washington, Seattle, WA (United States)

    2008-11-14

    Atomic-level structural information on αB-Crystallin (αB), a prominent member of the small heat-shock protein family, has been a challenge to obtain due its polydisperse oligomeric nature. We show that magic-angle spinning solid-state NMR can be used to obtain high-resolution information on an ~580-kDa human αB assembled from 175-residue 20-kDa subunits. An ~100-residue α-crystallin domain is common to all small heat-shock proteins, and solution-state NMR was performed on two different α- crystallin domain constructs isolated from αB. In vitro, the chaperone-like activities of full-length αB and the isolated α-crystallin domain are identical. Chemical shifts of the backbone and Cβ resonances have been obtained for residues 64–162 (α-crystallin domain plus part of the C-terminus) in αB and the isolated α-crystallin domain by solid-state and solution-state NMR, respectively. Both sets of data strongly predict six β-strands in the α-crystallin domain. A majority of residues in the α-crystallin domain have similar chemical shifts in both solid-state and solution-state, indicating similar structures for the domain in its isolated and oligomeric forms. Sites of intersubunit interaction are identified from chemical shift differences that cluster to specific regions of the α-crystallin domain. Multiple signals are observed for the resonances of M68 in the oligomer, identifying the region containing this residue as existing in heterogeneous environments within αB. Evidence for a novel dimerization motif in the human α-crystallin domain is obtained by a comparison of (i) solid-state and solution-state chemical shift data and (ii) 1H–15N heteronuclear single quantum coherence spectra as a function of pH. The isolated α-crystallin domain undergoes a dimer–monomer transition over the pH range 7.5–6.8. This steep pHdependent switch may be important for αB to function optimally (e.g., to preserve the filament integrity

  9. 1H NMR and FT-IR dataset based structural investigation of poly(amic acid)s and polyimides from 4,4′-diaminostilbene

    Science.gov (United States)

    Kumar, Amit; Tateyama, Seiji; Yasaki, Katsuaki; Ali, Mohammad Asif; Takaya, Naoki; Singh, Rajeev; Kaneko, Tatsuo

    2016-01-01

    Structural investigation of polymers by various available analytical methods is important in order to correlate the structure with polymer properties for which understanding of polymer structure is very important factor. The data presented here in this article shows the 1H NMR spectra used for the characterization of prepared poly(amic acid)s (PAAs). It is often difficult to assigns the peak in NMR of polymers due to its complexity. Data presented here helps in assigning the proton peak in complex NMR of PAAs prepared from aromatic diamines. Further functionality in polymer chains can be confirmed by FT-IR spectra. Change in functionality during some reaction or process can be monitored by disappearance or appearance of peaks in FT-IR. The complete imidization of PAAs to Polyimides (PIs) is difficult to analyze because of the chemical stability i.e. insolubility of PIs in most of the solvent therefore the completion of imidization process was confirmed using FTIR. PMID:26933669

  10. Structure and Permeability of Porous Silicon Investigated by Self-Diffusion NMR Measurements of Ethanol and Heptane

    Directory of Open Access Journals (Sweden)

    Puibasset J.

    2016-07-01

    Full Text Available The adsorption and phase transitions of confined fluids in nanoporous materials have been studied intensely because of both their fundamental interest and their crucial role in many technologies. Questions relating to the influence of the confinement of fluids, and the disorder or elastic deformation of porous solids on the liquid-gas phase transition are still under debate. Model systems are needed to understand the adsorption phenomenon. In this context, Porous Silicon (PoSi, which is a single crystal obtained by etching a (100 silicon wafer is an excellent candidate. Indeed, it consists of non-connected tubular pores running parallel to the [100] axis perpendicular to the wafer surface, with transverse sections with a polygonal shape of nanometric size whose areas are widely distributed. Once detached from the wafer, free PoSi membranes can be considered a nanoscale disordered honeycomb. Adsorption/desorption experiments have been performed to characterize the structure: they have shown that evaporation occurs collectively, an intriguing observation generally associated with a disordered pore structure with many interconnections through narrow necks. The characterization of fluid mobility inside the pores should give complementary information about the pore structure and topology. This paper focuses on the dynamics of a fluid confined inside the structure of porous silicon, and in particular the self-diffusion measurements (pulsed field gradient spin echo Nuclear Magnetic Resonance (NMR. The results show a strong anisotropy of the self-diffusion tensor, as expected in this highly anisotropic structure. However, a non-zero self-diffusion in the directions perpendicular to the pore axis is observed. In order to interpret these puzzling results, molecular and Brownian dynamics calculations are underway.

  11. Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin.

    Directory of Open Access Journals (Sweden)

    Gerrit Vortmeier

    Full Text Available The peptide hormone ghrelin activates the growth hormone secretagogue receptor 1a, also known as the ghrelin receptor. This 28-residue peptide is acylated at Ser3 and is the only peptide hormone in the human body that is lipid-modified by an octanoyl group. Little is known about the structure and dynamics of membrane-associated ghrelin. We carried out solid-state NMR studies of ghrelin in lipid vesicles, followed by computational modeling of the peptide using Rosetta. Isotropic chemical shift data of isotopically labeled ghrelin provide information about the peptide's secondary structure. Spin diffusion experiments indicate that ghrelin binds to membranes via its lipidated Ser3. Further, Phe4, as well as electrostatics involving the peptide's positively charged residues and lipid polar headgroups, contribute to the binding energy. Other than the lipid anchor, ghrelin is highly flexible and mobile at the membrane surface. This observation is supported by our predicted model ensemble, which is in good agreement with experimentally determined chemical shifts. In the final ensemble of models, residues 8-17 form an α-helix, while residues 21-23 and 26-27 often adopt a polyproline II helical conformation. These helices appear to assist the peptide in forming an amphipathic conformation so that it can bind to the membrane.

  12. Structural features of a bituminous coal and their changes during low-temperature oxidation and loss of volatiles investigated by advanced solid-state NMR spectroscopy

    Science.gov (United States)

    Mao, J.-D.; Schimmelmann, A.; Mastalerz, Maria; Hatcher, P.G.; Li, Y.

    2010-01-01

    Quantitative and advanced 13C solid-state NMR techniques were employed to investigate (i) the chemical structure of a high volatile bituminous coal, as well as (ii) chemical structural changes of this coal after evacuation of adsorbed gases, (iii) during oxidative air exposure at room temperature, and (iv) after oxidative heating in air at 75 ??C. The solid-state NMR techniques employed in this study included quantitative direct polarization/magic angle spinning (DP/MAS) at a high spinning speed of 14 kHz, cross polarization/total sideband suppression (CP/TOSS), dipolar dephasing, CH, CH2, and CHn selection, 13C chemical shift anisotropy (CSA) filtering, two-dimensional (2D) 1H-13C heteronuclear correlation NMR (HETCOR), and 2D HETCOR with 1H spin diffusion. With spectral editing techniques, we identified methyl CCH 3, rigid and mobile methylene CCH2C, methine CCH, quaternary Cq, aromatic CH, aromatic carbons bonded to alkyls, small-sized condensed aromatic moieties, and aromatic C-O groups. With direct polarization combined with spectral-editing techniques, we quantified 11 different types of functional groups. 1H-13C 2D HETCOR NMR experiments indicated spatial proximity of aromatic and alkyl moieties in cross-linked structures. The proton spin diffusion experiments indicated that the magnetization was not equilibrated at a 1H spin diffusion time of 5 ms. Therefore, the heterogeneity in spatial distribution of different functional groups should be above 2 nm. Recoupled C-H long-range dipolar dephasing showed that the fraction of large charcoal-like clusters of polycondensed aromatic rings was relatively small. The exposure of this coal to atmospheric oxygen at room temperature for 6 months did not result in obvious chemical structural changes of the coal, whereas heating at 75 ??C in air for 10 days led to oxidation of coal and generated some COO groups. Evacuation removed most volatiles and caused a significant reduction in aliphatic signals in its DP

  13. 99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex.

    Science.gov (United States)

    Mancini, Daiana T; Souza, Eugenio F; Caetano, Melissa S; Ramalho, Teodorico C

    2014-04-01

    The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the (99)Tc chemical shifts based on the ((99m)Tc)(CO)3 (NNO) complex conjugated to the antitumor agent 2-(4'-aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum-chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug-cc-pVTZ for the Tc and BPW91/IGLO-II for the other atoms) to compute the NMR parameters for the complex. We have calculated the (99)Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom-centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the (99)Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments.

  14. Syntheses, structures, and comprehensive NMR spectroscopic investigations of hetero-chalcogenidometallates: the right mix toward multinary complexes.

    Science.gov (United States)

    Ruzin, Eugen; Zent, Eldar; Matern, Eberhard; Massa, Werner; Dehnen, Stefanie

    2009-01-01

    Aqueous solutions of ternary ortho-chalcogenidostannate anions [SnE(1)(4-x)E(2)(x)](4-) (E(1), E(2) = S, Se, Te) have been generated following different routes that all lead to equilibria of all possible permutations of binary and ternary anions. This has been rationalized by means of NMR studies that can be explained by calculations using density functional theory (DFT) methods. Thus, if one reacts such solutions with transition-metal ions, quaternary M/Sn/E(1)/E(2) anions are obtained, which exhibit coordination by different ternary chalcogenidostannate ligands. The electronic excitation energies of the corresponding alkali metal salts lie between the E(g) values of compounds containing either M/Sn/E(1) or M/Sn/E(2) anions. In this way, we provide a simple approach toward a library of semiconductor compounds with finely-tuned optoelectronic properties.

  15. Structural biology applications of solid state MAS DNP NMR

    Science.gov (United States)

    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.

  16. Protein NMR structures refined without NOE data.

    Science.gov (United States)

    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.

  17. Investigating the Surface Structure of γ-Al 2 O 3 Supported WO X Catalysts by High Field 27 Al MAS NMR and Electronic Structure Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Chuan; Hu, Mary Y.; Jaegers, Nicholas R.; Shi, Dachuan; Wang, Huamin; Gao, Feng; Qin, Zhaohai; Wang, Yong; Hu, Jian Zhi

    2016-10-13

    The metal-support interaction in γ-Al2O3 supported WOX catalysts is investigated by a combination of high field quantitative single pulse (SP) 27Al MAS NMR spectroscopy, 2D MQMAS, 1H-27Al CP/MAS, and electronic structure calculations. NMR allows the observation of at least seven different Al sites, including a pentahedral Al site, three different tetrahedral Al sites, and three octahedral Al sites. It is found that the penta-coordinated Al (AlP) site density decreases monotonically with an increased WOX loading while the octahedral Al (AlO) site density increases concurrently. This suggests that the Alp sites are the preferred surface anchoring positions for the WOX species. Importantly, the AlP site isotropic chemical shift observed for the unsupported γ-Al2O3 at about 38 ppm migrates into the octahedral region with a new isotropic chemical shift value appearing near 7 ppm when the Alp site is anchored by WOX species. Density functional theory (DFT) computational modeling of the NMR parameters on proposed cluster models is carried out to accurately interpret the dramatic chemical shift changes from which the detailed anchoring mechanisms are obtained. It is found that tungsten dimers and monomers are the preferred supported surface species on γ-Al2O3, wherein one monomeric and several dimeric structures are identified as the most likely surface anchoring structures.

  18. NMR structural studies on antifreeze proteins.

    Science.gov (United States)

    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.

  19. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    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.

  20. Structural investigation of α-LaZr2F11 by coupling X-ray powder diffraction, 19F solid state NMR and DFT calculations

    Science.gov (United States)

    Martineau, Charlotte; Legein, Christophe; Body, Monique; Péron, Olivier; Boulard, Brigitte; Fayon, Franck

    2013-03-01

    α-LaZr2F11 has been synthesized by solid state reaction. Its crystal structure has been refined from X-ray powder diffraction data (space group no. 72 Ibam, a=7.785(1) Å, b=10.086(1) Å and c=11.102(1) Å). α-LaZr2F11 contains one La, one Zr and four F inequivalent crystallographic sites. F3 and F4 are shared between one ZrF73- polyhedron and one LaF85- polyhedron, while F1 and F2 bridge two ZrF73- polyhedra. 19F 1D MAS NMR spectra of α-LaZr2F11 are in agreement with the proposed structural model. Assignment of the 19F resonances to the corresponding crystallographic sites has been performed on the basis of both their relative intensities and their correlation patterns in a 19F 2D dipolar-based double-quantum recoupling MAS NMR spectrum. DFT calculations of the 19F chemical shielding tensors have been performed using the GIPAW method implemented in the NMR-CASTEP code, for the experimental structure and two PBE-DFT geometry optimized structures of α-LaZr2F11 (atomic position optimization and full geometry optimization with rescaling of the unit cell volume to the experimental value). Computations were done with and without using a modified La pseudopotential allowing the treatment of the 4f localized empty orbitals of La3+. A relatively nice agreement between the experimental 19F isotropic and anisotropic chemical shifts and the values calculated for the proposed structural model is obtained.

  1. NMR investigations of structural and dynamics features of natively unstructured drug peptide - salmon calcitonin: implication to rational design of potent sCT analogs.

    Science.gov (United States)

    Rawat, Atul; Kumar, Dinesh

    2013-01-01

    Backbone dynamics and conformational properties of drug peptide salmon calcitonin have been studied in aqueous solution using nuclear magnetic resonance (NMR). Although salmon calcitonin (sCT) is largely unfolded in solution (as has been reported in several circular dichroism studies), the secondary H(α) chemical shifts and three bond H(N) -H(α) coupling constants indicated that most of the residues of the peptide are populating the α-helical region of the Ramachandran (ϕ, ψ) map. Further, the peptide in solution has been found to exhibit multiple conformational states exchanging slowly on the NMR timescale (10(2) -10(3)  s(-1) ), inferred by the multiple chemical shift assignments in the region Leu4-Leu12 and around Pro23 (for residues Gln20-Tyr22 and Arg24). Possibly, these slowly exchanging multiple conformational states might inhibit symmetric self-association of the peptide and, in part, may account for its reduced aggregation propensity compared with human calcitonin (which lacks this property). The (15) N NMR-relaxation data revealed (i) the presence of slow (microsecond-to-millisecond) timescale dynamics in the N-terminal region (Cys1-Ser5) and core residues His17 and Asn26 and (ii) the presence of high frequency (nanosecond-to-picosecond) motions in the C-terminal arm. Put together, the various results suggested that (i) the flexible C-terminal of sCT (from Thr25-Thr31) is involved in identification of specific target receptors, (ii) whereas the N-terminal of sCT (from Cys1-Gln20) in solution - exhibiting significant amount of conformational plasticity and strong bias towards biologically active α-helical structure - facilitates favorable conformational adaptations while interacting with the intermembrane domains of these target receptors. Thus, we believe that the structural and dynamics features of sCT presented here will be useful guiding attributes for the rational design of biologically active sCT analogs.

  2. A novel Zn(4)O-based triazolyl benzoate MOF: synthesis, crystal structure, adsorption properties and solid state 13C NMR investigations.

    Science.gov (United States)

    Lincke, Jörg; Lässig, Daniel; Stein, Karolin; Moellmer, Jens; Kuttatheyil, Anusree Viswanath; Reichenbach, Christian; Moeller, Andreas; Staudt, Reiner; Kalies, Grit; Bertmer, Marko; Krautscheid, Harald

    2012-01-21

    The newly synthesized Zn(4)O-based MOF (3)(∞)[Zn(4)(μ(4)-O){(Metrz-pba)(2)mPh}(3)]·8 DMF (1·8 DMF) of rare tungsten carbide (acs) topology exhibits a porosity of 43% and remarkably high thermal stability up to 430 °C. Single crystal X-ray structure analyses could be performed using as-synthesized as well as desolvated crystals. Besides the solvothermal synthesis of single crystals a scalable synthesis of microcrystalline material of the MOF is reported. Combined TG-MS and solid state NMR measurements reveal the presence of mobile DMF molecules in the pore system of the framework. Adsorption measurements confirm that the pore structure is fully accessible for nitrogen molecules at 77 K. The adsorptive pore volume of 0.41 cm(3) g(-1) correlates well with the pore volume of 0.43 cm(3) g(-1) estimated from the single crystal structure.

  3. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  4. NMR Structural Studies on Alamethicin Dimers

    Institute of Scientific and Technical Information of China (English)

    李星

    2003-01-01

    15N labeled alamethicin dimer was synthesized. The structure and dynamics of alamethicin dimers were studied with nuclear magnetic resonance (NMR) spectroscopy. The data from 15N-labeled alamethicin dimer suggest little differences in conformation between the dimer and monomer in the Aib1-Pro14 region. Significant difference in the conformation of the C-terminus are manifest in the NH chemical shifts in the Val15-Pho20 region.

  5. New lanthanide complexes for sensitized visible and near-IR light emission: synthesis, 1H NMR, and X-ray structural investigation and photophysical properties.

    Science.gov (United States)

    Quici, Silvio; Marzanni, Giovanni; Forni, Alessandra; Accorsi, Gianluca; Barigelletti, Francesco

    2004-02-23

    We describe the syntheses, the 1H NMR studies in CD3OD and D2O as solvent, the X-ray characterization, and the luminescence properties in D2O solution of the two complexes Eu.1 and Er.1, where 1 is a dipartite ligand that includes (i) a 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A) unit serving as hosting site for the metal center; and (ii) a phenanthroline unit which plays the role of light antenna for the sensitization process of the metal centered luminescence. In a previous report (Inorg. Chem. 2002, 41, 2777), we have shown that for Eu.1 there are no water molecules within the first coordination sphere. X-ray and 1H NMR results reported here are consistent with full saturation of the nine coordination sites within the Eu.1 and Er.1 complexes. In addition, these studies provide important details regarding the conformations, square antiprism (SAP) and twisted square antiprism (TSAP), adopted in solution by these complexes. The luminescence results are consistent with both an effective intersystem crossing (ISC) at the light absorbing phenanthroline unit (lambda(exc) = 278 nm) and an effective energy transfer (en) process from the phenanthroline donor to the cation acceptor (with unit or close to unit efficiency for both steps). In D2O solvent, the overall sensitization efficiency, phi(se), is 0.3 and 5 x 10(-6), for Eu.1 (main luminescence peaks at 585, 612, 699 nm) and Er.1 (luminescence peak at 1530 nm), respectively. The photophysical properties of both complexes are discussed with reference to their structural features as elucidated by the obtained 1H NMR and X-ray results.

  6. Structural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Peter Tompa

    2013-09-01

    Full Text Available Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs and intrinsically disordered regions (IDRs which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as 13C-direct detected experiments, paramagnetic relaxation enhancements (PREs or residual dipolar couplings (RDCs for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.

  7. NMR and the local structure of relaxors

    Directory of Open Access Journals (Sweden)

    Blinc R.

    2002-01-01

    Full Text Available The relaxor transition in cubic perovskite relaxors (PMN, PSN and PST and tungsten bronze relaxor (SBN has been studied by NMR. The observed spectra are composed of a narrow -1/2 « 1/2 central transition superimposed on a broad background due to satellite transitions. The chemical heterogeneity, responsible for relaxor properties, is reflected here in the structure of the central transition part. The latter is composed of two components, one due to ordered and the other due to disordered regions. Despite of the fact that the macroscopic symmetry does not change when relaxor transition occurs, a non-zero quadruple coupling constant determined from NMR clearly demonstrates the broken local symmetry.

  8. Structural properties of carbon nanotubes derived from 13C NMR

    KAUST Repository

    Abou-Hamad, E.

    2011-10-10

    We present a detailed experimental and theoretical study on how structural properties of carbon nanotubes can be derived from 13C NMR investigations. Magic angle spinning solid state NMR experiments have been performed on single- and multiwalled carbon nanotubes with diameters in the range from 0.7 to 100 nm and with number of walls from 1 to 90. We provide models on how diameter and the number of nanotube walls influence NMR linewidth and line position. Both models are supported by theoretical calculations. Increasing the diameter D, from the smallest investigated nanotube, which in our study corresponds to the inner nanotube of a double-walled tube to the largest studied diameter, corresponding to large multiwalled nanotubes, leads to a 23.5 ppm diamagnetic shift of the isotropic NMR line position δ. We show that the isotropic line follows the relation δ = 18.3/D + 102.5 ppm, where D is the diameter of the tube and NMR line position δ is relative to tetramethylsilane. The relation asymptotically tends to approach the line position expected in graphene. A characteristic broadening of the line shape is observed with the increasing number of walls. This feature can be rationalized by an isotropic shift distribution originating from different diamagnetic shielding of the encapsulated nanotubes together with a heterogeneity of the samples. Based on our results, NMR is shown to be a nondestructive spectroscopic method that can be used as a complementary method to, for example, transmission electron microscopy to obtain structural information for carbon nanotubes, especially bulk samples.

  9. Investigating albendazole desmotropes by solid-state NMR spectroscopy.

    Science.gov (United States)

    Chattah, Ana K; Zhang, Rongchun; Mroue, Kamal H; Pfund, Laura Y; Longhi, Marcela R; Ramamoorthy, Ayyalusamy; Garnero, Claudia

    2015-03-02

    Characterization of the molecular structure and physicochemical solid-state properties of the solid forms of pharmaceutical compounds is a key requirement for successful commercialization as potential active ingredients in drug products. These properties can ultimately have a critical effect on the solubility and bioavailability of the final drug product. Here, the desmotropy of Albendazole forms I and II was investigated at the atomic level. Ultrafast magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy, together with powder X-ray diffraction, thermal analysis, and Fourier transform infrared spectroscopy, were performed on polycrystalline samples of the two solids in order to fully characterize and distinguish the two forms. High-resolution one-dimensional (1)H, (13)C, and (15)N together with two-dimensional (1)H/(1)H single quantum-single quantum, (1)H/(1)H single quantum-double quantum, and (1)H/(13)C chemical shift correlation solid-state NMR experiments under MAS conditions were extensively used to decipher the intramolecular and intermolecular hydrogen bonding interactions present in both solid forms. These experiments enabled the unequivocal identification of the tautomers of each desmotrope. Our results also revealed that both solid forms may be described as dimeric structures, with different intermolecular hydrogen bonds connecting the tautomers in each dimer.

  10. Structural investigation of a uronic acid-containing polysaccharide from abalone by graded acid hydrolysis followed by PMP-HPLC-MSn and NMR analysis.

    Science.gov (United States)

    Wang, Hong-xu; Zhao, Jun; Li, Dong-mei; Song, Shuang; Song, Liang; Fu, Ying-huan; Zhang, Li-peng

    2015-01-30

    A new strategy was applied to elucidate the structure of a polysaccharide from abalone gonad (AGSP). It was hydrolyzed by 0.05 M, 0.2 M, 0.5 M, and 2.0 M TFA at 100 °C for 1 h, sequentially. Every hydrolysate was ultrafiltrated (3000 Da) to collect oligo- and monosaccharides, and the final retentate was further hydrolyzed with 2.0 M TFA at 110 °C and 121 °C for 2 h, respectively. 1-Phenyl-3-methyl-5-pyrazolone (PMP) derivatization followed by HPLC-MSn analysis was applied to detect the sugar residues in these hydrolysates, which allowed proposing their location in the polysaccharide structure. The retentate after 0.5 M TFA hydrolysis was confirmed as the polysaccharide backbone, and it was further analyzed by 1D and 2D NMR spectroscopy. Thus, the structural elucidation of AGSP was accomplished, and it has a backbone of →4)-β-GlcA(1→2)-α-Man(1→ repeating unit with Fuc, Xyl and Gal in the branch. The analytical strategy demonstrated was useful to characterize the structure of polysaccharides.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-15

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

  12. Theoretical molecular structure, vibrational frequencies and NMR investigations of 2-[(1E-2-aza-2-(5-methyl(2-pyridylethenyl]-4-bromobenzen-1-ol

    Directory of Open Access Journals (Sweden)

    Cemal Parlak

    2012-08-01

    Full Text Available The normal mode frequencies and corresponding vibrational assignments, 1H and 13C NMR chemical shifts and structural parameters (bond lengths, bond and dihedral angles of 2-[(1E-2-aza-2-(5-methyl(2-pyridylethenyl]-4-bromobenzen-1-ol (2mpe-4bb Schiff base compound have been theoretically examined by means of Hartree-Fock (HF and Becke-3-Lee-Yang-Parr (B3LYP density functional methods with 6-31G(d and 6-311++G(d,p basis sets. Furthermore, reliable vibrational assignments have made on the basis of potential energy distribution (PED calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO of 2mpe-4bb have been predicted. Theoretical results have been successfully compared with available experimental data in the literature. Regarding the calculations, 2mpe-4bb prefers enol-imine form and DFT method is superior to HF approach except for predicting bond lengths.DOI: http://dx.doi.org/10.4314/bcse.v26i2.11

  13. Protein secondary structure prediction using NMR chemical shift data.

    Science.gov (United States)

    Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

    2010-10-01

    Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

    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.

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

    Science.gov (United States)

    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. Structure of some western Anatolia coals investigated by FTIR, Raman, C-13 solid state NMR spectroscopy and X-ray diffraction

    OpenAIRE

    Baysal, Mustafa; Yürüm, Alp; Yurum, Alp; Yıldız, Burçin; Yildiz, Burcin; YÜRÜM, YUDA; Yurum, Yuda

    2016-01-01

    Turkey has one of the largest lignite deposits in Europe but the low calorific values of Turkish lignites dictate new and environmentally safe new utilization technologies for further utilization. Research on coal chemical structures has long been of great interest as a fundamental issue for coal chemistry. Identifying the structures of organic material in lignites is important for lignite conversions to clean liquid fuels and value-added chemicals. Therefore, investigation of chemical and de...

  18. CASD-NMR: critical assessment of automated structure determination by NMR

    NARCIS (Netherlands)

    Rosato, A.; van der Schot, G.; Bonvin, A.M.J.J.

    2009-01-01

    NMR spectroscopy is currently the only technique for determining the solution structure of biological macromolecules. This typically requires both the assignment of resonances and a labor-intensive analysis of multidimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, in which peaks

  19. Structural investigation of aryllithium clusters in solution. I. A 13C and 7Li NMR studyof phenyllithium and some methyl-substituted phenyllithium derivatives

    NARCIS (Netherlands)

    Koten, G. van; Wehman, E.; Jastrzebski, J.T.B.H.; Ernsting, J.M.; Grove, D.M.

    1988-01-01

    }1{}3{C and }7{Li NMR spectra of phenyllithium and several methyl subsituted phenyllithium derivatives have been recorded in the presence of known amounts of coordinating solvents such as monodentate diethyl ether and THF and the potentially bidentate TMEDA (tetramethylethylenediamine). The relative

  20. Protein NMR Structure Refinement based on Bayesian Inference

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

    2015-08-15

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  2. Development and Investigation of NMR tools for chiral compound identification

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electronic, Optical and Nano Materials; Lansdon, Rick [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)

    2014-09-01

    The goal behind the assigned summer project was to investigate the ability of nuclear magnetic resonance spectroscopy (NMR) to identify enantiomers of select chiral organo-fluorophosphates (OFPs) compounds which are analogs of chemical warfare agents (CWAs, e.g. Sarin). This involved investigations utilizing chiral solvating agents (CSAs) and characterizing the binding phenomena with cyclodextrins. The resolution of OFPs enantiomers using NMR would be useful for research into toxicodynamics and toxicokinetics in biological systems due to the widely differing properties of the CWA enantiomers [1]. The optimization of decontamination abilities in the case of a CWA events, with this method’s potential rapidity and robustness, as well as the development of models correlating chiral compounds with CSAs for optimal resolution are all rational benefits of this research.

  3. Investigation of structure, vibrational, electronic, NBO and NMR analyses of 2-chloro-4-nitropyridine (CNP), 2-chloro-4-methyl-5-nitropyridine (CMNP) and 3-amino-2-chloro-4-methylpyridine (ACMP) by experimental and theoretical approach.

    Science.gov (United States)

    Velraj, G; Soundharam, S; Sridevi, C

    2015-02-25

    This study reports about the optimized molecular structures, vibrational wavenumbers, atomic charges, molecular electrostatic potentials, NBO, electronic properties, (1)H NMR and (13)C NMR chemical shifts for the molecules 2-chloro-4-nitropyridine (CNP), 2-chloro-4-methyl-5-nitropyridine (CMNP) and 3-amino-2-chloro-4-methylpyridine (ACMP). Theoretical calculations were performed by density functional theory (DFT)/B3LYP method using 6-311++G (d,p) basis set. The stability and charge delocalization of the title molecules were studied by natural bond orbital (NBO) analysis. Molecular electrostatic potential maps (MEP) were calculated to predict the reactive sites. The reactivity of the title compounds were investigated by HOMO-LUMO energies and global descriptors. The electronic properties of the compounds were also discussed and the transitions were found to be π→π(∗). In addition, the thermodynamic properties were studied for the title compounds and corresponding relations between the properties and temperature were also discussed. The hyperpolarizability values (βtot) were calculated for the title compounds. Hyperpolarizability value (βtot) of CMNP was found to be high and nineteen times greater than that of urea. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Conjoined use of EM and NMR in RNA structure refinement.

    Directory of Open Access Journals (Sweden)

    Zhou Gong

    Full Text Available More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM provides global shape information of macromolecules at nanometer resolution, which should be complementary to NMR for RNA structure determination. Here we developed a new energy term in Xplor-NIH against the density map obtained by EM. We conjointly used NMR and map restraints for the structure refinement of three RNA systems—U2/U6 small-nuclear RNA, genome-packing motif (Ψ(CD2 from Moloney murine leukemia virus, and ribosome-binding element from turnip crinkle virus. In all three systems, we showed that the incorporation of a map restraint, either experimental or generated from known PDB structure, greatly improves structural precision and accuracy. Importantly, our method does not rely on an initial model assembled from RNA duplexes, and allows full torsional freedom for each nucleotide in the torsion angle simulated annealing refinement. As increasing number of macromolecules can be characterized by both NMR and EM, the marriage between the two techniques would enable better characterization of RNA three-dimensional structures.

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

    Science.gov (United States)

    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

  6. Solid-phase enolate chemistry investigated using HR-MAS NMR spectroscopy.

    Science.gov (United States)

    Fruchart, Jean-Sébastien; Lippens, Guy; Kuhn, Cyrille; Gras-Masse, Hélène; Melnyk, Oleg

    2002-01-25

    Supported P4-t-Bu enolate chemistry of phenylacetyloxymethyl polystyrene (PS) resin was investigated using high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. Direct analysis of the crude reaction suspensions through the use of a diffusion filter (DF) allowed a rapid selection of the optimal experimental conditions, but also the characterization of the enolate on the solid phase. Comparison with solution experiments and literature data allowed us to address partially the structure of the enolate. HR-MAS NMR spectra of the enolate revealed also a tight interaction of P4-t-Bu base with the polymer matrix.

  7. A small-diameter NMR logging tool for groundwater investigations.

    Science.gov (United States)

    Walsh, David; Turner, Peter; Grunewald, Elliot; Zhang, Hong; Butler, James J; Reboulet, Ed; Knobbe, Steve; Christy, Tom; Lane, John W; Johnson, Carole D; Munday, Tim; Fitzpatrick, Andrew

    2013-01-01

    A small-diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively inexpensive, small-diameter probes that can be run in open or PVC-cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small-diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct-push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high-resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore-size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations.

  8. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae.

    Science.gov (United States)

    Li, Yiming; Syvitski, Ray T; Chu, Grace C; Ikeda-Saito, Masao; Mar, Gerd N La

    2003-02-28

    The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

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

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh

    2015-01-01

    different and cytolytic peptides were investigated in this work. The peptides were SPF-5506-A4 from Trichoderma sp, Conolysin-Mt1 from Conus mustelinus, and Alamethicin from Trichoderma viride. The studies employed solution and solid-state NMR spectroscopy in combination with different biophysical methods......- and 2H-labelled peptides. While the solution NMR experiments were performed to determine the structure of SPF-5506-A4 and Conolysin-Mt1, the oriented solid-state NMR experiments served to derive information about the orientation of the peptides with respect to the bilayer normal in order to understand...

  10. Using NMR Spectroscopy to Investigate the Solution Behavior of Nerve Agents and Their Binding to Acetylcholinesterase

    Science.gov (United States)

    2016-01-01

    USING NMR SPECTROSCOPY TO INVESTIGATE THE SOLUTION BEHAVIOR OF NERVE AGENTS AND THEIR BINDING TO...XX-01-2016 2. REPORT TYPE Final 3. DATES COVERED (From - To) Jan – Jun 2015 4. TITLE AND SUBTITLE Using NMR Spectroscopy to Investigate the...MOLECULAR MOTIONS AND NMR SPECTROSCOPY ...................................................................................................3 4. THE

  11. NMR structural studies of oligosaccharides and other natural products

    DEFF Research Database (Denmark)

    Kjærulff, Louise

    produce secondary metabolites for signaling and competing against other organisms, and these molecules are important in drug discovery due to their inherent biological activities. From a marine Photobacterium (P. halotolerans) we isolated the solonamides and the ngercheumicins, two families of cyclic....... fijiensis, was also investigated for production of novel secondary metabolites, and a new pyranonigrin (E) was isolated and structure elucidated by NMR spectroscopy along with JBIR-74 and decumbenone A, two known metabolites previously isolated from Aspergillus and Penicillium species. Oligosaccharides...... with respect to n+1JHH between these two experiments, observed in the nJCH HMBC cross peak. Through a double editing procedure this enables straightforward determination of both sign and magnitude of n+1JHH, including for very small coupling constants. Excellent results were obtained for the natural product...

  12. NMR structural studies of protein-small molecule interactions

    NARCIS (Netherlands)

    Shah, Dipen M.

    2014-01-01

    The research presented in the thesis describes the development and implementation of solution based NMR methods that provide 3D structural information on the protein-small molecule complexes. These methods can be critical for structure based drug design and can be readily applied in the early stages

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

    Science.gov (United States)

    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. Dilute Bicellar Solutions for Structural NMR Work

    Science.gov (United States)

    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.

  15. Structural analysis of N,N-diacyl-1,4-dihydropyrazine by variable-temperature NMR and DFT calculation

    Science.gov (United States)

    Song, Xiu-qing; Tan, Hong-bo; Yan, Hong; Chang, Yu

    2017-04-01

    N,N-diacyl-1,4-dihydropyrazine derivatives (1) were prepared via an efficient microwave-assisted synthesis. 1 was isolated and unambiguously confirmed by NMR spectra and high-resolution mass spectrometry. The NMR spectra of 1 showed complicated rather than conventional spectroscopy. Variable-temperature experiments and DFT calculation (PES) were used to investigate this phenomenon. DFT calculations confirmed that the structures of the two rotamers of 1 correspond to those determined by NMR in solution, and gave the syn-anti interconversion barriers of rotamers. The results showed that two isomers exist in solution (deuterated solvent) at room temperature, resulting in complicated NMR spectra.

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

    Science.gov (United States)

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

    2017-02-06

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

  17. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

    Science.gov (United States)

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

    2010-12-08

    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

  18. Structural Determination of Bis-histidinopeptide Zinc Complexes by 15N NMR (HMBC) Spectra

    Institute of Scientific and Technical Information of China (English)

    ZHOU,Cheng-He; Juan F.Miravet; M.Isabel Burguete; Santiago V.Luis; BAI,Xue; YUAN,Yong

    2004-01-01

    @@ Polynitrogen receptors such as bis-histidine peptides possess strong ability to bind metals, which play much important roles in medicinal, bioinorganic, bioorganic, biomimetic and supramolecular chemistry. In order to investigate the interaction of these hosts with a variety of neutral, cationic and anionic guests, several techniques, for example, NMR,potentiometric tirations and monocrystal X-ray diffraction have been employed. Among them NMR is a powerful technique for unraveling the structure of polynitrogen receptors as long as they are in solution where the rapid tumbling of molecules averages out the anisotropies such as chemical shift and dipole-dipole interactions. General 1H NMR approach has been widely used for the study of host-guest interaction, but it is difficult for the accurate measurement in complexes structures, particularly metal complexes structures in which how the polynitrogen receptors bind metal, and which nitrogen binds metal and so on.

  19. 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

    Science.gov (United States)

    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.

  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.

    Science.gov (United States)

    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.

  1. Investigations of adsorption sites on oxide surfaces using solid-state NMR and TPD-IGC

    Science.gov (United States)

    Golombeck, Rebecca A.

    The number and chemical identity of reactive sites on surfaces of glass affects the processing, reliability, and lifetime of a number of important commercial products. Surface site densities, distributions, and structural identities are closely tied to the formation and processing of the glass surface, and exert a direct influence on strength and coating performance. The surface of a glass sample may vary markedly from the composition and chemistry of the bulk glass. We are taking a physicochemical approach to understanding adsorption sites on pristine multicomponent glass fibers surfaces, directly addressing the effect of processing on surface reactivity. This project aimed to understand the energy distributions of surface adsorption sites, the chemical/structural identity of those sites, and the relationship of these glasses to glass composition, thermal history, and in future work, surface coatings. We have studied the bulk and surface structure as well as the surface reactivity of the glass fibers with solid-state nuclear magnetic resonance (NMR) spectroscopy, inverse gas chromatography (IGC), and computational chemistry methods. These methods, solid-state NMR and IGC, typically require high surface area materials; however, by using probe molecules for NMR experiments or packing a column at high density for IGC measurements, lower surface area materials, such as glass fibers, can be investigated. The glasses used within this study were chosen as representative specimens of fibers with potentially different reactive sites on their surfaces. The two glass compositions were centered around a nominal E-glass, which contains very little alkali cations and mainly alkaline earth cations, and wool glass, which contains an abundance of alkali cations. The concentration of boron was varied from 0 to 8 mole % in both fiber compositions. Fibers were drawn from each composition at a variety of temperatures and draw speeds to provide a range of glass samples with varying

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

    Science.gov (United States)

    Singh, Kawarpal; Blümich, Bernhard

    2017-05-02

    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

  3. Barbiturate bearing aroylhydrazine derivatives: Synthesis, NMR investigations, single crystal X-ray studies and biological activity

    Science.gov (United States)

    Giziroglu, Emrah; Sarikurkcu, Cengiz; Aygün, Muhittin; Basbulbul, Gamze; Soyleyici, H. Can; Firinci, Erkan; Kirkan, Bulent; Alkis, Ayse; Saylica, Tayfur; Biyik, Halil

    2016-03-01

    A series of barbituric acid aroylhydrazine derivatives have been prepared from their corresponding 1,3-dimethyl-5-acetyl barbituric acid and aroylhydrazines. All compounds have been fully characterized by using FT-IR, multinuclear NMR (1H, 13C) and Mass (MS) spectrometry. We also describe the X-ray crystal structure of 3a, which crystallizes in the monoclinic P21/n space group. The crystal structure is stabilized with infinite linear chains of dimeric units. Furthermore, all compounds were investigated for their tyrosinase inhibition, antioxidative and antimicrobial activies. The results from biological activity assays have shown that all of compounds have excellent antioxidant, significant tyrosinase inhibition and moderate antimicrobial activity.

  4. Fluorine dynamics in BaF{sub 2} superionic conductors investigated by NMR

    Energy Technology Data Exchange (ETDEWEB)

    Gumann, Patryk

    2008-07-01

    In this work the dynamics of fluorine in solid-state electrolytes having BaF{sub 2}-structure was investigated using three different NMR-methods: field cycling relaxometry, lineshape analysis, and static field gradient NMR. For this purpose a pure BaF{sub 2} crystal, as well as crystals doped with trivalent impurities (LaF{sub 3}), were studied as a function of temperature. Using MAS NMR it was possible to identify two lines in Ba{sub 0.9}La{sub 0.1}F{sub 2.1} having different chemical shift, and to refer them to the modified crystal structure. On this basis a model for the fluorine lineshape has been developed, taking into account three motional processes characterized by their correlation times. It includes jump diffusion of the fluorine ions among equivalent sites within two crystallographically distinct sublattices, and inter-lattice exchange processes. By measuring frequency and temperature-dependent spin lattice relaxation times, it was possible to gain information about fluorine dynamics on microscopic length scales. An attempt was also made to analyze the data for pure BaF{sub 2} and low admixture concentration samples with a non-exponential correlation function. (orig.)

  5. Two-dimensional NMR investigations of the dynamic conformations of phospholipids and liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Mei [Univ. of California, Berkeley, CA (United States). Applied Science and Technology

    1996-05-01

    Two-dimensional 13C, 1H, and 31P nuclear magnetic resonance (NMR) techniques are developed and used to study molecular structure and dynamics in liquid-crystalline systems, primarily phospholipids and nematic liquid crystals. NMR spectroscopy characterizes molecular conformation in terms of orientations and distances of molecular segments. In anisotropically mobile systems, this is achieved by measuring motionally-averaged nuclear dipolar couplings and chemical shift anisotropies. The short-range couplings yield useful bond order parameters, while the long-range interactions constrain the overall conformation. In this work, techniques for probing proton dipolar local fields are further developed to obtain highlyresolved dipolar couplings between protons and rare spins. By exploiting variable-angle sample spinning techniques, orientation-sensitive NMR spectra are resolved according to sitespecific isotropic chemical shifts. Moreover, the signs and magnitudes of various short-range dipolar couplings are obtained. They are used in novel theoretical analyses that provide information about segmental orientations and their distributions. Such information is obtained in a model-independent fashion or with physically reasonable assumptions. The structural investigation of phospholipids is focused on the dynam

  6. Molecular Structure of Humin and Melanoidin via Solid State NMR

    OpenAIRE

    Herzfeld, Judith; Rand, Danielle; Matsuki, Yoh; Daviso, Eugenio; Mak-Jurkauskas, Melody; Mamajanov, Irena

    2011-01-01

    Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective 13C substitution, 1H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simpl...

  7. Fourier Analysis and Structure Determination. Part II: Pulse NMR and NMR Imaging.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Uses simple pulse NMR experiments to discuss Fourier transforms. Studies the generation of spin echoes used in the imaging procedure. Shows that pulse NMR experiments give signals that are additions of sinusoids of differing amplitudes, frequencies, and phases. (MVL)

  8. NMR investigation of non-brominated and brominated epoxy ester prepolymers

    Science.gov (United States)

    Žigon, M.; Osredkar, U.; Šebenik, A.

    1992-03-01

    1H, 13C and two-dimensional NMR spectroscopy has been used to investigate the structure of epoxy ester prepolymers, based on non-brominated DGEBA-type or brominated DGETBBA-type epoxy resins, and on an oligomeric carboxylic acid. In the presence of a quaternary phosphonium salt, besides diglycidylether of bisphenol A (DGEBA) or diglycidylether of tetrabromobisphenol A (DGETBBA) and their higher oligomers, monoesters with characteristic R-CH 2-CH(OH)-CH 2-OCOR' groups were detected in prevailing quantities. In dependence of the epoxy-carboxy ratio, isomeric monoesters with hydroxymethyl groups, diesters and diols might also be present.

  9. Investigation of Oxidative Degradation in Polymers Using (17)O NMR Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd M.; Celina, Mathew; Assink, Roger A.; Clough, Roger L.; Gillen, Kenneth T.; Wheeler David R.

    1999-07-20

    The thermal oxidation of pentacontane (C{sub 50}H{sub 102}), and of the homopolymer polyisoprene, has been investigated using {sup 17}O NMR spectroscopy. By performing the oxidation using {sup 17}O labeled O{sub 2} gas, it is possible to easily identify degradation products, even at relatively low concentrations. It is demonstrated that details of the degradation mechanism can be obtained from analysis of the {sup 17}O NMR spectra as a function of total oxidation. Pentacontane reveals the widest variety of reaction products, and exhibits changes in the relative product distributions with increasing O{sub 2} consumption. At low levels of oxygen incorporation, peroxides are the major oxidation product, while at later stages of degradation these species are replaced by increasing concentrations of ketones, alcohols, carboxylic acids and esters. Analyzing the product distribution can help in identification of the different free-radical decomposition pathways of hydroperoxides, including recombination, proton abstraction and chain scission, as well as secondary reactions. The {sup 17}O NMR spectra of thermally oxidized polyisoprene reveal fewer degradation functionalities, but exhibit an increased complexity in the type of observed degradation species due to structural features such as unsaturation and methyl branching. Alcohols and ethers formed from hydrogen abstraction and free radical termination.

  10. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica

    1997-12-31

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

  12. PFG NMR investigations of TPA-TMA-silica mixtures.

    Science.gov (United States)

    Li, Xiang; Shantz, Daniel F

    2011-04-05

    Pulsed-field gradient (PFG) NMR studies of tetrapropylammonium (TPA)-tetramethylammonium (TMA)-silica mixtures are presented, and the effect of TMA as a foreign ion on the TPA-silica nanoparticle interactions before and after heating has been studied. Dynamic light scattering (DLS) results suggest that silica nanoparticles in these TPA-TMA systems grow via a ripening mechanism for the first 24 h of heating. PFG NMR of mixtures before heating show that TMA can effectively displace TPA from the nanoparticle surface. The binding isotherms of TPA at room temperature obtained via PFG NMR can be described by Langmuir isotherms, and indicate a decrease in the adsorbed amount of TPA upon addition of TMA. PFG NMR also shows a systematic increase in the self-diffusion coefficient of TPA in both the mixed TPA-TMA systems and pure TPA systems with heating time, indicating an increased amount of TPA in solution upon heating. By contrast, a much smaller amount of TMA is observed to desorb from the nanoparticles upon heating. These results point to the desorption of TPA from the nanoparticles being a kinetically controlled process. The apparent desorption rate constants were calculated from fitting the desorbed amount of TPA with time via a pseudosecond-order kinetic model. This analysis show the rate of TPA desorption in TPA-TMA mixtures increases with increasing TMA content, whereas for pure TPA mixtures the rate of TPA desorption is much less sensitive to the TPA concentration.

  13. Synthesis, characterization and spectroscopy studying of some metal complexes of a new Schiff base ligand; X-ray crystal structure, NMR and IR investigation of a new dodecahedron Cd(II) complex

    Science.gov (United States)

    Golbedaghi, Reza; Rezaeivala, Majid; Khalili, Maryam; Notash, Behrouz; Karimi, Javad

    2016-12-01

    Some new [Cd(H2L1)(NO3)]ClO4 (1), [Mn(H2L1)](ClO4)2 (2), [Ni(H2L1)](ClO4)2 (3) and [Cu(H2L1)](ClO4)2 (4) complexes were prepared by the reaction of a Schiff base ligand and M (II) metal ions in equimolar ratios (M = Cd, Mn, Ni and Cu). The ligand H2L1 was synthesized by reaction of 2-[2-(3-formyl phenoxy)propoxy]benzaldehyde and ethanol amine and characterized by IR, 1H,13C NMR spectroscopy and elemental analysis. The synthesized complexes were characterized with IR and elemental analysis in all cases and 1H, 13C NMR, and X-ray in the case of Cd(II) complex. The X-ray crystal structure of compound 1 showed that all nitrogen and oxygen atoms of Schiff base ligand (N2O4) and a molecule of nitrate with two donor oxygen atom have been coordinated to the metal ion and the Cd(II) ion is in an eight-coordinate environment that is best described as a distorted dodecahedron geometry.

  14. 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

    Science.gov (United States)

    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, and Δα) have been calculated using the finite-field approach.

  15. Solid state NMR investigation of silica aerogel supported Fischer-Tropsch catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Zhiru; Dunn, Brian C.; Turpin, Gregory C.; Eyring, Edward M.; Ernst, Richard D.; Pugmire, Ronald J. [Department of Chemistry, University of Utah, Salt Lake City, UT 84112 (United States)

    2007-01-15

    The Fischer-Tropsch (F-T) catalyst is the critical component for the F-T synthesis of a variety of hydrocarbons from syngas. Fischer-Tropsch cobalt, iron and ruthenium catalysts supported on silica aerogel have been prepared using a combination of sol-gel chemistry and vapor phase deposition methods. Solid state NMR spectroscopy, a very powerful technique for analyzing the structure and dynamics of various materials, was employed in the study of these F-T catalyst systems. The silica aerogel supported F-T catalysts have been investigated using both solid state {sup 29}Si and {sup 13}C NMR methods. The silica aerogel's tetrahedral sub-unit structure and the influence of the loaded metal compounds have been observed. Three types of Si(O{sub 1/2}){sub 4} tetrahedral unit structure (Q{sub 2}, Q{sub 3} and Q{sub 4}) are clearly resolved in the silica aerogel samples. The calcining process and the loading of metal compounds produce line broadening in the {sup 29}Si spectra sufficient to prevent clear resolution of the three distinct Q{sub n} spectral lines, but the broadened spectra indicate that the three Q sub-unit structures are still present. The ferrocene and ruthenocene molecules used in the vapor phase deposition method exhibit a rapid exchange within the silica aerogel support similar to what one would expect in the gas or liquid state. (author)

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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.

  19. Investigation of zinc alkali pyrophosphate glasses. Part II: Local and medium range orders analysed by 1D/2D NMR

    Energy Technology Data Exchange (ETDEWEB)

    Rajbhandari, P. [UCCS UMR-CNRS 8181, Université de Lille1, Villeneuve d' Ascq (France); Chen, Y. [LASIR UMR-CNRS 8516, Université de Lille1, Villeneuve d' Ascq (France); Doumert, B. [IMMCL CNRS-FR2638, Université de Lille1, Villeneuve d' Ascq (France); Montagne, L. [UCCS UMR-CNRS 8181, Université de Lille1, Villeneuve d' Ascq (France); Tricot, G., E-mail: gregory.tricot@univ-lille1.fr [UCCS UMR-CNRS 8181, Université de Lille1, Villeneuve d' Ascq (France); LASIR UMR-CNRS 8516, Université de Lille1, Villeneuve d' Ascq (France)

    2015-04-01

    The structure of the (66-x)ZnO-xNa{sub 2}O-33.4P{sub 2}O{sub 5} composition line, selected for the development of low-Tg and stable glasses, has been investigated by 1D/2D NMR spectroscopy. If standard 1D {sup 31}P MAS-NMR experiments give access to the Q{sup n} speciation and show the presence of Q{sup 0}, Q{sup 1} and Q{sup 2} sites within the glass structure, application of the homonuclear through-space correlation technique ({sup 31}P DQ-SQ) allows for a more accurate description of the phosphate units. Clear distinction between the Q{sup 1} sites involved in dimmers or in longer chains has been derived from 2D NMR correlation maps and leads to the re-assignment of Q{sup 1} into Q{sup 1,1} and Q{sup 1,2} species. {sup 23}Na and {sup 23}Na({sup 31}P) REDOR MAS-NMR experiments have been used to analyse the Na{sup +} ions distribution and its interaction with the phosphate network. {sup 67}Zn static NMR experiments, performed at very high field, were carried out and suggest a constant Zn{sup 2+} coordination state all along the composition line. The results have been used to discuss the impact of the Zn{sup 2+}/Na{sup +} ratio on the extent of disorder within the glass network expressed in terms of Q{sup n} dismutation equilibrium constant and phosphate chain length distribution. - Highlights: • Structure of zinc alkali pyrophosphate glasses have been analysed by 1D/2D NMR. • 2D {sup 31}P experiments allow to separate Q{sup 1,1} and Q{sup 1,2} species. • {sup 67}Zn static NMR shows a constant signal all along the composition line.

  20. NMR investigations of surfaces and interfaces using spin-polarized xenon

    Energy Technology Data Exchange (ETDEWEB)

    Gaede, Holly Caroline [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1995-07-01

    129Xe NMR is potentially useful for the investigation of material surfaces, but has been limited to high surface area samples in which sufficient xenon can be loaded to achieve acceptable signal to noise ratios. In Chapter 2 conventional 129Xe NMR is used to study a high surface area polymer, a catalyst, and a confined liquid crystal to determine the topology of these systems. Further information about the spatial proximity of different sites of the catalyst and liquid crystal systems is determined through two dimensional exchange NMR in Chapter 3. Lower surface area systems may be investigated with spin-polarized xenon, which may be achieved through optical pumping and spin exchange. Optically polarized xenon can be up to 105times more sensitive than thermally polarized xenon. In Chapter 4 highly polarized xenon is used to examine the surface of poly(acrylonitrile) and the formation of xenon clathrate hydrates. An attractive use of polarized xenon is as a magnetization source in cross polarization experiments. Cross polarization from adsorbed polarized xenon may allow detection of surface nuclei with drastic enhancements. A non-selective low field thermal mixing technique is used to enhance the 13C signal of CO2 of xenon occluded in solid CO2 by a factor of 200. High-field cross polarization from xenon to proton on the surface of high surface area polymers has enabled signal enhancements of ~1,000. These studies, together with investigations of the efficiency of the cross polarization process from polarized xenon, are discussed in Chapter 5. Another use of polarized xenon is as an imaging contrast agent in systems that are not compatible with traditional contrast agents. The resolution attainable with this method is determined through images of structured phantoms in Chapter 6.

  1. Structural analysis of complex saponins of Balanites aegyptiaca by 800 MHz 1H NMR spectroscopy.

    Science.gov (United States)

    Staerk, Dan; Chapagain, Bishnu P; Lindin, Therese; Wiesman, Zeev; Jaroszewski, Jerzy W

    2006-10-01

    The main saponin (1) present in the mesocarp of Balanites aegyptiaca fruit is a mixture of 22R and 22S epimers of 26-(O-beta-D-glucopyranosyl)-3-beta-[4-O-(beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyloxy]-22,26-dihydroxyfurost-5-ene. This structure differs from a previously reported saponin isolated from this source by the site of attachment of the rhamnosyl residue, and presumably represents a structural revision of the latter. The main saponin (2) present in the kernel is a xylopyranosyl derivative of 1. The use of high-field NMR enabled the practically complete assignment of 1H and 13C chemical shifts of these complex saponins, existing as a mixture of C-22 epimers. Moreover, the work represents a new approach to structural elucidation of saponins: direct preparative-scale HPLC-RID of crude extracts followed by high-field NMR investigations supported by ESI-MSn.

  2. A model for ensemble NMR quantum computer using antiferromagnetic structure

    CERN Document Server

    Kokin, A A

    2000-01-01

    The one-dimensional homonuclear periodic array of nuclear spins I = 1/2,owing to hyperfine interaction of nuclear spins with electronic magneticmoments in antiferromagnetic structure, is considered. The neighbor nuclearspins in such array are opposite oriented and have resonant frequenciesdetermined by hyperfine interaction constant, applied magnetic field value andinteraction with the left and right nuclear neighbor spins. The resonantfrequencies difference of nuclear spins, when the neighbor spins have differentand the same states, is used to control the spin dynamics by means of selectiveresonant RF-pulses both for single nuclear spins and for ensemble of nuclearspins with the same resonant frequency. A model for the NMR quantum computer of cellular-automata type based on anone-dimensional homonuclear periodic array of spins is proposed. This model maybe generalized to a large ensemble of parallel working one-dimensional arraysand to two-dimensional and three-dimensional structures.

  3. Effects of NMR spectral resolution on protein structure calculation.

    Directory of Open Access Journals (Sweden)

    Suhas Tikole

    Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

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

    Science.gov (United States)

    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.

  5. (17)O NMR and Raman Spectroscopies of Green Tea Infusion with Nanomaterial to Investigate Their Properties.

    Science.gov (United States)

    Zhou, Changyan; Zhang, Huiping; Yan, Ying; Zhang, Xinya

    2016-09-01

    (17)O NMR and Raman spectrograms of green tea infusions with nanomaterial were investigated. Different green tea infusions were prepared by steeping tea powder with different concentrations of nanomaterial aqueous solution. The tea infusions were tested with (17)O NMR and Raman spectroscopies. The (17)O NMR results showed that line width increased to 90 in the tea infusions after nanomaterial was added as a result of the effects of the self-association of Ca(2+) and tea polyphenol. The results of Raman spectroscopy showed that, in tea infusions, the enhancement of C─C and C─O stretching vibrations suggest an increase in the number of effective components in water.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  9. Rapid NMR screening of RNA secondary structure and binding

    Energy Technology Data Exchange (ETDEWEB)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

    2015-09-15

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.

  10. Investigating sorption on iron-oxyhydroxide soil minerals by solid-state NMR spectroscopy: a 6Li MAS NMR study of adsorption and absorption on goethite

    DEFF Research Database (Denmark)

    Nielsen, Ulla Gro; Paik, Younkee; Julmis, Keinia;

    2005-01-01

    High-resolution 2H MAS NMR spectra can be obtained for nanocrystalline particles of goethite (alpha-FeOOH, particle size approximately 4-10 nm) at room temperature, facilitating NMR studies of sorption under environmentally relevant conditions. Li sorption was investigated as a function of pH, th...

  11. Informing saccharide structural NMR studies with density functional theory calculations.

    Science.gov (United States)

    Klepach, Thomas; Zhao, Hongqiu; Hu, Xiaosong; Zhang, Wenhui; Stenutz, Roland; Hadad, Matthew J; Carmichael, Ian; Serianni, Anthony S

    2015-01-01

    Density functional theory (DFT) is a powerful computational tool to enable structural interpretations of NMR spin-spin coupling constants ( J-couplings) in saccharides, including the abundant (1)H-(1)H ( JHH), (13)C-(1)H ( JCH), and (13)C-(13)C ( JCC) values that exist for coupling pathways comprised of 1-4 bonds. The multiple hydroxyl groups in saccharides, with their attendant lone-pair orbitals, exert significant effects on J-couplings that can be difficult to decipher and quantify without input from theory. Oxygen substituent effects are configurational and conformational in origin (e.g., axial/equatorial orientation of an OH group in an aldopyranosyl ring; C-O bond conformation involving an exocyclic OH group). DFT studies shed light on these effects, and if conducted properly, yield quantitative relationships between a specific J-coupling and one or more conformational elements in the target molecule. These relationships assist studies of saccharide structure and conformation in solution, which are often challenged by the presence of conformational averaging. Redundant J-couplings, defined as an ensemble of J-couplings sensitive to the same conformational element, are particularly helpful when the element is flexible in solution (i.e., samples multiple conformational states on the NMR time scale), provided that algorithms are available to convert redundant J-values into meaningful conformational models. If the latter conversion is achievable, the data can serve as a means of testing, validating, and refining theoretical methods like molecular dynamics (MD) simulations, which are currently relied upon heavily to assign conformational models of saccharides in solution despite a paucity of experimental data needed to independently validate the method.

  12. Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

    Science.gov (United States)

    Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

    2017-01-01

    Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

  13. Simple NMR methods for evaluating higher order structures of monoclonal antibody therapeutics with quinary structure.

    Science.gov (United States)

    Chen, Kang; Long, Dianna S; Lute, Scott C; Levy, Michaella J; Brorson, Kurt A; Keire, David A

    2016-09-01

    Monoclonal antibody (mAb) drugs constitute the largest class of protein therapeutics currently on the market. Correctly folded protein higher order structure (HOS), including quinary structure, is crucial for mAb drug quality. The quinary structure is defined as the association of quaternary structures (e.g., oligomerized mAb). Here, several commonly available analytical methods, i.e., size-exclusion-chromatography (SEC) FPLC, multi-angle light scattering (MALS), circular dichroism (CD), NMR and multivariate analysis, were combined and modified to yield a complete profile of HOS and comparable metrics. Rituximab and infliximab were chosen for method evaluation because both IgG1 molecules are known to be homologous in sequence, superimposable in Fab crystal structure and identical in Fc structure. However, herein the two are identified to be significantly different in quinary structure in addition to minor secondary structure differences. All data collectively showed rituximab was mostly monomeric while infliximab was in mono-oligomer equilibrium driven by its Fab fragment. The quinary structure differences were qualitatively inferred from the less used but more reproducible dilution-injection-SEC-FPLC curve method. Quantitative principal component analysis (PCA) was performed on NMR spectra of either the intact or the in-situ enzymatic-digested mAb samples. The cleavage reactions happened directly in NMR tubes without further separation, which greatly enhanced NMR spectra quality and resulted in larger inter- and intra-lot variations based on PCA. The new in-situ enzymatic digestion method holds potential in identifying structural differences on larger therapeutic molecules using NMR.

  14. Combining (27)Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

    Science.gov (United States)

    Tu, Bingtian; Liu, Xin; Wang, Hao; Wang, Weimin; Zhai, Pengcheng; Fu, Zhengyi

    2016-12-19

    The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δiso, quadrupolar coupling constants, CQ, and asymmetry parameter, η) of Al22.5O28.5N3.5, predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the (27)Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al2.811O3.565N0.435 by quantitative analysis. The experimental δiso, CQ, and η of (27)Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the (27)Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al2.811O3.565N0.435. The results from (27)Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

  15. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  16. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

    Science.gov (United States)

    Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

    2008-02-01

    We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

  17. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra

    Science.gov (United States)

    Kose, Etem; Karabacak, Mehmet; Bardak, Fehmi; Atac, Ahmet

    2016-11-01

    One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The 1H and 13C NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm-1 (FT-IR) and 4000-10 cm-1 (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (1H and 13C) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of

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

    Science.gov (United States)

    Jaroniec, Christopher P.

    2015-04-01

    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.

  19. Solution state structure determination of silicate oligomers by 29SI NMR spectroscopy and molecular modeling.

    Science.gov (United States)

    Cho, Herman; Felmy, Andrew R; Craciun, Raluca; Keenum, J Patrick; Shah, Neil; Dixon, David A

    2006-02-22

    Evidence for nine new solution state silicate oligomers has been discovered by (29)Si NMR homonuclear correlation experiments of (29)Si-enriched samples. In addition to enhancing signal sensitivity, the isotopic enrichment increases the probability of the (29)Si-(29)Si two-bond scalar couplings that are necessary for the observation of internuclear correlations in 2-D experiments. The proposed assignments are validated by comparisons of experimental and simulated cross-peaks obtained with high digital resolution. The internuclear connectivity indicated by the NMR data suggests that several of these oligomers can have multiple stereoisomers, including conformers and/or diastereomers. The stabilities of these oligomers and their possible stereoisomers have been investigated by electronic structure calculations.

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

    Science.gov (United States)

    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

  1. Structural characterization of homogalacturonan by NMR spectroscopy - assignment of reference compounds

    DEFF Research Database (Denmark)

    Petersen, Bent O.; Meier, Sebastian; Duus, Jens Øllgaard;

    2008-01-01

    Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure of homogalac......Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure...

  2. Proton NMR studies on Megaphaera elsdenii flavodoxin : structure elucidation by 2D-NMR and implications

    NARCIS (Netherlands)

    Mierlo, van C.

    1990-01-01

    1H NMR techniques have been applied for a thorough study of the uncrystallizable Megasphaera elsdenii flavodoxin in its three redox states. The aim of the research project described in this thesis was to obtain answers regarding questions concerni

  3. Molecular structure of crude beeswax studied by solid-state 13C NMR.

    Science.gov (United States)

    Kameda, Tsunenori

    2004-01-01

    13C solid-state NMR experiments were performed to investigate the structure of beeswax in the native state (crude beeswax) for the first time. From quantitative direct polarization 13C MAS NMR spectrum, it was found that the fraction of internal-chain methylene (int-(CH2)) component compared to other components of crude beeswax was over 95%. The line shape of the int-(CH2) carbon resonance region was comprehensively analyzed in terms of NMR chemical shift. The 13C broad peak component covering from 31 to 35 ppm corresponds to int-(CH2) carbons with trans conformation in crystalline domains, whereas the sharp signal at 30.3 ppm corresponds to gauche conformation in the non-crystalline domain. From peak deconvolution of the aliphatic region, it was found that over 85% of the int-(CH2) has a crystal structure and several kinds of molecular packing for int-(CH2), at least three, exist in the crystalline domain.

  4. NMR investigation of imidazolium-based ionic liquids and their aqueous mixtures.

    Science.gov (United States)

    Cesare Marincola, Flaminia; Piras, Cristina; Russina, Olga; Gontrani, Lorenzo; Saba, Giuseppe; Lai, Adolfo

    2012-04-10

    (1)H and (13)C NMR spectroscopy is employed to investigate the interaction of water with two imidazolium-based ionic liquids (ILs), 1-hexyl-3-methylimidazolium bromide ([C(6)mim]Br) and 1-octyl-3-methylimidazolium bromide ([C(8)mim]Br), at IL concentrations well above the critical aggregation concentration (CAC). The results are compared with those of the neat samples. To this aim, a detailed analysis of the changes in the (1)H chemical shifts, (13)C relaxation parameters, and 2D ROESY data due to the presence of water is performed. The results for both neat ILs are consistent with a packed structure where head-to-head, head-to-tail, and tail-to-tail contacts occur and where the site of maximal mobility restriction is at the polar head. At the lowest investigated water content, the presence of water influences mainly the environment around the IL polar head, slowing down the motional dynamics of the aromatic ring with respect to the alkyl chain. At higher water contents this difference diminishes, the motional freedom of the whole molecule increasing. The presence of ROESY cross-peaks between protons in the polar and apolar IL regions, as well as between protons in non-neighboring alkyl groups, at all investigated water contents suggests that the alkyl tails are not fully segregated in hydrophobic domains, as expected for micelle-like structures.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Lola A. Brown

    2015-04-01

    Full Text Available 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(4,5P2]. 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(4,5P2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5P2 cellular signaling system to direct intracellular Gag trafficking during virus assembly.

  7. Stereochemical investigation of selegiline HCl with /sup 1/H and /sup 13/C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Podanyi, B. (CHINOIN Gyogyszer- es Vegyeszeti Termekek Gyara, Budapest (Hungary))

    1982-12-01

    Selegiline HCl, the bioactive substance of the antiparkinsonic medicine, JUMEX was investigated by NMR spectroscopy. The dominant conformer was determined. Optically active shift-reagent was used for the determination of optical purity. The /sup 13/C spectrum was analyzed, and molecular dynamics was investigated at different temperatures.

  8. DOSY-NMR and raman investigations on the self-aggregation and cyclodextrin complexation of vanillin.

    Science.gov (United States)

    Ferrazza, Ruggero; Rossi, Barbara; Guella, Graziano

    2014-06-26

    Vanillin (4-hydroxy-3-methoxybenzaldehyde) is a phenolic aldehyde with limited solubility in water; in this work, we investigate its self-aggregation, as well as its complexation equilibria with β-cyclodextrin by using nuclear magnetic resonance (NMR) and vibrational spectroscopy. In particular, diffusion-ordered NMR (DOSY) measurements allowing to detect diffusional changes caused by aggregation/inclusion phenomena lead to a reliable estimate of the equilibrium constants of these processes, while Raman spectroscopy was used to further characterize some structural details of vanillin self-aggregates and inclusion complexes. Although the self-association binding constant of vanillin in water was found to be low (K(a) ∼10), dimeric species are not negligible within the investigated range of concentration (3-65 mM); on the other hand, formation of β-cyclodextrin self-aggregates was not detected by DOSY measurements on aqueous solutions of β-cyclodextrin at different concentrations (2-12 mM). Finally, the binding of vanillin with β-cyclodextrin, as measured by the DOSY technique within a narrow range of concentrations (2-15 mM) by assuming the existence of only the monomeric 1:1 vanillin/β-CD complex, was about an order of magnitude higher (K(c) ∼ 90) than self-aggregation. However, the value of the equilibrium constant for this complexation was found to be significantly affected by the analytical concentrations of the host and guest system, thus indicating that K(c) is an "apparent" equilibrium constant.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rosato, Antonio [University of Florence, Department of Chemistry and Magnetic Resonance Center (Italy); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Fogh, Rasmus H.; Ragan, Timothy J. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H. [University of Georgia, Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium (United States); Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H. [University of Toronto, Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium (Canada); Kennedy, Michael [Miami University, Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (United States); Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers (United States); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    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.

  10. The structure of the cytochrome P450cam-putidaredoxin complex determined by paramagnetic NMR spectroscopy and crystallography

    NARCIS (Netherlands)

    Hiruma, Yoshitaka

    2014-01-01

    By utilizing paramagnetic NMR techniques, the structure and dynamics of the P450cam system were investigated. The analysis of PCS and RDC illuminated the stereo-specific final complex of Pdx and P450cam, while the results of PRE demonstrated the presence of a transient encounter complex.

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

    Science.gov (United States)

    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

  12. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  13. The aluminium effect on the structure of silico-phosphate glasses studied by NMR and FTIR

    Science.gov (United States)

    Sitarz, Maciej; Fojud, Zbigniew; Olejniczak, Zbigniew

    2009-04-01

    Silico-phosphate glasses of NaCaPO 4-SiO 2 and NaCaPO 4-AlPO 4-SiO 2 system have been the subject of the presented investigations. Glasses of these systems are the basis for the preparation of glassy-crystalline biomaterials [R.D. Rawlings, Clin. Mater. 14 (1993) 155]. Detailed knowledge of the precursor glass structure is necessary for proper design of the glassy-crystalline biomaterials preparation procedure. Since there is no long-range ordering in glasses, spectroscopic methods which make it possible to study the short range ordering should be applied. MIR studies carried out in the work have allowed to establish that the glasses of the systems studied show domain composition [L.L. Hench, R.J. Splinter, T.K. Greenlee, W.C. Allen, J. Biol. Res. Symp. 2 (1971) 117; L.L. Hench, R.J. Splinter, W.C. Allen, T.K. Greenlee, J. Biol. Res. 5 (1972) 117]. Domain structure is close to that of the corresponding crystalline phases. It has been shown that even small amount of aluminium in the glass (5 mol.% of AlPO 4) significantly influences both, its texture (microscopic and EDX studies) and its structure (spectroscopic studies). 27Al NMR investigations have made it possible to establish unequivocally that aluminium occurs exclusively in tetrahedral coordination, i.e. it is involved in the formation of glass framework. Presence of aluminium results in significant changes in the [SiO 4] 4- and [PO 4] 3- tetrahedra environment which is reflected in 23Na, 31P and 29Si NMR spectra. Changes in the shapes and positions of the bands in the NMR spectra of glasses belonging to the NaCaPO 4-AlPO 4-SiO 2 system confirm great influence of aluminium on silico-phosphate glasses structure.

  14. Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Leeflang, B.R.; Faber, E.J.; Erbel, P.J.A.

    2000-01-01

    The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a compu

  15. Structural characterization of homogalacturonan by NMR spectroscopy-assignment of reference compounds.

    Science.gov (United States)

    Petersen, Bent O; Meier, Sebastian; Duus, Jens Ø; Clausen, Mads H

    2008-11-03

    Complete assignment of (1)H and (13)C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2mg of sample making this method convenient for studying the structure of homogalacturonan oligosaccharides.

  16. Structure Elucidation of Tolperisone Hydrochloride by NMR%盐酸托哌酮的NMR研究

    Institute of Scientific and Technical Information of China (English)

    黄建设; 吴军; 肖志会; 张偲

    2005-01-01

    The structure of tolperisone hydrochloride was elucidated by 1D and 2D NMR techniques (i. e. , gCOSY, gNOESY, gHSQC and gHMBC). The 1H and 13C chemical shifts of this compound were completely assigned, and its stereochemistry was investigated by NOESY.%应用1D NMR和脉冲梯度场2D NMR技术深入研究盐酸托哌酮的溶液结构,对其1H和13C NMR化学位移进行全归属,并讨论其立体化学.

  17. {sup 17}O NMR investigation of oxidative degradation in polymers under gamma-irradiation

    Energy Technology Data Exchange (ETDEWEB)

    ALAM,TODD M.; CELINA,MATHIAS C.; ASSINK,ROGER A.; CLOUGH,ROGER LEE; GILLEN,KENNETH T.

    2000-03-08

    The {gamma}-irradiated-oxidation of pentacontane (C{sub 50}H{sub 102}) and the polymer polyisoprene was investigated as a function of oxidation level using {sup 17}O nuclear magnetic resonance (NMR) spectroscopy. It is demonstrated that by using {sup 17}O labeled O{sub 2} gas during the {gamma}-irradiation process, details about the oxidative degradation mechanisms can be directly obtained from the analysis of the {sup 17}O NMR spectra. Production of carboxylic acids is the primary oxygen-containing functionality during the oxidation of pentacontane, while ethers and alcohols are the dominant oxidation product observed for polyisoprene. The formation of ester species during the oxidation process is very minor for both materials, with water also being produced in significant amounts during the radiolytic oxidation of polyisoprene. The ability to focus on the oxidative component of the degradation process using {sup 17}O NMR spectroscopy demonstrates the selectivity of this technique over more conventional approaches.

  18. A Grid-enabled web portal for NMR structure refinement with AMBER.

    Science.gov (United States)

    Bertini, Ivano; Case, David A; Ferella, Lucio; Giachetti, Andrea; Rosato, Antonio

    2011-09-01

    The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols. We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER-based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of three different proteins are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein-ligand adducts. AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http://py-enmr.cerm.unifi.it/access/index/amps-nmr; its use requires registration with a digital certificate. ivanobertini@cerm.unifi.it Supplementary data are available at Bioinformatics online.

  19. Molecular structure, spectral investigation (1H NMR, 13C NMR, UV-Visible, FT-IR, FT-Raman), NBO, intramolecular hydrogen bonding, chemical reactivity and first hyperpolarizability analysis of formononetin [7-hydroxy-3(4-methoxyphenyl)chromone]: A quantum chemical study

    Science.gov (United States)

    Srivastava, Anubha; Mishra, Rashmi; Kumar, Sudhir; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

    2015-03-01

    Formononetin [7-hydroxy-3(4-methoxyphenyl)chromone or 4‧-methoxy daidzein] is a soy isoflavonoid that is found abundantly in traditional Chinese medicine Astragalus mongholicus (Bunge) and Trifolium pretense L. (red clover), and in an Indian medicinal plant, Butea (B.) monosperma. Crude extract of B.monosperma is used for rapid healing of fracture in Indian traditional medicine. In this study, a combined theoretical and experimental approach is used to study the properties of formononetin. The optimized geometry was calculated by B3LYP method using 6-311++G(d,p) as a large basis set. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution (PED) analysis. Density functional theory (DFT) is applied to explore the nonlinear optical properties of the molecule. Good consistency is found between the calculated results and observed data for the electronic absorption, IR and Raman spectra. The solvent effects have been calculated using time-dependent density functional theory in combination with the integral equation formalism polarized continuum model, and the results are in good agreement with observed measurements. The double well potential energy curve of the molecule about the respective bonds, have been plotted, as obtained from DFT/6-31G basis set. The computational results diagnose the most stable conformer of formononetin. The HOMO-LUMO energy gap of possible conformers has been calculated for comparing their chemical activity. Chemical reactivity has been measured by reactivity descriptors and molecular electrostatic potential surface (MEP). The 1H and 13C NMR chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. Furthermore, the role of CHsbnd O intramolecular hydrogen bond in the stability of molecule is investigated on the basis of the results of topological properties of AIM theory and NBO analysis. The calculated first hyperpolarizability shows

  20. Solid state NMR investigation of a novel Li ion ceramic electrolyte. Li doped BPO sub 4

    CERN Document Server

    Dodd, A J

    2002-01-01

    Over the last decade lithium ion conducting batteries have emerged as the leading technology in battery materials. Their performance, however, is limited to applications below around 50 deg C by the liquid nature of the electrolytes used. In the quest for a solid state electrolyte for use in high temperature applications the nano-crystalline ceramic lithium doped boron phosphate material was developed. Solid state nuclear magnetic resonance (NMR) has been employed to investigate some of the fundamental properties of this material including ionic mobility, defect structure, sample purity and ionic distribution. The findings of this work show that when synthesised at a reaction temperature above 600 deg C the loss of boron from the structure results in the incorporation of vacancy sites about which the Li ions gather in small clusters. Multiple-pulse multiple-quantum spin counting techniques are employed in an effort to count the number of quadrupolar sup 7 Li nuclei interacting in a cluster though it is ultima...

  1. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith;

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... the NH-tautomer with a hydrogen atom situated at the nitrogen of the quinoline moiety. Direct evidence of the presence of the NH-tautomer is provided by 1H–14N HMQC solid-state NMR at very fast MAS. Solid-state dispersion-corrected density functional theory calculations with BLYP-D3 confirm...

  2. 1H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    KAUST Repository

    Schmid, Marc R.

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

  3. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    Science.gov (United States)

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

  4. Determination of the structural changes by Raman and {sup 13}C CP/MAS NMR spectroscopy on native corn starch with plasticizers

    Energy Technology Data Exchange (ETDEWEB)

    Cozar, O. [Academy of Romanian Scientists, Splaiul Independentei 54, 050094, Bucharest, Romania and National Institute of Research-Development for Machines and Installations Designed to Agriculture and Food Industry - INMA Bucureşti - Cluj-Napoca Branch (Romania); Filip, C.; Tripon, C. [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Cioica, N.; Coţa, C.; Nagy, E. M. [National Institute of Research-Development for Machines and Installations Designed to Agriculture and Food Industry - INMA Bucureşti - Cluj-Napoca Branch, RO-400458 Cluj-Napoca (Romania)

    2013-11-13

    The plasticizing - antiplasticizing effect of water and glycerol contents on native corn starch samples is investigated by FT-Raman and {sup 13}C CP/MAS NMR spectroscopy. The presence of both amorphous and crystalline structural phases was evidenced in pure native corn starch and also in the samples containing plasticizers. Among the crystalline starch structures, the A- and V- types were suggested by CP/MAS NMR spectra.

  5. NMR Structures and Interactions of Temporin-1Tl and Temporin-1Tb with Lipopolysaccharide Micelles

    Science.gov (United States)

    Bhunia, Anirban; Saravanan, Rathi; Mohanram, Harini; Mangoni, Maria L.; Bhattacharjya, Surajit

    2011-01-01

    Temporins are a group of closely related short antimicrobial peptides from frog skin. Lipopolysaccharide (LPS), the major constituent of the outer membrane of Gram-negative bacteria, plays important roles in the activity of temporins. Earlier studies have found that LPS induces oligomerization of temporin-1Tb (TB) thus preventing its translocation across the outer membrane and, as a result, reduces its activity on Gram-negative bacteria. On the other hand, temporin-1Tl (TL) exhibits higher activity, presumably because of lack of such oligomerization. A synergistic mechanism was proposed, involving TL and TB in overcoming the LPS-mediated barrier. Here, to gain insights into interactions of TL and TB within LPS, we investigated the structures and interactions of TL, TB, and TL+TB in LPS micelles, using NMR and fluorescence spectroscopy. In the context of LPS, TL assumes a novel antiparallel dimeric helical structure sustained by intimate packing between aromatic-aromatic and aromatic-aliphatic residues. By contrast, independent TB has populations of helical and aggregated conformations in LPS. The LPS-induced aggregated states of TB are largely destabilized in the presence of TL. Saturation transfer difference NMR studies have delineated residues of TL and TB in close contact with LPS and enhanced interactions of these two peptides with LPS, when combined together. Fluorescence resonance energy transfer and 31P NMR have pointed out the proximity of TL and TB in LPS and conformational changes of LPS, respectively. Importantly, these results provide the first structural insights into the mode of action and synergism of antimicrobial peptides at the level of the LPS-outer membrane. PMID:21586570

  6. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Mishra

    2017-03-01

    Full Text Available The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

  7. Molecular mobility in Medicago truncatula seed during early stage of germination: Neutron scattering and NMR investigations

    Energy Technology Data Exchange (ETDEWEB)

    Falourd, Xavier [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France); Natali, Francesca [CNR-IOM-OGG, c/o Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Peters, Judith [Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Université Joseph Fourier UFR PhITEM, BP 53, 38041 Grenoble Cedex 9 (France); Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1 (France); Foucat, Loïc, E-mail: Loic.Foucat@nantes.inra.fr [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France)

    2014-01-15

    Highlights: • Neutron scattering and NMR approaches were used to characterize seed germination. • A parallel between macromolecular motions and water dynamics was established. • Freezing/thawing cycle revealed a hysteresis connected to the seed hydration level. - Abstract: First hours of Medicago truncatula (MT) seeds germination were investigated using elastic incoherent neutron scattering (EINS) and nuclear magnetic resonance (NMR), to follow respectively how macromolecular motions and water mobility evolve when water permeates into the seed. From EINS results, it was shown that there is an increase in macromolecular mobility with the water uptake. Changes in NMR relaxation parameters reflected microstructural changes associated with the recovery of the metabolic processes. The EINS investigation of the effect of temperature on macromolecular motions showed that there is a relationship between the amount of water in the seeds and the effect of freezing–thawing cycle. The NMR relaxometry results obtained at 253 K allowed establishing possible link between the freezing of water molecules tightly bound to macromolecules and their drastic motion restriction around 250 K, as observed with EINS at the highest water content.

  8. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

    Directory of Open Access Journals (Sweden)

    Bailey Timothy L

    2006-02-01

    Full Text Available Abstract Background The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structure, i.e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models. Results Several probabilistic models not only successfully estimate the continuum secondary structure, but also provide a categorical output on par with models directly trained on categorical data. Importantly, models trained on the continuum secondary structure are also better than their categorical counterparts at identifying the conformational state for structurally ambivalent residues. Conclusion Cascaded probabilistic neural networks trained on the continuum secondary structure exhibit better accuracy in structurally ambivalent regions of proteins, while sustaining an overall classification accuracy on par with standard, categorical prediction methods.

  9. Investigation of a polymer-dispersed liquid crystal system by NMR diffusometry and relaxometry

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Mingxue

    2013-02-26

    Polymer-dispersed liquid crystals (PDLCs) are polymer composites containing a dispersion of liquid crystal droplets in polymer networks. PDLCs have attracted much attention due to their unique properties and potential usage. The properties of PDLCs depend on the degree of phase separation and the size of liquid crystal droplets. To investigate the structure will help us to better understand and optimize PDLCs.The main aim of this PhD thesis was to investigate PDLCs by NMR techniques. Diffusion constants and spin-lattice relaxation times in the laboratory (T{sub 1}) and rotating frame (T{sub 1{rho}}) were measured for PDLCs as well as precursor mixtures based on the trifunctional monomer trimethylolpropane triacrylate (TMPTA) and the commercial nematic mixture E7. The variation of the main dipolar splitting of {sup 1}H spectra with increasing temperature was analyzed to obtain the nematic-to-isotropic phase transition temperature and the nematic order parameter of E7 and, for comparison, the nematic liquid crystal 5CB.Diffusion constants in TMPTA/E7 mixtures, measured by pulsed-field gradient NMR, increase for both E7 and TMPTA as the mass fraction of E7 increases, due to the lower viscosity of E7. E7 in the PDLC diffuses more slowly than in the bulk because of the hindrance by the polymer matrix. T{sub 1} and T{sub 1{rho}} relaxation times in the liquid or liquid-crystalline phases of TMPTA and bulk E7 are higher than in the PDLC and the pure polymer, due to the lower mobility in the polymer samples. T{sub 1{rho}} in the PDLC is even shorter than in the pure polymer, indicating an anti-softening effect caused by E7 molecules. In bulk E7, the well-ordered rod-like molecules exhibit a unique H-C dipolar coupling, which leads to oscillations in the cross-polarization curve. However, in the PDLC, the anchoring effect at the boundary between the polymer and LC droplets disturbs the molecular order resulting in a smooth cross polarization curve.

  10. 2D NMR Investigation of Dynamic Equilibrium of Tautomers of Gossypol

    Institute of Scientific and Technical Information of China (English)

    SHEN Ying-lin; YANG Sheng-hua; YAN Xiao-hua; MA Xue-yi

    2004-01-01

    Gossypol was obtained as an yellow platelike crystal with m.p. 210-214 . In CDCl3 there were three tautomers of gossypol: Ⅰ aldehyde, Ⅱ lactol, Ⅲ ketal, in equilibrium .Their total 1H NMR spectra were assigned by means of 1D and 2D NMR techniques including 1H-1H cosy ,DEPT, HMQC (1H Detected Heteronuclear Multiple Quantum Coherence) and HMBC (1H Detected Heteronuclear Multiple Bond Connectivity) experiments.This paper first reported that we took use of the 2D NMR techniques to assign all of 1H NMR chemical shifts of each tautomer , through the assignments of each peaks we investigated the tautomerism of gossypol . We concluded that when gossypol ( Ⅰ ) was put into CDCl3 , it would tautomerized three tautomers, they stable existed and attained tautomeric equilibrium in a molar ratio of 6:2:1 according to peaks intensity ratios in CDCl3. The result listed in table 1.Table 1. The 1H spectroscopy chemical shifts (ppm) for gossypol (Ⅰ), (Ⅱ) and (Ⅲ)All spectra were recorded at room tempreture in CDCl3 using TMS as an internal standard reported in δ units,hydroxyl protons were identified by D2O exchange.

  11. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

    Energy Technology Data Exchange (ETDEWEB)

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten, E-mail: torsten.herrmann@ens-lyon.fr [Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs (France)

    2015-08-15

    UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.

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

    Science.gov (United States)

    Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

    2010-09-03

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

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

    Science.gov (United States)

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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; Vries, Sjoerd de; Vuister, Geerten W; Wu, Bin; Yang, Yunhuang; Bonvin, Alexandre M J J

    2012-02-08

    The protocols currently used for protein structure determination by nuclear magnetic resonance (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 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nohaile, M J [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    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 {alpha}-helices and a five-stranded {beta}-sheet in a ({beta}/{alpha}){sub 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nohaile, Michael James [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    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.

  18. Enhanced efficiency of solid-state NMR investigations of energy materials using an external automatic tuning/matching (eATM) robot

    Science.gov (United States)

    Pecher, Oliver; Halat, David M.; Lee, Jeongjae; Liu, Zigeng; Griffith, Kent J.; Braun, Marco; Grey, Clare P.

    2017-02-01

    We have developed and explored an external automatic tuning/matching (eATM) robot that can be attached to commercial and/or home-built magic angle spinning (MAS) or static nuclear magnetic resonance (NMR) probeheads. Complete synchronization and automation with Bruker and Tecmag spectrometers is ensured via transistor-transistor-logic (TTL) signals. The eATM robot enables an automated "on-the-fly" re-calibration of the radio frequency (rf) carrier frequency, which is beneficial whenever tuning/matching of the resonance circuit is required, e.g. variable temperature (VT) NMR, spin-echo mapping (variable offset cumulative spectroscopy, VOCS) and/or in situ NMR experiments of batteries. This allows a significant increase in efficiency for NMR experiments outside regular working hours (e.g. overnight) and, furthermore, enables measurements of quadrupolar nuclei which would not be possible in reasonable timeframes due to excessively large spectral widths. Additionally, different tuning/matching capacitor (and/or coil) settings for desired frequencies (e.g.7Li and 31P at 117 and 122 MHz, respectively, at 7.05 T) can be saved and made directly accessible before automatic tuning/matching, thus enabling automated measurements of multiple nuclei for one sample with no manual adjustment required by the user. We have applied this new eATM approach in static and MAS spin-echo mapping NMR experiments in different magnetic fields on four energy storage materials, namely: (1) paramagnetic 7Li and 31P MAS NMR (without manual recalibration) of the Li-ion battery cathode material LiFePO4; (2) paramagnetic 17O VT-NMR of the solid oxide fuel cell cathode material La2NiO4+δ; (3) broadband 93Nb static NMR of the Li-ion battery material BNb2O5; and (4) broadband static 127I NMR of a potential Li-air battery product LiIO3. In each case, insight into local atomic structure and dynamics arises primarily from the highly broadened (1-25 MHz) NMR lineshapes that the eATM robot is uniquely

  19. Synthesis, spectroscopic investigations (X-ray, NMR and TD-DFT), antimicrobial activity and molecular docking of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone.

    Science.gov (United States)

    Barakat, Assem; Ghabbour, Hazem A; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Ali, M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Fun, Hoong-Kun

    2015-07-21

    The synthesis of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone 1 is described. The molecular structure of the title compound 1 was confirmed by NMR, FT-IR, MS, CHN microanalysis, and X-ray crystallography. The molecular structure was also investigated by a set of computational studies and found to be in good agreement with the experimental data obtained from the various spectrophotometric techniques. The antimicrobial activity and molecular docking of the synthesized compound was investigated.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    Science.gov (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  3. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    Science.gov (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

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

    NARCIS (Netherlands)

    Pauli, G.F.; Niemitz, M.; Bisson, J.; Lodewyk, M.W.; Soldi, C.; Shaw, J.T.; Tantillo, D.J.; Saya, J.M.; Vos, K.; Klein Nijenhuis, R.A.; Hiemstra, H.; Chen, S-N.; McAlpine, J.B.; Lankin, D.C.; Friesen, J.B.

    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 com

  5. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra.

    Science.gov (United States)

    Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M; Cinar, Mehmet

    2013-11-01

    The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.

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

    Science.gov (United States)

    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.

  7. Investigations of Nuclear Structure

    Energy Technology Data Exchange (ETDEWEB)

    Sarantites, Demetrios [Washington Univ., St. Louis, MO (United States); Reviol, W. [Washington Univ., St. Louis, MO (United States)

    2015-07-15

    The proposal addresses studies of nuclear structure at low-energies and development of instrumentation for that purpose. The structure studies deal with features of neutron-rich nuclei with unexplored shapes (football- or pear-shaped nuclei). The regions of interest are: neutron rich nuclei like 132-138Sn, or 48-54Ca, and the Zr, Mo, and Ru isotopes. The tools used can be grouped as follows: either Gammasphere or Gretina multi-gamma detector arrays and auxiliary detectors (Microball, Neutron Shell, and the newly completed Phoswich Wall).The neutron-rich nuclei are accessed by radioactive-beam binary reactions or by 252Cf spontaneous fission. The experiments with heavy radioactive beams aim at exciting the beam nuclei by pick-up or transfer a neutron or a proton from a light target like 13C, 9Be, 11B or 14N .For these binary-reaction studies the Phoswich Wall detector system is essential. It is based on four multi-anode photomultiplier tubes on which CsI and thin fast-timing plastic scintillators are attached. Their signals are digitized with a high density microchip system.

  8. Structural, vibrational, NMR, quantum chemical, DNA binding and protein docking studies of two flexible imine oximes

    Indian Academy of Sciences (India)

    YUNUS KAYA

    2016-09-01

    Two flexible imine oxime molecules, namely, 3-(pyridin-2-ylmethylimino)-butan-2-one oxime (HL¹) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL²) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated 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, three stable molecules and the most stable conformer were determined for the both imine oximes. The spectroscopic properties such as vibrational and NMR were calculated for the most stable conformer of the HL¹ and HL². The calculation results were applied to simulate infrared spectra of the title compounds, which show good agreement with observed spectra. In addition, the stable three molecules of the both imine oximes have been used to carry out DNA binding and protein docking studies with DNA and protein structures (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligands inside the DNA and protein cavity.

  9. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    Science.gov (United States)

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  10. STRUCTURAL STUDIES OF BIOMATERIALS USING DOUBLE-QUANTUM SOLID-STATE NMR SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

    Drobny, Gary P.; Long, J. R.; Karlsson, T.; Shaw, Wendy J.; Popham, Jennifer M.; Oyler, N.; Bower, Paula M.; Stringer, J.; Gregory, D.; Mehta, M.; Stayton, Patrick S.

    2004-10-31

    Proteins directly control the nucleation and growth of biominerals, but the details of molecular recognition at the protein-biomineral interface remain poorly understood. The elucidation of recognition mechanisms at this interface may provide design principles for advanced materials development in medical and ceramic composites technologies. Here, we describe both the theory and practice of double-quantum solid-stateNMR(ssNMR) structure-determination techniques, as they are used to determine the secondary structures of surface-adsorbed peptides and proteins. In particular, we have used ssNMR dipolar techniques to provide the first high-resolution structural and dynamic characterization of a hydrated biomineralization protein, salivary statherin, adsorbed to its biologically relevant hydroxyapatite (HAP) surface. Here, we also review NMR data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules using double-quantum ssNMR spectroscopy.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

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

  12. Investigating the Dissolution Performance of Amorphous Solid Dispersions Using Magnetic Resonance Imaging and Proton NMR.

    Science.gov (United States)

    Tres, Francesco; Coombes, Steven R; Phillips, Andrew R; Hughes, Leslie P; Wren, Stephen A C; Aylott, Jonathan W; Burley, Jonathan C

    2015-09-10

    We have investigated the dissolution performance of amorphous solid dispersions of poorly water-soluble bicalutamide in a Kollidon VA64 polymeric matrix as a function of the drug loading (5% vs. 30% bicalutamide). A combined suite of state-of-the-art analytical techniques were employed to obtain a clear picture of the drug release, including an integrated magnetic resonance imaging UV-Vis flow cell system and 1H-NMR. Off-line 1H-NMR was used for the first time to simultaneously measure the dissolution profiles and rates of both the drug and the polymer from a solid dispersion. MRI and 1H-NMR data showed that the 5% drug loading compact erodes linearly, and that bicalutamide and Kollidon VA64 are released at approximately the same rate from the molecular dispersion. For the 30% extrudate, data indicated a slower water ingress into the compact which corresponds to a slower dissolution rate of both bicalutamide and Kollidon VA64.

  13. Investigating the Dissolution Performance of Amorphous Solid Dispersions Using Magnetic Resonance Imaging and Proton NMR

    Directory of Open Access Journals (Sweden)

    Francesco Tres

    2015-09-01

    Full Text Available We have investigated the dissolution performance of amorphous solid dispersions of poorly water-soluble bicalutamide in a Kollidon VA64 polymeric matrix as a function of the drug loading (5% vs. 30% bicalutamide. A combined suite of state-of-the-art analytical techniques were employed to obtain a clear picture of the drug release, including an integrated magnetic resonance imaging UV-Vis flow cell system and 1H-NMR. Off-line 1H-NMR was used for the first time to simultaneously measure the dissolution profiles and rates of both the drug and the polymer from a solid dispersion. MRI and 1H-NMR data showed that the 5% drug loading compact erodes linearly, and that bicalutamide and Kollidon VA64 are released at approximately the same rate from the molecular dispersion. For the 30% extrudate, data indicated a slower water ingress into the compact which corresponds to a slower dissolution rate of both bicalutamide and Kollidon VA64.

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

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh

    2015-01-01

    Millions of people around the world take antimicrobial drugs every day to fight off bacterial infections. However, the microbes are starting to fight back and to develop resistance towards conventional antibiotics, posing a major challenge in the future. Therefore, there is a need for exploring...... the opportunities for alternative drugs that cannot be overcome by the bacteria. In this context, cytolytic peptides are being investigated and designed to target cell membranes of microbes specifically. In the search for information about the structure and dynamics of membrane-active peptides, three highly...... to characterize different properties of these peptides. Owing to the membrane-active nature of all three, the peptides were studied in model membranes including isotropic bicelles, magnetically aligned bilayers and mechanically aligned bilayers, employing a diverse set of NMR experiments on unlabeled and 15N...

  15. Two-dimensional NMR and structure determination of salmon calcitonin in methanol

    Energy Technology Data Exchange (ETDEWEB)

    Meadows, R.P.; Nikonowicz, E.P.; Jones, C.R.; Gorenstein, D.G. (Purdue Univ., Lafayette, IN (USA)); Bastian, J.W.

    1991-02-05

    The structure of the 32-residue peptide salmon calcitonin (sCT) in 90% MeOH-10% H{sub 2}O has been investigated by two-dimensional NMR techniques and molecular modeling. Sequential assignments for nearly all of the 32 spin systems have been obtained, and results indicate that the heptaresidue loop formed by the disulfide bond between Cys-1 and Cys-7 is followed by an {alpha}-helical segment from Val-8 through Tyr-22. A region of conformational heterogeneity is observed for residues 20-25, resulting from the slow isomerism of the cis and trans forms of Pro-23. The C-terminal segment is found to exist in an extended conformation.

  16. Solid-state NMR spectroscopic investigation at thermal waste products from embedded flame retardants and polymers; Festkoerper-NMR-Untersuchungen an thermischen Abbauprodukten von flammgeschuetzten Polymeren

    Energy Technology Data Exchange (ETDEWEB)

    Fichera, M.A.

    2008-07-01

    The author of the contribution under consideration describes the structural characterisation of embedded flame retardants and polymers. Analysis includes determination of the phase contents as well as description of their mutual interactions as a function of their thermal history in different atmospheres (air and nitrogen). Solid-state NMR spectroscopy enables structural information about the amorphous state of the decomposed products, determination of the thermal and thermo-oxidative conversion in different amorphous and crystalline structures, and predictions about the short-range order of the observed nuclei. In this context measurements of single pulse, rotor-synchronised spin echo (SP) and cross polarisation (CP) experiments, as well as REDOR (rotational echo double resonance) and TRAPDOR- (transfer of population in double resonance) have been conducted. Additionally, {sup 1}B SP and {sup 31}P RSE experiments have been used to study quantitatively the borate and both phosphorus and phosphate contents in the solid residues. Particular emphasis was put on quantifying crystalline and non-crystalline phosphate phases. The first system consists o a combination of the flame retardants red phosphorus and magnesium hydroxide in high impact polystyrene (HIPS). From the results of extensive NMR experiments it was deduced that most of inserted red phosphorus remains in amorphous phosphates phases (ortho, pyro, and chain/ring phosphates) besides some crystalline phosphate phases. Decomposition characteristics such as temperature and the availability of oxygen (N{sub 2} atmosphere/air) show a significant influence on the decomposition process and the formation of phosphate phases (crystalline/amorphous). By comparing the results of the annealing processes to the results of the cone calorimeter measurements an anaerobic decomposition way was confirmed. In a second system, thermal reactions between the two flame retardants bisphenol A bis diphenyl phosphate and zinc borate

  17. Solution Structure Determination of Proteins by Solution NMR: Application to a Envelope Protein, LAP2

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Recent advances in multidimensional NMR to obtain resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long range order, coupled with new methods of structure refinement, have permitted solution structures of proteins to be rapidly and quickly determined.

  18. 1H and 13C HR-MAS NMR investigations on native and enzymatically digested bovine nasal cartilage.

    Science.gov (United States)

    Schiller, J; Naji, L; Huster, D; Kaufmann, J; Arnold, K

    2001-08-01

    Rheumatic diseases are accompanied by a progressive destruction of the cartilage layer of the joints. Despite the frequency of the disease, degradation mechanisms are not yet understood and methods for early diagnosis are not available. Although some information on pathogenesis could be obtained from the analysis of degradation products of cartilage supernatants, the most direct information on degradation processes would come from the native cartilage as such. We have used 1H as well as 13C HR-MAS (high resolution magic angle spinning) NMR spectroscopy to obtain suitable line-widths of NMR resonances of native cartilage. 1D and 2D NMR spectra of native cartilage were compared with those of enzymatically-treated (collagenase and papain) samples. In the 1H NMR spectra of native cartilage, resonances of polysaccharides, lipids and a few amino acids of collagen were detectable, whereas the 13C NMR spectra primarily indicated the presence of chondroitin sulfate. Treatment with papain resulted only in small changes in the 1H NMR spectrum, whereas a clear diminution of all resonances was detectable in the 13C NMR spectra. On the other hand, treatment with collagenase caused the formation of peptides with an amino acid composition typical for collagen (glycine, proline, hydroxyproline and lysine). It is concluded that the HR-MAS NMR spectra of cartilage may be of significance for the investigation of cartilage degradation since they allow the fast evaluation of cartilage composition and only very small amounts of sample are required.

  19. Study of Structural Stability of Cyclophilin A by NMR and Circular Dichroism Spectra

    Institute of Scientific and Technical Information of China (English)

    SHI, Yan-Hong; LIN, Dong-Hai; HUANG, Jian-Ying; SHEN, Xu

    2006-01-01

    The structural stability of cyclophilin A (CypA) was investigated using H/D exchange and temperature coefficients of chemical shifts of amide protons, monitored by 2D heteronuclear NMR spectroscopy. Amide proton exchange rates were measured by H/D exchange experiments for slow-exchange protons and measured by SEA (Solvent Exposed Amides)-HSQC experiments for fast-exchange protons. Temperature coefficients of chemical shifts and hydrogen exchange rates of amide protons show reasonably good correlation with the protein structure. Totally,44 out of 153 non-proline assigned residues still exist in 86 d of hydrogen-deuterium exchange at 4 ℃, suggesting that CypA structure should be highly stable. Residues in secondary structures of α2, β1, β2, β5,β6 and β7 might constitute the hydrophobic core of the protein. The change in free energy of unfolding ( AGuH2O ) of CypA was estimated to be (21.99± 1.53) kJ·mol-1 by circular dichroism (CD). The large free energy change is also an indicator of the high structural stability.

  20. NMR investigation of field-induced magnetic order in barium manganese oxide

    Science.gov (United States)

    Suh, Steve

    the triangular Mn5+ magnetic lattice of Ba3Mn2O8 coupled with interdimer interaction is predicted to result in incommensurate spin structure when the symmetry axis of Ba3Mn2O8 is aligned parallel to the field. Because of single ion anisotropy of the system, Ba3Mn 2O8 has phase diagram that depends on its alignment with respect to the external field[5]. This means that the microscopic spin structure is different depending on whether the material's symmetry axis is aligned parallel or perpendicular to the field. Also, since we are dealing with S = 1, we have potential to investigate spin-gap closure due to singlet and triplet states as well as triplet and quintet states if we are able to access high enough fields (15T to 30T). Measurements at National High Magnetic Field Laboratory (NHMFL), gives us a superficial taste of what it is like to be in the phase created by triplet and quintet gap closure. The temperature range allowed by the Oxford dilution refrigerator system at Brown Lab, UCLA is from 1K down to 30mK. The magnetic field range allowed by the superconducting magnet at Brown Lab, UCLA is from 0T up to 12T. This combination of temperature and field range allows us to investigate the first quantum critical point (Hc1) in detail with various NMR measurements. Normal state frequency shift as a function of temperature near Hc1 reveals behavior consistent with dilute hardcore bose gas. Analysis of the lineshapes of NMR spectra going into spin order BEC phase as a function of field, we directly observe incommensurate nature of spin order and deduce development of order parameter consistent with mean-field theory. Finally, we verify that the language of dilute 3D Bosons also applies to Ba3Mn2O8 through T1 measurements. From critical behavior inferred in T1 measurements, we complete phase boundary diagram at low temperatures and apply general concept of softening in Goldstone mode near Hc1 to describe our T 1 dependence as a function of temperature.

  1. 113Cd-NMR investigation of a cadmium-substituted copper, zinc-containing superoxide dismutase from yeast

    DEFF Research Database (Denmark)

    Kofod, Pauli; Bauer, Rogert; Danielsen, Eva

    1991-01-01

    113Cd nuclear magnetic resonance spectroscopy has been used to investigate the metal binding sites of cadmium-substituted copper,zinc-containing superoxide dismutase from baker's yeast. NMR signals were obtained for 113Cd(II) at the Cu site as well as for 113Cd(II) at the Zn site. The two subunits...... an explanation for the discrepancy in the literature regarding 113Cd-NMR investigations of bovine superoxide dismutase....

  2. Does aluminium bind to histidine? An NMR investigation of amyloid β12 and amyloid β16 fragments.

    Science.gov (United States)

    Narayan, Priya; Krishnarjuna, Bankala; Vishwanathan, Vinaya; Jagadeesh Kumar, Dasappa; Babu, Sudhir; Ramanathan, Krishna Venkatachala; Easwaran, Kalpathy Ramaier Katchap; Nagendra, Holenarasipur Gundurao; Raghothama, Srinivasarao

    2013-07-01

    Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in Aβ (amyloid β) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal Aβ fragments, DAEFRHDSGYEV (Aβ12) and DAEFRHDSGYEVHHQK (Aβ16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with Aβ12 and Aβ16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in Aβ12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets. © 2013 John Wiley & Sons A/S.

  3. Structure-Correlation NMR Spectroscopy for Macromolecules Using Repeated Bidirectional Photoisomerization of Azobenzene.

    Science.gov (United States)

    Nagashima, Toshio; Ueda, Keisuke; Nishimura, Chiaki; Yamazaki, Toshio

    2015-11-17

    Control over macromolecular structure offers bright potentials for manipulation of macromolecular functions. We here present structure-correlation NMR spectroscopy to analyze the correlation between polymorphic macromolecular structures driven by photoisomerization of azobenzene. The structural conversion of azobenzene was induced within the mixing time of a NOESY experiment using a colored light source, and the reverse structural conversion was induced during the relaxation delay using a light source of another color. The correlation spectrum between trans- and cis-azobenzene was then obtained. To maximize the efficiency of the bidirectional photoisomerization of azobenzene-containing macromolecules, we developed a novel light-irradiation NMR sample tube and method for irradiating target molecules in an NMR radio frequency (rf) coil. When this sample tube was used for photoisomerization of an azobenzene derivative at a concentration of 0.2 mM, data collection with reasonable sensitivity applicable to macromolecules was achieved. We performed isomerization of an azobenzene-cross-linked peptide within the mixing time of a NOESY experiment that produced cross-peaks between helix and random-coil forms of the peptide. Thus, these results indicate that macromolecular structure manipulation can be incorporated into an NMR pulse sequence using an azobenzene derivative and irradiation with light of two types of wavelengths, providing a new method for structural analysis of metastable states of macromolecules.

  4. STUDIES ON THE CHEMICAL STRUCTURES OF ACTIVATED CARBON FIBERS BY SOLID STATE NMR

    Institute of Scientific and Technical Information of China (English)

    FURuowen; HuangWenqiang; 等

    1999-01-01

    The solid state C13-NMR spectra of different ACFs from various precursor fibers were recorded in this paper,The effects of activation conditions on chemical structures of ACFs,as well as the changes of chemical structures during carbonization and redox reaction were inverstigated by NMR technique,At same time,the soild state P31-NMR spectra of ACFS are studied.The C13-NMR spectra of ACFs can be divided into six bands that are assigned to methyl and methylene groups,hydroxyl and ether groups.acetal (or methylenedioxy) carbon,graphite-like aromatic carbon structure,phenol,and quinone groups,respectively.Only phosphorous pentoxide exists on ACFs and CFs.Moreover,most of them are stuck over the crystal face but not at the edge of graphite-like micro-crystal.The carbonization and activation conditions affect the C13-NMR spectra of ACFs.The experimental rsults indicate that the redox reaction of ACFs with oxidants greatly consumes C-H group.

  5. Double-resonance NMR probes of structural distortions in alkali-metal{endash}fulleride superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Pennington, C.H.; Hahm, C.; Stenger, V.A.; Gorny, K.; Recchia, C.H.; Martindale, J.A. [Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio 43210 (United States); Buffinger, D.R.; Ziebarth, R.P. [Department of Chemistry, The Ohio State University, 120 West 18th Avenue, Columbus, Ohio 43210 (United States)

    1996-09-01

    The {sup 87}Rb NMR line shape of the Rb{sub 3}C{sub 60} superconductor contains three distinct peaks: one associated with octahedrally coordinated Rb in the fcc lattice of C{sub 60} molecules and two others, labeled {ital T} and {ital T}{sup {prime}}, both associated with tetrahedrally coordinated Rb. This contrasts with the accepted crystal structure, in which all tetrahedral Rb sites are equivalent. We report multinuclear single and double resonance NMR experiments which probe for effects which could lead to the unexpected splitting, and discuss implications for electronic structure. {copyright} {ital 1996 The American Physical Society.}

  6. Production of stable isotope labelled lipase Lip2 from Yarrowia lipolytica for NMR: investigation of several expression systems.

    Science.gov (United States)

    Nars, G; Saurel, O; Bordes, F; Saves, I; Remaud-Siméon, M; André, I; Milon, A; Marty, A

    2014-09-01

    Extracellular lipase Lip2 from Yarrowia lipolytica is a promising biocatalyst with unusual structural features, as indicated by X-ray crystallography. These features comprise a mobile domain called the lid that controls access to the catalytic site. Conformational rearrangements of the lid have been suggested to regulate lipase enzymatic activities. We used nuclear magnetic resonance to investigate the dynamics of Lip2 by exploring four expression systems, Escherichia coli, cell-free, Pichia pastoris and Y. lipolytica to produce uniformly labelled enzyme. The expression of Lip2 was assessed by determining its specific activity and measuring (15)N-(1)H HSQC spectra. Y. lipolytica turned out to be the most efficient expression system. Here, we report the first use of Y. lipolytica as an expression host for the production of uniform stable isotopic labelled protein for further structural and dynamics studies using NMR.

  7. Sequence-specific Assignment of 1H-NMR Resonance and Determination of the Secondary Structure of Jingzhaotoxin-Ⅰ

    Institute of Scientific and Technical Information of China (English)

    Xiong-Zhi ZENG; Qi ZHU; Song-Ping LIANG

    2005-01-01

    Jingzhaotoxin-Ⅰ (JZTX-Ⅰ) purified from the venom of the spider Chilobrachys jingzhao is a novel neurotoxin preferentially inhibiting cardiac sodium channel inactivation by binding to receptor site 3.The structure of this toxin in aqueous solution was investigated using 2-D 1H-NMR techniques. The complete sequence-specific assignments of proton resonance in the 1H-NMR spectra of JZTX-Ⅰ were obtained by analyzing a series of 2-D spectra, including DQF-COSY, TOCSY and NOESY spectra, in H2O and D2O. All the backbone protons except for Gln4 and more than 95% of the side-chain protons were identified by dαN,dαδ, dβN and dNN connectivities in the NOESY spectrum. These studies provide a basis for the further determination of the solution conformation of JZTX-Ⅰ. Furthermore, the secondary structure of JZTX-Ⅰ was identified from NMR data. It consists mainly of a short triple-stranded antiparallel β-sheet with Trp7-Cys9, Phe20-Lys23 and Leu28-Trp31. The characteristics of the secondary structure of JZTX-Ⅰ are similar to those of huwentoxin-Ⅰ (HWTX-Ⅰ) and hainantoxin-Ⅳ (HNTX-Ⅳ), whose structures in solution have previously been reported.

  8. A solid state NMR investigation of char forming processes in polymer degradation

    CERN Document Server

    Dick, C M

    2002-01-01

    A detailed knowledge of the condensed phase chemistry occurring in polymers exposed to elevated temperatures is crucial to understanding the behaviour of polymers exposed to fire. This is particularly true when trying to reduce polymer flammability by means of promoting char-forming reactions. Until recently, however, structural information on highly crosslinked chars and their precursors has been difficult to obtain, and as a consequence many degradation workers have merely labelled degradation residues as 'intractable'. However, the application of solid state NMR techniques developed in our laboratories for the structural characterisation of coals has provided a considerable insight into the structure and chemistry of polymer chars formed under both oxidative and non-oxidative conditions. A series of polymers including poly(vinyl chloride), poly(vinyl acetate), polyurethanes, polychloropene, cis and trans polyisoprene have been studied. These polymers have been used to describe the application of quantitati...

  9. Studies on solution NMR structure of brazzein——Secondary structure and molecular scaffold

    Institute of Scientific and Technical Information of China (English)

    高广华; 戴继勋; 丁鸣; 王金凤; 王大成

    1999-01-01

    Brazzein is a sweet-tasting protein isolated from the fruit of West African plant Pentadiplandra 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 sideehain proton resonances were achieved using through-bond and through-space eonneetivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one α-helix (residues 21—29), one short 310-helix (residues 14—17), two strands of antiparallel β-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 ’eysteine-stabilized alpha-beta’ (CSαβ) motif with scorpion neurotoxins, insect defensins and plant γ-thionins. The significance of this multi-function motif, the possible active sites an

  10. A novel strategy for NMR resonance assignment and protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Lemak, Alexander [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada); Gutmanas, Aleksandras [European Bioinformatics Institute, Protein Data Bank Europe (United Kingdom); Chitayat, Seth; Karra, Murthy [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada); Fares, Christophe [Max-Planck-Institut f. Kohlenforschung (Germany); Sunnerhagen, Maria [Linkoeping University, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology (Sweden); Arrowsmith, Cheryl H., E-mail: carrow@uhnres.utoronto.ca [University of Toronto, Ontario Cancer Institute and Campbell Family Cancer Research Institute, Department of Medical Biophysics (Canada)

    2011-01-15

    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  11. ABACUS, a direct method for protein NMR structure computation via assembly of fragments.

    Science.gov (United States)

    Grishaev, A; Steren, C A; Wu, B; Pineda-Lucena, A; Arrowsmith, C; Llinás, M

    2005-10-01

    The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.

  12. Porous structure of membranes of an acrylonitrile copolymer. Porosity, ^1H-NMR permeability

    Science.gov (United States)

    Viallat, A.; Margulies, M. M.

    2000-06-01

    Nanoporous polymer membranes (porosity φ≈ 0.7) used for dialysis are studied from NMR relaxation times of water confined in the pore space. Fast interpore water diffusion is observed. Two structural parameters are evidenced: i) a reduced NMR relaxation time, tau, which reflects the width of the pore-size distribution; ii) the average polymer-grain size of the solid matrix deduced from NMR experiments performed on membranes partially filled by water. A relation is found between the ratio k/tau^2, where k is the permeability to water and the porosity. This relation is in qualitative agreement with numerical simulations reported in the literature on low-porosity systems and with experimental results obtained for sedimentary rocks and for fused glass model systems. It supports the idea that tau is the relevant structural parameter to describe convective transport in a wide class of porous systems.

  13. Complete {sup 1}H and {sup 13}C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Ana Carolina Ferreira; Silva, Aline Nazare; Matos, Priscilla Mendonca; Silva, Eder Henrique da; Heleno, Vladimir Constantino Gomes [Universidade de Franca, Franca, SP (Brazil). Nucleo de Pesquisas em Ciencias Exatas e Tecnologicas; Lopes, Norberto Peporine; Lopes, Joao Luis Callegari [Universidade de Sao Paulo (FCFRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Ciencias Farmaceuticas de Ribeirao Preto. Dept. de Quimica e Fisica; Sass, Daiane Cristina, E-mail: vheleno_05@yahoo.com.br [Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Filosofia, Ciencias e Letras de Ribeirao Preto. Dept. de Quimica

    2012-07-01

    Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. {sup 1}H NMR, {sup 13}C NMR {l_brace}{sup 1}H{r_brace}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables (author)

  14. Interaction between new synthesized derivative of (E,E)-azomethines and BN(6,6-7) nanotube for medical applications: Geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations

    Science.gov (United States)

    Sheikhi, Masoome; Shahab, Siyamak; Filippovich, Liudmila; Khaleghian, Mehrnoosh; Dikusar, Evgenij; Mashayekhi, Mahsa

    2017-10-01

    In this present work, first time interaction between new synthesized derivative of the 4-((E)-((4-((E)-phenyldiazenyl)phenyl)imino)methyl)benzoic acid (E-PABA) and the BN(6,6-7) Nanotube for medical applications were studied. The geometries of the compounds E-PABA, the BN(6,6-7) Nanotube and the Complex BN(6,6-7)/E-PABA were optimized by Density Functional Theory (DFT) in the gas phase. The adsorption effect of the compound E-PABA on the electronic properties, chemical shift tensors and natural charge of the BN(6,6-7) Nanotube was investigated and discussed. The electronic spectra of the E-PABA and the Complex BN(6,6-7)/E-PABA in the gas phase carried out by Time Dependent Density Functional Theory (TD-DFT) for the foundation adsorption effect on maximum wavelength of the E-PABA.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  17. Thermal and structural analysis of a cryogenic conduction cooling system for a HTS NMR magnet

    Energy Technology Data Exchange (ETDEWEB)

    In, Se Hwan; Hong, Yong Jun; Yeom, Han Kil; Ko, Hyo Bong; Park, Seong Je [Korea Institute of Machinery and Materials, Daejeon (Korea, Republic of)

    2016-03-15

    The superconducting NMR magnets have used cryogen such as liquid helium for their cooling. The conduction cooling method using cryocoolers, however, makes the cryogenic cooling system for NMR magnets more compact and user-friendly than the cryogen cooling method. This paper describes the thermal and structural analysis of a cryogenic conduction cooling system for a 400 MHz HTS NMR magnet, focusing on the magnet assembly. The highly thermo-conductive cooling plates between HTS double pancake coils are used to transfer the heat generated in coils, namely Joule heating at lap splice joints, to thermal link blocks and finally the cryocooler. The conduction cooling structure of the HTS magnet assembly preliminarily designed is verified by thermal and structural analysis. The orthotropic thermal properties of the HTS coil, thermal contact resistance and radiation heat load are considered in the thermal analysis. The thermal analysis confirms the uniform temperature distribution for the present thermal design of the NMR magnet within 0.2 K. The mechanical stress and the displacement by the electromagnetic force and the thermal contraction are checked to verify structural stability. The structural analysis indicates that the mechanical stress on each component of the magnet is less than its material yield strength and the displacement is acceptable in comparison with the magnet dimension.

  18. Investigating lanthanide dopant distributions in Yttrium Aluminum Garnet (YAG) using solid state paramagnetic NMR.

    Science.gov (United States)

    McCarty, Ryan J; Stebbins, Jonathan F

    2016-10-01

    This paper demonstrates the approach of using paramagnetic effects observed in NMR spectra to investigate the distribution of lanthanide dopant cations in YAG (yttrium aluminum garnet, Y3Al5O12) optical materials, as a complimentary technique to optical spectroscopy and other standard methods of characterization. We investigate the effects of Ce(3+), Nd(3+), Yb(3+), Tm(3+), and Tm(3+)-Cr(3+) on (27)Al and (89)Y NMR spectra. We note shifted resonances for both AlO4 and AlO6 sites. In some cases, multiple shifted peaks are observable, and some of these can be empirically assigned to dopant cations in known configurations to the observed nuclides. In many cases, AlO6 peaks shifted by more than one magnetic neighbor can be detected. In general, we observe that the measured intensities of shifted resonances, when spinning sidebands are included, are consistent with predictions from models with dopant cations that are randomly distributed throughout the lattice. In at least one set of (27)Al spectra, we identify two sub-peaks possibly resulting from two paramagnetic cations with magnetically coupled spin states neighboring the observed nucleus. We identify systematic changes in the spectra related to known parameters describing the magnetic effects of lanthanide cations, such as larger shift distances when the expectation value of electron spins is greater. We lastly comment on the promise of this technique in future analyses of laser and other crystalline oxide materials. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    Science.gov (United States)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  20. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-11-15

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

  1. Investigation of the role of stereoelectronic effects in the conformation of piperidones by NMR spectroscopy and X-ray diffraction

    Directory of Open Access Journals (Sweden)

    Cesar Garcias-Morales

    2015-10-01

    Full Text Available This paper reports the synthesis of a series of piperidones 1–8 by the Mannich reaction and analysis of their structures and conformations in solution by NMR and mass spectrometry. The six-membered rings in 2,4,6,8-tetraphenyl-3,7-diazabicyclo[3.3.1]nonan-9-ones, compounds 1 and 2, adopt a chair–boat conformation, while those in 2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-ones, compounds 3–8, adopt a chair–chair conformation because of stereoelectronic effects. These stereoelectronic effects were analyzed by the 1JC–H coupling constants, which were measured in the 13C satellites of the 1H NMR spectra obtained with the hetero-dqf pulse sequence. In the solid state, these stereoelectronic effects were investigated by measurement of X-ray diffraction data, the molecular geometry (torsional bond angles and bond distances, and inter- and intramolecular interactions, and by natural bond orbital analysis, which was performed using density functional theory at the ωB97XD/6311++G(d,p level. We found that one of the main factors influencing the conformational stability of 3–8 is the interaction between the lone-pair electrons of nitrogen and the antibonding sigma orbital of C(7–Heq (nN→σ*C–H(7eq, a type of hyperconjugative interaction.

  2. Quantification of protein secondary structure by (13)C solid-state NMR.

    Science.gov (United States)

    Andrade, Fabiana Diuk; Forato, Lucimara Aparecida; Bernardes Filho, Rubens; Colnago, Luiz Alberto

    2016-05-01

    High-resolution (13)C solid-state NMR stands out as one of the most promising techniques to solve the structure of insoluble proteins featuring biological and technological importance. The simplest nuclear magnetic resonance (NMR) spectroscopy method to quantify the secondary structure of proteins uses the areas of carbonyl and alpha carbon peaks. The quantification obtained by fitting procedures depends on the assignment of the peaks to the structure, type of line shape, number of peaks to be used, and other parameters that are set by the operator. In this paper, we demonstrate that the analysis of (13)C NMR spectra by a pattern recognition method-based on the singular value decomposition (SVD) regression, which does not depend on the operator-shows higher correlation coefficients for α-helix and β-sheet (0.96 and 0.91, respectively) than Fourier transform infrared spectroscopy (FTIR) method. Therefore, the use of (13)C solid-state NMR spectra and SVD is a simple and reliable method for quantifying the secondary structures of insoluble proteins in solid-state.

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

    NARCIS (Netherlands)

    Rosato, A.; Aramini, J.M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J.; Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Guntert, P.; He, Y.; Herrmann, T.; Huang, Y.J.; Jaravine, V.; Jonker, H.R.; Kennedy, M.A.; Lange, O.F.; Liu, G.; Malliavin, T.E.; Mani, R.; Mao, B.; Montelione, G.T.; Nilges, M.; Rossi, P.; Schot, G. van der; Schwalbe, H.; Szyperski, T.A.; Vendruscolo, M.; Vernon, R.; Vranken, W.F.; Vries, S.D. de; Vuister, G.W.; Wu, B.; Yang, Y.; Bonvin, A.M.

    2012-01-01

    The protocols currently used for protein structure determination by nuclear magnetic resonance (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 us

  4. Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

    Science.gov (United States)

    Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

    2015-10-06

    Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure.

  5. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  6. Magnetic and NMR investigation of RRh3B2 (R=La to Gd) compounds

    Science.gov (United States)

    Malik, S. K.; Dhar, S. K.; Vijayaraghavan, R.; Wallace, W. E.

    1982-11-01

    Magnetization (4.2 to 300 K) and 11B paramagnetic NMR (77 to 300 K) studies have been carried out on ternary borides RRh3B2 (R=La to Gd). These compounds crystallize in the CeCo3B2-type structure. From cell volume considerations Ce is in a mixed valent/quadrivalent state while the rest of the rare earth ions are in a trivalent state. With the exception of La and Pr compounds, all other compounds are found to order magnetically. From the high values of the ratio of paramagnetic moment to ordered state moment, the magnetic ordering is inferred to be the itinerant type in CeRh3B2 and EuRh3B2. In Nd and Gd compounds, magnetization data reveal that magnetic ordering is associated with the rare earth sublattice. A complex behavior of magnetization is observed in SmRh3B2. A first order quadrupole split 11B NMR spectrum is observed in Ce, Pr, Nd, and Sm compounds. The boron Knight shift in all these compounds is small and, within the limits of experimental error, scales linearly with susceptibility in Pr and Nd compounds. A temperature independent Knight shift is observed in SmRh3B2, indicating the influence of strong crystal fields.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Pei; Juang, Chilong; Harbison, G.S. (State Univ. of New York, Stony Brook (USA))

    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.

  8. NMR-based structural validation of therapeutic antibody produced in Nicotiana benthamiana.

    Science.gov (United States)

    Yagi, Hirokazu; Fukuzawa, Noriho; Tasaka, Yasushi; Matsuo, Kouki; Zhang, Ying; Yamaguchi, Takumi; Kondo, Sachiko; Nakazawa, Shiori; Hashii, Noritaka; Kawasaki, Nana; Matsumura, Takeshi; Kato, Koichi

    2015-06-01

    We successfully developed a method for metabolic isotope labeling of recombinant proteins produced in transgenic tobacco. This enabled assessment of structural integrity of plant-derived therapeutic antibodies by NMR analysis. A variety of expression vehicles have been developed for the production of promising biologics, including plants, fungi, bacteria, insects, and mammals. Glycoprotein biologics often experience altered folding and post-translational modifications that are typified by variant glycosylation patterns. These differences can dramatically affect their efficacy, as exemplified by therapeutic antibodies. However, it is generally difficult to validate the structural integrity of biologics produced using different expression vehicles. To address this issue, we have developed and applied a stable-isotope-assisted nuclear magnetic resonance (NMR) spectroscopy method for the conformational characterization of recombinant antibodies produced in plants. Nicotiana benthamiana used as a vehicle for the production of recombinant immunoglobulin G (IgG) was grown in a (15)N-enriched plant growth medium. The Fc fragment derived from the (15)N-labeled antibody thus prepared was subjected to heteronuclear two-dimensional (2D) NMR measurements. This approach enabled assessment of the structural integrity of the plant-derived therapeutic antibodies by comparing their NMR spectral properties with those of an authentic IgG-Fc derived from mammalian cells.

  9. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    Science.gov (United States)

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. Copyright 1998 Academic Press.

  10. Investigation of multiaxial molecular dynamics by 2H MAS NMR spectroscopy.

    Science.gov (United States)

    Kristensen, J H; Hoatson, G L; Vold, R L

    1998-11-01

    The technique of 2H MAS NMR spectroscopy is presented for the investigation of multiaxial molecular dynamics. To evaluate the effects of discrete random reorientation a Lie algebraic formalism based on the stochastic Liouville-von Neumann equation is developed. The solution to the stochastic Liouville-von Neumann equation is obtained both in the presence and absence of rf irradiation. This allows effects of molecular dynamics to be evaluated during rf pulses and extends the applicability of the formalism to arbitrary multiple pulse experiments. Theoretical methods are presented for the description of multiaxial dynamics with particular emphasis on the application of vector parameters to represent molecular rotations. Numerical time and powder integration algorithms are presented that are both efficient and easy to implement computationally. The applicability of 2H MAS NMR spectroscopy for investigating molecular dynamics is evaluated from theoretical spectra. To demonstrate the potential of the technique the dynamics of thiourea-2H4 is investigated experimentally. From a series of variable temperature MAS and quadrupole echo spectra it has been found that the dynamics can be described by composite rotation about the CS and CN bonds. Both experiments are sensitive to the fast CS rotation which is shown to be described by the Arrhenius parameters E(CS) = 46.4 +/- 2.3 kJ mol(-1) and ln(A(CS))= 32.6 +/- 0.9. The MAS experiment represents a significant improvement by simultaneously allowing the dynamics of the slow CN rotation to be fully characterized in terms of E(CN) = 56.3 +/- 3.4 kJ mol(-1) and ln(A(CN)) = 25.3 +/- 1.1.

  11. Theoretical investigation of nano zirconium carbide sheet: A study of NMR, NBO, EPR and Polar

    Directory of Open Access Journals (Sweden)

    Roya Rouhani

    2015-09-01

    Full Text Available In this work, we have focused on the zirconium carbide (ZrC sheet. The result exhibited that ZrC exhibits various outstanding physical and chemical properties, such as high hardness (25 Gpa, high melting point (3420°C, high corrosion and wear resistance, solid-state phase stability as well as chemical stability. Hence, ZrC has been considered a good potential material for ultra-high temperature applications. Applications range from cutting tools, grinding wheels and abrasives for mechanical as well as structural components in chemical and electronic industries. Abinitio calculation was carried out for Zirconium carbide sheet (ZrC using Gaussian 09 program for the first time (Fig 1. We choose B3LYP for calculating natural bond orbital (NBO, Nuclear magnetic resonance (NMR, Electron paramagnetic resonance (EPR and polar.

  12. Contribution to Structural Elucidation: Behaviours of Substructures Partially Defined from 2D NMR

    Institute of Scientific and Technical Information of China (English)

    EPOUHE, Celine; FAN, Bo-Tao; YUAN, Shen-Gang; PANAYE, A.; DOUCET, J. P

    2003-01-01

    Structural elucidation (automatic determination of the structure of a molecule from its spectra) is frequently hampered by combinatorial explosion when trying to assemble the identified substructures. We devised a new method which can avoid this pitfall by a systematic examination of allowed 13C chemical shifts ranges for all substructures chemically possible and combined with a progressive pruning thanks to neighbouring relationships appearing from 2D NMR. This method is explained by a detailed example.

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

    Science.gov (United States)

    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.

  14. Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

    Science.gov (United States)

    Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

    2015-02-01

    We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924.

  15. NMR structure of the integral membrane protein OmpX.

    Science.gov (United States)

    Fernández, César; Hilty, Christian; Wider, Gerhard; Güntert, Peter; Wüthrich, Kurt

    2004-03-05

    The structure of the integral membrane protein OmpX from Escherichia coli reconstituted in 60 kDa DHPC micelles (OmpX/DHPC) was calculated from 526 NOE upper limit distance constraints. The structure determination was based on complete sequence-specific assignments for the amide protons and the Val, Leu, and Ile(delta1) methyl groups in OmpX, which were selectively protonated on a perdeuterated background. The solution structure of OmpX in the DHPC micelles consists of a well-defined, eight-stranded antiparallel beta-barrel, with successive pairs of beta-strands connected by mobile loops. Several long-range NOEs observed outside of the transmembrane barrel characterize an extension of a four-stranded beta-sheet beyond the height of the barrel. This protruding beta-sheet is believed to be involved in intermolecular interactions responsible for the biological functions of OmpX. The present approach for de novo structure determination should be quite widely applicable to membrane proteins reconstituted in mixed micelles with overall molecular masses up to about 100 kDa, and may also provide a platform for additional functional studies.

  16. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde

    Science.gov (United States)

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data.

  17. Investigation of the conformation of aspartic acid by the NMR method

    Energy Technology Data Exchange (ETDEWEB)

    Tananaeva, N.N.; Gorokhovatskaya, M.Ya.; Tikhonova, R.V.; Kostromina, N.A.

    1986-01-01

    The conformations of aspartic acid were investigated in relation to the pH value by /sup 1/H and /sup 13/C NMR methods. It was shown that the form of the spectra becomes simpler in the transition from the alkaline to the acidic region and changes from an ABX to an A/sub 2/X system. The order of protonation of the donating groups was established. The spin-spin coupling constants at various pH values were calculated, and the conformational transitions were examined on the basis of their variation. The possibility of the closure of a six-membered ring in the molecule in the alkaline region and the opening of this ring in the acidic region was demonstrated.

  18. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde.

    Science.gov (United States)

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-05

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, (1)H and (13)C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data.

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

    KAUST Repository

    Li, Jianping

    2013-06-05

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

  20. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  1. Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy.

    Science.gov (United States)

    Nothias-Scaglia, Louis-Félix; Gallard, Jean-François; Dumontet, Vincent; Roussi, Fanny; Costa, Jean; Iorga, Bogdan I; Paolini, Julien; Litaudon, Marc

    2015-10-23

    Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available.

  2. Molecular-level secondary structure, polymorphism, and dynamics of full-length -synuclein fibrils studied by solid-state NMR

    Science.gov (United States)

    Heise, Henrike; Hoyer, Wolfgang; Becker, Stefan; Andronesi, Ovidiu C.; Riedel, Dietmar; Baldus, Marc

    2005-11-01

    The 140-residue protein -synuclein (AS) is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson's disease. We have investigated the structure and dynamics of full-length AS fibrils by high-resolution solid-state NMR spectroscopy. Homonuclear and heteronuclear 2D and 3D spectra of fibrils grown from uniformly 13C/15N-labeled AS and AS reverse-labeled for two of the most abundant amino acids, K and V, were analyzed. 13C and 15N signals exhibited linewidths of HR ALIGN=LEFT WIDTH=50% NOSHADE SIZE=1>

  3. High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles

    Energy Technology Data Exchange (ETDEWEB)

    Usachev, K. S., E-mail: k.usachev@kpfu.ru; Efimov, S. V.; Kolosova, O. A.; Filippov, A. V.; Klochkov, V. V. [Kazan Federal University (Russian Federation)

    2015-04-15

    PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.

  4. NMR as a tool in the investigation of fundamental problems in ordered liquids

    NARCIS (Netherlands)

    Burnell, E.E.; Lange, de C.A.

    2005-01-01

    An overview is presented of modern NMR techniques and a variety of experimental and theoretical tools employed in the study of solutes dissolved in liquid crystals. The NMR techniques involve multiple quantum and spectral subtraction methods, In addition, various experimental and theoretical tools a

  5. Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

    Directory of Open Access Journals (Sweden)

    Lorenzo Sborgi

    Full Text Available GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding. These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein

  6. NMR relaxation times of trabecular bone-reproducibility, relationships to tissue structure and effects of sample freezing

    Energy Technology Data Exchange (ETDEWEB)

    Prantner, Viktoria; Isaksson, Hanna; Nissi, Mikko J; Jurvelin, Jukka S [Department of Physics and Mathematics, University of Eastern Finland, PO Box 1627, 70211 Kuopio (Finland); Naervaeinen, Johanna; Groehn, Olli H J [Department of Neurobiology, A I Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio (Finland); Lammentausta, Eveliina [Department of Diagnostic Radiology, Oulu University Hospital, PO Box 50, 90029 OYS, Oulu (Finland); Avela, Janne, E-mail: hanna.isaksson@uef.f [Department of Biology of Physical Activity, University of Jyvaeskylae, PO Box 35, 40014 Jyvaeskylae (Finland)

    2010-12-07

    Nuclear magnetic resonance (NMR) spectroscopy provides a potential tool for non-invasive evaluation of the trabecular bone structure. The objective of this study was to determine the reproducibility of the NMR relaxation parameters (T{sub 2}, Carr-Purcel-T{sub 2}, T{sub 1}{rho}) for fat and water and relate those to the structural parameters obtained by micro-computed tomography ({mu}CT). Especially, we aimed to evaluate the effect of freezing on the relaxation parameters. For storing bone samples, freezing is the standard procedure during which the biochemical and cellular organization of the bone marrow may be affected. Bovine trabecular bone samples were stored at -20 {sup 0}C for 7 days and measured by NMR spectroscopy before and after freezing. The reproducibility of NMR relaxation parameters, as expressed by the coefficient of variation, ranged from 3.1% to 27.9%. In fresh samples, some correlations between NMR and structural parameters (Tb.N, Tb.Sp) were significant (e.g. the relaxation rate for T{sub 2} of fat versus Tb.Sp: r = -0.716, p < 0.01). Freezing did not significantly change the NMR relaxation times but the correlations between relaxation parameters and the {mu}CT structural parameters were not statistically significant after freezing, suggesting some nonsystematic alterations of the marrow structure. Therefore, the use of frozen bone samples for NMR relaxation studies may provide inferior information about the trabecular bone structure.

  7. Bacterial expression and isotope labeling of AIMP1/p43 codosome protein for structural studies by multidimensional NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Vorobyova N. V.

    2015-04-01

    Full Text Available AIMP1/p43 protein is a structural component of multisynthetase complex (codosome in eukaryotes, which reveals both tRNA binding and cytokine activities. Aim. Bacterial expression and purification of isotopically-labeled recombinant AIMP1/p43 protein in E. coli cells for studying its solution structure by multidimensional NMR spectroscopy. Methods. AIMP1/p43 protein was expressed in E. coli BL21(DE3pLysE cells on M9 minimal medium with 15N isotope labeling and purified by metal-chelated chromatography. Heteronuclear 2D 1H-15N NMR experiments were performed in solution at 293 K on Agilent DDR2 800 NMR spectrometer. Results. The AIMP1/p43 protein was obtained in uniformly 15N-labeled form as an NMR sample. A high dispersion of resonance signals in the 2D 1H-15N HSQC NMR spectra confirmed the presence of its compact 3D protein structure. The NMR spectrum of AIMP1/p43 demonstrated a high signal-to-noise ratio and sufficient stability to acquire other multidimensional NMR data sets for determination of the structure of AIMP1/p43 protein in solution. Conclusions. The 15N-labeled AIMP1/p43 protein was stable for 4–7 days, which makes possible acquiring the critical NMR experimental data for detailed structural analysis in solution. Our data on the initial NMR spectra indicated the presence of some additional signals in comparison with the NMR spectrum of EMAP II which could be assigned to amino acids of the N-terminal α-helical fragment of AIMP1/p43.

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

    Science.gov (United States)

    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

  9. NMR structure analysis of uniformly 13C-labeled carbohydrates.

    Science.gov (United States)

    Fontana, Carolina; Kovacs, Helena; Widmalm, Göran

    2014-06-01

    In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.

  10. Well-defined azazirconacyclopropane complexes supported on silica structurally determined by 2D NMR comparative elucidation

    KAUST Repository

    El Eter, Mohamad

    2013-01-01

    Grafting of Zr(NMe2)4 on mesoporous silica SBA-15 afforded selectively well-defined surface species SiOZr(NMe2) (η2NMeCH2). 2D solid-state NMR (1H- 13C HETCOR, Multiple Quantum) experiments have shown a unique structural rearrangement occurring on the immobilised zirconium bis methylamido ligand. © The Royal Society of Chemistry 2013.

  11. Analysis of Structural Variability in Pharmaceutical Excipients Using Solid-State NMR Spectroscopy

    OpenAIRE

    Sperger, Diana M.; Munson, Eric Jon

    2011-01-01

    Polysaccharide-based excipients comprise the majority of most solid dosage forms and can vary dramatically in terms of structural and functionally related properties. Analytical methods for characterizing these important formulation components are crucial. Solid-state NMR spectroscopy (SSNMR) can provide a wealth of information on these materials while offering the advantages of non-destructive sample preparation and selectivity. The overall objective of this work is to identify SSNMR paramet...

  12. Coordination Structure of Aluminum in Magnesium Aluminum Hydroxide Studied by 27Al NMR

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The coordination structure of aluminum in magnesium aluminum hydroxide was studiedby 27Al NMR. The result showed that tetrahedral aluminum (AlⅣ) existed in magnesiumaluminum hydroxide, and the contents of AlⅣ increased with the increase of the ratio of Al/Mg andwith the peptizing temperature. AlⅣ originated from the so-called Al13 polymer with the structureof one Al tetrahedron surrounded by twelve Al octahedrons.

  13. On the structure of the Nx phase of symmetric dimers: inferences from NMR.

    Science.gov (United States)

    Hoffmann, Anke; Vanakaras, Alexandros G; Kohlmeier, Alexandra; Mehl, Georg H; Photinos, Demetri J

    2015-02-07

    NMR measurements on a selectively deuterated liquid crystal dimer CB-C9-CB, exhibiting two nematic phases, show that the molecules in the lower temperature nematic phase, N(X), experience a chiral environment and are ordered about a uniformly oriented director throughout the macroscopic sample. The results are contrasted with previous interpretations that suggested a twist-bend spatial variation of the director. A structural picture is proposed wherein the molecules are packed into highly correlated chiral assemblies.

  14. Structure and Dynamics in Amphiphilic Bilayers: NMR and MD simulation Studies

    OpenAIRE

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations were employed to study molecular structure and dynamics in amphiphilic bilayers. This thesis reports on method development and practical applications to two types of bilayer systems: simple cell membrane models composed of phosphatidylcholine lipids and cholesterol; and liquid crystals composed of ethyleneoxide-based surfactants often used in technological applications and in fundamental studies ...

  15. Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA

    Energy Technology Data Exchange (ETDEWEB)

    Mareuil, Fabien [Institut Pasteur, Cellule d' Informatique pour la Biologie (France); Malliavin, Thérèse E.; Nilges, Michael; Bardiaux, Benjamin, E-mail: bardiaux@pasteur.fr [Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 (France)

    2015-08-15

    In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD–NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD–NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.

  16. NMR determines transient structure and dynamics in the disordered C-terminal domain of WASp interacting protein.

    Science.gov (United States)

    Haba, Noam Y; Gross, Renana; Novacek, Jiri; Shaked, Hadassa; Zidek, Lukas; Barda-Saad, Mira; Chill, Jordan H

    2013-07-16

    WASp-interacting protein (WIP) is a 503-residue proline-rich polypeptide expressed in human T cells. The WIP C-terminal domain binds to Wiskott-Aldrich syndrome protein (WASp) and regulates its activation and degradation, and the WIP-WASp interaction has been shown to be critical for actin polymerization and implicated in the onset of WAS and X-linked thrombocytopenia. WIP is predicted to be an intrinsically disordered protein, a class of polypeptides that are of great interest because they violate the traditional structure-function paradigm. In this first (to our knowledge) study of WIP in its unbound state, we used NMR to investigate the biophysical behavior of WIP(C), a C-terminal domain fragment of WIP that includes residues 407-503 and contains the WASp-binding site. In light of the poor spectral dispersion exhibited by WIP(C) and the high occurrence (25%) of proline residues, we employed 5D-NMR(13)C-detected NMR experiments with nonuniform sampling to accomplish full resonance assignment. Secondary chemical-shift analysis, (15)N relaxation rates, and protection from solvent exchange all concurred in detecting transient structure located in motifs that span the WASp-binding site. Residues 446-456 exhibited a propensity for helical conformation, and an extended conformation followed by a short, capped helix was observed for residues 468-478. The (13)C-detected approach allows chemical-shift assignment in the WIP(C) polyproline stretches and thus sheds light on their conformation and dynamics. The effects of temperature on chemical shifts referenced to a denatured sample of the polypeptide demonstrate that heating reduces the structural character of WIP(C). Thus, we conclude that the disordered WIP(C) fragment is comprised of regions with latent structure connected by flexible loops, an architecture with implications for binding affinity and function.

  17. A new method of evaluating tight gas sands pore structure from nuclear magnetic resonance (NMR) logs

    Science.gov (United States)

    Xiao, Liang; Mao, Zhi-qiang; Xie, Xiu-hong

    2016-04-01

    Tight gas sands always display such characteristics of ultra-low porosity, permeability, high irreducible water, low resistivity contrast, complicated pore structure and strong heterogeneity, these make that the conventional methods are invalid. Many effective gas bearing formations are considered as dry zones or water saturated layers, and cannot be identified and exploited. To improve tight gas sands evaluation, the best method is quantitative characterizing rock pore structure. The mercury injection capillary pressure (MICP) curves are advantageous in predicting formation pore structure. However, the MICP experimental measurements are limited due to the environment and economy factors, this leads formation pore structure cannot be consecutively evaluated. Nuclear magnetic resonance (NMR) logs are considered to be promising in evaluating rock pore structure. Generally, to consecutively quantitatively evaluate tight gas sands pore structure, the best method is constructing pseudo Pc curves from NMR logs. In this paper, based on the analysis of lab experimental results for 20 core samples, which were drilled from tight gas sandstone reservoirs of Sichuan basin, and simultaneously applied for lab MICP and NMR measurements, the relationships of piecewise power function between nuclear magnetic resonance (NMR) transverse relaxation T2 time and pore-throat radius Rc are established. A novel method, which is used to transform NMR reverse cumulative curve as pseudo capillary pressure (Pc) curve is proposed, and the corresponding model is established based on formation classification. By using this model, formation pseudo Pc curves can be consecutively synthesized. The pore throat radius distribution, and pore structure evaluation parameters, such as the average pore throat radius (Rm), the threshold pressure (Pd), the maximum pore throat radius (Rmax) and so on, can also be precisely extracted. After this method is extended into field applications, several tight gas

  18. Acoustic and NMR investigations of melting and crystallization of indium-gallium alloys in pores of synthetic opal matrices

    Science.gov (United States)

    Pirozerskii, A. L.; Charnaya, E. V.; Lee, M. K.; Chang, L. J.; Nedbai, A. I.; Kumzerov, Yu. A.; Fokin, A. V.; Samoilovich, M. I.; Lebedeva, E. L.; Bugaev, A. S.

    2016-05-01

    The paper presents the results of studying the crystallization and melting processes of Ga-In eutectic alloys, which are embedded in opal matrices, using acoustic and NMR methods. The indium concentrations in the alloys were 4, 6, 9, and 15 at %. Measurements were performed upon cooling from room temperature to complete crystallization of the alloys and subsequent heating. It is revealed how the size effects and alloy composition influence the formation of phases with α- and β-Ga structures and on changes in the melting-temperature ranges. A difference was observed between the results obtained using acoustic and NMR methods, which was attributed to different temperature measurement conditions.

  19. Structural Characterization of Lignins Isolated from Caragana sinica Using FT-IR and NMR Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    XIAOLing-ping; SHIZheng-jun; XUFeng; SUN Run-cang; Amar Kmohanty

    2011-01-01

    In order to efficiently explore and use woody biomass,six lignin fractions were isolated from dewaxed Caragana sinica via successive extraction with organic.solvents and alkaline solutions.The lignin structures were characterized by Fourier transform infrared spectroscopy (FT-IR) and 1D and 2D Nuclear Magnetic Resonance (NMR).FT-IR spectra revealed that the “core” of the lignin structure did not significantly change during the treatment under the conditions given.The results of 1 H and 13C NMR demonstrated that the lignin fraction L2,isolated with 70% ethanol containing 1% NaOH,was mainly composed of β-O-4 ether bonds together with G and S units and trace p-hydroxyphenyl unit.Based on the 2D HSQC NMR spectrum,the ethanol organosolv lignin fraction L1,extracted with 70% ethanol,presents a predominance of β-O-4' arylether linkages (61% of total side chains),and a low abundance of condensed carbon-carbon linked structures (such as β-β',β-1',and β-5') and a lower S/G ratio.Furthermore,a small percentage (ca.9%) of the linkage side chain was found to be acylated at the γ-carbon.

  20. Quantitative and Structure Analysis of Cellulose in Tobacco by 13C CP / MAS NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Zhu Xiaolan

    2016-07-01

    Full Text Available A new method utilizing 13C cross-polarization/magic angle spinning (CP/MAS nuclear magnetic resonance (NMR spectra was developed for the simultaneous quantitative determination and structure analysis of tobacco cellulose from hot water or acid detergent extraction. A reference spectrum of tobacco noncellulose components was subtracted from the spectrum of each sample to obtain a subspectrum of the cellulose components. The NMR spectra in combination with spectral fitting were analyzed in detail and some parameters, such as the content of cellulose, crystallinity, allomorph composition and lateral dimensions for cellulose elementary fibrils and microfibrils were determined. The quantitative results showed that the average recovery was 94.0% with a relative standard deviation (RSD of 4.6–4.8%. The structure results obtained by the spectral fitting for the cellulose C1-region showed that the main allomorph composition in tobacco cellulose was Iβ. The cellulose crystallinity calculated by the spectral fitting in C4 -region was about 50%. The lateral dimensions for cellulose elementary fibrils and microfibrils were in the range of 3.0–6.0 nm and 6.0–13.0 nm, respectively. Therefore, this NMR method could provide important information on both amount and structure of cellulose in tobacco.

  1. NMR strategies to support medicinal chemistry workflows for primary structure determination.

    Science.gov (United States)

    Oguadinma, Paul; Bilodeau, Francois; LaPlante, Steven R

    2017-01-15

    Central to drug discovery is the correct characterization of the primary structures of compounds. In general, medicinal chemists make great synthetic and characterization efforts to deliver the intended compounds. However, there are occasions which incorrect compounds are presented, such as those reported for Bosutinib and TIC10. This may be due to a variety of reasons such as uncontrolled reaction schemes, reliance on limited characterization techniques (LC-MS and/or 1D 1H NMR spectra), or even the lack of availability or knowledge of characterization strategies. Here, we present practical NMR approaches that support medicinal chemist workflows for addressing compound characterization issues and allow for reliable primary structure determinations. These strategies serve to differentiate between regioisomers and geometric isomers, distinguish between N- versus O-alkyl analogues, and identify rotamers and atropisomers. Overall, awareness and application of these available NMR methods (e.g. HMBC/HSQC, ROESY and VT experiments, to name only a few) should help practicing chemists to reveal chemical phenomena and avoid mis-assignment of the primary structures of compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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.

  3. Quadrupole Coupling Parameters and Structural Aspects of Crystalline and Amorphous Solids by NMR and Nqr.

    Science.gov (United States)

    Mao, Degen

    Nuclear quadrupole interaction is very sensitive to the local electron distribution and chemical bondings. NMR and NQR techniques have been 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. ^{71}Ga and ^{69}Ga NMR has been used to study crystalline beta-Ga _2O_3 and several gallate glasses. Quadrupole parameters were acquired for GaO_6 and GaO_4 units in beta-Ga_2 O_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. ^{51}V (I = 7/2) NQR resonances below 850 kHz have been detected for several metavanadates at both room temperature and liquid nitrogen temperature. Quadrupole parameters thus obtained are an order of magnitude more accurate than values obtained by previous NMR studies. For a spin 3/2 nucleus, the pure NQR frequency {Q_{cc}over 2}sqrt{1+{eta^2over 3}}is insufficient to determine either Q_{cc} or eta. However, two methods, Zeeman perturbed NQR powder pattern and ^{10}B NQR, can be employed to obtain both Q_{cc } and eta. An example is given for ^{11}B in CaO-B_2O_3. With a double coil tank circuit design, pure ^ {11}B NQR was used to determine the fraction of borons in BO_3 and BO _4 configurations in hydrated zinc borates. ^{11}B NMR and NQR were also used to study lead borate glasses. Small changes in Q_{cc} (less than 2%) and eta (less than 0.1) suggest that BO_3 units with non-bridging oxygens are not present in the lead borate glasses.

  4. The 1H NMR Structure of Bovine Pb2+- Osteocalcin and Implications for Lead Toxicity

    OpenAIRE

    Dowd, T. L.; Li, L.; Gundberg, C.M.

    2008-01-01

    Structural information on the effect of Pb2+ on proteins under physiologically relevant conditions is largely unknown. We have previously shown that low levels of lead increased the amount of osteocalcin bound to hydroxyapatite (BBA 1535:153)). This suggested that lead induced a more compact structure in the protein. We have determined the 3D structure of Pb2+-osteocalcin (49 amino acids), a bone protein from a target tissue, using 1H 2D NMR techniques. Lead, at a stoichiometry of only 1:1, i...

  5. Spectroscopic (infrared, Raman, UV and NMR) analysis, Gaussian hybrid computational investigation (MEP maps/HOMO and LUMO) on cyclohexanone oxime

    Science.gov (United States)

    Ramalingam, S.; Karabacak, M.; Periandy, S.; Puviarasan, N.; Tanuja, D.

    2012-10-01

    In the present analysis, FT-IR/FT-Raman spectra of the cyclohexanone oxime (CHO, C6H11NO) are recorded. The observed vibrational frequencies are assigned and the computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-311++G(d,p) basis set and the corresponding results are tabulated. In order to yield good coherence with observed values, the calculated frequencies are scaled by appropriate scale factors. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The alternation of structure of cyclohexanone due to the substitution of NOH is investigated. The vibrational sequence pattern of the molecule related to the substitutions is analyzed. Comparison of the observed fundamental vibrational frequencies of CHO and calculated results by density functional (B3LYP and B3PW91) and HF methods indicates that B3LYP is superior to the scaled HF and B3PW91 approach for molecular vibrational problems. Moreover, 13C NMR and 1H NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP/B3PW91 methods and the same basis set. A study on the electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, are performed by HF and DFT methods. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. NLO properties and Mulliken charges of the CHO was also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures are calculated in gas phase.

  6. Investigation of the binding of roxatidine acetate hydrochloride with cyclomaltoheptaose (β-cyclodextrin) using IR and NMR spectroscopy.

    Science.gov (United States)

    Maheshwari, Arti; Sharma, Manisha; Sharma, Deepak

    2011-09-27

    NMR chemical shift changes of the cyclomaltoheptaose (β-cyclodextrin, β-CD) cavity protons as well as roxatidine acetate hydrochloride aromatic ring protons revealed the formation of a RAH-β-CD inclusion complex. Detailed FTIR and NMR spectroscopic ((1)H NMR, COSY, NOESY, ROESY) studies have been done. The stoichiometry of the complex was determined to be 1:1, and the overall binding constant was also determined by Scott's method. The NOESY spectrum confirmed the selective penetration of the aromatic ring of RAH into the β-CD cavity in comparison to that of the piperidine ring. The mode of penetration of the guest into the CD cavity and structure of the complex has been established.

  7. Distributed computing and NMR constraint-based high-resolution structure determination: applied for bioactive Peptide endothelin-1 to determine C-terminal folding.

    Science.gov (United States)

    Takashima, Hiroyuki; Mimura, Norio; Ohkubo, Tadayasu; Yoshida, Takuya; Tamaoki, Haruhiko; Kobayashi, Yuji

    2004-04-14

    Distributed computing has been implemented to the solution structure determination of endothelin-1 to evaluate efficiency of the method for NMR constraint-based structure calculations. A key target of the investigation was determination of the C-terminal folding of the peptide, which had been dispersed in previous studies of NMR, despite its pharmacological significances. With use of tens of thousands of random initial structures to explore the conformational space comprehensively, we determined high-resolution structures with good convergences of C-terminal as well as previously defined N-terminal structures. The previous studies had missed the C-terminal convergence because of initial structure dependencies trapped in localized folding of the N-terminal region, which are strongly constricted by two disulfide bonds.

  8. Investigation of material properties by NMR in low and high magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Rata, D.G.

    2006-07-10

    In this work the experiments have been performed at both low and high field. The experiments cover various domains from simple relaxation experiments in low field to diffusion and spin-diffusion in high field. The applications of low-field investigations are: - quality control of chemical products. - water content determination inside of the walls of buildings. - determination of multilayer polymer coatings on a concrete. In high-field NMR several alkane molecules swollen at equilibrium in cross-linked natural rubber samples have been investigated and analyzed based on the assumptions of the Vrentras theory. A small diffusion anisotropy of the order of 10% has been discovered because of a deformation of free volume under compression. The anisotropy increases with the cross-link density and the compression ratio. The results presented in this study show that the solvent size influences the anisotropy of the diffusion process through the size parameter. The spin-diffusion measurements have been performed on Stanyl samples with different aged samples, at controlled temperature conditions. (orig.)

  9. Integration of XAS and NMR techniques for the structure determination of metalloproteins. Examples from the study of copper transport proteins.

    Science.gov (United States)

    Banci, Lucia; Bertini, Ivano; Mangani, Stefano

    2005-01-01

    Nuclear magnetic resonance (NMR) is a powerful technique for protein structure determination in solution. However, when dealing with metalloproteins, NMR methods are unable to directly determine the structure of the metal site and its coordination geometry. The capability of X-ray absorption spectroscopy (XAS) to provide the structure of a metal ion bound to a protein is then perfectly suited to complement the process of the structure determination. This aspect is particularly relevant in structural genomic projects where high throughput of structural results is the main goal. The synergism of the two techniques has been exploited in the structure determination of bacterial copper transport proteins.

  10. Ab initio study, investigation of NMR shielding tensors, NBO and vibrational frequency of catechol thioethers

    Directory of Open Access Journals (Sweden)

    A. Bagheri Gh

    2010-08-01

    Full Text Available The electrochemical oxidation of dopamine and 3,4-dihydroxymethamphetamine (HHMA has been studied in the presence of GSH and cysteine as a nucleophile. In order to determine the optimized geometries, energies, dipole moments, atomic charges, thermochemical analysis and other properties, we performed quantum chemical ab initio and density functional calculations at B3LYP level with 6-31G* basis set. The structural and vibrational properties of 5-S-glutathionyldopamine, 5-S-cysteinyldopamine and 5-S-N-acetylcysteinyldopamine are studied. The chemical shifts of anisotropy and Δδ are calculated. The gauge-invariant atomic orbital (GIAO method was employed to calculate isotropic atomic shielding of compounds. These calculations yield molecular geometries in good agreement with available experimental data. The bond lengths, bond angles, dipole moment, electron affinity, ionization potential, electronegativy, absolute hardness, highest occupied molecular orbital (HOMO and the energy of the lowest unoccupied molecular orbital (LUMO of the studied compounds were calculated in gas phase and water. NMR analysis of dopamine-o-quinone-glutathione conjugate revealed that the addition of glutathione was at C-5 to form glutathionyl-dopamine.

  11. Magnetic and structural properties of Cu-Co granular alloys measured with NMR

    CERN Document Server

    Sinnecker, J P; Tiberto, P; Guimarães, A P

    2000-01-01

    sup 5 sup 9 Co NMR experiments were performed in melt-spun Cu sub 1 sub 0 sub 0 sub - sub x Co sub x samples (x=10, 15 and 20). The NMR spectra are very similar for all concentrations. A seven-line structure equally spaced by 18 MHz was observed, with frequencies lower than that of metallic cobalt (217 MHz). This result is interpreted as a step decrease of the Co resonance frequency with each additional Cu impurity in the first coordination shell. The presence of the satellite lines indicates that the grains are very small, and the interface contributions prevail over those of the bulk. Regions with two different local anisotropy field values were observed for x=15 (approx 0.1 and approx 1 kG). For x=10 and 20, a single anisotropy value was found.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Volkman, B.F.

    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 {open_quote}receiver domain{close_quote} in the family of {open_quote}two-component{close_quote} 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.

  14. A review on the applications of the nuclear magnetic resonance (NMR) technology for investigating fractures

    Science.gov (United States)

    Golsanami, Naser; Sun, Jianmeng; Zhang, Zhiying

    2016-10-01

    This review focuses on the recent applications of nuclear magnetic resonance (NMR) technology for characterizing fractures. The paper aims to help researchers in extending the existing reservoir characterization methods (which are commonly used in conventional hydrocarbon reservoirs) for appropriate usage in unconventional resources. This is because some techniques for quantifying and qualifying fractures have been investigated in conventional sandstone and carbonate reservoirs, but the reality for unconventional resources is that such techniques are still poorly developed. Fractures are necessary for economical production of petroleum from many low-permeability reservoirs. The characterization of fractures by well logging technology is of great interest in the petroleum industry. The main purpose of this study is to review the characterization techniques that are developed either for identifying fractures or distinguishing fracture porosity from matrix porosity. This concept plays a leading role in providing availability of an optimized well completion program. The results of this study indicated that in terms of both sandstone and carbonate tight reservoirs, there have not been many steps taken toward the aforementioned goal up to now. Nevertheless, these steps are valuable enough to be counted on and could serve a meaningful function in treating hydrocarbon reservoirs. Because of the ongoing changes in today's petroleum industry, development of a comprehensive methodology will create greater economic benefits in unconventional reservoirs than in the conventional ones.

  15. The NMR structure of the inhibited catalytic domain of human stromelysin-1.

    Science.gov (United States)

    Gooley, P R; O'Connell, J F; Marcy, A I; Cuca, G C; Salowe, S P; Bush, B L; Hermes, J D; Esser, C K; Hagmann, W K; Springer, J P

    1994-02-01

    The three-dimensional structure of the catalytic domain of stromelysin-1 complexed with an N-carboxyl alkyl inhibitor has been determined by NMR methods. The global fold consists of three helices, a five stranded beta-sheet and a methionine located in a turn near the catalytic histidines, classifying stromelysin-1 as a metzincin. Stromelysin-1 is unique in having two independent zinc binding sites: a catalytic site and a structural site. The inhibitor binds in an extended conformation. The S1' subsite is a deep hydrophobic pocket, whereas S2' appears shallow and S3' open.

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

    Science.gov (United States)

    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.

  17. Local structure and molecular motions in imidazolium hydrogen malonate crystal as studied by {sup 2}H and {sup 13}C NMR

    Energy Technology Data Exchange (ETDEWEB)

    Mizuno, M., E-mail: mizuno@se.kanazawa-u.ac.jp; Chizuwa, M.; Umiyama, T.; Kumagai, Y.; Miyatou, T.; Ohashi, R.; Ida, T. [Kanazawa University, Kakuma, Department of Chemistry, Graduate School of Natural Science & Technology (Japan); Tansho, M.; Shimizu, T. [National Institute for Materials Science (Japan)

    2015-04-15

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

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

    Science.gov (United States)

    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

  19. An algebraic geometry approach to protein structure determination from NMR data.

    Science.gov (United States)

    Wang, Lincong; Mettu, Ramgopal R; Donald, Bruce Randall

    2005-01-01

    Our paper describes the first provably-efficient algorithm for determining protein structures de novo, solely from experimental data. We show how the global nature of a certain kind of NMR data provides quantifiable complexity-theoretic benefits, allowing us to classify our algorithm as running in polynomial time. While our algorithm uses NMR data as input, it is the first polynomial-time algorithm to compute high-resolution structures de novo using any experimentally-recorded data, from either NMR spectroscopy or X-Ray crystallography. Improved algorithms for protein structure determination are needed, because currently, the process is expensive and time-consuming. For example, an area of intense research in NMR methodology is automated assignment of nuclear Overhauser effect (NOE) restraints, in which structure determination sits in a tight inner-loop (cycle) of assignment/refinement. These algorithms are very time-consuming, and typically require a large cluster. Thus, algorithms for protein structure determination that are known to run in polynomial time and provide guarantees on solution accuracy are likely to have great impact in the long-term. Methods stemming from a technique called "distance geometry embedding" do come with provable guarantees, but the NP-hardness of these problem formulations implies that in the worst case these techniques cannot run in polynomial time. We are able to avoid the NP-hardness by (a) some mild assumptions about the protein being studied, (b) the use of residual dipolar couplings (RDCs) instead of a dense network of NOEs, and (c) novel algorithms and proofs that exploit the biophysical geometry of (a) and (b), drawing on a variety of computer science, computational geometry, and computational algebra techniques. In our algorithm, RDC data, which gives global restraints on the orientation of internuclear bond vectors, is used in conjunction with very sparse NOE data to obtain a polynomial-time algorithm for protein structure

  20. Several Applications of NMR in Organic Chemistry Research

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Modem NMR techniques, especially 2D-NMR have presented their powerful application in organic chemistry. Not only in structural determination, mechanism investigation, but also in solution conformation study for natural products. In this paper, various pulse field gradient NMR techniques such as COSY, NOESY, HMBC and HMQC were combined to study these problems.

  1. Several Applications of NMR in Organic Chemistry Research

    Institute of Scientific and Technical Information of China (English)

    CUI; yuxin; XU; hao

    2001-01-01

    Modem NMR techniques, especially 2D-NMR have presented their powerful application in organic chemistry. Not only in structural determination, mechanism investigation, but also in solution conformation study for natural products. In this paper, various pulse field gradient NMR techniques such as COSY, NOESY, HMBC and HMQC were combined to study these problems.  ……

  2. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  3. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  4. NMR structure of the cathelin-like domain of the protegrin-3 precursor.

    Science.gov (United States)

    Yang, Yinshan; Sanchez, Jean Frédéric; Strub, Marie-Paule; Brutscher, Bernhard; Aumelas, André

    2003-04-29

    In mammals, numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence of 94-114 residues, termed the cathelin-like domain. The cathelin-like domain of protegrin-3 (ProS) was overexpressed in Escherichia coli and uniformly labeled with (15)N or (15)N and (13)C, and its three-dimensional structure was determined by heteronuclear NMR at pH 6.2. Under these conditions and due to the cis-trans isomerization of the R(87)-P(88) and D(118)-P(119) amide bonds, the ProS structure was found to adopt four almost equally populated conformations in slow exchange on the NMR chemical shift time scale. The ProS structure consists of an N-terminal alpha-helix (Y(34)-N(48)) cradled by a four-stranded antiparallel beta-sheet (beta1, N(53)-L(60); beta2, K(74)-P(86); beta3, V(104)-V(111); and beta4, I(122)-C(124)). The solution structure of ProS, which is monomeric, allowed us to determine the structure of the L1 and L2 loops, which are too mobile in the crystal structure. The regions common to the solution and X-ray structures were found to be very similar. Finally, since the overall fold of ProS is very similar to that of cystatins despite a low degree of sequence identity, the ProS solution structure was compared to the solution and X-ray structures of the chicken cystatin. This comparison revealed that the structures of the L1 and L2 loops as well as that of the appending domain are quite different in the two proteins. These differences are mainly due to the high proline residue content (10%) which disorganizes the hydrogen bond network of a part of the ProS beta-sheet in contrast to that of the chicken cystatin structure.

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

    Science.gov (United States)

    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.

  6. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

    Science.gov (United States)

    2016-01-01

    Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5′-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography—the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry—to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4′ of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites. PMID:27779384

  7. NMR structure of integrin α4 cytosolic tail and its interactions with paxillin.

    Directory of Open Access Journals (Sweden)

    Geok-Lin Chua

    Full Text Available BACKGROUND: Integrins are a group of transmembrane signaling proteins that are important in biological processes such as cell adhesion, proliferation and migration. Integrins are α/β hetero-dimers and there are 24 different integrins formed by specific combinations of 18 α and 8 β subunits in humans. Generally, each of these subunits has a large extracellular domain, a single pass transmembrane segment and a cytosolic tail (CT. CTs of integrins are important in bidirectional signal transduction and they associate with a large number of intracellular proteins. PRINCIPAL FINDINGS: Using NMR spectroscopy, we determined the 3-D structure of the full-length α4 CT (Lys968-Asp999 and characterize its interactions with the adaptor protein paxillin. The α4 CT assumes an overall helical structure with a kink in its membrane proximal region. Residues Gln981-Asn997 formed a continuous helical conformation that may be sustained by potential ionic and/or hydrogen bond interactions and packing of aromatic-aliphatic side-chains. ¹⁵N-¹H HSQC NMR experiments reveal interactions of the α4 CT C-terminal region with a fragment of paxillin (residues G139-K277 that encompassed LD2-LD4 repeats. Residues of these LD repeats including their adjoining linkers showed α4 CT binding-induced chemical shift changes. Furthermore, NMR studies using LD-containing peptides showed predominant interactions between LD3 and LD4 of paxillin and α4 CT. Docked structures of the α4 CT with these LD repeats suggest possible polar and/or salt-bridge and non-polar packing interactions. SIGNIFICANCE: The current study provides molecular insights into the structural diversity of α CTs of integrins and interactions of integrin α4 CT with the adaptor protein paxillin.

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

    Science.gov (United States)

    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.

  9. The inclusion complex of rosmarinic acid into beta-cyclodextrin: A thermodynamic and structural analysis by NMR and capillary electrophoresis.

    Science.gov (United States)

    Aksamija, Amra; Polidori, Ange; Plasson, Raphaël; Dangles, Olivier; Tomao, Valérie

    2016-10-01

    This work focuses on the characterization of the rosmarinic acid (RA)-β-cyclodextrin (CD) complex in aqueous solution by (1)H NMR (1D- and 2D-ROESY), completed with studies by capillary electrophoresis (CE). From the (1)H NMR data, the stoichiometry of the complex was determined by a Job's plot and the binding constant was estimated from a linear regression (Scott's method). At pH 2.9, the results showed that RA binds CD with a 1:1 stoichiometry and a binding constant Kb of 445 (±53) M(-1) or 465 (±81) M(-1) depending on the CD protons (H-5 or H-3) selected for the evaluation. The Kb value was also calculated from the CD-induced chemical shifts of each RA proton in order to collect information on the structure of the complex. The pH dependence of Kb revealed that the RA carboxylic form displays the highest affinity for CD. An investigation by capillary electrophoresis fully confirmed these results. 2D ROESY analysis provided detailed structural information on the complex and showed a strong correlation between H-3 and H-5 of CD and most RA protons. In conclusion, RA, an efficient phenolic antioxidant from rosemary with a marketing authorization, spontaneously forms a relatively stable inclusion complex with CD in water.

  10. {sup 13}C solid-state NMR analysis of heterogeneous structure of beeswax in native state

    Energy Technology Data Exchange (ETDEWEB)

    Kameda, Tsunenori [National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8634 (Japan)

    2005-12-21

    I investigated the molecular structure of natural wax from Japanese bees (Apis cerana japonica) in its native state (neither purified nor recrystallized) by {sup 13}C and {sup 1}H solid-state NMR. Two strong {sup 13}C peaks at 32.9 and 34.0 ppm were attributed to signals from internal-chain methylene carbons [int-(CH{sub 2})] in two types of crystal form. The peak at 32.9 ppm was assigned to an orthorhombic crystal form, and that at 34.0 ppm was assigned to a triclinic or monoclinic form. In both crystalline regions, bi-exponential decay of {sup 13}C spin-lattice relaxation [T{sub 1}(C)] for the crystalline peaks due to chain diffusion was observed. {sup 1}H spin-lattice relaxation [T{sub 1}(H)] values for protons of the CH{sub 3} group and for int-(CH{sub 2}) in the crystalline and amorphous regions were identical; this was interpreted as being due to averaging of the T{sub 1}(H) relaxation rates via spin diffusion. In contrast, although the T{sub 1{sub {rho}}}(H) decay curves for protons of the CH{sub 3} group and for int-(CH{sub 2}) in the amorphous and orthorhombic forms were almost identical, those of the triclinic or monoclinic forms were different. This unhomogeneous character of T{sub 1{sub {rho}}}(H) was interpreted as resulting from differences in the molecular composition of each crystal form. Moreover, two components with long and short {sup 1}H spin-spin relaxation [T{sub 2}(H)] values, arising from the mobile and rigid phases, respectively, were observed at above about -30 deg. C.

  11. 13C solid-state NMR analysis of heterogeneous structure of beeswax in native state

    Science.gov (United States)

    Kameda, Tsunenori

    2005-12-01

    I investigated the molecular structure of natural wax from Japanese bees (Apis cerana japonica) in its native state (neither purified nor recrystallized) by 13C and 1H solid-state NMR. Two strong 13C peaks at 32.9 and 34.0 ppm were attributed to signals from internal-chain methylene carbons [int-(CH2)] in two types of crystal form. The peak at 32.9 ppm was assigned to an orthorhombic crystal form, and that at 34.0 ppm was assigned to a triclinic or monoclinic form. In both crystalline regions, bi-exponential decay of 13C spin-lattice relaxation [T1(C)] for the crystalline peaks due to chain diffusion was observed. 1H spin-lattice relaxation [T1(H)] values for protons of the CH3 group and for int-(CH2) in the crystalline and amorphous regions were identical; this was interpreted as being due to averaging of the T1(H) relaxation rates via spin diffusion. In contrast, although the T_{{1}_{\\rho}}(H) decay curves for protons of the CH3 group and for int-(CH2) in the amorphous and orthorhombic forms were almost identical, those of the triclinic or monoclinic forms were different. This unhomogeneous character of T_{{1}_{\\rho}}(H) was interpreted as resulting from differences in the molecular composition of each crystal form. Moreover, two components with long and short 1H spin-spin relaxation [T2(H)] values, arising from the mobile and rigid phases, respectively, were observed at above about -30 °C.

  12. Atomic structure of icosahedral B4C boron carbide from a first principles analysis of NMR spectra.

    Science.gov (United States)

    Mauri, F; Vast, N; Pickard, C J

    2001-08-20

    Density functional theory is demonstrated to reproduce the 13C and 11B NMR chemical shifts of icosahedral boron carbides with sufficient accuracy to extract previously unresolved structural information from experimental NMR spectra. B4C can be viewed as an arrangement of 3-atom linear chains and 12-atom icosahedra. According to our results, all the chains have a CBC structure. Most of the icosahedra have a B11C structure with the C atom placed in a polar site, and a few percent have a B (12) structure or a B10C2 structure with the two C atoms placed in two antipodal polar sites.

  13. Structural studies of lithium zinc borohydride by neutron powder diffraction, Raman and NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ravnsbaek, D.B. [Center for Materials Crystallography (CMC), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Frommen, C. [Institute for Energy Technology, P.O. Box 40, N-2027 Kjeller (Norway); Reed, D. [School of Metallurgy and Materials, University of Birmingham, Edgbaston, Birmingham, B15 2TT (United Kingdom); Filinchuk, Y. [Center for Materials Crystallography (CMC), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Swiss-Norwegian Beam Lines at ESRF, BP-220, 38043 Grenoble (France); Institute of Condensed Matter and Nanosciences, Universite Catholique de Louvain, 1 Place L. Pasteur, B-1348, Louvain-la-Neuve (Belgium); Sorby, M.; Hauback, B.C. [Institute for Energy Technology, P.O. Box 40, N-2027 Kjeller (Norway); Jakobsen, H.J. [Instrument Centre for Solid-State NMR Spectroscopy and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Book, D. [School of Metallurgy and Materials, University of Birmingham, Edgbaston, Birmingham, B15 2TT (United Kingdom); Besenbacher, F. [Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C (Denmark); Skibsted, J. [Instrument Centre for Solid-State NMR Spectroscopy and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Jensen, T.R., E-mail: trj@chem.au.dk [Center for Materials Crystallography (CMC), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark)

    2011-09-15

    Research highlights: > Structural study of the first interpenetrated framework hydride, LiZn{sub 2}(BH{sub 4}){sub 5} > Determination of deuterium positions and revision of crystal structure by PND. > Raman spectroscopy confirms the presence of isolated [Zn{sub 2}(BD{sub 4}){sub 5}]-bar complex anions. > Determination of quadrupole coupling parameters and chemical shifts by {sup 11}B MAS NMR. - Abstract: The crystal structure of LiZn{sub 2}(BH{sub 4}){sub 5} is studied in detail using a combination of powder neutron diffraction (PND), Raman spectroscopy, and {sup 11}B MAS NMR spectroscopy on LiZn{sub 2}(BH{sub 4}){sub 5} and LiZn{sub 2}({sup 11}BD{sub 4}){sub 5}. The aim is to obtain detailed structural knowledge of the first interpenetrated framework hydride compound, LiZn{sub 2}(BD{sub 4}){sub 5} which consists of doubly interpenetrated 3D frameworks built from dinuclear complex ions [Zn{sub 2}(BD{sub 4}){sub 5}]{sup -} and lithium ions. The positions of the deuterium atoms are determined using Rietveld refinement of the PND data and the orientation of one of the four independent BD{sub 4}{sup -} groups is revised. The current data reveal that the structure of [Zn{sub 2}(BD{sub 4}){sub 5}]{sup -} is more regular than previously reported, as are also the coordinations around the Zn and Li atoms. Both Zn and Li atoms are found to coordinate to the BD{sub 4}{sup -} units via the tetrahedral edges. Some distortion of the angles within the BD{sub 4} units is observed, relative to the expected angles of 109.4 for the ideal tetrahedral coordination. Raman spectroscopy confirms bending and stretching modes from the expected terminal and bridging bidentate BH{sub 4}{sup -} and BD{sub 4}{sup -} units. The {sup 11}B MAS NMR spectrum of the satellite transitions resolves two distinct manifolds of spinning sidebands, which allows estimation of the {sup 11}B quadrupole coupling parameters and isotropic chemical shifts for the four distinct {sup 11}B sites of [Zn{sub 2}(BD

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

    Science.gov (United States)

    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 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.

  15. Theoretical and experimental investigation of the 1H NMR spectrum of putrescine

    Science.gov (United States)

    Allouche, A. R.; Graveron-Demilly, D.; Fauvelle, F.; Aubert-Frécon, M.

    2008-12-01

    Chemical shifts δ and spin-spin coupling constants J have been calculated for the putrescine molecule, a polyamine present in prostate tissue, through a DFT/B3LYP/6-311++G(d,p)/PCM/(GIAO) approach, which has been shown to be accurate in previous work. From δ and J values, calculated for the first time for the isolated and the solvated putrescine, the 1H NMR spectra have been simulated. Comparisons between the calculated and the experimental NMR spectra at 400 MHz show a good agreement and allow to propose reliable values for the NMR spin Hamiltonian parameters of putrescine to be used as good starting values for further quantitation methods of metabolites in prostate tissue.

  16. Bis(pentamethylcyclopentadienyl)ytterbium: An investigation of weak interactions in solution using multinuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, D.J.

    1995-07-01

    NMR spectroscopy is ideal for studying weak interactions (formation enthalpy {le}20 kcal/mol) in solution. The metallocene bis(pentamethylcyclopentadienyl)ytterbium, Cp*{sub 2}Yb, is ideal for this purpose. cis-P{sub 2}PtH{sub 2}complexes (P = phosphine) were used to produce slow-exchange Cp*{sub 2}YbL adducts for NMR study. Reversible formation of (P{sub 2}PtH){sub 2} complexes from cis-P{sub 2}PtH{sub 2} complexes were also studied, followed by interactions of Cp*{sub 2}Yb with phosphines, R{sub 3}PX complexes. A NMR study was done on the interactions of Cp*{sub 2}Yb with H{sub 2}, CH{sub 4}, Xe, CO, silanes, stannanes, C{sub 6}H{sub 6}, and toluene.

  17. Molecular dynamics of spider dragline silk fiber investigated by 2H MAS NMR.

    Science.gov (United States)

    Shi, Xiangyan; Holland, Gregory P; Yarger, Jeffery L

    2015-03-09

    The molecular dynamics of the proteins that comprise spider dragline silk were investigated with solid-state (2)H magic angle spinning (MAS) NMR line shape and spin-lattice relaxation time (T1) analysis. The experiments were performed on (2)H/(13)C/(15)N-enriched N. clavipes dragline silk fibers. The silk protein side-chain and backbone dynamics were probed for Ala-rich regions (β-sheet and 31-helical domains) in both native (dry) and supercontracted (wet) spider silk. In native (dry) silk fibers, the side chains in all Ala containing regions undergo similar fast methyl rotations (>10(9) s(-1)), while the backbone remains essentially static (silk is wet and supercontracted, the presence of water initiates fast side-chain and backbone motions for a fraction of the β-sheet region and 31-helicies. β-Sheet subregion 1 ascribed to the poly(Ala) core exhibits slower dynamics, while β-sheet subregion 2 present in the interfacial, primarily poly(Gly-Ala) region that links the β-sheets to disordered 31-helical motifs, exhibits faster motions when the silk is supercontracted. Particularly notable is the observation of microsecond backbone motions for β-sheet subregion 2 and 31-helicies. It is proposed that these microsecond backbone motions lead to hydrogen-bond disruption in β-sheet subregion 2 and helps to explain the decrease in silk stiffness when the silk is wet and supercontracted. In addition, water mobilizes and softens 31-helical motifs, contributing to the increased extensibility observed when the silk is in a supercontracted state. The present study provides critical insight into the supercontraction mechanism and corresponding changes in mechanical properties observed for spider dragline silks.

  18. FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

    Science.gov (United States)

    Arjunan, V; Sakiladevi, S; Rani, T; Mythili, C V; Mohan, S

    2012-03-01

    The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. Computational Chemistry Meets Experiments for Explaining the Behavior of Bibenzyl: A Thermochemical and Spectroscopic (Infrared, Raman, and NMR) Investigation.

    Science.gov (United States)

    Latouche, Camille; Barone, Vincenzo

    2014-12-09

    The structure, conformational behavior, and spectroscopic parameters of bibenzyl have been investigated by a computational protocol including proper treatment of anharmonic and hindered rotor contributions. Conventional hybrid functionals overstabilize the anti conformer while low-order post-Hartree-Fock (MP2) approaches strongly favor the gauche conformer. However, inclusion of semiempirical dispersion effects in density functionals or coupled cluster post-Hartree-Fock models agree in forecasting the simultaneous presence of both conformers in the gas phase with a slightly larger stability (0.7 kcal·mol(-1)) of the gauche conformer. Addition of thermal and entropic effects finally leads to very close Gibbs free energies for both conformers and, thus, to a slight preference for the gauche form due to statistical factors (2 vs 1). The situation remains essentially the same in solution. On these grounds, perturbative vibrational computations including both electrical and mechanical anharmonicities lead to IR and Raman spectra in remarkable agreement with experiment. Full assignment of the IR spectra explains the presence of peaks from gauche or anti conformers. Comparison between computed and experimental Raman spectra confirms that both conformers are present in liquid phase, whereas the anti conformer seems to be preponderant in the solid state. Also computed NMR parameters are in good agreement with experiment.

  20. Applications of Solid State NMR to the Study of Molecular Structure

    Science.gov (United States)

    Curtis, Ronald Dean

    This thesis illustrates several applications of dilute spin I = 1over2 solid state nmr spectroscopy to the study of molecular structure in systems of chemical interest. Specifically, the compounds studied include benzylideneaniline and several related imines, the first stable iminophosphenium cation containing a N,P triple bond and several tetracyclines. The first two applications describe the use of dipolar-chemical shift nmr of "isolated" spin-pairs to fully characterize chemical shift tensors. For example, the carbon and nitrogen shift tensors of the C=N linkage of the Schiff base benzylideneaniline have been completely specified. The most shielded principal component of both carbon and nitrogen shift tensors is approximately perpendicular to the imine fragment. For the imine carbon, the intermediate component of the shift tensor is directed approximately along the C=N bond whereas the corresponding component of the nitrogen shift tensor is oriented along the direction of the nitrogen lone pair. Examination of the nitrogen chemical shift parameters for several related imines suggests that variations in the least shielded principal component are mainly responsible for changes in the nitrogen shieldings in the imine system. For the N,P moiety of the iminophosphenium cation, the most shielded principal component of both nitrogen and phosphorus tensors is oriented along the N,P bond axis. Comparison of both shift tensors with those of related compounds suggests that the electronic environment surrounding the N,P moiety is similar to other systems containing a formal triple bond. The final application section demonstrates the utility of high-resolution ^{13} C and ^{15}N cp/mas nmr for studying the molecular structure of solid tetracycline antibiotics. Comparison of ^{15} C chemical shifts in the solid state to those determined in (CD_3)_2SO solutions indicates for the first time that the structural integrity of the A ring of the tetracyclines is maintained in

  1. Synthesis of LaF{sub 3} nanosheets with high fluorine mobility investigated by NMR relaxometry and diffusometry

    Energy Technology Data Exchange (ETDEWEB)

    Gulina, L. B.; Tolstoy, V. P.; Murin, I. V. [Institute of Chemistry of St. Petersburg State University 198504, Universitetsky pr., 26 Peterhof, St. Petersburg (Russian Federation); Schäfer, M.; Privalov, A. F. [Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt (Germany)

    2015-12-21

    Ionically conducting lanthanum fluoride (LaF{sub 3}), displaying a nanoscopic lamellar structure, has been synthesized at the surface of an aqueous solution of LaCl{sub 3} and HF. The structure and the chemical composition of the conductor have been analyzed by SEM, electron probe microanalysis, X-ray powder diffraction, FTIR, and {sup 19}F magic angle spinning nuclear magnetic resonance (NMR) spectroscopy. The fluorine dynamics have been studied by NMR diffusometry and relaxometry in a temperature range from room temperature up to 875 K. The fluorine self-diffusion coefficient of the nanostructured LaF{sub 3} is about two orders of magnitude larger than that of bulk LaF{sub 3}. This novel material is highly promising for many typical applications of fluorine ionic systems.

  2. Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, D. Flemming; Vallurupalli, Pramodh; Kay, Lewis E. [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)], E-mail: kay@pound.med.utoronto.ca

    2008-07-15

    Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers are populated to only low levels and are often only transiently formed their study is not amenable to many of the tools of structural biology. In this perspective we discuss the role of CPMG-based relaxation dispersion NMR spectroscopy in characterizing these low populated, invisible states. It is shown that robust methods for measuring both backbone chemical shifts and residual anisotropic interactions in the excited state are in place and that these data provide valuable restraints for structural studies of invisible conformers.

  3. NMR solution structure of the RED subdomain of the Sleeping Beauty transposase.

    Science.gov (United States)

    Konnova, Tatiana A; Singer, Christopher M; Nesmelova, Irina V

    2017-03-27

    DNA transposons can be employed for stable gene transfer in vertebrates. The Sleeping Beauty (SB) DNA transposon has been recently adapted for human application and is being evaluated in clinical trials, however its molecular mechanism is not clear. SB transposition is catalyzed by the transposase enzyme, which is a multi-domain protein containing the catalytic and the DNA-binding domains. The DNA-binding domain of the SB transposase contains two structurally independent subdomains, PAI and RED. Recently, the structures of the catalytic domain and the PAI subdomain have been determined, however no structural information on the RED subdomain and its interactions with DNA has been available. Here, we used NMR spectroscopy to determine the solution structure of the RED subdomain and characterize its interactions with the transposon DNA.

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

    Science.gov (United States)

    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.

  5. Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard; Steinocher, Helena; Brooks, Andrew J.

    2015-01-01

    Despite the biological and pharmaceutical significance of membrane proteins, their tertiary structures constitute less than 3% of known structures. One of the major obstacles for initiating structural studies of membrane proteins by NMR spectroscopy is the generation of high amounts of isotope......-labeled protein. In this work, we have exploited the hydrophobic nature of membrane proteins to develop a simple and efficient production scheme for isotope-labeled single-pass transmembrane domains (TMDs) with or without intrinsically disordered regions. We have evaluated the applicability and limitations...... of the strategy using seven membrane protein variants that differ in their overall hydrophobicity and length and show a recovery for suitable variants of >70%. The developed production scheme is cost-efficient and easy to implement and has the potential to facilitate an increase in the number of structures...

  6. STUDY ON SEQUENCE STRUCTURE OF ACRYLAMIDE-ACRYLATE COPOLYMERS BY 13C-NMR METHOD

    Institute of Scientific and Technical Information of China (English)

    YUAN Dongwu; ZHU Shannong; YANG Xiaozhen

    1987-01-01

    Triad sequence distributions in a series of P(AM/AA) with different AA% were calculated from copolymerization reactivity ratio r1 and r2 based on first order Markov statistic model, and the calculated data compared with observed ones from 13C-NMR spectra showed good agreement with each other, The sequence distribution in P(AM/AA) obtained under our experimental conditions fits in with first order Markov statistic model. A significant sequence structure difference was observed between P(AM/AA) and alkaline hydrolyzed polyacrylamide, ABA triad (acrylate unit center), AAA and AAB triads (acrylamide unit center) dominated in hydrolyzed ones.

  7. NMR structure of mussel mytilin, and antiviral-antibacterial activities of derived synthetic peptides

    OpenAIRE

    Roch, Philippe; Yang, Y.; Toubiana, Mylene; Aumelas, A

    2008-01-01

    Mytilin is a 34-residue antibacterial peptide from the mussel Mytilus galloprovincialis, which in addition possesses in vitro antiviral activity. The three-dimensional solution structure of the synthetic mytilin was established by using 1H NMR and consists of the common cysteine-stabilized alpha beta motif close to the one observed in the mussel defensin MGD-1. Mytilin is characterized by 8 cysteines engaged in four disulfide bonds (2-27, 6-29, 10-31, and 15-34) only involving the beta-strand...

  8. Oligomeric structure of a cathelicidin antimicrobial peptide in dodecylphosphocholine micelle determined by NMR spectroscopy.

    Science.gov (United States)

    Saravanan, Rathi; Bhattacharjya, Surajit

    2011-01-01

    The broad spectrum of antibacterial activities of host defense cationic antimicrobial peptides (AMPs) arises from their ability to perturb membrane integrity of the microbes. The mechanisms are often thought to require assembly of AMPs on the membrane surface to form pores. However, three dimensional structures in the oligomeric form of AMPs in the context of lipid membranes are largely limited. Here, we demonstrate that a 22-residue antimicrobial peptide, termed VK22, derived from fowlicidin-1, a cathelicidin family of AMP from chicken oligomerizes into a predominantly tetrameric state in zwitterionic dodecylphosphocholine (DPC) micelles. An ensemble of NMR structures of VK22 determined in 200mM perdeuterated DPC, from 755 NOE constrains including 19 inter-helical NOEs, had revealed an assembly of four helices arranged in anti-parallel fashion. Hydrogen bonds, C(α)H-O=C types, and van der Waals interactions among the helical sub-units appear to be involved in the stabilization of the quaternary structures. The central region of the barrel shaped tetrameric bundle is non-polar with clusters of aromatic residues, whereas all the cationic residues are positioned at the termini. Paramagnetic spin labeled NMR experiments indicated that the tetrameric structure is embedded into micelles such that the non-polar region located inside the lipid acyl chains. Structure and micelle localization of a monomeric version, obtained from substitution of two Tyr residues with Ala, of the peptide is also compared. The mutated peptide VK22AA has been found be localized at the surface of the micelles. The tetrameric structure of VK22 delineates a small water pore that can be larger in the higher order oligomers. As these results provide structural insights, at atomic resolution, into the oligomeric states of a helical AMP in lipid environment, the structural details may be further utilized for the design of novel self-assembled membrane protein mimics.

  9. Structural characterization of functionalized gold nanoparticles for drug delivery in cancer therapy: a NMR based approach.

    Science.gov (United States)

    Coelho, Sílvia C; Rangel, Maria; Pereira, Maria C; Coelho, Manuel A N; Ivanova, Galya

    2015-07-15

    In the present paper, we report results from a study of the structure and physicochemical properties of gold nanoparticles modified with poly(ethylene glycol) (PEG) designed for the drug delivery of the proteasome inhibitor Bortezomib (BTZ) in cancer therapy. A number of advanced analytical techniques were used to define important physicochemical characteristics such as composition, structure, surface properties, particle size and morphology. A new approach based on detailed NMR studies was employed to define specific intermolecular interactions and mechanisms of drug immobilization and location into surface modified gold nanoparticles (AuNPs). Particularly important information was gained from analysis of NMR spectroscopic parameters such as the spectral line shape, translation diffusion, the nuclear Overhauser effect (NOE) and spin-lattice relaxation (T1). The results confirmed the coexistence of two different types of BTZ inclusion into polyethylene glycol coated gold nanoparticles: (i) association with the polymer chains by weak H-bonds and/or dipole-charge interactions and (ii) adsorption on the surface of the gold nanoparticles. The results allowed for determination of the overall structure of Bortezomib loaded PEG coated AuNPs, which is related to the therapeutic drug efficacy and activity in the treatment of cancer.

  10. NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein.

    Science.gov (United States)

    Biverståhl, Henrik; Andersson, August; Gräslund, Astrid; Mäler, Lena

    2004-11-30

    The structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein (bPrPp) has been investigated by NMR spectroscopy in phospholipid membrane mimetic systems. CD spectroscopy revealed that the peptide adopts a largely alpha-helical structure in zwitterionic bicelles as well as in DHPC micelles but has a less degree of alpha-helix structure in partly charged bicelles. The solution structure of bPrPp was determined in DHPC micelles, and an alpha-helix was found between residues Ser8 and Ile21. The residues within the helical region show slow amide hydrogen exchange. Translational diffusion measurements in zwitterionic q = 0.5 bicelles show that the peptide does not induce aggregation of the bicelles. Increased quadrupolar splittings were observed in the outer part of the (2)H spectrum of DMPC in q = 3.5 bicelles, indicating that the peptide induces a certain degree of order in the bilayer. The amide hydrogen exchange and the (2)H NMR results are consistent with a slight positive hydrophobic mismatch and that bPrPp forms a stable helix that inserts in a transmembrane location in the bilayer. The structure of bPrPp and its position in the membrane may be relevant for the understanding of how the N-terminal (1-30) part of the bovine PrP functions as a cell-penetrating peptide. These findings may lead to a better understanding of how the prion protein accumulates at the membrane surface and also how the conversion into the scrapie form is carried out.

  11. Radiation induced crosslinking in a silica-filled silicone elastomer as investigated by multiple quantum H NMR

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, R S; Chinn, S C; Solyom, D; Cohenour, R

    2005-05-24

    DC745 is a commercially available silicone elastomer consisting of dimethyl, methylphenyl, and vinyl-methyl siloxane monomers crosslinked with a peroxide vinyl specific curing agent. It is generally considered to age gracefully and to be resistant to chemical and thermally harsh environments. However, little data exists on the radiation resistance of this commonly used silicone elastomer. We report static {sup 1}H NMR studies of residual dipolar couplings in DC745 solid elastomers subject to exposure to ionizing gamma radiation. {sup 1}H spin-echo NMR data shows that with increasing dose, the segmental dynamics decrease is consistent with radiatively induced crosslinking. {sup 1}H multiple quantum NMR was used to assess changes in the network structure and observed the presence of a bimodal distribution of residual dipolar couplings, <{Omega}{sub d}>, that were dose dependent. The domain with the lower <{Omega}{sub d}> has been assigned to the polymer network while the domain with the higher <{Omega}{sub d}> has been assigned to polymer chains interacting with the inorganic filler surfaces. In samples exposed to radiation, the residual dipolar couplings in both reservoirs were observed to increase and the populations were observed to be dose dependent. The NMR results are compared to Differential Scanning Calorimetry (DSC) and a two-step solvent swelling technique. The solvent swelling data lend support to the interpretation of the NMR results and the DSC data show both a decrease in the melt temperature and the heat of fusion with cumulative dose, consistent with radiative crosslinking. In addition, DSC thermograms obtained following a 3 hr isothermal soak at -40 C showed the presence of a second melt feature at T{sub m} {approx} -70 C consistent with a network domain with significantly reduced segmental motion.

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

    Science.gov (United States)

    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.

  13. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    Energy Technology Data Exchange (ETDEWEB)

    Marassi, Francesca M., E-mail: fmarassi@sbmri.org; Ding, Yi [Sanford-Burnham Medical Research Institute (United States); Schwieters, Charles D. [National Institutes of Health, Division of Computational Bioscience, Center for Information Technology (United States); Tian, Ye; Yao, Yong [Sanford-Burnham Medical Research Institute (United States)

    2015-09-15

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

  14. USING HIGH-RESOLUTION SOLUTION-STATE NMR SPECTROSCOPY TO INVESTIGATE PMDI REACTIONS WITH WOOD

    Science.gov (United States)

    Solution-state NMR spectroscopy provides a powerful tool for understanding the formation of chemical bonds between wood components and adhesives. Finely ground cell wall (CW) material fully dissolves in a solvent system containing dimethylsulfoxide (DMSO-d6) and N-methyl¬imidazole (NMI-d6), keeping ...

  15. 13C NMR spectra of tectonic coals and the effects of stress on structural components

    Institute of Scientific and Technical Information of China (English)

    JU Yiwen; JIANG Bo; HOU Quanlin; WANG Guiliang; NI Shanqin

    2005-01-01

    High-resolution 13C Nuclear Magnetic Resonance (NMR) spectra of different kinds of tectonic coals were obtained using the NMR (CP/MAS+TOSS) method. On the basis of this, after simulation synthesis and division of spectra, the relative contents of carbon functional groups were calculated. Combined with results of Ro, max, XRD testing and element analysis, stress effects on the composition of macromolecular structures in tectonic coals were studied further. The results showed that Ro, max was not only the important index for describing coal rank, but was also effective for estimating the stress effect of tectonic coals. Under tectonic stress action, Ro, max was the most direct indicator of the coal structure and chemical components. Changes in the stacking Lc of the coal basic structure unit (BSU) and La/Lc parameters could distinguish the temperature and stress effects on metamorphic-deformed environments, and reflected the degree of structural deformation. Therefore, on the whole, Lc and La/Lc can be used to index of the degree of structural deformation of tectonic coals. In different metamorphic and deformed environments, different kinds of tectonic coals are formed under structural stress. The changes in characteristics of the macromolecular structure and chemical composition are such that as the increase in structural deformation becomes stronger, from the brittle deformation coal to ductile deformation coal, the ratio of width at the half height of the aromatic carbon and aliphatic carbon peaks (Hfa/Hfal ) was increased. As carbon aromaticity was raised further, carbon aliphaticity reduced obviously and different compositions of macromolecular structure appeared as a jump and wave pattern except for in wrinkle structure coal, which might result chiefly from stress effects on the macromolecular structure of different kinds of tectonic coals. The macromoecular changes of wrinkle structure coal are reflected mainly on physical structure. In the metamorphic and

  16. Solution NMR of MPS-1 reveals a random coil cytosolic domain structure.

    Science.gov (United States)

    Li, Pan; Shi, Pan; Lai, Chaohua; Li, Juan; Zheng, Yuanyuan; Xiong, Ying; Zhang, Longhua; Tian, Changlin

    2014-01-01

    Caenorhabditis elegans MPS1 is a single transmembrane helical auxiliary subunit that co-localizes with the voltage-gated potassium channel KVS1 in the nematode nervous system. MPS-1 shares high homology with KCNE (potassium voltage-gated channel subfamily E member) auxiliary subunits, and its cytosolic domain was reported to have a serine/threonine kinase activity that modulates KVS1 channel function via phosphorylation. In this study, NMR spectroscopy indicated that the full length and truncated MPS-1 cytosolic domain (134-256) in the presence or absence of n-dodecylphosphocholine detergent micelles adopted a highly flexible random coil secondary structure. In contrast, protein kinases usually adopt a stable folded conformation in order to implement substrate recognition and phosphoryl transfer. The highly flexible random coil secondary structure suggests that MPS-1 in the free state is unstructured but may require a substrate or binding partner to adopt stable structure required for serine/threonine kinase activity.

  17. NMR and structural data for Connexin 32 and Connexin 26 N-terminal peptides

    Directory of Open Access Journals (Sweden)

    Yuksel Batir

    2016-12-01

    Full Text Available In this article we present 1H and 13C chemical shift assignments, secondary structural propensity data and normalized temperature coefficient data for N-terminal peptides of Connexin 26 (Cx26, Cx26G12R and Cx32G12R mutants seen in syndromic deafness and Charcot Marie Tooth Disease respectively, published in “Structural Studies of N-Terminal Mutants of Connexin 26 and Connexin 32 Using 1H NMR Spectroscopy” (Y. Batir, T.A. Bargiello, T.L. Dowd, 2016 [1]. The mutation G12R affects the structure of both Cx26 and Cx32 peptides differently. We present data from secondary structure propensity chemical shift analysis which calculates a secondary structure propensity (SSP score for both disordered or folded peptides and proteins using the difference between the 13C secondary chemical shifts of the Cα and Cβ protons. This data supplements the calculated NMR structures from NOESY data [1]. We present and compare the SSP data for the Cx26 vs Cx26G12R peptides and the Cx32 and Cx32G12R peptides. In addition, we present plots of temperature coefficients obtained for Cx26, Cx26G12R and Cx32G12R peptides collected previously [1] and normalized to their random coil temperature coefficients, “Random coil 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG” (G. Merutka, H.J. Dyson, P.E. Wright, 1995 [2]. Reductions in these normalized temperature coefficients are directly observable for residues in different segments of the peptide and this data informs on solvent accessibility of the NH protons and NH protons which may be more constrained due to the formation of H bonds.

  18. A tabu search approach for the NMR protein structure-based assignment problem.

    Science.gov (United States)

    Cavuşlar, Gizem; Çatay, Bülent; Apaydın, Mehmet Serkan

    2012-01-01

    Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this computationally challenging problem by using prior information about the protein obtained from a homologous structure. NVR-BIP used the Nuclear Vector Replacement (NVR) framework to model SBA as a binary integer programming problem. In this paper, we prove that this problem is NP-hard and propose a tabu search (TS) algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVR-TS uses a quadratic penalty relaxation of NVR-BIP where the violations in the Nuclear Overhauser Effect constraints are penalized in the objective function. Experimental results indicate that our algorithm finds the optimal solution on NVRBIP’s data set which consists of seven proteins with 25 templates (31 to 126 residues). Furthermore, it achieves relatively high assignment accuracies on two additional large proteins, MBP and EIN (348 and 243 residues, respectively), which NVR-BIP failed to solve. The executable and the input files are available for download at http://people.sabanciuniv.edu/catay/NVR-TS/NVR-TS.html.

  19. Adsorption-desorption induced structural changes of Cu-MOF evidenced by solid state NMR and EPR spectroscopy.

    Science.gov (United States)

    Jiang, Yijiao; Huang, Jun; Kasumaj, Besnik; Jeschke, Gunnar; Hunger, Michael; Mallat, Tamas; Baiker, Alfons

    2009-02-18

    Adsorption-desorption induced structural changes of Cu(bpy)(H(2)O)(2)(BF(4)),(bpy) (bpy = 4,4'-bipyridine) [Cu-MOF] have been evidenced by combined NMR and EPR spectroscopy. Upon adsorption of probe molecules even at a few mbar, EPR spectra show that they are activated to form complexes at Cu(II) sites, which results in a change of the Cu-MOF's structure as indicated by a high-field shift of the (11)B MAS NMR. After desorption, both EPR and (11)B MAS NMR spectra evidenced that the structure of the Cu-MOF reversibly shifted to the original state. This observation indicates that MOFs can undergo structural changes during processes where adsorption-desorption steps are involved such as gas storage, separation, and catalysis.

  20. Correlations between (51)V solid-state NMR parameters and chemical structure of vanadium (V) complexes as models for related metalloproteins and catalysts.

    Science.gov (United States)

    Fenn, Annika; Wächtler, Maria; Gutmann, Torsten; Breitzke, Hergen; Buchholz, Axel; Lippold, Ines; Plass, Winfried; Buntkowsky, Gerd

    2009-12-01

    The parameters describing the quadrupolar and CSA interactions of 51V solid-state MAS NMR investigations of model complexes mimicking vanadoenzymes as well as vanadium containing catalysts and enzyme complexes are interpreted with respect to the chemical structure. The interpretation is based on the data of 15 vanadium complexes including two new complexes with previously unpublished data and 13 complexes with data previously published by us. Correlations between the chemical structure and the 51V solid-state NMR data of this class of compounds have been established. Especially for the isotropic chemical shift delta(iso) and the chemical shift anisotropy delta(sigma), correlations with specific structural features like the coordination number of the vanadium atom, the number of coordinating nitrogens, the number of oxygen atoms and the chemical surrounding of the complex could be established for these compounds. Moreover, quantitative correlations between the solid-state NMR parameters and specific bond angles and bond lengths have been obtained. Our results can be of particular interest for future investigations concerning the structure and the mode of action of related vanadoenzymes and vanadate protein assemblies, including the use of vanadate adducts as transition state analogs for phosphate metabolizing systems.

  1. NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison.

    Science.gov (United States)

    Bjorndahl, Trent C; Andrew, Lena C; Semenchenko, Valentyna; Wishart, David S

    2007-11-13

    The human rhinovirus (HRV) is a positive sense RNA virus responsible for about 30% of "common colds". It relies on a 182 residue cysteine protease (3C) to proteolytically process its single gene product. Inhibition of this enzyme in vitro and in vivo has consistently demonstrated cessation of viral replication. This suggests that 3C protease inhibitors could serve as good drug candidates. However, significant proteolytic substrate diversity exists within the 110+ known rhinovirus serotypes. To investigate this variability we used NMR to solve the structure of the rhinovirus serotype 14 3C protease (subgenus B) covalently bound to a peptide (acetyl-LEALFQ-ethylpropionate) inhibitor. The inhibitor-bound structure was determined to an overall rmsd of 0.82 A (backbone atoms) and 1.49 A (all heavy atoms). Comparison with the X-ray structure of the serotype 2 HRV 3C protease from subgenus A (51% sequence identity) bound to the inhibitor ruprintrivir allowed the identification of conserved intermolecular interactions involved in proximal substrate binding as well as subgenus differences that might account for the variability observed in SAR studies. To better characterize the 3C protease and investigate the structural and dynamic differences between the apo and bound states we also solved the solution structure of the apo form. The apo structure has an overall rmsd of 1.07 +/- 0.17 A over backbone atoms, which is greater by 0.25 A than what is seen for the inhibited enzyme (2B0F.pdb). This increase is localized to the enzyme's C-terminal beta-barrel domain, which is responsible for recognizing and binding proteolytic substrates. Amide hydrogen exchange dynamics revealed dramatic differences between the two enzyme states. Furthermore, a number of residues exhibited exchange-broadened amide NMR signals in the apo state compared to the inhibited state. The majority of these residues are associated with proteolytic substrate interaction.

  2. Molecular Structure, NMR, HOMO, LUMO, and Vibrational Analysis of O-Anisic Acid and Anisic Acid Based on DFT Calculations

    Directory of Open Access Journals (Sweden)

    R. Mathammal

    2013-01-01

    Full Text Available This work deals with the vibrational spectroscopy of O-Anisic acid (OAA and Anisic acid (AA. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT with standard B3LYP/6-31G** method and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. The effects of carbonyl and methyl substitutions on the structure and vibrational frequencies have been investigated. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The 13C and 1H NMR chemical shifts of the DFA and CA molecules were calculated using the gauge-invariant-atomic orbital (GIAO method in DMSO solution using IEF-PCM model and compared with experimental data.

  3. {sup 103}Rh NMR investigation of the superconductor Rh{sub 17}S{sub 15}

    Energy Technology Data Exchange (ETDEWEB)

    Koyama, T., E-mail: t-koyama@sci.u-hyogo.ac.j [Graduate School of Material Science, University of Hyogo, Kamigori, Hyogo 678-1297 (Japan); Kanda, K.; Motoyama, G.; Ueda, K.; Mito, T.; Kohara, T. [Graduate School of Material Science, University of Hyogo, Kamigori, Hyogo 678-1297 (Japan); Nakamura, H. [Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501 (Japan)

    2010-12-15

    We present {sup 103}Rh NMR studies for the superconductor Rh{sub 17}S{sub 15} (T{sub c} 5.4 K). We have identified the observed NMR lines corresponding to four different Rh sites in the cubic unit cell and deduced the temperature (T) dependence of the Knight shift components in Rh 24m site whose point symmetry is not axial. The isotropic part of the Knight shift K decreases with T in the normal state, indicating the negative hyperfine coupling and the enhancement of the spin susceptibility at lower T. The sudden change of K below T{sub c} is an indication of the spin-singlet Cooper paring.

  4. Synthesis, crystal structure analysis, spectral (NMR, FT-IR, FT-Raman and UV-Vis) investigations, molecular docking studies, antimicrobial studies and quantum chemical calculations of a novel 4-chloro-8-methoxyquinoline-2(1H)-one: An effective antimicrobial agent and an inhibition of DNA gyrase and lanosterol-14α-demethylase enzymes

    Science.gov (United States)

    Murugavel, S.; Sundramoorthy, S.; Lakshmanan, D.; Subashini, R.; Pavan Kumar, P.

    2017-03-01

    The novel title compound 4-chloro-8-methoxyquinoline-2(1H)-one (4CMOQ) has been synthesized by slow evaporation solution growth technique at room temperature. The synthesized 4CMOQ molecule was characterized experimentally by FT-IR, FT-Raman, UV-Vis, NMR and single crystal diffraction (XRD) and theoretically by quantum chemical calculations. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311++G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. The nuclear magnetic resonance spectra (1H and 13C NMR) are obtained by using the gauge-invariant atomic orbital (GIAO) method. The change in electron density (ED) in the antibonding orbital's and stabilization energies E(2) of the molecule have been evaluated by natural bond orbital (NBO) analysis to give clear evidence of stabilization. Moreover, electronic characteristics such as HOMO and LUMO energies, Mulliken atomic charges and molecular electrostatic potential surface are investigated. Absorption spectrum analysis, nonlinear optical properties, chemical reactivity descriptors and thermodynamic features are also outlined theoretically. Molecular docking studies were executed to understand the inhibitory activity of 4CMOQ against DNA gyrase and Lanosterol 14 α-demethylase. The antimicrobial activity of 4CMOQ was determined against bacterial strains such as Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and fungal strains such as Aspergillus niger, Monascus purpureus and Penicillium citrinum. The obtained results show that the compound exhibited good to moderate antimicrobial activity.

  5. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Marin, Antoine; Malliavin, Therese E. [Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Theorique, CNRS UPR 9080 (France)], E-mail: therese.malliavin@ibpc.fr; Nicolas, Pierre; Delsuc, Marc-Andre [INRA - Domaine de Vilvert, Unite Mathematique Informatique et Genome (France)

    2004-09-15

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C{sub {beta}} and H{sub {beta}}, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H{sub {beta}}, C{sub {beta}}, C{sub {alpha}} and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.

  6. Bis(pentamethylcyclopentadienyl)ytterbium: An investigation of weak interactions in solution using multinuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, David Joel [Univ. of California, Berkeley, CA (United States)

    1995-07-01

    NMR spectroscopy is ideal for studying weak interactions (formation enthalpy ≤20 kcal/mol) in solution. The metallocene bis(pentamethylcyclopentadienyl)ytterbium, Cp*2Yb, is ideal for this purpose. cis-P2PtH2complexes (P = phosphine) were used to produce slow-exchange Cp*2YbL adducts for NMR study. Reversible formation of (P2PtH)2 complexes from cis-P2PtH2 complexes were also studied, followed by interactions of Cp*2Yb with phosphines, R3PX complexes. A NMR study was done on the interactions of Cp*2Yb with H2, CH4, Xe, CO, silanes, stannanes, C6H6, and toluene.

  7. 17O-Dynamic NMR and DFT Investigation of Bis(acyloxyiodoarenes

    Directory of Open Access Journals (Sweden)

    Giovanni Cerioni

    2012-10-01

    Full Text Available Bis(acetoxyiodobenzene and related acyloxy derivatives of hypervalent I(III were studied by variable temperature solution-state 17O-NMR and DFT calculations. The 17O-NMR spectra reveal a dynamic process that interchanges the oxygen atoms of the acyloxy groups. For the first time, coalescence events could be detected for such compounds, allowing the determination of activation free energy data which are found to range between 44 and 47 kJ/mol. The analysis of the 17O linewidth measured for bis(acetoxyiodobenzene indicates that the activation entropy is negligible. DFT calculations show that the oxygen atom exchange arises as a consequence of the [1,3]-sigmatropic shift of iodine. The calculated activation barriers are in excellent agreement with the experimental results. Both the 17O-NMR and DFT studies show that the solvent and chemical alterations, such as modification of the acyl groups or para- substitution of the benzene ring, hardly affect the energetics of the dynamic process. The low I-O Wiberg bond index (0.41–0.42 indicates a possible explanation of the invariance of both the energy barrier and the 17O chemical shift with para-substitution.

  8. Structural Dynamics and Conformational Equilibria of SERCA Regulatory Proteins in Membranes by Solid-State NMR Restrained Simulations

    Science.gov (United States)

    De Simone, Alfonso; Mote, Kaustubh R.; Veglia, Gianluigi

    2014-01-01

    Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes. PMID:24940774

  9. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    Science.gov (United States)

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

  10. NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.

    Science.gov (United States)

    Isernia, Carla; Bucci, Enrico; Leone, Marilisa; Zaccaro, Laura; Di Lello, Paola; Digilio, Giuseppe; Esposito, Sabrina; Saviano, Michele; Di Blasio, Benedetto; Pedone, Carlo; Pedone, Paolo V; Fattorusso, Roberto

    2003-03-03

    Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors. Plant proteins contain from one to four zinc finger domains, which are characterized by high conservation of the sequence QALGGH, shown to be critical for DNA-binding activity. The Arabidopsis thaliana SUPERMAN protein, which contains a single QALGGH zinc finger, is necessary for proper spatial development of reproductive floral tissues and has been shown to specifically bind to DNA. Here, we report the synthesis and UV and NMR spectroscopic structural characterization of a 37 amino acid SUPERMAN region complexed to a Zn(2+) ion (Zn-SUP37) and present the first high-resolution structure of a classical zinc finger domain from a plant protein. The NMR structure of the SUPERMAN zinc finger domain consists of a very well-defined betabetaalpha motif, typical of all other Cys(2)-His(2) zinc fingers structurally characterized. As a consequence, the highly conserved QALGGH sequence is located at the N terminus of the alpha helix. This region of the domain of animal zinc finger proteins consists of hypervariable residues that are responsible for recognizing the DNA bases. Therefore, we propose a peculiar DNA recognition code for the QALGGH zinc finger domain that includes all or some of the amino acid residues at positions -1, 2, and 3 (numbered relative to the N terminus of the helix) and possibly others at the C-terminal end of the recognition helix. This study further confirms that the zinc finger domain, though very simple, is an extremely versatile DNA binding motif.

  11. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations.

    Science.gov (United States)

    Toukach, Filip V; Ananikov, Valentine P

    2013-11-07

    All living systems are comprised of four fundamental classes of macromolecules--nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three principal hierarchical levels of the living world: (1) the molecular level (pathogenic agents and vaccine recognition by the immune system, metabolic pathways involving saccharides that provide cells with energy, and energy accumulation via photosynthesis); (2) the nanoscale level (cell membrane mechanics, structural support of biomolecules, and the glycosylation of macromolecules); (3) the microscale and macroscale levels (polymeric materials, such as cellulose, starch, glycogen, and biomass). NMR spectroscopy is the most powerful research approach for getting insight into the solution structure and function of carbohydrates at all hierarchical levels, from monosaccharides to oligo- and polysaccharides. Recent progress in computational procedures has opened up novel opportunities to reveal the structural information available in the NMR spectra of saccharides and to advance our understanding of the corresponding biochemical processes. The ability to predict the molecular geometry and NMR parameters is crucial for the elucidation of carbohydrate structures. In the present paper, we review the major NMR spectrum simulation techniques with regard to chemical shifts, coupling constants, relaxation rates and nuclear Overhauser effect prediction applied to the three levels of glycomics. Outstanding development in the related fields of genomics and proteomics has clearly shown that it is the advancement of research tools (automated spectrum analysis, structure elucidation, synthesis, sequencing and amplification) that drives the large challenges in modern science. Combining NMR spectroscopy and the computational analysis of structural information encoded in the NMR spectra reveals a way to the automated elucidation of the structure of carbohydrates.

  12. NMR spectroscopy reveals unexpected structural variation at the protein-protein interface in MHC class I molecules

    Energy Technology Data Exchange (ETDEWEB)

    Beerbaum, Monika; Ballaschk, Martin; Erdmann, Natalja [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany); Schnick, Christina [Freie Universitaet Berlin, Institut fuer Immungenetik, Charite-Universitaetsmedizin Berlin (Germany); Diehl, Anne [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany); Uchanska-Ziegler, Barbara; Ziegler, Andreas [Freie Universitaet Berlin, Institut fuer Immungenetik, Charite-Universitaetsmedizin Berlin (Germany); Schmieder, Peter, E-mail: schmieder@fmp-berlin.de [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2013-10-15

    {beta}{sub 2}-Microglobulin ({beta}{sub 2}m) is a small, monomorphic protein non-covalently bound to the heavy chain (HC) in polymorphic major histocompatibility complex (MHC) class I molecules. Given the high evolutionary conservation of structural features of {beta}{sub 2}m in various MHC molecules as shown by X-ray crystallography, {beta}{sub 2}m is often considered as a mere scaffolding protein. Using nuclear magnetic resonance (NMR) spectroscopy, we investigate here whether {beta}{sub 2}m residues at the interface to the HC exhibit changes depending on HC polymorphisms and the peptides bound to the complex in solution. First we show that human {beta}{sub 2}m can effectively be produced in deuterated form using high-cell-density-fermentation and we employ the NMR resonance assignments obtained for triple-labeled {beta}{sub 2}m bound to the HLA-B*27:09 HC to examine the {beta}{sub 2}m-HC interface. We then proceed to compare the resonances of {beta}{sub 2}m in two minimally distinct subtypes, HLA-B*27:09 and HLA-B*27:05, that are differentially associated with the spondyloarthropathy Ankylosing Spondylitis. Each of these subtypes is complexed with four distinct peptides for which structural information is already available. We find that only the resonances at the {beta}{sub 2}m-HC interface show a variation of their chemical shifts between the different complexes. This indicates the existence of an unexpected plasticity that enables {beta}{sub 2}m to accommodate changes that depend on HC polymorphism as well as on the bound peptide through subtle structural variations of the protein-protein interface.

  13. Binding and NMR structural studies on indoloquinoline-oligonucleotide conjugates targeting duplex DNA.

    Science.gov (United States)

    Eick, Andrea; Riechert-Krause, Fanny; Weisz, Klaus

    2012-06-20

    An 11-phenyl-indolo[3,2-b]quinoline (PIQ) was tethered through an aminoalkyl linker to the 5'-end of four pyrimidine oligonucleotides with T/C scrambled sequences at their two 5'-terminal positions. Binding to different double-helical DNA targets formed parallel triple helices with a PIQ-mediated stabilization that strongly depends on pH and the terminal base triad at the 5'-triplex-duplex junction. The most effective stabilization was observed with a TAT triplet at the 5'-junction under low pH conditions, pointing to a protonated ligand with a high triplex binding affinity and unfavorable charge repulsions in the case of a terminal C(+)GC triplet at the junction. The latter preference of the PIQ ligand for TAT over CGC is alleviated yet still preserved at higher pH. Intercalation of PIQ at the 5'-triplex-duplex junction as suggested by the triplex melting experiments was confirmed by homonuclear and heteronuclear NMR structural studies on a specifically isotope-labeled triplex. The NMR analysis revealed two coexisting species that only differ by a 180° rotation of the indoloquinoline within the intercalation pocket. NOE-derived molecular models indicate extensive stacking interactions of the indoloquinoline moiety with the TAT base triplet and CG base pair at the junction and a phenyl substituent that is positioned in the major groove and oriented almost perpendicular to the plane of the indoloquinoline.

  14. Assessment of the structure of pegylated-recombinant protein therapeutics by the NMR fingerprint assay.

    Science.gov (United States)

    Hodgson, Derek J; Aubin, Yves

    2017-05-10

    A number of recombinant protein therapeutic products, such as filgrastim (methionyl granulocyte colony stimulating factor [Met-GCSF] used to boost the immune system in chemotherapy treated cancer patients), and interferon alpha-2 (used for the treatment of various viral infections), have been chemically modified with the addition of a polyethylene glycol (PEG) chain. This modification prolongs residency of the drug in the body and reduces metabolic degradation, which allows less frequent administration of the products. Here we show how NMR spectroscopy methods can assess the higher order structure (HOS) of pegylated-filgrastim (Neulasta®), pegylated interferon-α2a (Pegasys®) pegylated interferon-α2b (PEG-Intron®) purchased from the marketplace. The addition of the PEG moiety effectively doubles the molecular weight of the three products. This presents a significant challenge for the application of NMR techniques. Nevertheless, the results showed that high-resolution spectra could be recorded for two of the three products. Comparison of the spectra of the pegylated protein and the non-pegylated protein shows that the chemical modification did not alter the HOS of these proteins.

  15. 29Si NMR study of structural ordering in aluminosilicate geopolymer gels.

    Science.gov (United States)

    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.

  16. Structure and dynamics of cationic membrane peptides and proteins: Insights from solid-state NMR

    Science.gov (United States)

    Hong, Mei; Su, Yongchao

    2011-01-01

    Many membrane peptides and protein domains contain functionally important cationic Arg and Lys residues, whose insertion into the hydrophobic interior of the lipid bilayer encounters significant energy barriers. To understand how these cationic molecules overcome the free energy barrier to insert into the lipid membrane, we have used solid-state NMR spectroscopy to determine the membrane-bound topology of these peptides. A versatile array of solid-state NMR experiments now readily yields the conformation, dynamics, orientation, depth of insertion, and site-specific protein–lipid interactions of these molecules. We summarize key findings of several Arg-rich membrane peptides, including β-sheet antimicrobial peptides, unstructured cell-penetrating peptides, and the voltage-sensing helix of voltage-gated potassium channels. Our results indicate the central role of guanidinium-phosphate and guanidinium-water interactions in dictating the structural topology of these cationic molecules in the lipid membrane, which in turn account for the mechanisms of this functionally diverse class of membrane peptides. PMID:21344534

  17. Dynamic Nuclear Polarization NMR as a new tool to investigate the nature of organic compounds occluded in plant silica particles.

    Science.gov (United States)

    Masion, Armand; Alexandre, Anne; Ziarelli, Fabio; Viel, Stéphane; Santos, Guaciara M

    2017-06-13

    The determination of the chemical nature of the organic matter associated with phytoliths remains a challenge. This difficulty mainly stems from amounts of organic carbon (C) that are often well below the detection limit of traditional spectroscopic tools. Conventional solid-state (13)C Nuclear Magnetic Resonance (NMR) is widely used to examine the nature and structure of organic molecules, but its inherent low sensitivity prohibits the observation of diluted samples. The recent advent of commercial microwave source in the terahertz range triggered a renewed interest in the Dynamic Nuclear Polarization (DNP) technique to improve the signal to noise ratio of solid-state NMR experiments. With this technique, the (13)C spectrum of a phytolith sample containing 0.1% w/w C was obtained overnight with sufficient quality to permit a semi-quantitative analysis of the organic matter, showing the presence of peptides and carbohydrates as predominant compounds. Considering the natural abundance of the (13)C isotope, this experiment demonstrates that DNP NMR is sufficiently sensitive to observe spin systems present in amounts as low as a few tens of ppm.

  18. Investigating fatty acids inserted into magnetically aligned phospholipid bilayers using EPR and solid-state NMR spectroscopy

    Science.gov (United States)

    Nusair, Nisreen A.; Tiburu, Elvis K.; Dave, Paresh C.; Lorigan, Gary A.

    2004-06-01

    This is the first time 2H solid-state NMR spectroscopy and spin-labeled EPR spectroscopy have been utilized to probe the structural orientation and dynamics of a stearic acid incorporated into magnetically aligned phospholipid bilayers or bicelles. The data gleaned from the two different techniques provide a more complete description of the bilayer membrane system. Both methods provided similar qualitative information on the phospholipid bilayer, high order, and low motion for the hydrocarbon segment close to the carboxyl groups of the stearic acid and less order and more rapid motion at the end towards the terminal methyl groups. However, the segmental order parameters differed markedly due to the different orientations that the nitroxide and C-D bond axes transform with the various stearic acid acyl chain conformations, and because of the difference in dynamic sensitivity between NMR and EPR over the timescales examined. 5-, 7-, 12-, and 16-doxylstearic acids spin-labels were used in the EPR experiments and stearic acid-d 35 was used in the solid-state NMR experiments. The influence of the addition of cholesterol and the variation of temperature on the fatty acid hydrocarbon chain ordering in the DMPC/DHPC phospholipid bilayers was also studied. Cholesterol increased the degree of ordering of the hydrocarbon chains. Conversely, as the temperature of the magnetically aligned phospholipid bilayers increased, the order parameters decreased due to the higher random motion of the acyl chain of the stearic acid. The results indicate that magnetically aligned phospholipid bilayers are an excellent model membrane system and can be used for both NMR and EPR studies.

  19. Compact NMR

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-06-01

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

  20. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

    Science.gov (United States)

    Henriksen, Niel M; Davis, Darrell R; Cheatham, Thomas E

    2012-08-01

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to "update" older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  1. Analysis of the structural quality of the CASD-NMR 2013 entries

    Energy Technology Data Exchange (ETDEWEB)

    Ragan, Timothy J.; Fogh, Rasmus H. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Montelione, Gaetano T. [Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (United States); Rosato, Antonio [University of Florence, Magnetic Resonance Center, Department of Chemistry (Italy); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

  2. Crystal structure and n.m.r. analysis of lactulose trihydrate.

    Science.gov (United States)

    Jeffrey, G A; Huang, D B; Pfeffer, P E; Dudley, R L; Hicks, K B; Nitsch, E

    1992-03-16

    The 13C CPMAS n.m.r. spectrum of 4-O-beta-D-galactopyranosyl-D-fructose (lactulose) trihydrate, C12H22O11.3 H2O, identifies the isomer in the crystals as the beta-furanose. This is confirmed by a crystal structure analysis, using CuK alpha X-ray data at room temperature. The space group is P212121, with Z = 4 and cell dimensions a = 9.6251(3), b = 12.8096(3), c = 17.7563(4) A. The structure was refined to R = 0.031 and Rw 0.025 for 1929 observed structure amplitudes. All the hydrogen atoms were unambigously located on difference syntheses. The conformation of the pyranose ring is the normal 4C1 chair and that of the furanose ring is 4T3. The 1----4 linkage torsion angles are O-5'-C-1'-O-1'-C-4 = 79.9(2) degrees and C-1'-O-1'-C-4-C-5 = -170.3(2) degrees. All hydroxyls, ring and glycosidic oxygens, and water molecules are involved in the hydrogen bonding, which consists of infinite chains linked together by water molecules to form a three-dimensional network. There is a three-centered intramolecular, interresidue hydrogen bond from O-3-H to O-5' and O-6'. The n.m.r. spectrum of the amorphous, dehydrated trihydrate suggests the occurrence of a solid-state reaction forming the same isomeric mixture as was observed in crystalline anhydrous lactulose, although the mutarotation of the trihydrate when dissolved in Me2SO is very slow.

  3. Solid state structure by X-ray and 13C CP/MAS NMR of new 5-[2-(N,N-dimethylamino)ethoxy]-4,7-dimethylcoumarins

    Science.gov (United States)

    Ostrowska, Kinga; Maciejewska, Dorota; Dobrzycki, Łukasz; Socha, Pawel

    2016-05-01

    5-[2-(N,N-dimethylamino)ethoxy]-4,7-dimethylcoumarin (1) and 6-acetyl-5-[2-(N,N-dimethylamino)ethoxy]-4,7-dimethylcoumarin (2), structurally related, were synthesized using both conventional and microwave-assisted approach. An impact of acetyl groups on the molecular structure of coumarin derivatives has been examined. Crystals of 2 were investigated using single crystal and powder X-ray diffraction techniques. Compound 2 crystallizes forming two polymorphs (denoted as 2_1 and 2_2), both belonging to P21/c space group. Both polymorphs are comparably stable and can be formed simultaneously during crystallization process. The solid state structure was also analysed using the fully resolved 13C CP/MAS NMR. The double signals with the intensity ratio of about 1:1 which were observed in the 13C CP/MAS NMR spectrum of compound 1 must arise due to the presence of two conformers of 1. In contrast, NMR spectrum recorded for powder mixture of two polymorphs of compound 2 displays no signal splitting. This is related to structural similarities of molecules in both polymorphs.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-01

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

  5. 1H NMR investigation of self-association of vanillin in aqueous solution

    Science.gov (United States)

    Bogdan, Mircea; Floare, Calin G.; Pîrnau, Adrian

    2009-08-01

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

  6. Stereochemical investigations on the diketopiperazine derivatives of enalapril and lisinopril by NMR spectroscopy

    Science.gov (United States)

    Demeter, Ádám; Fodor, Tamás; Fischer, János

    1998-11-01

    Stereochemical analysis of epimeric diketopiperazine (DKP) derivatives of enalapril and lisinopril has been performed by NMR spectroscopy. The present study focuses on the configurational assignment and conformational characteristics of the epimeric DKPs obtained from cyclization and subsequent base-catalyzed hydrolysis. We report full 1H and 13C assignments as obtained by a concerted use of 1D and 2D methods. The configuration of the respective stereogenic centres and the main conformational features were derived from the measured scalar and NOE connections. One conspicuous conformational feature of the sidechain is its tendency to bend over the piperazinedione ring.

  7. Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Zhou Jianjun; Liang Yongjie; Lin Guohui; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2012-07-15

    In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating 'equivalent resolution' from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 A) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure 'Resolution-by-Proxy' or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect. The ResProx web server is available at http://www.resprox.cahttp://www.resprox.ca.

  8. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    Science.gov (United States)

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.

  9. NMR structure of stem-loop D from human rhinovirus-14.

    Science.gov (United States)

    Headey, Stephen J; Huang, He; Claridge, Jolyon K; Soares, Giselle A; Dutta, Kaushik; Schwalbe, Martin; Yang, Daiwen; Pascal, Steven M

    2007-03-01

    The 5'-cloverleaf of the picornavirus RNA genome is essential for the assembly of a ribonucleoprotein replication complex. Stem-loop D (SLD) of the cloverleaf is the recognition site for the multifunctional viral protein 3Cpro. This protein is the principal viral protease, and its interaction with SLD also helps to position the viral RNA-dependent RNA polymerase (3Dpol) for replication. Human rhinovirus-14 (HRV-14) is distinct from the majority of picornaviruses in that its SLD forms a cUAUg triloop instead of the more common uYACGg tetraloop. This difference appears to be functionally significant, as 3Cpro from tetraloop-containing viruses cannot bind the HRV-14 SLD. We have determined the solution structure of the HRV-14 SLD using NMR spectroscopy. The structure is predominantly an A-form helix, but with a central pyrimidine-pyrimidine base-paired region and a significantly widened major groove. The stabilizing hydrogen bonding present in the uYACGg tetraloop was not found in the cUAUg triloop. However, the triloop uses different structural elements to present a largely similar surface: sequence and underlying architecture are not conserved, but key aspects of the surface structure are. Important structural differences do exist, though, and may account for the observed cross-isotype binding specificities between 3Cpro and SLD.

  10. Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

    Science.gov (United States)

    Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

    2012-07-10

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

  11. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

    Energy Technology Data Exchange (ETDEWEB)

    Tang Ming; Sperling, Lindsay J.; Berthold, Deborah A. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Schwieters, Charles D. [National Institutes of Health, Division of Computational Bioscience, Center for Information Technology (United States); Nesbitt, Anna E.; Nieuwkoop, Andrew J.; Gennis, Robert B.; Rienstra, Chad M., E-mail: rienstra@scs.illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2011-11-15

    X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 A crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 A in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

  12. NMR structure of the first Ig module of mouse FGFR1

    DEFF Research Database (Denmark)

    Kiselyov, V.V.; Bock, Elisabeth Marianne; Berezin, V.;

    2006-01-01

    Fibroblast growth factor (FGF) receptors (FGFRs) regulate a multitude of cellular processes during embryogenesis and in the adult. The extracellular part of the prototypical FGFR consists of three Ig modules (Ig1 - Ig3), in which Ig2 and Ig3 determine affinity and specificity for FGF and heparin...... of this module. We describe here the NMR structure of the Ig1 module of mouse FGFR1. The three-dimensional fold of the module belongs to the intermediate Ig subgroup and can be described as a beta-barrel consisting of two beta-sheets. One sheet is formed by A', G, F, C, and C', and the other by A, B, B', E...

  13. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    Science.gov (United States)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  14. Biosimilar structural comparability assessment by NMR: from small proteins to monoclonal antibodies

    Science.gov (United States)

    Japelj, Boštjan; Ilc, Gregor; Marušič, Jaka; Senčar, Jure; Kuzman, Drago; Plavec, Janez

    2016-01-01

    Biosimilar drug products must have a demonstrated similarity with respect to the reference product’s molecules in order to ensure both the effectiveness of the drug and the patients’ safety. In this paper the fusion framework of a highly sensitive NMR fingerprinting approach for conformational changes and mathematically-based biosimilarity metrics is introduced. The final goal is to translate the complex spectral information into biosimilarity scores, which are then used to estimate the degree of similarity between the biosimilar and the reference product. The proposed method was successfully applied to a small protein, i.e., filgrastim (neutropenia treatment), which is the first biosimilar approved in the United States, and a relatively large protein, i.e., monoclonal antibody rituximab (lymphoma treatment). This innovative approach introduces a new level of sensitivity to structural changes that are induced by, e.g., a small pH shift or other changes in the protein formulation. PMID:27578487

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

    Science.gov (United States)

    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.

  16. Structure of the novel steroidal antibiotic squalamine determined by two-dimensional NMR spectroscopy.

    Science.gov (United States)

    Wehrli, S L; Moore, K S; Roder, H; Durell, S; Zasloff, M

    1993-08-01

    Squalamine is a novel aminosterol recently isolated from the dogfish shark, Squalus acanthias. This water-soluble steroid exhibits potent antibacterial activity against both gram-negative and gram-positive bacteria. In addition, squalamine is fungicidal and induces osmotic lysis of protozoa. We report here the structural determination of squalamine, 3 beta-N-1-[N(3-[4-aminobutyl])-1,3 diaminopropane]-7 alpha,24 zeta-dihydroxy-5 alpha-cholestane 24-sulfate, which was deduced from the analysis of fast atom bombardment spectra and a series of two-dimensional nuclear magnetic resonance (NMR) spectra. Squalamine is a cationic steroid characterized by a condensation of an anionic bile salt intermediate with the polyamine, spermidine. This molecule is a potential host-defense agent in the shark, and provides insight into a new class of vertebrate antimicrobial molecules.

  17. Biosimilar structural comparability assessment by NMR: from small proteins to monoclonal antibodies

    Science.gov (United States)

    Japelj, Boštjan; Ilc, Gregor; Marušič, Jaka; Senčar, Jure; Kuzman, Drago; Plavec, Janez

    2016-08-01

    Biosimilar drug products must have a demonstrated similarity with respect to the reference product’s molecules in order to ensure both the effectiveness of the drug and the patients’ safety. In this paper the fusion framework of a highly sensitive NMR fingerprinting approach for conformational changes and mathematically-based biosimilarity metrics is introduced. The final goal is to translate the complex spectral information into biosimilarity scores, which are then used to estimate the degree of similarity between the biosimilar and the reference product. The proposed method was successfully applied to a small protein, i.e., filgrastim (neutropenia treatment), which is the first biosimilar approved in the United States, and a relatively large protein, i.e., monoclonal antibody rituximab (lymphoma treatment). This innovative approach introduces a new level of sensitivity to structural changes that are induced by, e.g., a small pH shift or other changes in the protein formulation.

  18. Structural investigation of an extracellular polysaccharide produced by the cariogenic bacterium Streptococcus mutans strain UA159

    NARCIS (Netherlands)

    Li, Bo; Dobruchowska, Justyna M.; Hoogenkamp, Michel A.; Gerwig, Gerrit J.

    2012-01-01

    The structure of an extracellular polysaccharide EPS159 produced from sucrose by Streptococcus mutans UA159 was investigated through the main oligosaccharides obtained from partial acid hydrolysis, monosaccharide/methylation analysis, and 1D/2D H-1 NMR spectroscopy. The results showed that EPS159 co

  19. Lipid–protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy

    OpenAIRE

    Fernández, César; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

    2002-01-01

    Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and dihexanoylphosphatidylcholine (DHPC) provided a detailed description of protein–detergent interactions. The NOEs were measured in 3D 15N- and 13C-resolved [1H,1H]-NOESY spectra recorded with selectively methyl-protonated and otherwise uniformly 2H,13C,15N-labeled OmpX in micelles of DHPC at natural isotope abundance. In these mixed micelles the NMR structure of OmpX cons...

  20. Lipid–protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy

    OpenAIRE

    Fernández, César; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

    2002-01-01

    Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and dihexanoylphosphatidylcholine (DHPC) provided a detailed description of protein–detergent interactions. The NOEs were measured in 3D 15N- and 13C-resolved [1H,1H]-NOESY spectra recorded with selectively methyl-protonated and otherwise uniformly 2H,13C,15N-labeled OmpX in micelles of DHPC at natural isotope abundance. In these mixed micelles the NMR structure of OmpX cons...

  1. Preparation of Uniformly 13C,15N-Labeled Recombinant Human Amylin for Solid-State NMR Investigation

    DEFF Research Database (Denmark)

    Kosicka, Iga; Kristensen, Torsten; Bjerring, Morten

    2014-01-01

    of amyloidogenic proteins in large amounts remains challenging due to their aggregation potential, toxicity for cells and difficult purification. In this work, we report a method for the production of large amounts of uniformly labeled 13C,15N-human amylin, being one of the most amyloidogenic peptides known...... crystal ordering, solid-state NMR forms the most suited method to determine the structures of the fibrils with atomic resolution. To exploit this potential, large amounts of isotopic-labeled protein need to be obtained through recombinant protein expression. However, expression and purification...

  2. NMR structural characterization of the N-terminal domain of the adenylyl cyclase-associated protein (CAP) from Dictyostelium discoideum

    Energy Technology Data Exchange (ETDEWEB)

    Mavoungou, Chrystelle [Max Planck Institute for Biochemistry (Germany); Israel, Lars [Ludwig Maximilians-University, Adolf Butenandt Institute, Cell Biology (Germany); Rehm, Till; Ksiazek, Dorota; Krajewski, Marcin; Popowicz, Grzegorz [Max Planck Institute for Biochemistry (Germany); Noegel, Angelika A. [University of Cologne, Institute for Biochemistry (Germany); Schleicher, Michael [Ludwig Maximilians-University, Adolf Butenandt Institute, Cell Biology (Germany); Holak, Tad A. [Max Planck Institute for Biochemistry (Germany)

    2004-05-15

    Cyclase-associated proteins (CAPs) are highly conserved, ubiquitous actin binding proteins that are involved in microfilament reorganization. The N-termini of CAPs play a role in Ras signaling and bind adenylyl cyclase; the C-termini bind to G-actin. We report here the NMR characterization of the amino-terminal domain of CAP from Dictyostelium discoideum (CAP(1-226)). NMR data, including the steady state {sup 1}H-{sup 15}N heteronuclear NOE experiments, indicate that the first 50 N-terminal residues are unstructured and that this highly flexible serine-rich fragment is followed by a stable, folded core starting at Ser 51. The NMR structure of the folded core is an {alpha}-helix bundle composed of six antiparallel helices, in a stark contrast to the recently determined CAP C-terminal domain structure, which is solely built by {beta}-strands.

  3. NMR structural characterization of the N-terminal domain of the adenylyl cyclase-associated protein (CAP) from Dictyostelium discoideum.

    Science.gov (United States)

    Mavoungou, Chrystelle; Israel, Lars; Rehm, Till; Ksiazek, Dorota; Krajewski, Marcin; Popowicz, Grzegorz; Noegel, Angelika A; Schleicher, Michael; Holak, Tad A

    2004-05-01

    Cyclase-associated proteins (CAPs) are highly conserved, ubiquitous actin binding proteins that are involved in microfilament reorganization. The N-termini of CAPs play a role in Ras signaling and bind adenylyl cyclase; the C-termini bind to G-actin. We report here the NMR characterization of the amino-terminal domain of CAP from Dictyostelium discoideum (CAP(1-226)). NMR data, including the steady state (1)H-(15)N heteronuclear NOE experiments, indicate that the first 50 N-terminal residues are unstructured and that this highly flexible serine-rich fragment is followed by a stable, folded core starting at Ser 51. The NMR structure of the folded core is an alpha-helix bundle composed of six antiparallel helices, in a stark contrast to the recently determined CAP C-terminal domain structure, which is solely built by beta-strands.

  4. Secondary structure and zinc ligation of human recombinant short-form stromelysin by multidimensional heteronuclear NMR.

    Science.gov (United States)

    Gooley, P R; Johnson, B A; Marcy, A I; Cuca, G C; Salowe, S P; Hagmann, W K; Esser, C K; Springer, J P

    1993-12-07

    Stromelysin-1, a member of the matrix metalloendoprotease family, is a zinc protease involved in the degradation of connective tissue in the extracellular matrix. As a step toward determining the structure of this protein, multidimensional heteronuclear NMR experiments have been applied to an inhibited truncated form of human stromelysin-1. Extensive 1H, 13C, and 15N sequential assignments have been obtained with a combination of three- and four-dimensional experiments. On the basis of sequential and short-range NOEs and 13C alpha chemical shifts, two helices have been delineated, spanning residues Asp-111 to Val-127 and Leu-195 to Ser-206. A third helix spanning residues Asp-238 to Gly-247 is characterized by sequential NOEs and 13C alpha chemical shifts, but not short-range NOEs. The lack of the latter NOEs suggests that this helix is either distorted or mobile. Similarly, sequential and interstrand NOEs and 13C alpha chemical shifts characterize a four-stranded beta-sheet with three parallel strands (Arg-100 to Ile-101, Ile-142 to Ala-147, Asp-177 to Asp-181) and one antiparallel strand (Ala-165 to Tyr-168). Two zinc sites have been identified in stromelysin [Salowe et al. (1992) Biochemistry 31, 4535-4540]. The NMR spectral properties, including chemical shift, pH dependence, and proton coupling of the imidazole nitrogens of six histidine residues (151, 166, 179, 201, 205, and 211), invariant in the matrix metalloendoprotease family, suggest that these residues are zinc ligands. NOE data indicate that these histidines form two clusters: one ligates the catalytic zinc (His-201, -205, and -211), and the other ligates a structural zinc (His-151, -166, and -179). Heteronuclear multiple quantum correlated spectra and specific labeling experiments indicate His-151, -179, -201, -205, and -211 are in the N delta 1H tautomer and His-166 is in the N epsilon 2H tautomer.

  5. 15N NMR study of nitrate ion structure and dynamics in hydrotalcite-like compounds

    Science.gov (United States)

    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.

  6. Structure and dynamics of bacteriophage IKe major coat protein in MPG micelles by solution NMR.

    Science.gov (United States)

    Williams, K A; Farrow, N A; Deber, C M; Kay, L E

    1996-04-23

    The structure and dynamics of the 53-residue filamentous bacteriophage IKe major coat protein in fully protonated myristoyllysophosphatidylglycerol (MPG) micelles were characterized using multinuclear solution NMR spectroscopy. Detergent-solubilized coat protein [sequence: see text] mimics the membrane-bound "assembly intermediate" form of the coat protein which occurs during part of the phage life cycle. NMR studies of the IKe coat protein show that the coat protein is largely alpha-helical, exhibiting a long amphipathic surface. helix (Asn 4 to Ser 26) and a shorter "micelle-spanning" C-terminal helix which begins at TRP 29 and continues at least to Phe 48. Pro 30 likely occurs in the first turn of the C-terminal helix, where it is ideally situated given the hydrogen bonding and steric restrictions imposed by this residue. The similarity of 15N relaxation values (T1, T2, and NOE and 500 MHz and T2 at 600 MHz) among much of the N-terminal helix and all of the TM helix indicates that the N-terminal helix is as closely associated with the micelle as the TM helix. The description of the protein in the micelle is supported by the observation of NOEs between lysolipid protons and protein amide protons between asn 8 and Ser 50. The N-terminal and TM helices exhibit substantial mobility on the microsecond to second time scale, which likely reflects changes in the orientation between the two helices. The overall findings serve to clarify the role of individual residues in the context of a TM alpha-helix and provide an understanding of the secondary structure, dynamics, and aqueous and micellar environments of the coat protein.

  7. Microsolvation of methylmercury: structures, energies, bonding and NMR constants ((199)Hg, (13)C and (17)O).

    Science.gov (United States)

    Flórez, Edison; Maldonado, Alejandro F; Aucar, Gustavo A; David, Jorge; Restrepo, Albeiro

    2016-01-21

    Hartree-Fock (HF) and second order perturbation theory (MP2) calculations within the scalar and full relativistic frames were carried out in order to determine the equilibrium geometries and interaction energies between cationic methylmercury (CH3Hg(+)) and up to three water molecules. A total of nine structures were obtained. Bonding properties were analyzed using the Quantum Theory of Atoms In Molecules (QTAIM). The analyses of the topology of electron densities reveal that all structures exhibit a partially covalent HgO interaction between methylmercury and one water molecule. Consideration of additional water molecules suggests that they solvate the (CH3HgOH2)(+) unit. Nuclear magnetic shielding constants σ((199)Hg), σ((13)C) and σ((17)O), as well as indirect spin-spin coupling constants J((199)Hg-(13)C), J((199)Hg-(17)O) and J((13)C-(17)O), were calculated for each one of the geometries. Thermodynamic stability and the values of NMR constants correlate with the ability of the system to directly coordinate oxygen atoms of water molecules to the mercury atom in methylmercury and with the formation of hydrogen bonds among solvating water molecules. Relativistic effects account for 11% on σ((13)C) and 14% on σ((17)O), which is due to the presence of Hg (heavy atom on light atom, HALA effect), while the relativistic effects on σ((199)Hg) are close to 50% (heavy atom on heavy atom itself, HAHA effect). J-coupling constants are highly influenced by relativity when mercury is involved as in J((199)Hg-(13)C) and J((199)Hg-(17)O). On the other hand, our results show that the values of NMR constants for carbon and oxygen, atoms which are connected through mercury (C-HgO), are highly correlated and are greatly influenced by the presence of water molecules. Water molecules introduce additional electronic effects to the relativistic effects due to the mercury atom.

  8. NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

    Science.gov (United States)

    Harris, Kimberly A; Bobay, Benjamin G; Sarachan, Kathryn L; Sims, Alexis F; Bilbille, Yann; Deutsch, Christopher; Iwata-Reuyl, Dirk; Agris, Paul F

    2015-08-14

    The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in the biosynthesis of t(6)A37, the details of the enzymatic mechanism remain unsolved. Therefore, the solution structure of Escherichia coli TsaC was characterized by NMR to further study the interactions with ATP and L-threonine, both substrates of TsaC in the biosynthesis of L-threonylcarbamoyl-AMP. Several conserved amino acids were identified that create a hydrophobic binding pocket for the adenine of ATP. Additionally, two residues were found to interact with L-threonine. Both binding sites are located in a deep cavity at the center of the protein. Models derived from the NMR data and molecular modeling reveal several sites with considerable conformational flexibility in TsaC that may be important for L-threonine recognition, ATP activation, and/or protein/protein interactions. These observations further the understanding of the enzymatic reaction catalyzed by TsaC, a threonylcarbamoyl-AMP synthase, and provide structure-based insight into the mechanism of t(6)A37 biosynthesis.

  9. Spin state and orbital ordering in CuCr2O4 investigated by NMR

    Science.gov (United States)

    Jo, Euna; Kang, Byeongki; Kim, Changsoo; Kwon, Sangil; Lee, Soonchil

    2013-09-01

    63,65Cu and 53Cr nuclear magnetic resonance spectra for CuCr2O4 were measured at various magnetic fields and temperatures. The microscopic evidence of orbital ordering in CuCr2O4 was obtained from a dipolar hyperfine field, NQR, and magnetic anisotropy analysis of the linewidth broadening of the Cu and Cr NMR spectra measured in the external magnetic field. The energy gap in the dispersion relation of the spin wave excitation was measured from the temperature dependence of the resonance frequency of Cu and Cr ions in CuCr2O4. The energy gap of the Cu ions is about 10 K (± 5 K), and that of the Cr ions is about 40 K (± 5 K). These values imply that the spin-orbit coupling of Cr ions is stronger than that of Cu ions related to the orbital ordering in CuCr2O4. The magnetic field dependence of the Cr NMR frequency shows that the angle between the Cr3+ magnetic moment and the Cu2+ magnetic moment is about 98∘ (± 2∘).

  10. Differential Isotope Labeling Strategy for Determining the Structure of Myristoylated Recoverin by NMR Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Toshiyuki [University of Tsukuba, Center for Tsukuba Advanced Research Alliance and Institute of Applied Biochemistry (Japan); Ames, James B. [Stanford University School of Medicine, Department of Neurobiology (United States); Kainosho, Masatsune [Tokyo Metropolitan University, Department of Chemistry (Japan); Stryer, Lubert [Stanford University School of Medicine, Department of Neurobiology (United States); Ikura, Mitsuhiko [University of Tsukuba, Center for Tsukuba Advanced Research Alliance and Institute of Applied Biochemistry (Japan)

    1998-02-15

    The three-dimensional solution structure of recombinant bovine myristoylated recoverin in the Ca2+-free state has been refined using an array of isotope-assisted multidimensional heteronuclear NMR techniques. In some experiments, the myristoyl group covalently attached to the protein N-terminus was labeled with 13C and the protein was unlabeled or vice versa; in others, both were 13C-labeled. This differential labeling strategy was essential for structural refinement and can be applied to other acylated proteins. Stereospecific assignments of 41 pairs of {beta}-methylene protons and 48 methyl groups of valine and leucine were included in the structure refinement. The refined structure was constructed using a total of 3679 experimental NMR restraints, comprising 3242 approximate interproton distance restraints (including 153 between the myristoyl group and the polypeptide), 140 distance restraints for 70 backbone hydrogen bonds, and 297 torsion angle restraints. The atomic rms deviations about the averaged minimized coordinate positions for the secondary structure region of the N-terminal and C-terminal domains are 0.44 {+-} 0.07 and 0.55 {+-} 0.18 A for backbone atoms, and 1.09 {+-} 0.07 and 1.10 {+-} 0.15 A for all heavy atoms, respectively. The refined structure allows for a detailed analysis of the myristoyl binding pocket. The myristoyl group is in a slightly bent conformation: the average distance between C1 and C14 atoms of the myristoyl group is 14.6 A. Hydrophobic residues Leu28, Trp31, and Tyr32 form a cluster that interacts with the front end of the myristoyl group (C1-C8), whereas residues Phe49, Phe56, Tyr86, Val87, and Leu90 interact with the tail end (C9-C14). The relatively deep hydrophobic pocket that binds the myristoyl group (C14:0) could also accommodate other naturally occurring acyl groups such as C12:0, C14:1, and C14:2 chains.

  11. NMR assignment of structural motifs in intact β-limit dextrin and its α-amylase degradation products in situ.

    Science.gov (United States)

    Petersen, Bent O; Meier, Sebastian; Duus, Jens Ø

    2012-10-01

    An increasingly detailed and realistic view of biological processes often hinges on atomic-level characterization of biomacromolecules and of the processes they are involved in, preferably under near-physiological conditions. Structure, degradation, and synthesis of glucose storage polymers have been studied for decades with a range of analytical tools, but the detailed in situ analysis has remained an analytical challenge. Here, we report the NMR assignment of different structural motifs in the β-limit dextrin from lintnerized maize starch as a branched α-glucan model system for starch, which is depleted of repetitive α-(1→4) glycosidic bonds at non-reducing ends but has the α-(1→6) branch points intact. By NMR spectroscopy at 18.7T magnetic field, we assign 12 discernible α-glucopyranosyl spin systems and identify them with different structural motifs. Amylolysis of the β-limit dextrin is directly followed by real-time NMR spectroscopy and four major cleavage products are identified and assigned to different branch point structures. Overall, these NMR assignments facilitate in situ assays under realistic conditions of substrate competition, transglycosylation, and product inhibition and shed light on chemical shift tendencies in different structural motifs of branched α-glucans.

  12. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    Science.gov (United States)

    Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J

    2012-03-14

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.

  13. Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

    Directory of Open Access Journals (Sweden)

    Malliavin Thérèse E

    2008-06-01

    Full Text Available Abstract Background The Ambiguous Restraints for Iterative Assignment (ARIA approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. Results ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i an interactive contact map, serving as a tool for the analysis of assignments, and (ii graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. Conclusion The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

  14. Investigation on silver complexes of novel 1,2,3-triazole linked crown ethers by NMR analysis

    Indian Academy of Sciences (India)

    Piotr Seliger; Natalia Gutowska; Monika Stefaniak; Jarosław Romański

    2015-10-01

    The novel derivatives of 1,2,3-triazole linked crown ethers were investigated towards silver(I) ion coordination. The NMR measurements in deuterated methanol in different ratios of ligand and silver cation were studied. The experiments were performed in order to examine the way of binding Ag(I) ion by the selected ligands. The results are presented for complexes with the Ag:L stoichiometry 0.5:1, 1:1 and 2:1, respectively. Depending on the type of crown ether moiety incorporated into the macrocyclic skeleton, interesting differences in the mode of stepwise coordination of the ion were noticed.

  15. Zero in on Key Open Problems in Automated NMR Protein Structure Determination

    KAUST Repository

    Abbas, Ahmed

    2015-11-12

    Nuclear magnetic resonance (NMR) is one of the main approaches for protein struc- ture determination. The biggest advantage of this approach is that it can determine the three-dimensional structure of the protein in the solution phase. Thus, the natural dynamics of the protein can be studied. However, NMR protein structure determina- tion is an expertise intensive and time-consuming process. If the structure determi- nation process can be accelerated or even automated by computational methods, that will significantly advance the structural biology field. Our goal in this dissertation is to propose highly efficient and error tolerant methods that can work well on real and noisy data sets of NMR. Our first contribution in this dissertation is the development of a novel peak pick- ing method (WaVPeak). First, WaVPeak denoises the NMR spectra using wavelet smoothing. A brute force method is then used to identify all the candidate peaks. Af- ter that, the volume of each candidate peak is estimated. Finally, the peaks are sorted according to their volumes. WaVPeak is tested on the same benchmark data set that was used to test the state-of-the-art method, PICKY. WaVPeak shows significantly better performance than PICKY in terms of recall and precision. Our second contribution is to propose an automatic method to select peaks pro- duced by peak picking methods. This automatic method is used to overcome the limitations of fixed number-based methods. Our method is based on the Benjamini- Hochberg (B-H) algorithm. The method is used with both WaVPeak and PICKY to automatically select the number of peaks to return from out of hundreds of candidate peaks. The volume (in WaVPeak) and the intensity (in PICKY) are converted into p-values. Peaks that have p-values below some certain threshold are selected. Ex- perimental results show that the new method is better than the fixed number-based method in terms of recall. To improve precision, we tried to eliminate false peaks using

  16. N-acetylglyoxylic amide bearing a nitrophenyl group as anion receptors: NMR and X-ray investigations on anion binding and selectivity

    Science.gov (United States)

    Suryanti, Venty; Bhadbhade, Mohan; Black, David StC; Kumar, Naresh

    2017-10-01

    N-Nitrophenylglyoxylic amides 1 and 2 in presence of tetrabutylammonium cation (TBA) act as receptors for anions HSO4-, Cl-, Br- and NO3- as investigated by NMR studies. The receptors formed 1:1 host-guest complexes in solution. X-ray structure of 1 along with TBA that bind a chloride anion is reported. Molecule 1 showed the highest selectivity for HSO4- anion over others measured. X-ray structure of the bound Cl- revealed a pocket containing the anion making strong (Nsbnd H⋯Cl) and weak hydrogen bonds (Csbnd H⋯Cl) that contribute to the recognition of the chloride anion. Nsbnd H and Csbnd H hydrogen bonds resulted in a relatively strong binding for chloride ions.

  17. NMR and Electrochemical Investigation of the Transport Properties of Methanol and Water in Nafion and Clay-Nanocomposites Membranes for DMFCs

    Directory of Open Access Journals (Sweden)

    Vincenzo Baglio

    2012-06-01

    Full Text Available Water and methanol transport behavior, solvents adsorption and electrochemical properties of filler-free Nafion and nanocomposites based on two smectite clays, were investigated using impedance spectroscopy, DMFC tests and NMR methods, including spin-lattice relaxation and pulsed-gradient spin-echo (PGSE diffusion under variable temperature conditions. Synthetic (Laponite and natural (Swy-2 smectite clays, with different structural and physical parameters, were incorporated into the Nafion for the creation of exfoliated nanocomposites. Transport mechanism of water and methanol appears to be influenced from the dimensions of the dispersed platelike silicate layers as well as from their cation exchange capacity (CEC. The details of the NMR results and the effect of the methanol solution concentration are discussed. Clays particles, and in particular Swy-2, demonstrate to be a potential physical barrier for methanol cross-over, reducing the methanol diffusion with an evident blocking effect yet nevertheless ensuring a high water mobility up to 130 °C and for several hours, proving the exceptional water retention property of these materials and their possible use in the DMFCs applications. Electrochemical behavior is investigated by cell resistance and polarization measurements. From these analyses it is derived that the addition of clay materials to recast Nafion decreases the ohmic losses at high temperatures extending in this way the operating range of a direct methanol fuel cell.

  18. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

    Science.gov (United States)

    Tian, Ye; Schwieters, Charles D; Opella, Stanley J; Marassi, Francesca M

    2017-01-01

    Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

  19. Concurrent combined verification: reducing false positives in automated NMR structure verification through the evaluation of multiple challenge control structures.

    Science.gov (United States)

    Golotvin, Sergey S; Pol, Rostislav; Sasaki, Ryan R; Nikitina, Asya; Keyes, Philip

    2012-06-01

    Automated structure verification using (1)H NMR data or a combination of (1)H and heteronuclear single-quantum correlation (HSQC) data is gaining more interest as a routine application for qualitative evaluation of large compound libraries produced by synthetic chemistry. The goal of this automated software method is to identify a manageable subset of compounds and data that require human review. In practice, the automated method will flag structure and data combinations that exhibit some inconsistency (i.e. strange chemical shifts, conflicts in multiplicity, or overestimated and underestimated integration values) and validate those that appear consistent. One drawback of this approach is that no automated system can guarantee that all passing structures are indeed correct structures. The major reason for this is that approaches using only (1)H or even (1)H and HSQC spectra often do not provide sufficient information to properly distinguish between similar structures. Therefore, current implementations of automated structure verification systems allow, in principle, false positive results. Presented in this work is a method that greatly reduces the probability of an automated validation system passing incorrect structures (i.e. false positives). This novel method was applied to automatically validate 127 non-proprietary compounds from several commercial sources. Presented also is the impact of this approach on false positive and false negative results.

  20. Investigation of Ti-doped NaAlH4 by solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, R; Majzoub, E; Herberg, J

    2003-11-24

    In recent years, the development of Ti-doped NaAlH{sub 4} as a hydrogen storage material has gained attention because of its large weight percentage of hydrogen ({approx}5%) compared to traditional interstitial hydrides. The addition of transition-metal dopants, in the form of Ti-halides, such as TiCl{sub 3}, dramatically improves the kinetics of the absorption and desorption of hydrogen from NaAlH{sub 4}. However, the role that Ti plays in enhancing the absorption and desorption of H{sub 2} is still unknown. In the present study, {sup 27}Al, {sup 23}Na, and {sup 1}H MAS (Magic Angle Spinning) NMR (Nuclear Magnetic Resonance) has been performed to understand the titanium speciation in Ti-doped NaAlH{sub 4}. All experiments were performed on a sample of crushed single crystals exposed to Ti during growth, a sample of solvent-mixed 4TiCl{sub 3} + 112NaAlH{sub 4}, a reacted sample of solvent-mixed TiCl{sub 3} + {sup 3}NaAlH{sub 4} with THF, and a reacted sample of ball-milled TiCl3 + 3NaAlH{sub 4}. The {sup 27}Al MAS NMR has shown differences in compound formation between solvent-mixed TiCl{sub 3} + 3NaAlH{sub 4} with THF and the mechanically ball-milled TiCl{sub 3} + 3NaAlH{sub 4}. {sup 27}Al MAS NMR of the mechanically ball-milled mixture of fully-reacted TiCl{sub 3} + 3NaAlH{sub 4} showed spectral signatures of TiAl{sub 3} while, the solvent-mixed 4TiCl{sub 3} + 112NaAlH{sub 4}, which is totally reacted, does not show the presences of TiAl{sub 3}, but shows the existence of Al{sub 2}O{sub 3}.

  1. NMR and IR Spectroscopy for the Structural Characterization of Edible Fats and Oils: An Instrumental Analysis Laboratory

    Science.gov (United States)

    Crowther, Molly W.

    2008-01-01

    This article describes an upper-level instrumental laboratory for undergraduates that explores the complementary nature of IR and NMR spectroscopy for analysis of several edible fats and oils that are structurally similar but differ in physical properties and health implications. Five different fats and oils are analyzed for average chain length,…

  2. Structural analysis of a melaminium polyphosphate from X-ray powder diffraction and solid-state NMR data

    NARCIS (Netherlands)

    Brodski, V.; Peschar, R.; Schenk, H.; Brinkmann, A.; Bloemberg, T.G.; Eck, E.R.H. van; Kentgens, A.P.M.

    2005-01-01

    The crystal structure of the environmentally friendly flame retardant melaminium polyphosphate (MPoly) (2,4,6-triamino-1,3,5-triazinium-PO3)(n) was determined by a direct-space global optimization technique from X-ray powder diffraction data. Solid-state NMR was used to corroborate the proposed

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

    Science.gov (United States)

    Akutsu, H; Nishimoto, S; Kyogoku, Y

    1994-08-01

    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.

  4. Structural investigations on lipid nanoparticles containing high amounts of lecithin.

    Science.gov (United States)

    Schubert, Martin Alexander; Harms, Meike; Müller-Goymann, Christel Charlotte

    2006-02-01

    Solid lipid nanoparticles (SLN), an alternative colloidal drug delivery system to polymer nanoparticles, emulsions and liposomes, possess inherent low incorporation rates resulting from the crystalline structure of the solid lipid. To increase the drug loading capacity of SLN, matrix modification by incorporation of the amphiphilic lipid lecithin within the lipid matrices has been proposed as a promising alternative. The objective of this work is to investigate the effects of the lecithin on the microstructure of matrix modified SLN. In addition, these systems were checked for the existence of aggregates like mixed micelles, liposomes, etc., which could possibly be formed by lecithin leakage into the aqueous phase during the preparation process. For this purpose, laser diffraction, photon correlation spectroscopy (PCS), small angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM) were performed to investigate the structure, mobility, and molecular environment of the compounds. Lecithin incorporation within the lipid matrices resulted in a concentration dependent decrease in particle size up to a critical concentration of 30%. Lecithin incorporation up to 50% was investigated but caused no further particle size decrease. TEM revealed anisometrical and crystalline platelets of ellipsoidal to disc-like shape. Furthermore, SAXS and TEM showed no signs of lecithin and nonionic emulsifier derived aggregates in the aqueous phase. This points in agreement with NMR measurements to a strong attachment of both substances to the SLN surfaces. The proposed structure of the particles after melt emulsification consists of two different layers: a crystalline triglyceride-rich core is covered in dependence of the lecithin content either by a monomolecular or multimolecular lecithin/Solutol HS15 (SOL) layer.

  5. A subzero 1H NMR relaxation investigation of water dynamics in tomato pericarp.

    Science.gov (United States)

    Foucat, Loïc; Lahaye, Marc

    2014-09-01

    (1)H NMR relaxation times (T1 and T2) were measured at low field (0.47 T) in pericarp tissues of three tomato genotypes (Ferum, LA0147 and Levovil) at subzero temperature (-20 °C) and two ripening stages (mature green and red). The unfrozen water dynamics was characterised by two T1 and three T2 components. The relaxation time values and their associated relative populations allowed differentiating the ripening stage of only LA0147 and Levovil lines. But the three genotypes were unequivocally discriminated at the red ripe stage. The unfrozen water distribution was discussed in terms of specific interactions, especially with sugars, in relation with their osmoprotectant effects.

  6. A Solid State NMR Investigation of Recent Marine Siliceous Sponge Spicules

    Directory of Open Access Journals (Sweden)

    Sylvie Masse

    2016-03-01

    Full Text Available The composition of four recent siliceous marine sponge spicules was studied and compared. In particular, multinuclear (29Si, 13C, 31P solid state nuclear magnetic resonance (NMR allowed the characterization of both the mineral and organic constituents in a non-destructive manner. The silica network condensation was similar for all samples. The organic matter showed a similar pattern but varied in abundance as a function of the sponge group (Hexactinellida or Demospongiae and sampling conditions (living or dead organisms. This indicates that the striking morphological differences observed at the macroscale for the various samples do not lead to significant fingerprints in the spectroscopic signatures of the mineral and organic constituents.

  7. Investigating the mechanisms of amylolysis of starch granules by solution-state NMR.

    Science.gov (United States)

    Baldwin, Andrew J; Egan, Danielle L; Warren, Fredrick J; Barker, Paul D; Dobson, Christopher M; Butterworth, Peter J; Ellis, Peter R

    2015-05-11

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

  8. Conformational and stereoeletronic investigations of muscarinic agonists of acetylcholine by NMR and theoretical calculations

    Science.gov (United States)

    da Silva, Julio Cesar A.; Ducati, Lucas C.; Rittner, Roberto

    2012-05-01

    NMR solvent effects and theoretical calculations showed muscarinic agonists present a large stability for their near synclinal conformations, indicating the presence of significant stabilization factors. Analysis of the results clearly indicated that this stability is not determined by the dihedral around the substituted C-C ethane bond, as stated by some authors, but a consequence of the geometry adopted in order to maximize N+/O interactions in this type of molecules. It can be assumed that acetylcholine and its muscarinic agonists exhibit their biologic activity when the positively charged nitrogen and the oxygen atoms are in the same side of the molecule within an interatomic distance ranging from 3.0 to 6.0 Å.

  9. Supra-molecular structure and chemical reactivity of cellulose I studied using CP/MAS (sup)13 C-NMR

    CSIR Research Space (South Africa)

    Chunilall, Viren

    2013-08-01

    Full Text Available medium, provided the original work is properly cited. Supra-Molecular Structure and Chemical Reactivity of Cellulose I Studied Using CP/MAS 13C-NMR Viren Chunilall, Tamara Bush and Per Tomas Larsson Additional information is available at the end... of Cellulose I Studied Using CP/MAS 13C-NMR 71 1.1.2. Dissolving pulp The unbleached pulp that results after acid bi-sulphite pulping is used as raw material for dissolving pulp production. Lignin and hemicelluloses in the unbleached pulp are considered...

  10. Structural investigation of hybrid nanocomposites

    Science.gov (United States)

    Lo Celso, F.; Triolo, A.; Negroni, F.; Hainbuchner, M.; Baron, M.; Strunz, P.; Rauch, H.; Triolo, R.

    Ultra small (USANS) and small angle neutron scattering (SANS) techniques were employed to study an elastomer styrene-butadiene, where two kinds of silica fillers have been added in different amounts. Small silica-particle fillers are expected to modify morphological and mechanical properties when dispersed in the copolymer matrix. The USANS and SANS techniques can span a wide range of momentum transfer, investigating morphological properties of the filled elastomer over a number of decades in length scale. Surface and mass fractal behavior has been observed over different length scales.

  11. Structure investigations of electrodeposited nickel

    Energy Technology Data Exchange (ETDEWEB)

    Vertes, A.; Czako-Nagy, I.; Lakatos-Varsani, M. (Eoetvoes Lorand Tudomanyegyetem, Budapest (Hungary). Dept. of Physical Chemistry); Kajcsos, Z. (Hungarian Academy of Sciences, Budapest. Central Research Inst. for Physics); Csordas, L. (Eoetvoes Lorand Tudomanyegyetem, Budapest (Hungary). Dept. of Solid State Physics); Brauer, G. (Zentralinstitut fuer Kernforschung, Rossendorf bei Dresden (German Democratic Republic)); Leidheiser, H. Jr. (Lehigh Univ., Bethlehem, PA (USA). Center for Surface and Coatings Research)

    1982-08-01

    Nickel, electrodeposited under different conditions and yielding different values of stress, was investigated by positron annihilation (lifetime and Doppler-broadening), Moessbauer effect and X-ray diffraction measurements. Two-component positron lifetime spectra were obtained. The first component is thought to result from bulk annihilation and trapping at single trapping centres (TC). Estimations of TC-concentrations are obtained by means of the trapping model. The second one possibly denotes annihilation at voids, the number of which is dependent on the stress in the deposit. Results of Doppler-broadening measurements support this interpretation. The Moessbauer results show differences in the magnetic orientation in the three samples examined.

  12. The NMR Structure of Human Obestatin in Membrane-Like Environments: Insights into the Structure-Bioactivity Relationship of Obestatin

    Science.gov (United States)

    Gurriarán-Rodríguez, Uxía; Mosteiro, Carlos S.; Álvarez-Pérez, Juan C.; Otero-Alén, María; Camiña, Jesús P.; Gallego, Rosalía; García-Caballero, Tomás; Martín-Pastor, Manuel; Casanueva, Felipe F.; Jiménez-Barbero, Jesús; Pazos, Yolanda

    2012-01-01

    The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1). Other analogues, including human non-amidated obestatin (2) and the fragment peptides (6–23)-obestatin (3), (11–23)-obestatin (4), and (16–23)-obestatin (5) have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS). Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation). Our findings emphasize the importance of both the primary structure (composition and size) and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively) at both the structural and bioactivity levels. PMID:23056203

  13. Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

    2014-11-19

    Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

  14. Investigating the interaction between peptides of the amphipathic helix of Hcf106 and the phospholipid bilayer by solid-state NMR spectroscopy

    Science.gov (United States)

    Zhang, Lei; Liu, Lishan; Maltsev, Sergey; Lorigan, Gary A.; Dabney-Smith, Carole

    2013-01-01

    The chloroplast twin arginine translocation (cpTat) system transports highly folded precursor proteins into the thylakoid lumen using the protonmotive force as its only energy source. Hcf106, as one of the core components of the cpTat system, is part of the precursor receptor complex and functions in the initial precursor-binding step. Hcf106 is predicted to contain a single amino terminal transmembrane domain followed by a Pro-Gly hinge, a predicted amphipathic α-helix (APH), and a loosely structured carboxy terminus. Hcf106 has been shown biochemically to insert spontaneously into thylakoid membranes. To better understand the membrane active capabilities of Hcf106, we used solid-state NMR spectroscopy to investigate those properties of the APH. In this study, synthesized peptides of the predicted Hcf106 APH (amino acids 28–65) were incorporated at increasing mol% into 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) and POPC/MGDG (monogalactosyldiacylglycerol; mole ratio 85:15) multilamellar vesicles (MLVs) to probe the peptide-lipid interaction. Solid-state 31P NMR and 2H NMR spectroscopic experiments revealed that the peptide perturbs the headgroup and the acyl chain regions of phospholipids as indicated by changes in spectral lineshape, chemical shift anisotropy (CSA) line width, and 2H order SCD parameters. In addition, the comparison between POPC MLVs and POPC/MGDG MLVs indicated that the lipid bilayer composition affected peptide perturbation of the lipids, and such perturbation appeared to be more intense in a system more closely mimicking a thylakoid membrane. PMID:24144541

  15. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    Science.gov (United States)

    Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

    2015-01-01

    A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

  16. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    Science.gov (United States)

    Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

    2015-01-01

    A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

  17. Structure of UC{sub 2} and U{sub 2}C{sub 3}:XRD, {sup 13}C NMR and EXAFS study

    Energy Technology Data Exchange (ETDEWEB)

    Carvajal Nuñez, U. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany); Eloirdi, R., E-mail: rachel.eloirdi@ec.europa.eu [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany); Prieur, D.; Martel, L. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany); López Honorato, E. [Centro de Investigatión y de Estudios Avanzados del IPN (CINVESTAV), Unidad Saltillo, Av. Industria Metalúrgica 1062, Ramos Arizpe, Coahuila 25900 (Mexico); Farnan, I. [University of Cambridge, Cambridge CB2 1TN (United Kingdom); Vitova, T. [Institut für Nukleare Entsorgung (INE), P.O. Box 3640, D- 76021 Karlsruhe (Germany); Somers, J. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany)

    2014-03-15

    Highlights: • A structural investigation of UC{sub 2} and U{sub 2}C{sub 3} phases was made with XRD, NMR and EXAFS. • Heat treatment of a pulverised UC{sub 2} ingot, repressed into a pellet yields a U{sub 2}C{sub 3} phase coexisting with UC{sub 2−z}. • Heat treatment of UC{sub 2} as cast ingots results in a partial decomposition to UC. • EXAFS data confirmed the CaC{sub 2} and Pu{sub 2}C{sub 3} type structure for UC{sub 2} and U{sub 2}C{sub 3} respectively. • {sup 13}C MAS NMR identified a contribution of a well and less ordered phases in UC{sub 2}. -- Abstract: In this study, uranium dicarbide (UC{sub 2}) has been prepared by arc melting and heat treated under vacuum to form uranium sequicarbide (U{sub 2}C{sub 3}) in the presence of a second phase UC{sub 2−z}. Both samples, as cast and heat treated, have been characterised by chemical analyses, X-ray diffraction (XRD), {sup 13}C magic angle spinning nuclear magnetic resonance (MAS-NMR) and by extended X-ray absorption fine structure (EXAFS). The composition, the purity, the various environments of both U and C atoms as well as the bonds length with the coordination number have been determined. By combining a long-range order method (XRD) and short-range order spectroscopy techniques (EXAFS and NMR), a unique view on the microstructure of UC{sub 2}, before and after heat treatment, and of U{sub 2}C{sub 3} phase has been achieved.

  18. Temperature effects on structure and dynamics in borate and borosilicate liquids: High-resolution and high-temperature NMR results

    Energy Technology Data Exchange (ETDEWEB)

    Stebbins, J.F.; Ellsworth, S.E. [Stanford Univ., Stanford, CA (United States)

    1996-09-01

    The fictive temperature dependence of the relative abundances of three- and four-coordinated boron was investigated in several sodium borate and borosilicate glasses using high-resolution {sup 11}B nuclear magnetic resonance (NMR). In the compositions with low sodium/boron ratios, no effect was observed, but in the borosilicates, the fraction of the tetrahedral species decreased significantly as the fictive temperature increased because of the higher content of nonbridging oxygens. In situ, high-temperature magic-angle spinning NMR demonstrated the exchange of the two species at a rate comparable to the shear relaxation rate, indicating a close link between B-O bond breaking and viscous flow.

  19. Segmental motions of poly(ethylene glycol) chains adsorbed on Laponite platelets in clay-based hydrogels: a NMR investigation.

    Science.gov (United States)

    Lorthioir, Cédric; Khalil, Mouhamad; Wintgens, Véronique; Amiel, Catherine

    2012-05-22

    The segmental dynamics of poly(ethylene glycol) (PEG) chains adsorbed on the clay platelets within nanocomposite PEG/Laponite hydrogels was investigated over the tens of microseconds time scale, using combined solution and solid-state NMR approaches. In a first step, the time evolution of the molecular mobility displayed by the PEG chains following the addition to a Laponite aqueous dispersion was monitored during the aggregation of the clay disks and the hydrogel formation, by means of (1)H solution-state NMR. Part of the PEG repeat units were found to get strongly constrained during the gelation process. Comparisons between this time evolution of the PEG local dynamics in the PEG/Laponite/water systems and the increase of the macroscopic storage shear modulus, mainly governed by the assembling of the Laponite disks, indicate that the slowing down of the segmental motions arises from adsorbed PEG repeat units or chain portions strongly constrained between aggregated clay layers. In a second step, after completion of the gelation process, the molecular motions of the adsorbed PEG chains were probed by (1)H solid-state NMR spectroscopy. (1)H double-quantum experiments indicate that the adsorbed PEG repeat units, though reported to be frozen over a few tens of nanoseconds, still display significant reorientational motions over the tens of microseconds time scale. Using a comparison with a model system of amorphized PEG chains, the characteristic frequency of these segmental motions was found to range between 78.0 kHz and 100.7 MHz at 300 K. Interestingly, at this temperature, the level of reorientational motions detected for these adsorbed PEG chain portions was found to be as restricted as the one of bulk amorphous PEG chains, cooled at a slightly lower temperature (about 290 K).

  20. Analysis of structural variability in pharmaceutical excipients using solid-state NMR spectroscopy.

    Science.gov (United States)

    Sperger, Diana M; Munson, Eric Jon

    2011-09-01

    Polysaccharide-based excipients comprise the majority of most solid dosage forms and can vary dramatically in terms of structural and functionally related properties. Analytical methods for characterizing these important formulation components are crucial. Solid-state NMR spectroscopy (SSNMR) can provide a wealth of information on these materials while offering the advantages of non-destructive sample preparation and selectivity. The overall objective of this work is to identify SSNMR parameters that can be used to detect differences among these excipients. Excipients were obtained from a wide range of suppliers and analyzed as received; (13)C SSNMR spectra were acquired using a Chemagnetics CMX-300 spectrometer operating at approximately 75 MHz. The resolution of SSNMR signals of many excipients allows for positive identification of the major form present. Alginic acid and sodium alginate can be differentiated based on carbonyl peak position. Analysis of relative peak intensities provides insight into the purity of a carrageenan sample compared to known standards. The SSNMR spectrum of starch can be used to identify the source and to quantitate the amorphous and crystalline content. Relaxation values and peak areas of starch derivatives can be related to the degree of hydrolysis, providing an alternative method for determining dextrose equivalent. Differences in peak intensities and relaxation time values of HPMC samples can be correlated to the amount of methoxy subsituent groups. Important characteristics of excipients such as form identification, structural differences, crystalline and amorphous content, and water content variations can be detected using SSNMR spectroscopy.

  1. Structural dynamics of a single-stranded RNA–helix junction using NMR

    Science.gov (United States)

    Eichhorn, Catherine D.; Al-Hashimi, Hashim M.

    2014-01-01

    Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, 13C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A6-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA–helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition. PMID:24742933

  2. Three-dimensional solution structure of ω-conotoxin SO3 determined by 1H NMR

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Cone snails (Conus) elaborate a series of conotoxin (CTX) peptides in their venoms to paralyze their prey. Among these toxins, ω-CTX's specifically target to presynaptic voltage-gated calcium channel subsets, causing inhibition of neurotransmitter release. Ω-CTX SO3 was isolated from the venom of Conus striatus, which is the only available fish-hunting snail near the coast of the South China Sea. The three-dimensional solution structure of ω-CTX SO3, a peptide which is the only ω-conotoxin reported to show high homology with another ω-CTX (MVIIA from C. Magus), has been determined by 1H NMR techniques. The molecular structure of ω-CTX SO3 is stabilized by three disulfide bridges and a short triple-stranded antiparallel ω-sheet with four turns. A comprehensive comparison suggested that the backbone conformation of ω-CTX's was quite conserved, while the length of ω-sheet and the type of some turns might have minor differences.

  3. Quantitative 2D HSQC NMR determination of polymer structures by selecting suitable internal standard references.

    Science.gov (United States)

    Zhang, Liming; Gellerstedt, Göran

    2007-01-01

    A new analytical method based on the 2D HSQC NMR sequence is presented, which can be applied for quantitative structural determination of complicated polymers. The influence of T1 and T2 relaxations, off-resonance effects, coupling constants and homonuclear couplings are discussed. It was found that the T2 values measured on polymeric samples with the conventional HSQC-CPMG sequence could not be used to correct the errors caused by T2 relaxations during the polarization transfer delay. A unique way of selecting the proper internal standard reference signal(s) is therefore proposed to eliminate the major errors caused by T2 relaxations, resonance offsets, coupling constant deviations and homonuclear couplings. Two polymer samples, a cellulose triacetate and an acetylated lignin, have been used to illustrate the principles. The methodology developed in this work is robust to instrument miss-setting and it can find wide-spread applications in areas where a quantitative analysis of structurally complicated polymers is necessary. Copyright (c) 2006 John Wiley & Sons, Ltd.

  4. MAS NMR of HIV-1 protein assemblies

    Science.gov (United States)

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

    2015-04-01

    The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.

  5. Thermodynamic and structural behaviour of equimolar POPC/CnE4 (n=8, 12, 16) mixtures by sorption gravimetry, 2H NMR spectroscopy and X-ray diffraction.

    Science.gov (United States)

    Pfeiffer, H; Klose, G; Heremans, K

    2010-03-01

    The hydration behaviour of equimolar mixtures of phospholipids and nonionic surfactants with different chain length was investigated by gravimetric sorption, NMR spectroscopy and X-ray diffraction. At the most hydration degrees investigated, the incorporation of nonionic surfactants in a phospholipid bilayer leads to an increase of the hydrophilicity, which can be shown by the presence of excess hydration. The increased hydrophilicity could be explained by the excavation of additional water binding sites due to the "dilution" of the dipole field of the phospholipid bilayer. Another related contribution arises from the increase of the accessible surface area due to the increase of gauche conformers that result from the steric mismatch when surfactants are incorporated into the phospholipid matrix. (2)H NMR spectroscopy was used to determine the quadrupolar splitting representing a measure of the order state of water. The swelling behaviour could be assessed by small-angle X-ray diffraction. (31)P NMR spectroscopy was applied for the assignment of phase structures to the respective hydration range.

  6. Interference of spin-, charge- and orbital degrees of freedom in low-carrier rare earth compounds, investigated by NMR

    Science.gov (United States)

    Wada, S.

    2006-05-01

    In rare earth compounds, the concentration of charge carriers is known to strongly influence the nature, and the charge carriers caused by valence fluctuations result in a complete suppression of the magnetic state, as typically observed for YbInCu4. The notable exception has been reported for the cubic (NaCl structure) TmX and YbX families with low carrier, that exhibits antiferro-magnetic (AFM) order at low temperatures. Among these families, TmTe and YbSb with degenerate low-lying multiplets have an additional transition of antiferro-quadrupolar (AFQ) orderings. To elucidate the interplay between the electronic transport and magnetic and/or orbital phenomena close to a semiconductor-to-metal transition, we have carried NMR measurements of 63Cu in YbInCu4, 125Te in TmTe, and 121Sb in YbSb down to 1.2 K and the implication of NMR findings is discussed in terms of the CEF splitting.

  7. 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.

    Science.gov (United States)

    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.

  8. Visualizing the principal component of {sup 1}H,{sup 15}N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Ian M.; Boyko, Robert F.; Sykes, Brian D., E-mail: brian.sykes@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2011-09-15

    Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding {sup 1}H,{sup 15}N-HSQC NMR spectra for homologous proteins, we investigated whether structural information could be ascertained for a new homolog solely from its {sup 1}H,{sup 15}N-HSQC NMR spectrum. We addressed this question with two different approaches. First, we used a semi-automated approach with the program, ORBplus. ORBplus looks for patterns in the chemical shifts and correlates these commonalities to the explicit property of interest. ORBplus ranks resonances based on consistency of the magnitude and direction of the chemical shifts within the database, and the chemical shift correlation of the unknown protein with the database. ORBplus visualizes the results by a histogram and a vector diagram, and provides residue specific predictions on structural similarities with the database. The second method we used was partial least squares (PLS), which is a multivariate statistical technique used to correlate response and predictor variables. We investigated the ability of these methods to predict the tertiary structure of the contractile regulatory protein troponin C. Troponin C undergoes a closed-to-open conformational change, which is coupled to its function in muscle. We found that both ORBplus and PLS were able to identify patterns in the {sup 1}H,{sup 15}N-HSQC NMR data from different states of troponin C that correlated to its conformation.

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

    Science.gov (United States)

    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.

  10. Molecular mobility in dense protein systems: an investigation through 1H NMR relaxometry and diffusometry.

    Science.gov (United States)

    Bouchoux, Antoine; Schorr, Diane; Daffé, Awa; Cambert, Mireille; Gésan-Guiziou, Geneviève; Mariette, François

    2012-09-27

    Understanding how proteins behave in highly concentrated systems is a major issue in many fields of research, including biology, biophysics, and chemical engineering. In this paper, we provide a comprehensive (1)H NMR study of molecular mobility in dilute to highly concentrated dispersions of the exact same protein (casein) but organized in two distinct supramolecular forms: spongelike casein micelles or soft casein aggregates. Both relaxometry and diffusometry experiments were performed, so that three different parameters are reported: spin-spin relaxation rates of non-water protons (1/T(2,ne)), spin-spin relaxation rates of water protons (1/T(2,e+w)), and water self-diffusion coefficients (D(w)). The results are discussed in an effort to understand the respective effects of protein crowding and protein supramolecular organization on each mobility indicator. We also examine if connections exist between the observed changes in molecular mobility and the already documented changes in rheological and osmotic properties of casein dispersions as concentration is increased.

  11. 1D 13C-NMR Data as Molecular Descriptors in Spectra — Structure Relationship Analysis of Oligosaccharides

    Directory of Open Access Journals (Sweden)

    Florbela Pereira

    2012-03-01

    Full Text Available Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the α or β anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1→2, 1→3, 1→4, or 1→6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1 classification of the anomeric configuration of the first unit, second unit and reducing end; (2 classification of the type of first and second linkages; (3 classification of the three residues: reducing end, middle and first residue; and (4 classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set—it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds for the nine tasks, respectively, on the basis of unassigned chemical shifts.

  12. Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation.

    Science.gov (United States)

    Hamley, I W; Nutt, D R; Brown, G D; Miravet, J F; Escuder, B; Rodríguez-Llansola, F

    2010-01-21

    The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide Abeta16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations. The solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one

  13. Probing Membrane Protein Structure Using Water Polarization Transfer Solid-State NMR

    Science.gov (United States)

    Williams, Jonathan K.; Hong, Mei

    2014-01-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected 1H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane peptide of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins. PMID:25228502

  14. Chemical structure and intra-molecular effects on NMR-NQR tensors of harmine and harmaline alkaloids

    Science.gov (United States)

    Ahmadinejad, Neda; Tahan, Arezoo; Talebi Tari, Mostafa

    2016-02-01

    Density functional theory (DFT) methods were used to analyze the effects of molecular structure and ring currents on the NMR chemical shielding tensors and NQR frequencies of harmine and harmaline alkaloids in the gas phase. The results demonstrated that NMR tensors and NQR frequencies of 15N nuclei in these compounds depend on chemical environment and resonance interactions. Hence, their values are obviously different in the mentioned structures. The interpretation of natural bond orbital (NBO) data suggests that in harmine structure, the lone pair participation of N9 in π-system electron clouds causes to development of aromaticity nature in pyrrole ring. However, the chemical shielding around N9 atom in harmine structure is higher than in harmaline, while in harmaline structure, lone pair participation of N2 in π-system electron clouds causes to development of aromaticity nature in pyridine ring. Hence, chemical shielding around N2 atom in harmaline structure is higher than in harmine. It can be deduced that by increasing lone pair electrons contribution of nitrogen atoms in ring resonance interactions and aromaticity development, the values of NMR chemical shielding around them increase, while χ and q zz values of these nuclei decrease.

  15. Vibrational spectroscopic (FT-IR, FT-Raman, ¹H NMR and UV) investigations and computational study of 5-nitro-2-(4-nitrobenzyl) benzoxazole.

    Science.gov (United States)

    Bhagyasree, J B; Varghese, Hema Tresa; Panicker, C Yohannan; Samuel, Jadu; Van Alsenoy, Christian; Bolelli, Kayhan; Yildiz, Ilkay; Aki, Esin

    2013-02-01

    The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 5-nitro-2-(4-nitrobenzyl) benzoxazole have been investigated experimentally and theoretically using Gaussian09 software package. Potential energy distribution of the normal modes of vibrations was done using GAR2PED program. The energy and oscillator strength calculated by time dependent density functional theory almost compliments with experimental findings. Gauge-including atomic orbital (1)H NMR chemical shifts calculations were carried out by using B3LYP functional with 6-31G basis set. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization have been analyzed using NBO analysis. MEP was performed by the DFT method and the predicted infrared intensities and Raman activities have also been reported. The calculated geometrical parameters are in agreement with that of similar derivatives.

  16. Differential scanning calorimetry to investigate G-quadruplexes structural stability.

    Science.gov (United States)

    Pagano, Bruno; Randazzo, Antonio; Fotticchia, Iolanda; Novellino, Ettore; Petraccone, Luigi; Giancola, Concetta

    2013-11-01

    Differential Scanning Calorimetry (DSC) is a straightforward methodology to characterize the energetics of thermally-induced transitions of DNA and other biological macromolecules. Therefore, DSC has been used to study the thermodynamic stability of several nucleic acids structures. G-quadruplexes are among the most important non-canonical nucleic acid architectures that are receiving great consideration. This article reports examples on the contribution of DSC to the knowledge of G-quadruplex structures. The selected case studies show the potential of this method in investigating the structure stability of G-quadruplex forming nucleic acids, and in providing information on their structural complexity. Indeed, DSC can determine thermodynamic parameters of G-quadruplex folding/unfolding processes, but it can also be useful to reveal the formation of multiple conformations or the presence of intermediate states along the unfolding pathway, and to evaluate the impact of chemical modifications on their structural stability. This article aims to show that DSC is an important complementary methodology to structural techniques, such as NMR and X-ray crystallography, in the study of G-quadruplex forming nucleic acids. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Composition of mortar as a function of distance to the brick-mortar interface : A study on the formation of cured mortar structure in masonry using NMR, PFM and XRD

    NARCIS (Netherlands)

    Brocken, H.J.P.; Larbi, J.A.; Pel, L.; Pers, N.M. van der

    1999-01-01

    The formation of cured mortar structure in masonry was studied using multiple experimental techniques. Starting with fresh mortar, nuclear magnetic resonance (NMR) was used to measure the water extraction during brick laying. After curing, the composition of cured mortar was investigated with polari

  18. Composition of mortar as a function of distance to the brick-mortar interface: A study on the formation of cured mortar structure in masonry using NMR, PFM and XRD

    NARCIS (Netherlands)

    Brocken, H.J.P.; Larbi, J.A.; Pel, L.; Van der Pers, N.M.

    1999-01-01

    The formation of cured mortar structure in masonry was studied using multiple experimental techniques. Starting with fresh mortar, nuclear magnetic resonance (NMR) was used to measure the water extraction during brick laying. After curing, the composition of cured mortar was investigated with polari

  19. Composition of mortar as a function of distance to the brick-mortar interface : A study on the formation of cured mortar structure in masonry using NMR, PFM and XRD

    NARCIS (Netherlands)

    Brocken, H.J.P.; Larbi, J.A.; Pel, L.; Pers, N.M. van der

    1999-01-01

    The formation of cured mortar structure in masonry was studied using multiple experimental techniques. Starting with fresh mortar, nuclear magnetic resonance (NMR) was used to measure the water extraction during brick laying. After curing, the composition of cured mortar was investigated with

  20. Composition of mortar as a function of distance to the brick-mortar interface: A study on the formation of cured mortar structure in masonry using NMR, PFM and XRD

    NARCIS (Netherlands)

    Brocken, H.J.P.; Larbi, J.A.; Pel, L.; Van der Pers, N.M.

    1999-01-01

    The formation of cured mortar structure in masonry was studied using multiple experimental techniques. Starting with fresh mortar, nuclear magnetic resonance (NMR) was used to measure the water extraction during brick laying. After curing, the composition of cured mortar was investigated with

  1. Variable-temperature 13C solid-state NMR study of the molecular structure of honeybee wax and silk.

    Science.gov (United States)

    Kameda, Tsunenori; Tamada, Yasushi

    2009-01-01

    To elucidate the native-state crystal structure of beeswax from the Japanese bee, Apis cerana japonica, we determined the relationship between temperature and the 13C solid-state nuclear magnetic resonance (NMR) chemical shift of methylene carbon of beeswax, with comparison to n-alkanes and polyethylene in the orthorhombic, monoclinic, or triclinic crystal form. Variable-temperature 13C solid-state NMR observations of n-alkanes and polyethylene revealed that the chemical shifts of methylene carbon in the orthorhombic crystal form increased linearly with increasing temperature, that of the triclinic form decreased, and that of the monoclinic form was unaltered. These relations were compared with results of variable-temperature 13C solid-state NMR observation of beeswax. Results clarified that the two crystal forms comprising the beeswax in the native state are orthorhombic and monoclinic. The variable-temperature 13C solid-state NMR observations were also applied to interpret the differential scanning calorimetry (DSC) curve of beeswax. They were used to clarify the structural changes of beeswax for widely various temperatures. For beeswax secreted by the Japanese bee, the transition from the orthorhombic form to the rotator phase occurred at 36 degrees C, that is from the crystalline to the intermediate state at 45 degrees C. Moreover, the variable-temperature 13C solid-state NMR spectrum of honeybee silk in the native state was observed. Results demonstrated that the secondary structures of honeybee silk proteins in the native state comprised coexisting alpha-helix and beta-sheet conformations and that the amount of alpha-helices was greater. The alpha-helix content of honeybee silk was compared with that of hornet silk produced by Vespa larvae.

  2. High-resolution (19)F MAS NMR spectroscopy: structural disorder and unusual J couplings in a fluorinated hydroxy-silicate.

    Science.gov (United States)

    Griffin, John M; Yates, Jonathan R; Berry, Andrew J; Wimperis, Stephen; Ashbrook, Sharon E

    2010-11-10

    High-resolution (19)F magic angle spinning (MAS) NMR spectroscopy is used to study disorder and bonding in a crystalline solid. (19)F MAS NMR reveals four distinct F sites in a 50% fluorine-substituted deuterated hydrous magnesium silicate (clinohumite, 4Mg(2)SiO(4)·Mg(OD(1-x)F(x))(2) with x = 0.5), indicating extensive structural disorder. The four (19)F peaks can be assigned using density functional theory (DFT) calculations of NMR parameters for a number of structural models with a range of possible local F environments generated by F(-)/OH(-) substitution. These assignments are supported by two-dimensional (19)F double-quantum MAS NMR experiments that correlate F sites based on either spatial proximity (via dipolar couplings) or through-bond connectivity (via scalar, or J, couplings). The observation of (19)F-(19)F J couplings is unexpected as the fluorines coordinate Mg atoms and the Mg-F interaction is normally considered to be ionic in character (i.e., there is no formal F-Mg-F covalent bonding arrangement). However, DFT calculations predict significant (19)F-(19)F J couplings, and these are in good agreement with the splittings observed in a (19)F J-resolved MAS NMR experiment. The existence of these J couplings is discussed in relation to both the nature of bonding in the solid state and the occurrence of so-called "through-space" (19)F-(19)F J couplings in solution. Finally, we note that we have found similar structural disorder and spin-spin interactions in both synthetic and naturally occurring clinohumite samples.

  3. NMR Structure of Calmodulin Complexed to an N-terminally Acetylated α-Synuclein Peptide

    Science.gov (United States)

    Gruschus, James M.; Yap, Thai Leong; Pistolesi, Sara; Maltsev, Alexander S.; Lee, Jennifer C.

    2013-01-01

    Calmodulin (CaM) is a calcium binding protein that plays numerous roles in Ca-dependent cellular processes, including uptake and release of neurotransmitters in neurons. α-Synuclein (α-syn), one of the most abundant proteins in central nervous system neurons, helps maintain presynaptic vesicles containing neurotransmitters and moderates their Ca-dependent release into the synapse. Ca-bound CaM interacts with α-syn most strongly at its N-terminus. The N-terminal region of α-syn is important for membrane binding, thus CaM could modulate membrane association of α-syn in a Ca-dependent manner. In contrast, Ca-free CaM has negligible interaction. The interaction with CaM leads to significant signal broadening in both CaM and α-syn NMR spectra, most likely due to conformational exchange. The broadening is much reduced when binding a peptide consisting of the first 19 residues of α-syn. In neurons, most α-syn is acetylated at the N-terminus, and acetylation leads to a ten-fold increase in binding strength for the α-syn peptide (KD = 35 ± 10 μM). The N-terminally acetylated peptide adopts a helical structure at the N-terminus with the acetyl group contacting the N-terminal domain of CaM, and with less ordered helical structure towards the C-terminus of the peptide contacting the CaM C-terminal domain. Comparison with known structures shows the CaM/α-syn complex most closely resembles Ca-bound CaM in a complex with an IQ motif peptide. However, a search comparing the α-syn peptide sequence with known CaM targets, including IQ motifs, found no homologies, thus the N-terminal α-syn CaM binding site appears to be a novel CaM target sequence. PMID:23607618

  4. Heparin sodium compliance to USP monograph: structural elucidation of an atypical 2.18 ppm NMR signal.

    Science.gov (United States)

    Mourier, Pierre A J; Guichard, Olivier Y; Herman, Fréderic; Viskov, Christian

    2012-01-01

    The ¹H nuclear magnetic resonance (NMR) acceptance criteria in the new heparin US Pharmacopeia (USP) monograph do not take into account potential structural modifications responsible for any extra signals observed in ¹H NMR spectra, some purified heparins may be non-compliant under the proposed new USP guidelines and incorrectly classified as unsuitable for pharmaceutical use. Heparins from the "ES" source, containing an extra signal at 2.18 ppm, were depolymerized under controlled conditions using heparinases I, II, and III. The oligosaccharides responsible for the 2.18 ppm signal were enriched using orthogonal chromatographic techniques. After multiple purification steps, we obtained an oligosaccharide mixture containing a highly enriched octasaccharide bearing the structural modification responsible for the extra signal. Following heparinase I depolymerization, a pure tetrasaccharide containing the fingerprint structural modification was isolated for full structural determination. Using 1D and 2D ¹H NMR spectroscopy, the structural moiety responsible for the extra signal at 2.18 ppm was identified as an acetyl group on the heparin backbone, most likely resulting from a very minor manufacturing process side reaction that esterifies the uronic acid at position 3. Such analytical peculiarity has always been present in this heparin source and it was used safety over the years. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Solution NMR structure and histone binding of the PHD domain of human MLL5.

    Directory of Open Access Journals (Sweden)

    Alexander Lemak

    Full Text Available Mixed Lineage Leukemia 5 (MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. In addition to its catalytic domain, MLL5 contains a PHD finger domain, a protein module that is often involved in binding to the N-terminus of histone H3. Here we report the NMR solution structure of the MLL5 PHD domain showing a variant of the canonical PHD fold that combines conserved H3 binding features from several classes of other PHD domains (including an aromatic cage along with a novel C-terminal α-helix, not previously seen. We further demonstrate that the PHD domain binds with similar affinity to histone H3 tail peptides di- and tri-methylated at lysine 4 (H3K4me2 and H3K4me3, the former being the putative product of the MLL5 catalytic reaction. This work establishes the PHD domain of MLL5 as a bone fide 'reader' domain of H3K4 methyl marks suggesting that it may guide the spreading or further methylation of this site on chromatin.

  6. Theoretical Studies on Electronic Structures and NMR Spectra of Ollgo(4-vinylpyridine)

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hongjian; ZHOU Jia; HU Lingjing; TENG Qiwen

    2009-01-01

    Poly(4-vinylpyridine)was determined to possess conductivity in the experiment.In order to understand properties of the polymer,a series of 4-vinylpyridine oligomers were designed.The structures of these oligomers were optimized using density function theory(DFT)at B3LYP/6-31G(d)level.The energy gaps and thermal stabilities of the oligomers were decreased when the chain lengths were increased.These properties were also decreased owing to the protonation of the pyridine ring.The holes were easily injected into the oligomers in the presence of hydrochloride.The electrons were conducted in the side chain composed of the pytidine rings rather than the main chain owing to the saturation of the main chain.The 13C nuclear magnetic resonance(NMR)spectra and nucleus independent chemical shifts(NICS)of these compounds were calculated at B3LYP/6-31G(d)level.The chemical shifts of the carbon atoms connected with the nitrogen atoms in the protonated pyridines were moved upfield in comparison with those of the pyridines.The addition of hydrochioride on the pyridine ring in the oligomers led to the increase of the aromaficifies,namely the aromaticities of the oligomers were obviously improved when the pyridine rings were protonated.

  7. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

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

    Science.gov (United States)

    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.

  9. Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Nemmers, S; Tobias, B

    1992-06-15

    15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5-Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31, 898-904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly29 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.

  10. Interactions of acetylcholinesterase with salvianolic acid B and rosmarinic acid from Salvia miltiorhiza water extract investigated by NMR relaxation rate

    Institute of Scientific and Technical Information of China (English)

    Guo Wei Yin; Yi Ming Li; Wei Wei; Shan Hao Jiang; Da Yuan Zhu; Wei Hong Du

    2008-01-01

    In order to understand whether the ameliorating effect on old ages memory disorder by the root of Salvia miltiorhiza is related to the acetylcholinesterase (AChE) inhibition, two main ingredients, salvianolic acid B (1) and rosmarinic acid (2), which were isolated from S. Miltiorhiza water extract, were investigated in vitro by NMR relaxation rate in this work. The results showed that the proton selective relaxation rates and the molecular rotational correlation time of proton pairs for compounds 1 and 2 increased significantly by adding of AChE in mixing solution. The study reveals that the two compounds might bind to the enzyme and have AChE inhibitory effect, which could contribute to the ameliorating effect at some extent on old ages memory disorder.

  11. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    KAUST Repository

    Jang, Richard

    2011-03-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  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.

    Science.gov (United States)

    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.

  13. Which kind of aromatic structures are produced during biomass charring? New insights provided by modern solid-state NMR spectroscopy

    Science.gov (United States)

    Knicker, Heike; Paneque-Carmona, Marina; Velasco-Molina, Marta; de la Rosa, José Maria; León-Ovelar, Laura Regina; Fernandez-Boy, Elena

    2017-04-01

    Intense research on biochar and charcoal of the last years has revealed that depending on the production conditions, the chemical and physical characteristics of their aromatic network can greatly vary. Since such variations are determining the behavior and stability of charred material in soils, a better understanding of the structural changes occurring during their heating and the impact of those changes on their function is needed. One method to characterize pyrogenic organic matter (PyOM) represents solid-state 13C NMR spectroscopy applying the cross polarization (CP) magic angle spinning technique (MAS). A drawback of this technique is that the quantification of NMR spectra of samples with highly condensed and proton-depleted structures is assumed to be bias. Typical samples with such attributes are charcoals produced at temperatures above 700°C under pyrolytic conditions. Commonly their high condensation degree leads to graphenic structures that are not only reducing the CP efficiency but create also a conductive lattice which acts as a shield and prevents the entering of the excitation pulse into the sample during the NMR experiments. Since the latter can damage the NMR probe and in the most cases the obtained NMR spectra show only one broad signal assignable to aromatic C, this technique is rarely applied for characterizing high temperature chars or soot. As a consequence, a more detailed knowledge of the nature of the aromatic ring systems is still missing. The latter is also true for the aromatic domains of PyOM produced at lower temperatures, since older NMR instruments operating at low magnetic fields deliver solid-state 13C NMR spectra with low resolution which turns a more detailed analysis of the aromatic chemical shift region into a challenging task. In order to overcome this disadvantages, modern NMR spectroscopy offers not only instruments with greatly improved resolution but also special pulse sequences for NMR experiments which allow a more

  14. Secondary structure, dynamics, and architecture of the p7 membrane protein from hepatitis C virus by NMR spectroscopy.

    Science.gov (United States)

    Cook, Gabriel A; Opella, Stanley J

    2011-06-01

    P7 is a small membrane protein that is essential for the infectivity of hepatitis C virus. Solution-state NMR experiments on p7 in DHPC micelles, including hydrogen/deuterium exchange, paramagnetic relaxation enhancement and bicelle 'q-titration,' demonstrate that the protein has a range of dynamic properties and distinct structural segments. These data along with residual dipolar couplings yield a secondary structure model of p7. We were able to confirm previous proposals that the protein has two transmembrane segments with a short interhelical loop containing the two basic residues K33 and R35. The 63-amino acid protein has a remarkably complex structure made up of seven identifiable sections, four of which are helical segments with different tilt angles and dynamics. A solid-state NMR two-dimensional separated local field spectrum of p7 aligned in phospholipid bilayers provided the tilt angles of two of these segments. A preliminary structural model of p7 derived from these NMR data is presented.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kharkov, B. B. [Department of Chemistry, Royal Institute of Technology KTH, Stockholm, SE 10044 (Sweden); Chizhik, V. I. [Faculty of Physics, St. Petersburg State University, St. Petersburg 198504 (Russian Federation); Dvinskikh, S. V., E-mail: sergeid@kth.se [Department of Chemistry, Royal Institute of Technology KTH, Stockholm, SE 10044 (Sweden); Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034 (Russian Federation)

    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. Polymeric Structure and Solid NMR Spectra of Cadmuim ( Ⅱ)Dialkyldithiophosphates(Alkyl=Propyl,Butyl,Isopropyl and Isobutyl)

    Institute of Scientific and Technical Information of China (English)

    尹业高; WILLIS; ,Forsling; 等

    2003-01-01

    By dropwise adding thio ligands to concentrated aqueous solutions of Cd(ClO4)2·6H2O ,polymeric complexes,Cd(Ⅱ)O,O′-dipropyldithiophosphate(1),O,O′-dibutyl-dithiophosphate(2),O,O′-diisopropyl-dithiophosphate(3) and O,O′-diisobutyl-dithiophos phate(4) were obtained.The structure of 4 was determined by Xray diffraction analysis,showing that the metal ion sits in distorted tetrahedral sulphur coordination sphere and that the eight-memberd bimetallic rings take the twist chair and boat conformations, alternately.Based on facts that the S(1)-Cd Bond length [0.25099(12)nm] is shorter than the other S-Cd bond length [0.25399(12)-0.25701(18)nm] and that the S(1)-involving angles [113.45(4)°-118.43(5)°] are systematically large than the normal angles of a tetrahedron,the ligands are hypothesized to be erratically functionalized to Cd(Ⅱ).To certify the steric nonequivalence of ligands,the compounds were investigated by solid 13C,31P and 113Cd NMR spectroscopy.

  17. Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

    Science.gov (United States)

    Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

    2016-06-01

    In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

  18. NMR studies of metalloproteins.

    Science.gov (United States)

    Li, Hongyan; Sun, Hongzhe

    2012-01-01

    Metalloproteins represent a large share of the proteomes, with the intrinsic metal ions providing catalytic, regulatory, and structural roles critical to protein functions. Structural characterization of metalloproteins and identification of metal coordination features including numbers and types of ligands and metal-ligand geometry, and mapping the structural and dynamic changes upon metal binding are significant for understanding biological functions of metalloproteins. NMR spectroscopy has long been used as an invaluable tool for structure and dynamic studies of macromolecules. Here we focus on the application of NMR spectroscopy in characterization of metalloproteins, including structural studies and identification of metal coordination spheres by hetero-/homo-nuclear metal NMR spectroscopy. Paramagnetic NMR as well as (13)C directly detected protonless NMR spectroscopy will also be addressed for application to paramagnetic metalloproteins. Moreover, these techniques offer great potential for studies of other non-metal binding macromolecules.

  19. Si-29 NMR Results on Forsterite, Wadsleyite and Ringwoodite: Structural Disorder and Effects of Magnetic Cations

    Science.gov (United States)

    Stebbins, J. F.; Smyth, J. R.; Panero, W. R.; Frost, D. J.

    2008-12-01

    The most abundant mineral in the lower part of the transition zone of the Earth's mantle is probably ringwoodite (spinel structured [Mg,Fe]2SiO4). Recent theoretical calculations (Panero, JGR, in press) have shown that significant, thermally activated Mg,Si disorder should occur in ringwoodite at mantle pressures and temperatures, with important consequences for elastic constants and seismic wave velocities. However, direct characterization of the extent of this disorder, marked by tetrahedral Mg and octahedral Si, has been difficult because of the similar x-ray scattering of Mg and Si. Iron-free, Si-29 enriched, anhydrous synthetic forsterite starting material was used to synthesize ringwoodite and wadsleyite in the 5000-tonne multi-anvil press at the Bayerisches Geoinstitut, at 1500 +- 50 deg C and 24 and 20 GPa, respectively. Estimated temperature-quench times from 1500 to 1000) would allow octahedral Si to be detected at the level of a fraction of 1 %. However, only tetrahedral Si was observed in all samples. This suggests that Mg,Si site disorder present in ringwoodite at high temperature may revert to an ordered distribution on cooling, as has been observed directly for the highest temperature component of the Mg,Al disorder in MgAl2O4 spinel. An additional, small, broad SiO4 peak seen in ringwoodite may be a result of imperfect re-ordering during the rapid quench process. The effects of minor components of paramagnetic dopant cations (e.g. 0.2 % added Co2+ and "natural" impurities in the reagents) on the NMR spectra and on spin-lattice relaxation have also been studied to better understand the small details of the spectra revealed by such high S/N. As is typical for Si-29 in silicates, relaxation is clearly non-exponential and instead initially follows a power law, as expected when controlled by direct coupling to magnetic impurities. Remarkably, in the forsterite, at least 12 small, "extra" NMR peaks are observed, many of which are at chemical shifts well

  20. The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

    Science.gov (United States)

    Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

    2017-10-01

    A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

  1. MAS-NMR investigations of the crystallization behaviour of lithium aluminum silicate (LAS) glasses containing P 2O 5 and TiO 2 nucleants

    Science.gov (United States)

    Ananthanarayanan, A.; Kothiyal, G. P.; Montagne, L.; Revel, B.

    2010-06-01

    Lithium aluminum silicate (LAS) glass of composition (mol%) 20.4Li 2O-4.0Al 2O 3-68.6SiO 2-3.0K 2O-2.6B 2O 3-0.5P 2O 5-0.9TiO 2 was prepared by melt quenching. The glass was then nucleated and crystallized based on differential thermal analysis (DTA) data and was characterized by 29Si, 31P, 11B and 27Al MAS-NMR. XRD and 29Si NMR showed that lithium metasilicate (Li 2SiO 3) is the first phase to c form followed by cristobalite (SiO 2) and lithium disilicate (Li 2Si 2O 5). 29Si MAS-NMR revealed a change in the network structure already for the glasses nucleated at 550 °C. Since crystalline Li 3PO 4, as observed by 31P MAS-NMR, forms concurrently with the silicate phases, we conclude that crystalline Li 3PO 4 does not act as a nucleating agent for lithium silicate phases. Moreover, 31P NMR indicates the formation of M-PO 4 ( M=B, Al or Ti) complexes. The presence of BO 3 and BO 4 structural units in all the glass/glass-ceramic samples is revealed through 11B MAS-NMR. B remains in the residual glass and the crystallization of silicate phases causes a reduction in the number of alkali ions available for charge compensation. As a result, the number of trigonally coordinated B (BO 3) increases at the expense of tetrahedrally coordinated B (BO 4). The 27Al MAS-NMR spectra indicate the presence of tetrahedrally coordinated Al species, which are only slightly perturbed by the crystallization.

  2. NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B.

    Science.gov (United States)

    Zhou, Zheng; Feng, Hanqiao; Hansen, D Flemming; Kato, Hidenori; Luk, Ed; Freedberg, Daron I; Kay, Lewis E; Wu, Carl; Bai, Yawen

    2008-08-01

    The NMR structure of budding yeast chaperone Chz1 complexed with histones H2A.Z-H2B has been determined. Chz1 forms a long irregular chain capped by two short alpha-helices, and uses both positively and negatively charged residues to stabilize the histone dimer. A molecular model that docks Chz1 onto the nucleosome has implications for its potential functions.

  3. NMR structure of mussel mytilin, and antiviral-antibacterial activities of derived synthetic peptides.

    Science.gov (United States)

    Roch, Philippe; Yang, Yinshan; Toubiana, Mylène; Aumelas, André

    2008-01-01

    Mytilin is a 34-residue antibacterial peptide from the mussel Mytilus galloprovincialis, which in addition possesses in vitro antiviral activity. The three-dimensional solution structure of the synthetic mytilin was established by using 1H NMR and consists of the common cysteine-stabilized alphabeta motif close to the one observed in the mussel defensin MGD-1. Mytilin is characterized by 8 cysteines engaged in four disulfide bonds (2-27, 6-29, 10-31, and 15-34) only involving the beta-strand II. Hydrophilic and hydrophobic areas of mytilin account for 63% and 37%, respectively, a ratio very close to that of MGD-1 (64% and 36%). One linear and three cyclic fragments were designed from the interstrand loop sequence known to retain the biological activities in MGD-1. Only the fragment of 10 amino acids (C10C) constrained by two disulfide bonds in a stable beta-hairpin structure was able to inhibit the mortality of Palaemon serratus shrimp injected with white spot syndrome virus (WSSV). Fifty percent inhibition was obtained by in vitro pre-incubation of WSSV with 45 microM of C10C compared with 7 microM for mytilin. Interaction between the fragment and the virus occurred very rapidly as 40% survival was recorded after only 1 min of pre-incubation. In addition, C10C was capable of inhibiting in vitro growth of Vibrio splendidus LGP32 (MIC 125 microM), Vibrio anguillarum (MIC 2mM), Micrococcus lysodeikticus and Escherichia coli (MIC 1mM). Destroying the cysteine-stabilized alphabeta structure or shortening the C10C fragment to the C6C fragment with only one disulfide bond resulted in loss of both antiviral and antibacterial activities. Increasing the positive net charge did not enforce the antibacterial activity and completely suppressed the antiviral one. The C10C-designed peptide from mytilin appeared comparable in composition and structure with protegrin, tachyplesin and polyphemusin.

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

    Science.gov (United States)

    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.

  5. Structural analysis of alkali cations in mixed alkali silicate glasses by 23Na and 133Cs MAS NMR

    Directory of Open Access Journals (Sweden)

    T. Minami

    2014-12-01

    Full Text Available We report the structural analysis of Na+ and Cs+ in sodium cesium silicate glasses by using 23Na and 133Cs magic-angle spinning nuclear magnetic resonance (MAS NMR spectroscopy. In the NMR spectra of cesium silicate crystals, the peak position shifted to higher magnetic field for structures with larger Cs+ coordination numbers and to lower magnetic field for smaller Cs+ coordination numbers. The MAS NMR spectra of xNa2O-yCs2O-2SiO2 (x = 0, 0.2, 0.33, 0.5, 0.66, 0.8, 1.0; x + y = 1 glass reveal that the average coordination number of both the alkali cations decreases with increasing Cs+/(Na+ + Cs+ ratio. In addition, the coordination number of Na+ in xNa2O-yCs2O-2SiO2 glass is smaller than that of Cs+. This difference between the average coordination numbers of the alkali cations is considered to be one structural reason of the mixed alkali effect.

  6. Unlocking the molecular structure of fungal melanin using 13C biosynthetic labeling and solid-state NMR.

    Science.gov (United States)

    Tian, Shiying; Garcia-Rivera, Javier; Yan, Bin; Casadevall, Arturo; Stark, Ruth E

    2003-07-15

    Melanins are enigmatic pigments found in all biological kingdoms that are associated with a variety of functions, including microbial virulence. Despite being ubiquitous in nature, melanin pigments have long resisted atomic-level structural examination because of their insolubility and amorphous organization. Cryptococcus neoformans is a human pathogenic fungus that melanizes only when provided with exogenous substrate, thus offering a unique system for exploring questions related to melanin structure at the molecular level. We have exploited the requirement for exogenous substrate in melanin synthesis as well as the capabilities of high-resolution solid-state nuclear magnetic resonance (NMR) to establish the predominantly aliphatic composition of l-dopa melanin and to introduce (13)C labels that permit the identification of proximal carbons in the developing biopolymer. By swelling solid melanin samples in organic solvents and using two-dimensional heteronuclear NMR in conjunction with magic-angle spinning, we have identified chemical bonding patterns typical of alkane, alkene, alcohol, ketone, ester, and indole functional groups. These findings demonstrate the feasibility of a novel approach to determining the structure of melanin using metabolic labeling and NMR spectroscopy.

  7. Determination of the Three-dimensional Structure of Gynoside A in Solution using NMR and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Wen-Cai Ye

    2007-04-01

    Full Text Available The three-dimensional structure of Gynoside A, an ocotillone-type triterpenoid glycoside isolated from Gynostemma pentaphyllum, was determined in pyridine-d5 and DMSO-d6 solution through constrained molecular modeling using constraints derived from proton NMR spectra. The calculation yielded well-defined global minima. Except for some quantitative details the overall structure of Gynoside A in pyridine-d5 shared many common features with that in DMSO-d6. The structure in pyridine-d5 had lower energies than that in DMSO-d6 solution.

  8. An NMR metabolomics investigation of perturbations after treatment with Chinese herbal medicine formula in an experimental model of sepsis.

    Science.gov (United States)

    Li, Yunzhi; Liu, Hongbin; Wu, Xianzhong; Li, Donghua; Huang, Jing

    2013-05-01

    Sepsis is a leading cause of morbidity and mortality in critically ill patients. OMICS and systems pharmacology approaches offer the promise of new therapeutic candidates for the treatment of patients with sepsis. Qin-Re-Jie-Du (QRJD) and Liang-Xue-Huo-Xue (LXHX) are two traditional Chinese herbal medicine (CHM) formulas with putative effects in sepsis treatment. The present study aimed to assess their efficacy in an experimental model of sepsis in rats (cecal ligation and punctures) and investigate their mechanism of action using a 1H-NMR metabolomics approach. Rats were randomly divided into four groups (i.e., model group, sham control group, and two CHM treatment groups). Water extracts of QRJD and LXHX were orally administered to the two CHM treatment groups at a dose of 24 g/kg of body weight, once daily for 3 consecutive days. The same volume of 0.9% saline solution was orally administered to the model and sham surgery groups. Plasma samples were collected and measured using 600 MHz 1H-NMR spectroscopy. As a result, 18 potential metabolite biomarkers involved in multiple metabolic pathways, including increased energy metabolism, fat mobilization, and disrupted amino acid metabolism, were identified in septic rats. The principal component analysis (PCA) and partial least squares discriminant (PLS-DA) plots of the metabolic state correlated well with the mortality and clinical biochemistry results. An analysis of potential biomarkers verified the holistic effects of the two CHM formulas. The Cori cycle was positively regulated in the QRJD-treated formulas treatment group but also inhibited in the LXHX-treated group, which demonstrates the different efficacies of these solutions in septic rats.

  9. Assignments of 1H and 13C NMR Signals of Mogroside IVa

    Institute of Scientific and Technical Information of China (English)

    ZHANGJian-ye; YANGXiu-wei

    2003-01-01

    Aim To investigate the structure of mogroside IVa isolated from traditional Chinese medicine fructus momordicae [fruits of Siraitia grosvenori (Swingle) C. Jeffery] and summarize the NMR characteristics of the structure. Methods Cormnon extraction, separafion and purification methods were used. Various NMR techniques including 1H NMR,13C NMR, DEPT, 1H-1H COSY, HSQC, HMBC, NOESY and molecular model simulated by comtmter were used to elucidate the structure. Results 1H and 13C NMR signals of mogroside IVa were assigned, and spectroscopic basis was obtained for identification of such type of compounds. Conclusion 1D and 2D NMR techniques including 1H-1H COSY, HSQC, HMBC, NOESY spectra are powerful tools for structure analysis. The structure determined by NMR methods is identical with energy minimized conformation simulated by computer.

  10. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.

    Science.gov (United States)

    Wirmer-Bartoschek, Julia; Bendel, Lars Erik; Jonker, Hendrik R A; Grün, J Tassilo; Papi, Francesco; Bazzicalupi, Carla; Messori, Luigi; Gratteri, Paola; Schwalbe, Harald

    2017-06-12

    Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes.

    Science.gov (United States)

    Vícha, Jan; Patzschke, Michael; Marek, Radek

    2013-05-28

    A methodology for optimizing the geometry and calculating the NMR shielding constants is calibrated for octahedral complexes of Pt(IV) and Ir(III) with modified nucleic acid bases. The performance of seven different functionals (BLYP, B3LYP, BHLYP, BP86, TPSS, PBE, and PBE0) in optimizing the geometry of transition-metal complexes is evaluated using supramolecular clusters derived from X-ray data. The effects of the size of the basis set (ranging from SVP to QZVPP) and the dispersion correction (D3) on the interatomic distances are analyzed. When structural deviations and computational demands are employed as criteria for evaluating the optimizations of these clusters, the PBE0/def2-TZVPP/D3 approach provides excellent results. In the next step, the PBE0/def2-TZVPP approach is used with the continuum-like screening model (COSMO) to optimize the geometry of single molecules for the subsequent calculation of the NMR shielding constants in solution. The two-component zeroth-order regular approximation (SO-ZORA) is used to calculate the NMR shielding constants (PBE0/TZP/COSMO). The amount of exact exchange in the PBE0 functional is validated for the nuclear magnetic shieldings of atoms in the vicinity of heavy transition metals. For the PBE0/TZP/COSMO setup, an exact exchange of 40% is found to accurately reproduce the experimental NMR shielding constants for both types of complexes. Finally, the effect of the amount of exact exchange on the NMR shielding calculations (which is capable of compensating for the structural deficiencies) is analyzed for various molecular geometries (SCS-MP2, BHLYP, and PBE0) and the influence of a trans-substituent on the NMR chemical shift of nitrogen is discussed. The observed dependencies for an iridium complex cannot be rationalized by visualizing the Fermi-contact (FC) induced spin density and probably originate from changes in the d-d transitions that modulate the spin-orbit (SO) part of the SO/FC term.

  12. Investigation on water status and distribution in broccoli and the effects of drying on water status using NMR and MRI methods

    NARCIS (Netherlands)

    Xu, Fangfang; Jin, Xin; Zhang, Lu; Chen, Xiao Dong

    2017-01-01

    Many quality attributes of food products are influenced by the water status and the microstructure. Low-field nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) methods are applied to non-destructively monitor the water status and structure of food. The aim of this study is to

  13. 核磁共振技术在构效关系研究中的应用%Progress on Structure-Activity Relationship by NMR Methods

    Institute of Scientific and Technical Information of China (English)

    王明安

    2000-01-01

      In this paper, two kinds of NMR methods which were used in structure-activity relationship research were introduced. They were structure-activity relationship by 13C NMR and 2D 15N/1H HSQC spectrum.%  介绍了核磁共振技术在构效关系研究中的应用,包括:1)13C NMR在构效关系研究中的应用;2) SAR by NMR 新方法的应用,重点介绍第二种方法。

  14. Choosing the best pulse sequences, acquisition parameters, postacquisition processing strategies, and probes for natural product structure elucidation by NMR spectroscopy.

    Science.gov (United States)

    Reynolds, William F; Enríquez, Raúl G

    2002-02-01

    The relative merits of different pairs of two-dimensional NMR pulse sequences (COSY-90 vs COSY-45, NOESY vs T-ROESY, HSQC vs HMQC, HMBC vs CIGAR, etc.) are compared and recommendations are made for the preferred choice of sequences for natural product structure elucidation. Similar comparisons are made between different selective 1D sequences and the corresponding 2D sequences. Many users of 2D NMR use longer than necessary relaxation delays and neglect to use forward linear prediction processing. It is shown that using shorter relaxation delays in combination with forward linear prediction allows one to get better resolved spectra in less time. The relative merits of different probes and likely future probe developments are also discussed.

  15. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    Science.gov (United States)

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  16. Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof;

    2015-01-01

    A combined experimental and theoretical study has been performed on 9-benzyl-3,6-diiodo-9H-carbazole. Experimental X-ray (100.0 K) and room-temperature 13C NMR studies were supported by advanced density functional theory (DFT) calculations. The non relativistic structure optimization was performed.......57 ppm dropped to 5.6 ppm). A good linear correlation between experimental and theoretically predicted structural and NMR parameters was observed....

  17. **1**5N-NMR INVESTIGATION OF HYDROXYLAMINE DERIVATIZED HUMIC SUBSTANCES.

    Science.gov (United States)

    Thorn, Kevin A.; Arterburn, Jeffrey B.; Mikita, Michael A.

    1986-01-01

    Humic substances are the most abundant naturally occurring refactory organic compounds in soils and water. They have a broad range of physical, chemical and physiological properties. In soils, humic substances contribute to the cation exchange capacity, help maintain the physical structure, and play a role in plant growth and nutrition. In aquatic systems, humic substances serve to regulate the levels of inorganic constituents, yield trihalomethanes upon chlorination, and transport or concentrate organic and inorganic pollutants. The oxygen containing functional groups of humic and fulvic acids are believed to play a key role in the chemical properties of humic substances. This study was undertaken to gain additional information on the specific types of oxygen functionalities in humic substances. Since the analysis of hydroxyl moieties had been earlier established, we focused our attention on the analysis of ketone and aldehyde functional groups in humic substances.

  18. Towards identifying the new structures formed on the {gamma}-radiolysis of Ultem[Ultem; {gamma}-Radiolysis; NMR; Partial structures

    Energy Technology Data Exchange (ETDEWEB)

    Brereton, Ian; Devasahayam, Sheila; Hill, D.J.T. E-mail: hill@chemistry.uq.edu.au; Whittaker, A.K

    2004-01-01

    Ultem irradiated up to 10.0 MGy has been analysed using {sup 13}C, {sup 1}H and 2D proton-carbon and proton-proton correlation NMR spectroscopy to shed light on the formation of new structures. Chemical shifts and correlation data were used to determine the structure or partial structures of several new components. The spectra indicated the presence of new groups and structures involving the isopropylidene group, the imide ring, and hydrogen-abstraction reactions. Possible pathways for formation of the new structures are proposed and the G-values for their formation have been estimated.

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

    Science.gov (United States)

    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.

  20. Synthesis, NMR characterization, X-ray structural analysis and theoretical calculations of amide and ester derivatives of the coumarin scaffold

    Science.gov (United States)

    Matos, Maria J.; Uriarte, Eugenio; Santana, Lourdes; Vilar, Santiago

    2013-06-01

    Compounds 1 (4-methyl-N-(coumarin-3-yl)benzamide) and 2 ((coumarin-3-yl)-4-methylbenzoate) were synthesized by linking the coumarin system (3-aminocoumarin or 3-hydroxycoumarin, respectively) to a p-toluoylchloride. 1H and 13C NMR and X-ray diffractometry determined the molecular structures of both derivatives. The X-ray results were compared to those obtained by conformational analysis followed by semiempirical methodologies (AM1 and PM3). The theoretical calculations yielded results reproducing the whole three-dimensional (3D) structure of both molecules in a good agreement with X-ray structural analysis. The global structures of the two compounds are very similar in the two studied environments, meaning that the structural determination in the gas phase can be extrapolated. A comparative study between compounds 1 and 2, based on the structural results, was carried out.

  1. Communication: Proton NMR dipolar-correlation effect as a method for investigating segmental diffusion in polymer melts

    Science.gov (United States)

    Lozovoi, A.; Mattea, C.; Herrmann, A.; Rössler, E. A.; Stapf, S.; Fatkullin, N.

    2016-06-01

    A simple and fast method for the investigation of segmental diffusion in high molar mass polymer melts is presented. The method is based on a special function, called proton dipolar-correlation build-up function, which is constructed from Hahn Echo signals measured at times t and t/2. The initial rise of this function contains additive contributions from both inter- and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution depends on the relative mean squared displacements (MSDs) of polymer segments from different macromolecules, while the intramolecular part reflects segmental reorientations. Separation of both contributions via isotope dilution provides access to segmental displacements in polymer melts at millisecond range, which is hardly accessible by other methods. The feasibility of the method is illustrated by investigating protonated and deuterated polybutadiene melts with molecular mass 196 000 g/mol at different temperatures. The observed exponent of the power law of the segmental MSD is close to 0.32 ± 0.03 at times when the root MSD is in between 45 Å and 75 Å, and the intermolecular proton dipole-dipole contribution to the total proton Hahn Echo NMR signal is larger than 50% and increases with time.

  2. NMR Investigation of the complexation of (S-2-isopropyl- 1-(o-nitrophenylsulfonylaziridine with -cyclodextrin

    Directory of Open Access Journals (Sweden)

    Mohamed Z. Sliman

    2014-07-01

    Full Text Available Aziridines are known to undergo hydrolysis in the presence of cyclodextrins, whereas the latter are largely investigated as potential vectors of biologically active compounds. Despite this easy cyclodextrin-induced cleavage of aziridines in aqueous medium, it was of interest to find out a model aziridine derivative that would be sufficiently water-stable and form a stable complex with b-cyclodextrin in aqueous medium, so that it could be used as a reference in future formulations or vectorization work. Among compounds we have investigated, we found out that only (S-2-isopropyl-1-(o-nitrophenylsulfonylaziridine complied with the above-mentioned solubility and stability requirements. NMR studies of the inclusion complex of this derivative with b-cyclodextrin provided useful parameters related to the stoichiometry of the complex and the association constant Ka. The geometry of the complex was assessed by 2D-ROESY experiments, suggesting a deep insertion of the aziridine into the cavity of b-cyclodextrin.

  3. Vibrational, NMR and UV-visible spectroscopic investigation and NLO studies on benzaldehyde thiosemicarbazone using computational calculations

    Science.gov (United States)

    Moorthy, N.; Prabakar, P. C. Jobe; Ramalingam, S.; Pandian, G. V.; Anbusrinivasan, P.

    2016-04-01

    In order to investigate the vibrational, electronic and NLO characteristics of the compound; benzaldehyde thiosemicarbazone (BTSC), the XRD, FT-IR, FT-Raman, NMR and UV-visible spectra were recorded and were analysed with the calculated spectra by using HF and B3LYP methods with 6-311++G(d,p) basis set. The XRD results revealed that the stabilized molecular systems were confined in orthorhombic unit cell system. The cause for the change of chemical and physical properties behind the compound has been discussed makes use of Mulliken charge levels and NBO in detail. The shift of molecular vibrational pattern by the fusing of ligand; thiosemicarbazone group with benzaldehyde has been keenly observed. The occurrence of in phase and out of phase molecular interaction over the frontier molecular orbitals was determined to evaluate the degeneracy of the electronic energy levels. The thermodynamical studies of the temperature region 100-1000 K to detect the thermal stabilization of the crystal phase of the compound were investigated. The NLO properties were evaluated by the determination of the polarizability and hyperpolarizability of the compound in crystal phase. The physical stabilization of the geometry of the compound has been explained by geometry deformation analysis.

  4. Phase Structures of Nascent Polyethylene Powder Studied by Wideline Proton NMR

    Institute of Scientific and Technical Information of China (English)

    YAN,Xiao-Wei; WANG,Jing-Dai; REN,Xiao-Hong; YANG,Yong-Rong; JIANG,Bin-Bo; VODA,Mihai Adrian; BERTMER,Marko; STAFF,Siegfried

    2007-01-01

    The wideline proton NMR spectra of polyethylene powder samples were analyzed in terms of contributions from three components: (1) a rigid part with immobile chains, (2) a soft region with liquid-like character which produces a Lorentzian contribution to the spectrum, and (3) an intermediate region in which the rotation of me-thylene groups about C-C bonds is partially hindered. The relative mass fractions as well as chain mobilities varied greatly among samples produced by different polymerization techniques. The NMR crystallinity agreed well with that estimated by WAXD and was much higher than DSC crystallinity, indicating an inclusion of the contribution from a crystalline-amorphous interphase. The crystalline defects in the rigid part could be significantly affected by processing parameters when employing the same type of polymerization technique. The intermediate region in the NMR spectra was analyzed according to the comparison between bimodal high density polyethylene and corresponding linear unimodal one. It was found that the mass fraction of the NMR interphase could be an indication of the percentage of tie molecules between crystalline lamellae and thus may significantly affect the mechanical properties of polymeric material.

  5. Systematic NMR/NQR investigation of the local charge environment in iron pnictides

    Energy Technology Data Exchange (ETDEWEB)

    Graefe, Uwe; Bruening, Eva-Maria; Lang, Guillaume; Veyrat, Louis; Baek, Seung-Ho; Grafe, Hans-Joachim; Hammerath, Franziska; Manthey, Katarina; Behr, Guenther; Werner, Jochen; Wurmehl, Sabine; Buechner, Bernd [IFW Dresden, Institute for Solid State Research, P.O. Box 270116, D-01171 Dresden (Germany); Paar, Dalibor [IFW Dresden, Institute for Solid State Research, P.O. Box 270116, D-01171 Dresden (Germany); Dept. of Physics, Faculty of Science, Univ. of Zagreb, P.O. Box 331, HR-10002 Zagreb (Croatia)

    2012-07-01

    As iron-based superconductors are a striking example of a system featuring unconventional superconductivity close to a region of static magnetism in the phase diagram, much attention has been devoted to the study of ground-state coexistence and/or competition. In this regard, a more general question is the existence and the role played by electronic inhomogeneities, whether in ordered states or in the paramagnetic state. A powerful tool to investigate these issues is Nuclear Magnetic/Quadrupole Resonance, which allows to probe locally the electric charge environment and the spin fluctuations. Here, we present a summary of recent results and on-going studies at the As site of 1111 iron pnictides.

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  8. Extra-framework aluminium species in hydrated faujasite zeolite as investigated by two-dimensional solid-state NMR spectroscopy and theoretical calculations.

    Science.gov (United States)

    Li, Shenhui; Zheng, Anmin; Su, Yongchao; Fang, Hanjun; Shen, Wanling; Yu, Zhiwu; Chen, Lei; Deng, Feng

    2010-04-21

    Extra-framework aluminium (EFAL) species in hydrated dealuminated HY zeolite were thoroughly investigated by various two-dimensional solid-state NMR techniques as well as density functional theoretical calculations. (27)Al MQ MAS NMR experiments demonstrated that five-coordinated and four-coordinated extra-framework aluminium subsequently disappeared with the increase of water loading, and the quadrupole interaction of each aluminium species decreased gradually during the hydration process. (1)H double quantum MAS NMR revealed that the EFAL species in the hydrated zeolite consisted of three components: a hydroxyl AlOH group, and two types of water molecule (rigid and mobile water). (1)H-(27)Al LG-CP HETCOR experiments indicated that both the extra-framework and the framework Al atoms were in close proximity to the rigid water in the fully rehydrated zeolite. The experimental results were further confirmed by DFT theoretical calculations. Moreover, theoretical calculation results further demonstrated that the EFAL species in the hydrated zeolite consisted of the three components and the calculated (1)H NMR chemical shift for each component agreed well with our NMR observations. It is the rigid water that connects the extra-framework aluminium with the four-coordinated framework aluminium through strong hydrogen bonds.

  9. The influence of membrane electrode assembly water content on the performance of a polymer electrolyte membrane fuel cell as investigated by 1H NMR microscopy.

    Science.gov (United States)

    Feindel, Kirk W; Bergens, Steven H; Wasylishen, Roderick E

    2007-04-21

    The relation between the performance of a self-humidifying H(2)/O(2) polymer electrolyte membrane fuel cell and the amount and distribution of water as observed using (1)H NMR microscopy was investigated. The integrated (1)H NMR image signal intensity (proportional to water content) from the region of the polymer electrolyte membrane between the catalyst layers was found to correlate well with the power output of the fuel cell. Several examples are provided which demonstrate the sensitivity of the (1)H NMR image intensity to the operating conditions of the fuel cell. Changes in the O(2)(g) flow rate cause predictable trends in both the power density and the image intensity. Higher power densities, achieved by decreasing the resistance of the external circuit, were found to increase the water in the PEM. An observed plateau of both the power density and the integrated (1)H NMR image signal intensity from the membrane electrode assembly and subsequent decline of the power density is postulated to result from the accumulation of H(2)O(l) in the gas diffusion layer and cathode flow field. The potential of using (1)H NMR microscopy to obtain the absolute water content of the polymer electrolyte membrane is discussed and several recommendations for future research are provided.

  10. Automatic Tuning Matching Cycler (ATMC) In Situ NMR Spectroscopy as a Novel Approach for Real-Time Investigations of Li- and Na-Ion Batteries

    OpenAIRE

    2016-01-01

    This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.jmr.2016.02.008 We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., sign...

  11. What Is the True Color of Fresh Meat? A Biophysical Undergraduate Laboratory Experiment Investigating the Effects of Ligand Binding on Myoglobin Using Optical, EPR, and NMR Spectroscopy

    Science.gov (United States)

    Linenberger, Kimberly; Bretz, Stacey Lowery; Crowder, Michael W.; McCarrick, Robert; Lorigan, Gary A.; Tierney, David L.

    2011-01-01

    With an increased focus on integrated upper-level laboratories, we present an experiment integrating concepts from inorganic, biological, and physical chemistry content areas. Students investigate the effects of ligand strength on the spectroscopic properties of the heme center in myoglobin using UV-vis, [superscript 1]H NMR, and EPR…

  12. What Is the True Color of Fresh Meat? A Biophysical Undergraduate Laboratory Experiment Investigating the Effects of Ligand Binding on Myoglobin Using Optical, EPR, and NMR Spectroscopy

    Science.gov (United States)

    Linenberger, Kimberly; Bretz, Stacey Lowery; Crowder, Michael W.; McCarrick, Robert; Lorigan, Gary A.; Tierney, David L.

    2011-01-01

    With an increased focus on integrated upper-level laboratories, we present an experiment integrating concepts from inorganic, biological, and physical chemistry content areas. Students investigate the effects of ligand strength on the spectroscopic properties of the heme center in myoglobin using UV-vis, [superscript 1]H NMR, and EPR…

  13. Investigation on Acute Biochemical Effects of Ce(NO3)3 on Liver and Kidney Tissues by MAS 1H NMR Spectroscopic-Based Metabonomic Approach

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    High resolution magic angle spinning (MAS)-1 H nuclear magnetic resonance (NMR) spectroscopic-based metabonomic approach was applied to the investigation on the acute biochemical effects of Ce(NO3)3. Male Wistar rats were liver and kidney tissues were analyzed using principal component analysis to extract toxicity information. The biochemical effects of Ce(NO3)3 were characterized by the increase of triglycerides and lactate and the decrease of glycogen in rat liver tissue, together with an elevation of the triglyceride level and a depletion of glycerophosphocholine and betaine in kidney tissues. The target lesions of Ce(NO3)3 on liver and kidney were found by MAS NMR-based metabonomic method. This study demonstrates that the combination of MAS 1H NMR and pattern recognition analysis can be an effective method for studies of biochemical effects of rare earths.

  14. Investigation of the energy barrier to the rotation of amide CN bonds in ACE inhibitors by NMR, dynamic HPLC and DFT.

    Science.gov (United States)

    Bouabdallah, S; Ben Dhia, M T; Driss, M R; Touil, S

    2016-09-01

    The isomerizations of Enalapril, Perindopril, Enalaprilat and Lisinopril have been investigated using NMR spectroscopic, dynamic chromatographic, unified equation and DFT theoretical calculations. The thermodynamic parameters (ΔH, ΔS and ΔG) were determined by varying the temperature in the NMR experiments. At the coalescence temperature, we can evaluate the isomerization barrier to the rotation (ΔG(≠)) around the amide bond. Using dynamics chromatography and an unified equation introduced by Trap, we can determine isomerization rate constants and Gibbs activation energies. Molecular mechanics calculations also provided evidence for the presence of low energy conformers for the ACE due to restricted amide rotation. With the value of barriers (ΔE) between them of the order of (20kJmol(-1)), which is in agreement with the dynamic NMR results and DFT calculations.

  15. Investigations on Synperiplanar and Antiperiplanar Isomers of Losartan: Theoretical and Experimental NMR Studies.

    Science.gov (United States)

    Kujawski, Jacek; Czaja, Kornelia; Ratajczak, Tomasz; Jodłowska, Elżbieta; Chmielewski, Marcin K

    2015-06-29

    Losartan inhibits the renin-angiotensin-aldosterone system by blocking the angiotensin II receptor. It is commonly used in cardiovascular diseases, such as hypertension. Several publications applied the ab initio and density functional theory methods to investigate the molecule of losartan. Only in one of them were the nuclear magnetic resonance spectra calculations carried out, and their results were correlated with the experimental values. The authors focused their attention on calculations of the anion form of losartan, taking into consideration both its synperiplanar and antiperiplanar configurations. Coefficients of determination and mean absolute deviation parameters were calculated for the experimental and calculated chemical shifts for every used basis set. They showed a noticeably stronger correlation for the anti-isomers than for the syn-isomers. Moreover, the solvation model increased the value of this parameter. The results of calculations confirmed that an anti-conformation of the analyte seems to be the preferred one, and such an orientation might be most potent within the receptor cavity, which is in agreement with the results of previous studies.

  16. Investigations on Synperiplanar and Antiperiplanar Isomers of Losartan: Theoretical and Experimental NMR Studies

    Directory of Open Access Journals (Sweden)

    Jacek Kujawski

    2015-06-01

    Full Text Available Losartan inhibits the renin-angiotensin-aldosterone system by blocking the angiotensin II receptor. It is commonly used in cardiovascular diseases, such as hypertension. Several publications applied the ab initio and density functional theory methods to investigate the molecule of losartan. Only in one of them were the nuclear magnetic resonance spectra calculations carried out, and their results were correlated with the experimental values. The authors focused their attention on calculations of the anion form of losartan, taking into consideration both its synperiplanar and antiperiplanar configurations. Coefficients of determination and mean absolute deviation parameters were calculated for the experimental and calculated chemical shifts for every used basis set. They showed a noticeably stronger correlation for the anti-isomers than for the syn-isomers. Moreover, the solvation model increased the value of this parameter. The results of calculations confirmed that an anti-conformation of the analyte seems to be the preferred one, and such an orientation might be most potent within the receptor cavity, which is in agreement with the results of previous studies.

  17. Lipid-protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy.

    Science.gov (United States)

    Fernández, César; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

    2002-10-15

    Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and dihexanoylphosphatidylcholine (DHPC) provided a detailed description of protein-detergent interactions. The NOEs were measured in 3D (15)N- and (13)C-resolved [(1)H,(1)H]-NOESY spectra recorded with selectively methyl-protonated and otherwise uniformly (2)H,(13)C,(15)N-labeled OmpX in micelles of DHPC at natural isotope abundance. In these mixed micelles the NMR structure of OmpX consists of an eight-stranded antiparallel beta-barrel. The OmpX surface area covered with intermolecular NOEs to the DHPC hydrophobic tails forms a continuous cylinder jacket of approximately 28 A in height, which is centered about the middle of the long axis through the beta-barrel. In addition, some intermolecular NOEs with methyl groups of the DHPC polar head were identified along both boundaries of this cylinder jacket. The experimental data suggest that the hydrophobic surface areas of OmpX are covered with a monolayer of DHPC molecules, which appears to mimic quite faithfully the embedding of the beta-barrel in a double-layer lipid membrane.

  18. Lipid–protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy

    Science.gov (United States)

    Fernández, César; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

    2002-01-01

    Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and dihexanoylphosphatidylcholine (DHPC) provided a detailed description of protein–detergent interactions. The NOEs were measured in 3D 15N- and 13C-resolved [1H,1H]-NOESY spectra recorded with selectively methyl-protonated and otherwise uniformly 2H,13C,15N-labeled OmpX in micelles of DHPC at natural isotope abundance. In these mixed micelles the NMR structure of OmpX consists of an eight-stranded antiparallel β-barrel. The OmpX surface area covered with intermolecular NOEs to the DHPC hydrophobic tails forms a continuous cylinder jacket of approximately 28 Å in height, which is centered about the middle of the long axis through the β-barrel. In addition, some intermolecular NOEs with methyl groups of the DHPC polar head were identified along both boundaries of this cylinder jacket. The experimental data suggest that the hydrophobic surface areas of OmpX are covered with a monolayer of DHPC molecules, which appears to mimic quite faithfully the embedding of the β-barrel in a double-layer lipid membrane. PMID:12370417

  19. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical s...

  20. Vibrational, NMR and quantum chemical investigations of acetoacetanilde, 2-chloroacetoacetanilide and 2-methylacetoacetanilide.

    Science.gov (United States)

    Arjunan, V; Kalaivani, M; Senthilkumari, S; Mohan, S

    2013-11-01

    The vibrational assignment and analysis of the fundamental modes of the compounds acetoacetanilide (AAA), 2-chloroacetoacetanilide (2CAAA) and 2-methylacetoacetanilide (2MAAA) have been performed. Density functional theory studies have been carried out with B3LYP method utilising 6-311++G(**) and cc-pVTZ basis sets to determine structural, thermodynamic and vibrational characteristics of the compounds and also to understand the influence of chloro and methyl groups on the characteristic frequencies of amide (CONH) group. Intramolecular hydrogen bond exists in acetoacetanilide and o-substituted acetoacetanilide molecules and the N⋯O distance is found to be around 2.7Å. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecules were determined and the same have been calculated using the gauge independent atomic orbital (GIAO) method. The energies of the frontier molecular orbitals have been determined. In AAA, 2CAAA and 2MAAA molecules, the nN→πCO(∗) interaction between the nitrogen lone pair and the amide CO antibonding orbital gives strong stabilization of 64.75, 62.84 and 64.18kJmol(-1), respectively. The blue shift in amide-II band of 2MAAA is observed by 45-50cm(-1) than that of AAA. The steric effect of ortho methyl group significantly operating on the NH bond properties. The amide-III, the CN stretching mode of methyl and chloro substituted acetoacetanilide compounds are not affected by the substitution while the amide-V band, the NH out of plane bending mode of 2-chloroacetoacetanilide compound is shifted to a higher frequency than that of AAA. The substituent chlorine plays significantly and the blue shift in o-substituted compounds than the parent in the amide-V vibration is observed. The amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA are significantly raised than that of AAA. A blue shift of amide-VI, CO out of plane bending modes of 2MAAA and 2CAAA than AAA is observed.

  1. Combination of NMR and MRI quantitation of moisture and structure changes for convection cooking of fresh chicken meat.

    Science.gov (United States)

    Shaarani, Sharifudin Md; Nott, Kevin P; Hall, Laurance D

    2006-03-01

    This study demonstrates that a combination of bulk NMR and magnetic resonance imaging measurements of the T(2)-values of water protons can be used to determine the heat-induced changes in the structure and moisture content of fresh chicken meat which had been cooked in a convection oven at 200°C for a range of times. The gravimetric moisture content was also determined for both the raw and cooked meat. Multi-exponential fitting of the bulk NMR T(2) relaxation time data demonstrated three distinct water populations T(21) (39-43ms), T(22) (82-99ms) and T(23) (2-3ms) for raw meat which changed to 18-31ms (T(21)), 61-208ms (T(22)) and 3-7ms (T(23)) after the meat had been cooked. The T(1) and T(2) values obtained by MRI for cooked meat decreased progressively with increased heating time. There are highly significant correlations between the T(2) values from MRI and the T(21) values from bulk NMR measurements of cooked meat (r=0.986; p<0.01), and also between the normalised M(0) values from MRI and the gravimetric moisture content (r=0.953; p<0.01).

  2. Setting the anomeric effect against steric effects in simple acyclic acetals. Non-anomeric non-classical conformations. An n.m.r. and molecular mechanics investigation

    DEFF Research Database (Denmark)

    Anderson, J. Edgar; Heki, Katsuhiko; Hirota, Minoru

    1987-01-01

    N.m.r. parameters for a series of simple aliphatic acetals indicate that the preferred conformation changes from the anomeric one found in formaldehyde dimethyl acetal (formal), to a new one whose structure is suggested by molecular mechanics calculations.......N.m.r. parameters for a series of simple aliphatic acetals indicate that the preferred conformation changes from the anomeric one found in formaldehyde dimethyl acetal (formal), to a new one whose structure is suggested by molecular mechanics calculations....

  3. NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1.

    Science.gov (United States)

    Lyukmanova, Ekaterina N; Shenkarev, Zakhar O; Shulepko, Mikhail A; Mineev, Konstantin S; D'Hoedt, Dieter; Kasheverov, Igor E; Filkin, Sergey Yu; Krivolapova, Alexandra P; Janickova, Helena; Dolezal, Vladimir; Dolgikh, Dmitry A; Arseniev, Alexander S; Bertrand, Daniel; Tsetlin, Victor I; Kirpichnikov, Mikhail P

    2011-03-25

    Discovery of proteins expressed in the central nervous system sharing the three-finger structure with snake α-neurotoxins provoked much interest to their role in brain functions. Prototoxin LYNX1, having homology both to Ly6 proteins and three-finger neurotoxins, is the first identified member of this family membrane-tethered by a GPI anchor, which considerably complicates in vitro studies. We report for the first time the NMR spatial structure for the water-soluble domain of human LYNX1 lacking a GPI anchor (ws-LYNX1) and its concentration-dependent activity on nicotinic acetylcholine receptors (nAChRs). At 5-30 μM, ws-LYNX1 competed with (125)I-α-bungarotoxin for binding to the acetylcholine-binding proteins (AChBPs) and to Torpedo nAChR. Exposure of Xenopus oocytes expressing α7 nAChRs to 1 μM ws-LYNX1 enhanced the response to acetylcholine, but no effect was detected on α4β2 and α3β2 nAChRs. Increasing ws-LYNX1 concentration to 10 μM caused a modest inhibition of these three nAChR subtypes. A common feature for ws-LYNX1 and LYNX1 is a decrease of nAChR sensitivity to high concentrations of acetylcholine. NMR and functional analysis both demonstrate that ws-LYNX1 is an appropriate model to shed light on the mechanism of LYNX1 action. Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding.

  4. NMR Structure and Action on Nicotinic Acetylcholine Receptors of Water-soluble Domain of Human LYNX1*

    Science.gov (United States)

    Lyukmanova, Ekaterina N.; Shenkarev, Zakhar O.; Shulepko, Mikhail A.; Mineev, Konstantin S.; D'Hoedt, Dieter; Kasheverov, Igor E.; Filkin, Sergey Yu.; Krivolapova, Alexandra P.; Janickova, Helena; Dolezal, Vladimir; Dolgikh, Dmitry A.; Arseniev, Alexander S.; Bertrand, Daniel; Tsetlin, Victor I.; Kirpichnikov, Mikhail P.

    2011-01-01

    Discovery of proteins expressed in the central nervous system sharing the three-finger structure with snake α-neurotoxins provoked much interest to their role in brain functions. Prototoxin LYNX1, having homology both to Ly6 proteins and three-finger neurotoxins, is the first identified member of this family membrane-tethered by a GPI anchor, which considerably complicates in vitro studies. We report for the first time the NMR spatial structure for the water-soluble domain of human LYNX1 lacking a GPI anchor (ws-LYNX1) and its concentration-dependent activity on nicotinic acetylcholine receptors (nAChRs). At 5–30 μm, ws-LYNX1 competed with 125I-α-bungarotoxin for binding to the acetylcholine-binding proteins (AChBPs) and to Torpedo nAChR. Exposure of Xenopus oocytes expressing α7 nAChRs to 1 μm ws-LYNX1 enhanced the response to acetylcholine, but no effect was detected on α4β2 and α3β2 nAChRs. Increasing ws-LYNX1 concentration to 10 μm caused a modest inhibition of these three nAChR subtypes. A common feature for ws-LYNX1 and LYNX1 is a decrease of nAChR sensitivity to high concentrations of acetylcholine. NMR and functional analysis both demonstrate that ws-LYNX1 is an appropriate model to shed light on the mechanism of LYNX1 action. Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding. PMID:21252236

  5. Spectroscopic (FTIR, FT-Raman, UV and NMR) investigation and NLO, HOMO-LUMO, NBO analysis of 2-Benzylpyridine based on quantum chemical calculations.

    Science.gov (United States)

    Mathammal, R; Sudha, N; Guru Prasad, L; Ganga, N; Krishnakumar, V

    2015-02-25

    In this work, the vibrational characteristics of 2-Benzylpyridine have been investigated. The structure of the molecule has been optimized and the structural characteristics of the molecule have been determined by density functional theory B3LYP method with 6-31G(d,p) basis set. The infrared and Raman spectra have been simulated from calculated intensities. Both the experimental and theoretical vibrational data confirms the presence of functional groups in the title compound. The (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital method. UV-Visible spectrum of the title compound was recorded in the region 190-1100 nm and the electronic properties HOMO and LUMO energies were calculated by CIS approach. Nonlinear optical and thermodynamic properties were interpreted. All the calculated results were compared with the available experimental data of the title molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Investigation of drug-excipient interactions in lapatinib amorphous solid dispersions using solid-state NMR spectroscopy.

    Science.gov (United States)

    Song, Yang; Yang, Xinghao; Chen, Xin; Nie, Haichen; Byrn, Stephen; Lubach, Joseph W

    2015-03-02

    This study investigated the presence of specific drug-excipient interactions in amorphous solid dispersions of lapatinib (LB) and four commonly used pharmaceutical polymers, including Soluplus, polyvinylpyrrolidone vinyl acetate (PVPVA), hydroxypropylmethylcellulose acetate succinate (HPMCAS), and hydroxypropylmethylcellulose phthalate (HPMCP). Based on predicted pKa differences, LB was hypothesized to exhibit a specific ionic interaction with HPMCP, and possibly with HPMCAS, while Soluplus and PVPVA were studied as controls without ionizable functionality. Thermal studies showed a single glass transition (Tg) for each dispersion, in close agreement with predicted values for Soluplus, PVPVA, and HPMCAS systems. However, the Tg values of LB-HPMCP solid dispersions were markedly higher than predicted values, indicating a strong intermolecular interaction between LB and HPMCP. (15)N solid-state NMR provided direct spectroscopic evidence for protonation of LB (i.e., salt formation) within the HPMCP solid dispersions. (1)H T1 and (1)H T1ρ relaxation studies of the dispersions supported the ionic interaction hypothesis, and indicated multiple phases in the cases of excess drug or polymer. In addition, the dissolution and stability behavior of each system was examined. Both acidic polymers, HPMCAS and HPMCP, effectively inhibited the crystallization of LB on accelerated stability, likely owing to beneficial strong intermolecular hydrogen and/or specific ionic bonds with the acidic polymers. Soluplus and PVPVA showed poor physical properties on stability and subsequently poor crystallization inhibition.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Hiroshi [Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School (United States); Swapna, G. V. T. [State University of New Jersey, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers (United States); Wu, Kuen-Phon; Afinogenova, Yuliya [Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School (United States); Conover, Kenith; Mao, Binchen [State University of New Jersey, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers (United States); Montelione, Gaetano T.; Inouye, Masayori, E-mail: inouye@cabm.rutgers.edu [Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School (United States)

    2012-04-15

    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{sub 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{sub 2}-tag is replaced with non-isotope labeled PrS{sub 2}-tag, silencing the NMR signals from PrS{sub 2}-tag in isotope-filtered {sup 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 (RbfA{Delta}25). Using the PrS{sub 2}-tag, full-length well-behaved RbfA samples could be successfully prepared for NMR studies. PrS{sub 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{sub 2}-tagged RbfA superimposes with the TROSY-HSQC spectrum of RbfA{Delta}25, indicating that PrS{sub 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 {sup 1}H, {sup 15}N and {sup 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 {sup 1}H-{sup 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 RbfA{Delta}25 construct. CS-Rosetta calculations also demonstrate that the core structure of full-length RbfA is similar to that of the RbfA{Delta}25

  9. 29 Si NMR and SAXS investigation of the hybrid organic–inorganic glasses obtained by consolidation of the melting gels

    Energy Technology Data Exchange (ETDEWEB)

    Jitianu, Andrei; Cadars, Sylvian; Zhang, Fan; Rodriguez, Gabriela; Picard, Quentin; Aparicio, Mario; Mosa, Jadra; Klein, Lisa C.

    2017-01-01

    This study is focused on structural characterization of hybrid glasses obtained by consolidation of melting gels. The melting gels were prepared in molar ratios of methyltriethoxysilane (MTES) and dimethyldiethoxysilane (DMDES) of 75%MTES-25%DMDES and 65%MTES-35%DMDES. Following consolidation, the hybrid glasses were characterized using Raman, 29Si and 13C Nuclear Magnetic Resonance (NMR) spectroscopies, synchrotron Small Angle X-Ray Scattering (SAXS) and scanning electron microscopy (SEM). Raman spectroscopy revealed the presence of Si–C bonds in the hybrid glasses and 8-membered ring structures in the Si–O–Si network. Qualitative NMR spectroscopy identified the main molecular species, while quantitative NMR data showed that the ratio of trimers (T) to dimers (D) varied between 4.6 and 3.8. Two-dimensional 29Si NMR data were used to identify two distinct types of T3 environments. SAXS data showed that the glasses are homogeneous across the nm to micrometer length scales. The scattering cross section was one thousand times lower than what is expected when phase separation occurs. The SEM images show a uniform surface without defects, in agreement with the SAXS results, which further supports that the hybrid glasses are nonporous.

  10. NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition.

    Science.gov (United States)

    Mukherjee, Munia; Dutta, Kaushik; White, Mark A; Cowburn, David; Fox, Robert O

    2006-06-01

    Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E-D3) is considered to be the primary viral determinant involved in the virus-host-cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL-2 TBE virus and is a model for the pathogenic BSL-3 and BSL-4 viruses in the serogroup. We have determined the solution structure of LGT-E-D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT-E-D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT-E-D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design.

  11. 13C-NMR STUDY ON THE CHAIN TERMINAL STRUCTURE OF POLY-1,3-PENTADIENE POLYMERIZED WITH RARE EARTH CATALYST

    Institute of Scientific and Technical Information of China (English)

    XIE Demin; GONG Zhi; WANG Fosong

    1987-01-01

    The sequence distribution and the terminal structures of poly-1,3-pentadiene chains obtained by rare earth catalyst and effect of polymerization temperature on microstructure of the polymer have been investigated by 13C-NMR method. According to experimental results it was supposed that terminal active growing chain of the polymer would be four types of anti- and syn-η3-allyl structures. When polymerization temperature was reduced, the content of cis-1,4-poly-1,3-pentadiene increases. It can be explained by isomerization between anti- and syn-η3-allyl. The process forming trans-1,2 unit instead of 3,4-unit were also described.

  12. Development of Solid State NMR Methods for the Structural Characterization of Membrane Proteins: Applications to Understand Multiple Sclerosis

    Energy Technology Data Exchange (ETDEWEB)

    Cosman, M; Tran, A T; Ulloa, J; Maxwell, R S

    2003-03-04

    Multiple sclerosis (MS) is a relapsing-remitting disorder of the central nervous system that results in the loss of the myelin sheaths insulating nerve fibers (axons). Strong evidence suggests that MS is an autoimmune disease mediated by T-cell and antibody responses against myelin antigens. Myelin oligodendrocyte glycoprotein (MOG) is a 26 kD to 28 kD an integral membrane protein of the central nervous system implicated as a target for autoaggressive antibodies in MS. To date, the conformation of MOG in association with the myelin membrane is unknown and the exact nature of the interactions between this protein and disease-inducing immune responses have not been determined. Since membrane associated proteins are typically characterized by decreased correlation times, solution state NMR methodologies are often impracticable. Membrane proteins are also often difficult to crystallize for X-ray diffraction studies, Consequently, there is an urgent need to develop new structure characterization tools for this important class of biomolecules. The research described here overviews the initial stages of our effort to develop an integrated, NMR based approach to structural studies of MOG over the many structural domains it is postulated to posses. The structural knowledge gained about this important MS antigen in its native environment will contribute significantly to our understanding of its function in vivo. This project will also aid in the development of therapeutics to inhibit the antigedantibody interaction and thus prevent demyelination in MS patients.

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

    Science.gov (United States)

    Alsanousi, Nesreen; Sugiki, Toshihiko; Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi; Kojima, Chojiro

    2016-09-02

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

  14. Teaching NMR Using Online Textbooks

    Directory of Open Access Journals (Sweden)

    Joseph P. Hornak

    1999-12-01

    Full Text Available Nuclear magnetic resonance (NMR spectroscopy has almost become an essential analytical tool for the chemist. High-resolution one- and multi-dimensional NMR, timedomain NMR, and NMR microscopy are but a few of the NMR techniques at a chemist's disposal to determine chemical structure and dynamics. Consequently, even small chemistry departments are finding it necessary to provide students with NMR training and experience in at least some of these techniques. The hands-on experience is readily provided with access to state-of-the-art commercial spectrometers. Instruction in the principles of NMR is more difficult to achieve as most instructors try to teach NMR using single organic or analytical chemistry book chapters with static figures. This paper describes an online textbook on NMR spectroscopy called The Basics of NMR (http://www.cis.rit.edu/htbooks/nmr/ suitable for use in teaching the principles of NMR spectroscopy. The book utilizes hypertext and animations to present the principles of NMR spectroscopy. The book can be used as a textbook associated with a lecture or as a stand-alone teaching tool. Conference participants are encouraged to review the textbook and evaluate its suitability for us in teaching NMR spectroscopy to undergraduate chemistry majors.

  15. High-performance liquid chromatography on-line coupled to high-field NMR and mass spectrometry for structure elucidation of constituents of Hypericum perforatum L

    DEFF Research Database (Denmark)

    Hansen, S. H.; Jensen, A. G.; Cornett, Claus

    1999-01-01

    The on-line separation and structure elucidation of naphthodianthrones, flavonoids, and other constituents of an extract from Hypericum perforatum L, using high performance liquid chromatography (HPLC) coupled on-line with ultraviolet-visible, nuclear magnetic resonance (NMR), and mass spectrometry...... (MS) is described. A conventional reversed-phase HPLC system using ammonium acetate as the buffer substance in the eluent tvas used, and proton NMR spectra were obtained on a 500 MHz NMR instrument. The MS and MS/MS analyses were performed using negative electrospray ionization, In the present study...

  16. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.

  17. Structural Modifications of Deoxycholic Acid to Obtain Three Known Brassinosteroid Analogues and Full NMR Spectroscopic Characterization.

    Science.gov (United States)

    Herrera, Heidy; Carvajal, Rodrigo; Olea, Andrés F; Espinoza, Luis

    2016-08-27

    An improved synthesis route for obtaining known brassinosteroid analogues, i.e., methyl 2α,3α-dihydroxy-6-oxo-5α-cholan-24-oate (11), methyl 3α-hydroxy-6-oxo-7-oxa-5α-cholan-24-oate (15) and methyl 3α-hydroxy-6-oxa-7-oxo-5α-cholan-24-oate (16), from hyodeoxycholic acid (4) maintaining the native side chain is described. In the alternative procedure, the di-oxidized product 6, obtained in the oxidation of methyl hyodeoxycholate 5, was converted almost quantitatively into the target monoketone 7 by stereoselective reduction with NaBH₄, increasing the overall yield of this synthetic route to 96.8%. The complete ¹H- and (13)C-NMR assignments for all compounds synthesized in this work have been made by 1D and 2D heteronuclear correlation gs-HSQC and gs-HMBC techniques. Thus, it was possible to update the spectroscopic information of ¹H-NMR and to accomplish a complete assignment of all (13)C-NMR signals for analogues 5-16, which were previously reported only in partial form.

  18. The Expanding Role of NMR in Drug Discovery and Development

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ The role of NMR in the pharmaceutical industry has changed dramatically over the last decade. Once thought of as an analytical technique used primarily to support synthetic chemistry, NMR now has an important role in the investigation of biochemical changes involved in clinical diseases and drug toxicity. It is also used extensively to elucidate the structures of drug metabolites. Data obtained using LC NMR MS and 19F NMR will be used to illustrate the utility of hyphenated methods in identifying xenobiotic metabolites as part of a drug development program. The application of NMR to the study of potential drug toxicity will also be described using the cationic, amphiphilic drugs chloroquine and amiodarone. These drugs are known to induce phospholipidosis characterized by lysosomal lamellar bodies and drug accumulation. Using a metabonomic approach, NMR spectroscopy of urine allowed the identification of a combination of urinary biomarkers of phospholipidosis.

  19. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy.

    Science.gov (United States)

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

    2013-10-01

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

  20. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Chemistry (United States)

    2013-10-15

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

  1. Synthesis,Crystal Structure of Cis—dioxo—catecholatotungsten(VI) Complex and Its NMR Studies on the Interaction with ATP

    Institute of Scientific and Technical Information of China (English)

    鲁晓明; 刘顺成; 姜凌; 毛希安; 叶朝晖

    2003-01-01

    Cis-dioxo-catecholatotungsten(VI) complex anion[W(VI)O2-(OC6H4O)2]2- was obtained with discrete protonated ethylenediamine (NH2CH2CH2NH3)+ cations by the reaction of tetrabutyl ammonium decatungstate with catechol in the mixed solvent of CH3OH,CH3CN and ethylenediamine,and compared with its molybdenum anaogue [Mo(V) O2(OC6H4O)2]3- by crystal structure,UV,EPR,The results of the UV and EPR spectra show that tungsten is less redox active than molybdenum since the molybdenum is reduced from Mo(VI) to Mo(V) but tungsten stays in the original highest oxidized state Mo(VI) when they are crystallized from the solution above.It is worthy to note that [W(VI)O2(OC6H4O)]2- shows the same coordination structure as its molybdenum analogue in which the metal center exhibits distorted octahedral coordination geometry with two cis-dioxocatecholate ligands and might have the related coordination structure feature with the cofactor of flavoenzyme because [Mo(V)O2(OC6H4O)2]3- presented essentially the same EPR spectra as flavoenzyme.The NMR studies on the interaction of the title complex with ATP reveal that the reduction of W(VI) to W(V) occurs when the title complex is dissolved in D2O and the W(V) is oxidized again when ATP solution is mixed with original solution and the hydrolysis of the catecholato ligand take places at mean time being monitored by 1H NMR and 13C NMR spectra.

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

    Science.gov (United States)

    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.

  3. Synthesis of 24-phenyl-24-oxo steroids derived from bile acids by palladium-catalyzed cross coupling with phenylboronic acid. NMR characterization and X-ray structures.

    Science.gov (United States)

    Mayorquín-Torres, Martha C; Romero-Ávila, Margarita; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

    2013-11-01

    Palladium-catalyzed cross coupling of phenyboronic acid with acetylated bile acids in which the carboxyl functions have been activated by formation of a mixed anhydride with pivalic anhydride afforded moderate to good yield of 24-phenyl-24-oxo-steroids. Unambiguous assignments of the NMR signals were made with the aid of combined 1D and 2D NMR techniques. X-ray diffraction studies confirmed the obtained structures.

  4. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.

    Science.gov (United States)

    Lange, Oliver F; Rossi, Paolo; Sgourakis, Nikolaos G; Song, Yifan; Lee, Hsiau-Wei; Aramini, James M; Ertekin, Asli; Xiao, Rong; Acton, Thomas B; Montelione, Gaetano T; Baker, David

    2012-07-03

    We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the "best effort" structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.

  5. Sequential sup 1 H NMR assignments and secondary structure of an IgG-binding domain from protein G

    Energy Technology Data Exchange (ETDEWEB)

    Lian, L.Y.; Yang, J.C.; Derrick, J.P.; Sutcliffe, M.J.; Roberts, G.C.K. (Univ. of Leicester (England)); Murphy, J.P.; Goward, C.R.; Atkinson, T. (PHLS Center for Applied Microbiology and Research, Porton Down, Salisbury (England))

    1991-06-04

    Protein G is a member of a class of cell surface bacterial proteins from Streptococcus that bind IgG with high affinity. A fragment of molecular mass 6,988, which retains IgG-binding activity, has been generated by proteolytic digestion and analyzed by {sup 1}H NMR. Two-dimenstional DQF-COSY, TOCSY, and NOESY spectra have been employed to assign the {sup 1}H NMR spectrum of the peptide. Elements of regular secondary structure have been identified by using nuclear Overhauser enhancement, coupling constant, and amide proton exchange data. The secondary structure consists of a central {alpha}-helix (Ala28-Val44), flanked by two portions of {beta}-sheet (Val5-Val26 and Asp45-Lys62). This is a fundamentally different arrangement of secondary structure from that of protein A, which is made up of three consecutive {alpha}-helics in free solution. The authors conclude that the molecular mechanisms underlying the association of protein A and protein G with IgG are different.

  6. Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

    Science.gov (United States)

    Pawlak, Tomasz; Potrzebowski, Marek J

    2014-03-27

    This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

  7. Electronic structure investigation of biphenylene films

    Science.gov (United States)

    Totani, R.; Grazioli, C.; Zhang, T.; Bidermane, I.; Lüder, J.; de Simone, M.; Coreno, M.; Brena, B.; Lozzi, L.; Puglia, C.

    2017-02-01

    Photoelectron Spectroscopy (PS) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The obtained results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, NEXAFS measurements allowed characterizing the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.

  8. Beta-alanine-oxalic acid (1:1) hemihydrate crystal: structure, 13C NMR and vibrational properties, protonation character.

    Science.gov (United States)

    Godzisz, D; Ilczyszyn, M; Ilczyszyn, M M

    2003-03-01

    The crystal structure of beta-alanine-oxalic acid (1:1) hemihydrate complex has been reinvestigated by X-ray diffraction method at 293 K. Formation of monoclinic crystal system belonging to C2/c space group and consisting of semi-oxalate chains, diprotonated beta-alanine dimers and water molecules bonded to both these units is confirmed. New results are obtained for distances in the carboxylic groups and hydrogen bonds. These structural observations are used for protonation degree monitoring on the carboxylic oxygen atoms. They are in accordance with our vibrational study. The 13C NMR spectra provide insights into the solid structure of this complex, character of its hydrogen bonds and the beta-alanine protonation.

  9. Contribution of proton NMR relaxation to the investigation of molecular dynamics in columnar mesophases of discotic and polycatenar molecules

    Indian Academy of Sciences (India)

    A C Ribeiro; P J Sebastiao; C Cruz

    2003-08-01

    We present in this work a review concerning wide frequency range 1 proton NMR relaxation studies performed in compounds exhibiting columnar mesophases, namely the Colho mesophase in the case of a liquid crystal of discotic molecules and the h mesophase in the case of a liquid crystal of biforked molecules. These NMR relaxation studies were performed combining conventional and fast field cycling NMR techniques in a frequency range between 100 Hz and 300 MHz. The possibility of probing such a large frequency range has provided a way to effectively distinguish the influence, on the 1 relaxation profiles, of the different molecular movements observed in this type of mesophases. In addition, we present a comparison between the molecular dynamics in columnar (h) and lamellar (SmC) mesophases exhibited by the same biforked compound.

  10. Direct Speciation of Phosphorus in Alum-Amended Poultry Litter: Solid-State 31P NMR Investigation

    Energy Technology Data Exchange (ETDEWEB)

    Hunger, Stefan; Cho, Herman M.; Sims, James T.; Sparks, Donald L.

    2004-02-01

    Amending poultry litter (PL) with aluminum sulfate (alum) has proven to be effective in reducing water-soluble phosphorus (P) in the litter and in runoff from fields that have received PL applications; it has therefore been suggested as a best management practice. Although its effectiveness has been demonstrated on a macroscopic scale in the field, little is known about P speciation in either alumamended or unamended litter. This knowledge is important for the evaluation of the long-term stability and bioavailability of P, which is a necessary prerequisite for the assessment of the sustainability of intensive poultry operations. Both solid state MAS and CP-MAS {sup 31}P NMR as well as {sup 31}P({sup 27}Al) TRAPDOR were used to investigate P speciation in alumamended and unamended PL. The results indicate the presence of a complex mixture of organic and inorganic orthophosphate phases. A calcium phosphate phase, probably a surface precipitate on calcium carbonate, could be identified in both unamended and alum-amended PL, as well as physically bound HPO{sub 4}{sup 2-}. Phosphate associated with Al was found in the alum-amended PL, most probably a mixture of a poorly ordered wavellite and phosphate surface complexes on aluminum hydroxide that had been formed by the hydrolysis of alum. However, a complex mixture of organic and inorganic phosphate species could not be resolved. Phosphate associated with Al comprised on average 40{+-}14% of the total P in alum-amended PL, whereas calcium phosphate phases comprised on average 7{+-}4% in the alum-amended PL and 14{+-}5% in the unamended PL.

  11. 1H NMR-based metabolomics investigation of copper-laden rat: a model of Wilson's disease.

    Directory of Open Access Journals (Sweden)

    Jingjing Xu

    Full Text Available Wilson's disease (WD, also known as hepatoleticular degeneration (HLD, is a rare autosomal recessive genetic disorder of copper metabolism, which causes copper to accumulate in body tissues. In this study, rats fed with copper-laden diet are used to render the clinical manifestations of WD, and their copper toxicity-induced organ lesions are studied. To investigate metabolic behaviors of 'decoppering' process, penicillamine (PA was used for treating copper-laden rats as this chelating agent could eliminate excess copper through the urine. To date, there has been limited metabolomics study on WD, while metabolic impacts of copper accumulation and PA administration have yet to be established.A combination of 1HNMR spectroscopy and multivariate statistical analysis was applied to examine the metabolic profiles of the urine and blood serum samples collected from the copper-laden rat model of WD with PA treatment.Copper accumulation in the copper-laden rats is associated with increased lactate, creatinine, valine and leucine, as well as decreased levels of glucose and taurine in the blood serum. There were also significant changes in p-hydroxyphenylacetate (p-HPA, creatinine, alpha-ketoglutarate (α-KG, dimethylamine, N-acetylglutamate (NAG, N-acetylglycoprotein (NAC in the urine of these rats. Notably, the changes in p-HPA, glucose, lactate, taurine, valine, leucine, and NAG were found reversed following PA treatment. Nevertheless, there were no changes for dimethylamine, α-KG, and NAC as a result of the treatment. Compared with the controls, the concentrations of hippurate, formate, alanine, and lactate were changed when PA was applied and this is probably due to its side effect. A tool named SMPDB (Small Molecule Pathway Database is introduced to identify the metabolic pathway influenced by the copper-laden diet.The study has shown the potential application of NMR-based metabolomic analysis in providing further insights into the molecular