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Sample records for nmr structure analysis

  1. Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

    PubMed

    Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

    2016-06-01

    NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html.

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

    PubMed

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

    2015-08-01

    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.

  3. NMR analysis and crystal structure of hydroxyclerodanes from Mexican Salvia species

    NASA Astrophysics Data System (ADS)

    Ortega, Alfredo; Ortiz-Pastrana, Naytzé; Bedolla-García, Brenda Y.; Toscano, Rubén A.; Bautista, Elihú

    2017-08-01

    NMR and single crystal X-ray diffraction analysis of seven clerodanes from Mexican Salvia species was performed. We focused on clerodanes with tertiary hydroxyl group at C-4, C-8, and C-10, in which the establishment of absolute configuration around these chiral centers is nontrivial and the 13C NMR signals can be misassigned. In addition, the analysis by 1H NMR in aprotic solvent allowed us to establish a common pattern that correlates the chemical shift with the position of the hydroxyl groups, which constitute a good methodology for future structural elucidation of these kinds of compounds. The obtained data allowed us to establish the absolute configuration of five of these diterpenes and the structural revision of salvimicrophyllin D (7).

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

    PubMed Central

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

    2015-01-01

    RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson–Crick stem and the “canonical” UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9–G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements. PMID:25805858

  5. Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data.

    PubMed

    Toukach, F V; Shashkov, A S

    2001-09-28

    A computer-assisted approach to the prediction of the primary structures of regular glycopolymers is described. The analysis is based on comparing the calculated 13C NMR spectra of all the possible structures of the repeating unit (for the given monomeric composition) to an experimental 13C NMR spectrum. The spectra generation is based on the spectral database containing information on the 13C chemical shifts of monomers, di- and trimeric fragments. If the required data are missing from this database, the special database for average glycosylation effects is used. The analysis reveals those structures with the calculated 13C NMR spectrum most close to observed. The structures of repeating units of any topology containing up to six residues linked by glycosidic, amidic or phospho-diester bridges can be predicted. Unambiguous selection of the proper structure from the output list of possible structures may require additional experimental data. Testing the created program and databases on bacterial polysaccharides and their derivatives containing up to three non-sugar residues (alditols, amino acids, phosphate groups etc.) per repeating unit revealed the good convergence of prediction with independently obtained structural data.

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

    PubMed

    Fontana, Carolina; Kovacs, Helena; Widmalm, Göran

    2014-06-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-05-01

    RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements. © 2015 Giambaşu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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

    PubMed

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

    2011-12-01

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

  10. Tannin structural elucidation and quantitative ³¹P NMR analysis. 2. Hydrolyzable tannins and proanthocyanidins.

    PubMed

    Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

    2013-10-02

    An unprecedented analytical method that allows simultaneous structural and quantitative characterization of all functional groups present in tannins is reported. In situ labeling of all labile H groups (aliphatic and phenolic hydroxyls and carboxylic acids) with a phosphorus-containing reagent (Cl-TMDP) followed by quantitative ³¹P NMR acquisition constitutes a novel fast and reliable analytical tool for the analysis of tannins and proanthocyanidins with significant implications for the fields of food and feed analyses, tannery, and the development of natural polyphenolics containing products.

  11. Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

    PubMed

    Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

    2013-10-02

    Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series.

  12. Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

    PubMed Central

    2015-01-01

    The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

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

    PubMed

    Ragan, Timothy J; Fogh, Rasmus H; Tejero, Roberto; Vranken, Wim; Montelione, Gaetano T; Rosato, Antonio; Vuister, Geerten W

    2015-08-01

    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.

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

    PubMed

    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.

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

    SciTech Connect

    Zilm, K.W.

    1989-01-01

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

  16. NMR and IR Spectroscopy for the Structural Characterization of Edible Fats and Oils: An Instrumental Analysis Laboratory

    ERIC Educational Resources Information Center

    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,…

  17. NMR and IR Spectroscopy for the Structural Characterization of Edible Fats and Oils: An Instrumental Analysis Laboratory

    ERIC Educational Resources Information Center

    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,…

  18. Structural, vibrational, electronic and NMR spectral analysis of 3-chloro-6-methoxypyridazine by DFT calculations.

    PubMed

    Vijaya Chamundeeswari, S P; James Jebaseelan Samuel, E; Sundaraganesan, N

    2013-06-01

    In this work, the FT-Raman and FT-Infrared spectra of 3-chloro-6-methoxypyridazine sample were measured to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm(-1) and 4000-400 cm(-1), respectively. The molecular geometry and vibrational frequencies of 3-chloro-6-methoxypyridazine in the ground state were calculated using the DFT/B3LYP/6-31G(d),6-311G(d,p) level. The recorded FT-IR and FT-Raman spectral measurements favor the calculated structural parameters which are further supported by spectral simulation. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The UV-Visible absorption spectrum of the compound that dissolved in methanol was recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. The isotropic chemical shift computed by (13)C and (1)H NMR analysis also shows good agreement with experimental observations. In addition, the molecular electrostatic potential (MEP) and frontier molecular orbitals (FMOs) analysis of the title compound were investigated using theoretical calculations. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    PubMed

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

    1998-01-01

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

  20. Improving NMR Structures of RNA

    PubMed Central

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

    2016-01-01

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

  1. Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection

    SciTech Connect

    Qu, Yi; Feng, Ju; Deng, Shuang; Cao, Li; Zhang, Qibin; Zhao, Rui; Zhang, Zhaorui; Jiang, Yuxuan; Zink, Erika M.; Baker, Scott E.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Hu, Jian Z.; Wu, Si

    2014-11-19

    Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation,) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we employed SEC, Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), and ZIC-HILIC coupled with dialysis strategies to enrich the glycopeptides from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is the most efficient, which was thus applied to the analysis of biological complex sample, the pronase E digest of the secreted proteins from the fungi Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core and O-linked glycans bearing mannose and glucose with 1->3 and 1->6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled to dialysis is superior to the commonly used SEC separation to prepare glycopeptides for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.

  2. Analysis of structural variability in pharmaceutical excipients using solid-state NMR spectroscopy.

    PubMed

    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.

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

    PubMed

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

    2006-10-01

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

  4. NMR analysis of biodiesel

    USDA-ARS?s Scientific Manuscript database

    Biodiesel is usually analyzed by the various methods called for in standards such as ASTM D6751 and EN 14214. Nuclear magnetic resonance (NMR) is not one of these methods. However, NMR, with 1H-NMR commonly applied, can be useful in a variety of applications related to biodiesel. These include monit...

  5. Advanced NMR-based techniques for pore structure analysis of coal. Final project report

    SciTech Connect

    Smith, D.M.; Hua, D.W.

    1996-02-01

    During the 3 year term of the project, new methods have been developed for characterizing the pore structure of porous materials such as coals, carbons, and amorphous silica gels. In general, these techniques revolve around; (1) combining multiple techniques such as small-angle x-ray scattering (SAXS) and adsorption of contrast-matched adsorbates or {sup 129}Xe NMR and thermoporometry (the change in freezing point with pore size), (2) combining adsorption isotherms over several pressure ranges to obtain a more complete description of pore filling, or (3) applying NMR ({sup 129}Xe, {sup 14}N{sub 2}, {sup 15}N{sub 2}) techniques with well-defined porous solids with pores in the large micropore size range (>1 nm).

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  7. NMR structural studies on antifreeze proteins.

    PubMed

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

    1998-01-01

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

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

    SciTech Connect

    Zilm, K.W.

    1989-01-01

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

  9. 1H NMR assignments of apo calcyclin and comparative structural analysis with calbindin D9k and S100 beta.

    PubMed Central

    Potts, B. C.; Carlström, G.; Okazaki, K.; Hidaka, H.; Chazin, W. J.

    1996-01-01

    The homodimeric S100 protein calcyclin has been studied in the apo state by two-dimensional 1H NMR spectroscopy. Using a combination of scalar correlation and NOE experiments, sequence-specific 1H NMR assignments were obtained for all but one backbone and > 90% of the side-chain resonances. To our knowledge, the 2 x 90 residue (20 kDa) calcyclin dimer is the largest protein system for which such complete assignments have been made by purely homonuclear methods. Sequential and medium-range NOEs and slowly exchanging backbone amide protons identified directly the four helices and the short antiparallel beta-type interaction between the two binding loops that comprise each subunit of the dimer. Further analysis of NOEs enabled the unambiguous assignment of 556 intrasubunit distance constraints, 24 intrasubunit hydrogen bonding constraints, and 2 x 26 intersubunit distance constraints. The conformation of the monomer subunit was refined by distance geometry and restrained molecular dynamics calculations using the intrasubunit constraints only. Calculation of the dimer structure starting from this conformational ensemble has been reported elsewhere. The extent of structural homology among the apo calcyclin subunit, the monomer subunit of apo S100 beta, and monomeric apo calbindin D9k has been examined in detail by comparing 1H NMR chemical shifts and secondary structures. This analysis was extended to a comprehensive comparison of the three-dimensional structures of the calcyclin monomer subunit and calbindin D9k, which revealed greater similarity in the packing of their hydrophobic cores than was anticipated previously. Together, these results support the hypothesis that all members of the S100 family have similar core structures and similar modes of dimerization. Analysis of the amphiphilicity of Helix IV is used to explain why calbindin D9k is monomeric, but full-length S100 proteins form homodimers. PMID:8931135

  10. Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

    PubMed Central

    Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

    2009-01-01

    15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

  11. Magic Angle Spinning NMR Spectroscopy: A Versatile Technique for Structural and Dynamic Analysis of Solid-Phase Systems

    PubMed Central

    Polenova, Tatyana; Gupta, Rupal; Goldbourt, Amir

    2016-01-01

    Magic Angle Spinning (MAS) NMR spectroscopy is a powerful method for analysis of a broad range of systems, including inorganic materials, pharmaceuticals, and biomacromolecules. The recent developments in MAS NMR instrumentation and methodologies opened new vistas to atomic-level characterization of a plethora of chemical environments previously inaccessible to analysis, with unprecedented sensitivity and resolution. PMID:25794311

  12. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    PubMed

    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.

  13. Protein structure determination from NMR chemical shifts.

    PubMed

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

    2007-06-05

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  15. Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies.

    PubMed

    Gupta, Rupal; Lu, Manman; Hou, Guangjin; Caporini, Marc A; Rosay, Melanie; Maas, Werner; Struppe, Jochem; Suiter, Christopher; Ahn, Jinwoo; Byeon, In-Ja L; Franks, W Trent; Orwick-Rydmark, Marcella; Bertarello, Andrea; Oschkinat, Hartmut; Lesage, Anne; Pintacuda, Guido; Gronenborn, Angela M; Polenova, Tatyana

    2016-01-21

    Mature infectious HIV-1 virions contain conical capsids composed of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20-64-fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar-based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4-18.8 T) and temperature (109-180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of the temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine side-chain conformers; unique intermolecular correlations across two CA molecules; and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR spectroscopy as an excellent tool for the characterization of HIV-1 assemblies.

  16. Dynamic Nuclear Polarization Enhanced MAS NMR for Structural Analysis of HIV-1 Protein Assemblies

    PubMed Central

    Gupta, Rupal; Lu, Manman; Hou, Guangjin; Caporini, Marc A.; Rosay, Melanie; Maas, Werner; Struppe, Jochem; Suiter, Christopher; Ahn, Jinwoo; Byeon, In-Ja L.; Franks, W. Trent; Orwick-Rydmark, Marcella; Bertarello, Andrea; Oschkinat, Hartmut; Lesage, Anne; Pintacuda, Guido; Gronenborn, Angela M.; Polenova, Tatyana

    2016-01-01

    Mature infectious HIV-1 virions contain conical capsids comprised of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20 – 64 fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4 – 18.8 T) and temperature (109 – 180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine sidechain conformers, unique intermolecular correlations across two CA molecules, and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR as an excellent tool for characterization of HIV-1 assemblies. PMID:26709853

  17. NMR-based Structural Analysis of the Complete Rough-type Lipopolysaccharide Isolated from Capnocytophaga canimorsus*

    PubMed Central

    Zähringer, Ulrich; Ittig, Simon; Lindner, Buko; Moll, Hermann; Schombel, Ursula; Gisch, Nicolas; Cornelis, Guy R.

    2014-01-01

    We here describe the NMR analysis of an intact lipopolysaccharide (LPS, endotoxin) in water with 1,2-dihexanoyl-sn-glycero-3-phosphocholine as detergent. When HPLC-purified rough-type LPS of Capnocytophaga canimorsus was prepared, 13C,15N labeling could be avoided. The intact LPS was analyzed by homonuclear (1H) and heteronuclear (1H,13C, and 1H,31P) correlated one- and two-dimensional NMR techniques as well as by mass spectrometry. It consists of a penta-acylated lipid A with an α-linked phosphoethanolamine attached to C-1 of GlcN (I) in the hybrid backbone, lacking the 4′-phosphate. The hydrophilic core oligosaccharide was found to be a complex hexasaccharide with two mannose (Man) and one each of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo), Gal, GalN, and l-rhamnose residues. Position 4 of Kdo is substituted by phosphoethanolamine, also present in position 6 of the branched ManI residue. This rough-type LPS is exceptional in that all three negative phosphate residues are “masked” by positively charged ethanolamine substituents, leading to an overall zero net charge, which has so far not been observed for any other LPS. In biological assays, the corresponding isolated lipid A was found to be endotoxically almost inactive. By contrast, the intact rough-type LPS described here expressed a 20,000-fold increased endotoxicity, indicating that the core oligosaccharide significantly contributes to the endotoxic potency of the whole rough-type C. canimorsus LPS molecule. Based on these findings, the strict view that lipid A alone represents the toxic center of LPS needs to be reassessed. PMID:24993825

  18. NMR-based structural analysis of the complete rough-type lipopolysaccharide isolated from Capnocytophaga canimorsus.

    PubMed

    Zähringer, Ulrich; Ittig, Simon; Lindner, Buko; Moll, Hermann; Schombel, Ursula; Gisch, Nicolas; Cornelis, Guy R

    2014-08-22

    We here describe the NMR analysis of an intact lipopolysaccharide (LPS, endotoxin) in water with 1,2-dihexanoyl-sn-glycero-3-phosphocholine as detergent. When HPLC-purified rough-type LPS of Capnocytophaga canimorsus was prepared, (13)C,(15)N labeling could be avoided. The intact LPS was analyzed by homonuclear ((1)H) and heteronuclear ((1)H,(13)C, and (1)H,(31)P) correlated one- and two-dimensional NMR techniques as well as by mass spectrometry. It consists of a penta-acylated lipid A with an α-linked phosphoethanolamine attached to C-1 of GlcN (I) in the hybrid backbone, lacking the 4'-phosphate. The hydrophilic core oligosaccharide was found to be a complex hexasaccharide with two mannose (Man) and one each of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo), Gal, GalN, and l-rhamnose residues. Position 4 of Kdo is substituted by phosphoethanolamine, also present in position 6 of the branched Man(I) residue. This rough-type LPS is exceptional in that all three negative phosphate residues are "masked" by positively charged ethanolamine substituents, leading to an overall zero net charge, which has so far not been observed for any other LPS. In biological assays, the corresponding isolated lipid A was found to be endotoxically almost inactive. By contrast, the intact rough-type LPS described here expressed a 20,000-fold increased endotoxicity, indicating that the core oligosaccharide significantly contributes to the endotoxic potency of the whole rough-type C. canimorsus LPS molecule. Based on these findings, the strict view that lipid A alone represents the toxic center of LPS needs to be reassessed. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    ERIC Educational Resources Information Center

    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…

  20. A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

    ERIC Educational Resources Information Center

    Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

    2004-01-01

    An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

  1. A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

    ERIC Educational Resources Information Center

    Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

    2004-01-01

    An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

  2. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    ERIC Educational Resources Information Center

    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…

  3. Multispectral Analysis of NMR Imagery

    NASA Technical Reports Server (NTRS)

    Butterfield, R. L.; Vannier, M. W. And Associates; Jordan, D.

    1985-01-01

    Conference paper discusses initial efforts to adapt multispectral satellite-image analysis to nuclear magnetic resonance (NMR) scans of human body. Flexibility of these techniques makes it possible to present NMR data in variety of formats, including pseudocolor composite images of pathological internal features. Techniques do not have to be greatly modified from form in which used to produce satellite maps of such Earth features as water, rock, or foliage.

  4. Multispectral Analysis of NMR Imagery

    NASA Technical Reports Server (NTRS)

    Butterfield, R. L.; Vannier, M. W. And Associates; Jordan, D.

    1985-01-01

    Conference paper discusses initial efforts to adapt multispectral satellite-image analysis to nuclear magnetic resonance (NMR) scans of human body. Flexibility of these techniques makes it possible to present NMR data in variety of formats, including pseudocolor composite images of pathological internal features. Techniques do not have to be greatly modified from form in which used to produce satellite maps of such Earth features as water, rock, or foliage.

  5. Solid-state NMR analysis of the PGLa peptide orientation in DMPC bilayers: structural fidelity of 2H-labels versus high sensitivity of 19F-NMR.

    PubMed

    Strandberg, Erik; Wadhwani, Parvesh; Tremouilhac, Pierre; Dürr, Ulrich H N; Ulrich, Anne S

    2006-03-01

    The structure and alignment of the amphipathic alpha-helical antimicrobial peptide PGLa in a lipid membrane is determined with high accuracy by solid-state 2H-NMR. Orientational constraints are derived from a series of eight alanine-3,3,3-d3-labeled peptides, in which either a native alanine is nonperturbingly labeled (4x), or a glycine (2x) or isoleucine (2x) is selectively replaced. The concentration dependent realignment of the alpha-helix from the surface-bound "S-state" to a tilted "T-state" by 30 degrees is precisely calculated using the quadrupole splittings of the four nonperturbing labels as constraints. The remaining, potentially perturbing alanine-3,3,3-d3 labels show only minor deviations from the unperturbed peptide structure and help to single out the unique solution. Comparison with previous 19F-NMR constraints from 4-CF3-phenylglycine labels shows that the structure and orientation of the PGLa peptide is not much disturbed even by these bulky nonnatural side chains, which contain CF3 groups that offer a 20-fold better NMR sensitivity than CD3 groups.

  6. (13)C NMR Metabolomics: INADEQUATE Network Analysis.

    PubMed

    Clendinen, Chaevien S; Pasquel, Christian; Ajredini, Ramadan; Edison, Arthur S

    2015-06-02

    The many advantages of (13)C NMR are often overshadowed by its intrinsically low sensitivity. Given that carbon makes up the backbone of most biologically relevant molecules, (13)C NMR offers a straightforward measurement of these compounds. Two-dimensional (13)C-(13)C correlation experiments like INADEQUATE (incredible natural abundance double quantum transfer experiment) are ideal for the structural elucidation of natural products and have great but untapped potential for metabolomics analysis. We demonstrate a new and semiautomated approach called INETA (INADEQUATE network analysis) for the untargeted analysis of INADEQUATE data sets using an in silico INADEQUATE database. We demonstrate this approach using isotopically labeled Caenorhabditis elegans mixtures.

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

    SciTech Connect

    Wright, P.E.

    1994-12-01

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

  8. A unilateral NMR magnet for sub-structure analysis in the built environment: the Surface GARField.

    PubMed

    McDonald, P J; Aptaker, P S; Mitchell, J; Mulheron, M

    2007-03-01

    A new, portable NMR magnet with a tailored magnetic field profile and a complementary radio frequency sensor have been designed and constructed for the purpose of probing in situ the sub-surface porosity of cement based materials in the built environment. The magnet is a one sided device akin to a large NMR-MOUSE with the additional design specification of planes of constant field strength /B0/ parallel to the surface. There is a strong gradient G in the field strength perpendicular to these planes. As with earlier GARField magnets, the ratio G//:B0/ is a system constant although the method of achieving this condition is substantially different. The new magnet as constructed is able to detect signals 50mm (1H NMR at 3.2 MHz) away from the surface of the magnet and can profile the surface layers of large samples to a depth of 35-40 mm by moving the magnet, and hence the resonant plane of the polarising field, relative to the sample surface. The matching radio frequency excitation/detector coil has been designed to complement the static magnetic field such that the polarising B0 and sensing B1 fields are, in principal, everywhere orthogonal. Preliminary spatially resolved measurements are presented of cement based materials, including two-dimensional T1-T2 relaxation correlation spectra.

  9. Computer-assisted analysis of the structure of regular branched polysaccharides containing 2,3-disubstituted rhamnopyranose and mannopyranose residues on the basis of 13C NMR data.

    PubMed

    Lipkind, G M; Shashkov, A S; Nifant'ev, N E; Kochetkov, N K

    1992-12-31

    A computer-assisted approach to the analysis of the structure of branched polysaccharides that contain 2,3-di-O-glycosylated alpha-rhamnopyranose and alpha-mannopyranose residues is based on evaluation of the 13C NMR spectra, using glycosylation effects and their deviations from additivity (delta delta values) at the branch points. This approach, in combination with monosaccharide and methylation analysis data, has been verified on a series of bacterial polysaccharides of known structure.

  10. Lead optimization of antifungal peptides with 3D NMR structures analysis

    PubMed Central

    Landon, Céline; Barbault, Florent; Legrain, Michèle; Menin, Laure; Guenneugues, Marc; Schott, Valérie; Vovelle, Françoise; Dimarcq, Jean-Luc

    2004-01-01

    Antimicrobial peptides are key components of the innate immune response in most multicellular organisms. These molecules are considered as one of the most innovative class of anti-infective agents that have been discovered over the last two decades, and therefore, as a source of inspiration for novel drug design. Insect cystein-rich antimicrobial peptides with the CSαβ scaffold (an α-helix linked to a β-sheet by two disulfide bridges) represent particularly attractive templates for the development of systemic agents owing to their remarkable resistance to protease degradation. We have selected heliomicin, a broad spectrum antifungal CSαβ peptide from Lepidoptera as the starting point of a lead optimization program based on phylogenic exploration and fine tuned mutagenesis. We report here the characterization, biological activity, and 3D structure of heliomicin improved analogs, namely the peptides ARD1, ETD-135, and ETD-151. The ARD1 peptide was initially purified from the immune hemolymph of the caterpillars of Archeoprepona demophoon. Although it differs from heliomicin by only two residues, it was found to be more active against the human pathogens Aspergillus fumigatus and Candida albicans. The peptides ETD-135 and ETD-151 were engineered by site-directed mutagenesis of ARD1 in either cationic or hydrophobic regions. ETD-135 and ETD-151 demonstrated an improved antifungal activity over the native peptides, heliomicin and ARD1. A comparative analysis of the 3D structure of the four molecules highlighted the direct impact of the modification of the amphipathic properties on the molecule potency. In addition, it allowed to characterize an optimal organization of cationic and hydrophobic regions to achieve best antifungal activity. PMID:14978308

  11. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

    PubMed Central

    NISHIMURA, Chiaki

    2017-01-01

    The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic

  12. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

    PubMed

    Nishimura, Chiaki

    2017-01-01

    The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

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

    PubMed Central

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

    2016-01-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases 15N-1H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include 1) using a global metric of structural accuracy, the Discriminating Power (DP) score, for guiding model selection during the iterative NOE interpretation process, and 2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

  15. Structural analysis of a signal peptide inside the ribosome tunnel by DNP MAS NMR

    PubMed Central

    Lange, Sascha; Franks, W. Trent; Rajagopalan, Nandhakishore; Döring, Kristina; Geiger, Michel A.; Linden, Arne; van Rossum, Barth-Jan; Kramer, Günter; Bukau, Bernd; Oschkinat, Hartmut

    2016-01-01

    Proteins are synthesized in cells by ribosomes and, in parallel, prepared for folding or targeting. While ribosomal protein synthesis is progressing, the nascent chain exposes amino-terminal signal sequences or transmembrane domains that mediate interactions with specific interaction partners, such as the signal recognition particle (SRP), the SecA–adenosine triphosphatase, or the trigger factor. These binding events can set the course for folding in the cytoplasm and translocation across or insertion into membranes. A distinction of the respective pathways depends largely on the hydrophobicity of the recognition sequence. Hydrophobic transmembrane domains stabilize SRP binding, whereas less hydrophobic signal sequences, typical for periplasmic and outer membrane proteins, stimulate SecA binding and disfavor SRP interactions. In this context, the formation of helical structures of signal peptides within the ribosome was considered to be an important factor. We applied dynamic nuclear polarization magic-angle spinning nuclear magnetic resonance to investigate the conformational states of the disulfide oxidoreductase A (DsbA) signal peptide stalled within the exit tunnel of the ribosome. Our results suggest that the nascent chain comprising the DsbA signal sequence adopts an extended structure in the ribosome with only minor populations of helical structure. PMID:27551685

  16. A consensus on protein structure accuracy in NMR?

    PubMed

    Billeter, Martin

    2015-02-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed

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

    2014-01-24

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

  19. Photoprotein Aequorin Structure Determination by NMR Spectroscopy

    DTIC Science & Technology

    1993-07-09

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

  20. Protein NMR structures refined without NOE data.

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-10-01

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

  2. Application of comprehensive NMR-based analysis strategy in annotation, isolation and structure elucidation of low molecular weight metabolites of Ricinus communis seeds.

    PubMed

    Vučković, Ivan; Rapinoja, Marja-Leena; Vaismaa, Matti; Vanninen, Paula; Koskela, Harri

    2016-01-01

    Powder-like extract of Ricinus communis seeds contain a toxic protein, ricin, which has a history of military, criminal and terroristic use. As the detection of ricin in this "terrorist powder" is difficult and time-consuming, related low mass metabolites have been suggested to be useful for screening as biomarkers of ricin. To apply a comprehensive NMR-based analysis strategy for annotation, isolation and structure elucidation of low molecular weight plant metabolites of Ricinus communis seeds. The seed extract was prepared with a well-known acetone extraction approach. The common metabolites were annotated from seed extract dissolved in acidic solution using (1)H NMR spectroscopy with spectrum library comparison and standard addition, whereas unconfirmed metabolites were identified using multi-step off-line HPLC-DAD-NMR approach. In addition to the common plant metabolites, two previously unreported compounds, 1,3-digalactoinositol and ricinyl-alanine, were identified with support of MS analyses. The applied comprehensive NMR-based analysis strategy provided identification of the prominent low molecular weight metabolites with high confidence. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Molecular structure, vibrational analysis (FT-IR, FT-Raman), NMR, UV, NBO and HOMO-LUMO analysis of N,N-Diphenyl Formamide based on DFT calculations.

    PubMed

    Mathammal, R; Monisha, N R; Yasaswini, S; Krishnakumar, V

    2015-03-15

    In this work, the vibrational spectral analysis is carried out by using Raman and infrared spectroscopy in the range 4000-400 cm(-1) and 4000-50 cm(-1) respectively for N,N-Diphenyl Formamide (DPF) molecule. The optimized molecular structures, vibrational frequencies and corresponding vibrational assignments, nuclear magnetic resonance (NMR) and ultraviolet-visible (UV-VIS) spectra of the title molecule are evaluated using density functional theory (DFT) with standard B3LYP/6-31G(d,p) basis set. The harmonic vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond (NBO) analysis. The possible electronic transitions are determined by HOMO-LUMO orbital shapes and their energies. Thermodynamic properties (heat capacity, entropy and enthalpy) and the first hyperpolarizability of the title compound are calculated. The Mulliken charges and electric dipole moment of the molecule are computed using DFT calculations. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shift of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints

    PubMed Central

    Heller, Davide Martin; Giorgetti, Alejandro

    2010-01-01

    Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper limits for the distances (constraints) between pairs of atoms. If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the macromolecule satisfying the data. Thus, the more constraints are measured, the better defined these structures will be. The availability of a user-friendly tool able to help in the analysis and interpretation of the number of experimental constraints per residue, is thus of valuable importance when assessing the levels of structure definition of NMR solved biological macromolecules, in particular, when high-quality structures are needed in techniques such as, computational biology approaches, site-directed mutagenesis experiments and/or drug design. Here, we present a free publicly available web-server, i.e. NMR Constraints Analyser, which is aimed at providing an automatic graphical analysis of the NMR experimental constraints atom by atom. The NMR Constraints Analyser server is available from the web-page http://molsim.sci.univr.it/constraint PMID:20513646

  5. NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.

    PubMed

    Heller, Davide Martin; Giorgetti, Alejandro

    2010-07-01

    Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper limits for the distances (constraints) between pairs of atoms. If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the macromolecule satisfying the data. Thus, the more constraints are measured, the better defined these structures will be. The availability of a user-friendly tool able to help in the analysis and interpretation of the number of experimental constraints per residue, is thus of valuable importance when assessing the levels of structure definition of NMR solved biological macromolecules, in particular, when high-quality structures are needed in techniques such as, computational biology approaches, site-directed mutagenesis experiments and/or drug design. Here, we present a free publicly available web-server, i.e. NMR Constraints Analyser, which is aimed at providing an automatic graphical analysis of the NMR experimental constraints atom by atom. The NMR Constraints Analyser server is available from the web-page http://molsim.sci.univr.it/constraint.

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

    SciTech Connect

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

    2008-12-26

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

  7. Structural Studies of Biological Solids Using NMR

    NASA Astrophysics Data System (ADS)

    Ramamoorthy, Ayyalusamy

    2011-03-01

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

  8. Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Yehl, Jenna; Kudryashova, Elena; Reisler, Emil; Kudryashov, Dmitri; Polenova, Tatyana

    2017-01-01

    Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin. PMID:28303963

  9. Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy.

    PubMed

    Loy, Brian A; Lesser, Adam B; Staveness, Daryl; Billingsley, Kelvin L; Cegelski, Lynette; Wender, Paul A

    2015-03-18

    Protein kinase C (PKC) modulators are currently of great importance in preclinical and clinical studies directed at cancer, immunotherapy, HIV eradication, and Alzheimer's disease. However, the bound conformation of PKC modulators in a membrane environment is not known. Rotational echo double resonance (REDOR) NMR spectroscopy could uniquely address this challenge. However, REDOR NMR requires strategically labeled, high affinity ligands to determine interlabel distances from which the conformation of the bound ligand in the PKC-ligand complex could be identified. Here we report the first computer-guided design and syntheses of three bryostatin analogues strategically labeled for REDOR NMR analysis. Extensive computer analyses of energetically accessible analogue conformations suggested preferred labeling sites for the identification of the PKC-bound conformers. Significantly, three labeled analogues were synthesized, and, as required for REDOR analysis, all proved highly potent with PKC affinities (∼1 nM) on par with bryostatin. These potent and strategically labeled bryostatin analogues are new structural leads and provide the necessary starting point for projected efforts to determine the PKC-bound conformation of such analogues in a membrane environment, as needed to design new PKC modulators and understand PKC-ligand-membrane structure and dynamics.

  10. Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP from Escherichia coli

    PubMed Central

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

    2014-01-01

    The solution NMR structure of the α-helical integral membrane protein YgaP from Escherichia coli in mixed 1,2-diheptanoyl-sn-glycerol-3-phosphocholine/1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1′-rac-glycerol) micelles is presented. In these micelles, YgaP forms a homodimer with the two transmembrane helices being the dimer interface, whereas the N-terminal cytoplasmic domain includes a rhodanese-fold in accordance to its sequence homology to the rhodanese family of sulfurtransferases. The enzymatic sulfur transfer activity of full-length YgaP as well as of the N-terminal rhodanese domain only was investigated performing a series of titrations with sodium thiosulfate and potassium cyanide monitored by NMR and EPR. The data indicate the thiosulfate concentration-dependent addition of several sulfur atoms to the catalytic Cys-63, which process can be reversed by the addition of potassium cyanide. The catalytic reaction induces thereby conformational changes within the rhodanese domain, as well as on the transmembrane α-helices of YgaP. These results provide insights into a potential mechanism of YgaP during the catalytic thiosulfate activity in vivo. PMID:24958726

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

    PubMed

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

    2017-05-01

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

  12. Two-Dimensional NMR Lineshape Analysis

    NASA Astrophysics Data System (ADS)

    Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

    2016-04-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.

  13. Two-Dimensional NMR Lineshape Analysis

    PubMed Central

    Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

    2016-01-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions. PMID:27109776

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

    SciTech Connect

    LeMaster, D.M.

    1994-12-01

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

  15. Automated Solid Phase Extraction (SPE) LC/NMR Applied to the Structural Analysis of Extractable Compounds from a Pharmaceutical Packaging Material of Construction.

    PubMed

    Norwood, Daniel L; Mullis, James O; Davis, Mark; Pennino, Scott; Egert, Thomas; Gonnella, Nina C

    2013-01-01

    The structural analysis (i.e., identification) of organic chemical entities leached into drug product formulations has traditionally been accomplished with techniques involving the combination of chromatography with mass spectrometry. These include gas chromatography/mass spectrometry (GC/MS) for volatile and semi-volatile compounds, and various forms of liquid chromatography/mass spectrometry (LC/MS or HPLC/MS) for semi-volatile and relatively non-volatile compounds. GC/MS and LC/MS techniques are complementary for structural analysis of leachables and potentially leachable organic compounds produced via laboratory extraction of pharmaceutical container closure/delivery system components and corresponding materials of construction. Both hyphenated analytical techniques possess the separating capability, compound specific detection attributes, and sensitivity required to effectively analyze complex mixtures of trace level organic compounds. However, hyphenated techniques based on mass spectrometry are limited by the inability to determine complete bond connectivity, the inability to distinguish between many types of structural isomers, and the inability to unambiguously determine aromatic substitution patterns. Nuclear magnetic resonance spectroscopy (NMR) does not have these limitations; hence it can serve as a complement to mass spectrometry. However, NMR technology is inherently insensitive and its ability to interface with chromatography has been historically challenging. This article describes the application of NMR coupled with liquid chromatography and automated solid phase extraction (SPE-LC/NMR) to the structural analysis of extractable organic compounds from a pharmaceutical packaging material of construction. The SPE-LC/NMR technology combined with micro-cryoprobe technology afforded the sensitivity and sample mass required for full structure elucidation. Optimization of the SPE-LC/NMR analytical method was achieved using a series of model compounds

  16. A New Microcell Technique for NMR Analysis.

    ERIC Educational Resources Information Center

    Yu, Sophia J.

    1987-01-01

    Describes a new laboratory technique for working with small samples of compounds used in nuclear magnetic resonance (NMR) analysis. Demonstrates how microcells can be constructed for each experiment and samples can be recycled. (TW)

  17. A New Microcell Technique for NMR Analysis.

    ERIC Educational Resources Information Center

    Yu, Sophia J.

    1987-01-01

    Describes a new laboratory technique for working with small samples of compounds used in nuclear magnetic resonance (NMR) analysis. Demonstrates how microcells can be constructed for each experiment and samples can be recycled. (TW)

  18. Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.

    PubMed

    Cornilescu, Gabriel; Didychuk, Allison L; Rodgers, Margaret L; Michael, Lauren A; Burke, Jordan E; Montemayor, Eric J; Hoskins, Aaron A; Butcher, Samuel E

    2016-02-27

    NMR and SAXS (small-angle X-ray scattering)/WAXS (wide-angle X-ray scattering) are highly complementary approaches for the analysis of RNA structure in solution. Here we describe an efficient NMR-SAXS/WAXS approach for structural investigation of multi-helical RNAs. We illustrate this approach by determining the overall fold of a 92-nt 3-helix junction from the U4/U6 di-snRNA. The U4/U6 di-snRNA is conserved in eukaryotes and is part of the U4/U6.U5 tri-snRNP, a large ribonucleoprotein complex that comprises a major subunit of the assembled spliceosome. Helical orientations can be determined by X-ray scattering data alone, but the addition of NMR RDC (residual dipolar coupling) restraints improves the structure models. RDCs were measured in two different external alignment media and also by magnetic susceptibility anisotropy. The resulting alignment tensors are collinear, which is a previously noted problem for nucleic acids. Including WAXS data in the calculations produces models with significantly better fits to the scattering data. In solution, the U4/U6 di-snRNA forms a 3-helix junction with a planar Y-shaped structure and has no detectable tertiary interactions. Single-molecule Förster resonance energy transfer data support the observed topology. A comparison with the recently determined cryo-electron microscopy structure of the U4/U6.U5 tri-snRNP illustrates how proteins scaffold the RNA and dramatically alter the geometry of the U4/U6 3-helix junction.

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

    SciTech Connect

    Zilm, K.W.

    1988-01-01

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

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

    SciTech Connect

    Zilm, K.W.

    1988-01-01

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

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

    SciTech Connect

    Zilm, K.W.

    1990-01-01

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

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

    PubMed

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

    2013-10-04

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

  3. NMR studies of protein structure and dynamics

    NASA Astrophysics Data System (ADS)

    Kay, Lewis E.

    2011-12-01

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

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

    PubMed

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

    2013-09-17

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

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

    SciTech Connect

    Zilm, K.W.

    1992-05-27

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

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

    SciTech Connect

    Zilm, K.W.

    1989-01-01

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

  7. Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz.

    PubMed

    Struppe, Jochem; Quinn, Caitlin M; Lu, Manman; Wang, Mingzhang; Hou, Guangjin; Lu, Xingyu; Kraus, Jodi; Andreas, Loren B; Stanek, Jan; Lalli, Daniela; Lesage, Anne; Pintacuda, Guido; Maas, Werner; Gronenborn, Angela M; Polenova, Tatyana

    2017-07-03

    The recent breakthroughs in NMR probe technologies resulted in the development of MAS NMR probes with rotation frequencies exceeding 100 kHz. Herein, we explore dramatic increases in sensitivity and resolution observed at MAS frequencies of 110-111 kHz in a novel 0.7 mm HCND probe that enable structural analysis of fully protonated biological systems. Proton- detected 2D and 3D correlation spectroscopy under such conditions requires only 0.1-0.5 mg of sample and a fraction of time compared to conventional (13)C-detected experiments. We discuss the performance of several proton- and heteronuclear- ((13)C-,(15)N-) based correlation experiments in terms of sensitivity and resolution, using a model microcrystalline fMLF tripeptide. We demonstrate the applications of ultrafast MAS to a large, fully protonated protein assembly of the 231-residue HIV-1 CA capsid protein. Resonance assignments of protons and heteronuclei, as well as (1)H-(15)N dipolar and (1)H(N) CSA tensors are readily obtained from the high sensitivity and resolution proton-detected 3D experiments. The approach demonstrated here is expected to enable the determination of atomic-resolution structures of large protein assemblies, inaccessible by current methodologies. Copyright © 2017. Published by Elsevier Inc.

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

    SciTech Connect

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

    1999-11-14

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

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

    PubMed

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

    2017-08-08

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

  10. Synthesis, NMR analysis and X-ray crystal structure of 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazatetraasterane

    NASA Astrophysics Data System (ADS)

    Tan, Hong-bo; Song, Xiu-qing; Yan, Hong; Xin, Hong-xing

    2017-02-01

    Novel 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazatetraasterane (3, Tetraethyl 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazapentacyclo [6.4.0.02,7.04,11.05,10]dodecane-1,5,7,11-tetracarboxylate) was prepared by naphthoylation of 3,9-diazatetraasterane (2). The target compound was isolated and unambiguously confirmed by NMR spectra, high-resolution mass spectrometry, and single-crystal X-ray diffraction analysis. In order to discuss the spatial effects on the NMR of 3 by the naphthoyl group, spectra analysis (1D-NMR and 2D-NMR) of 2 and 3 was conducted in details by the shifts and assignments of signals. Single-crystal X-ray diffraction assists to explain the molecular asymmetry of 3 and elucidates the effects of naphthoyl group on the geometry of the central cage of 3,9-diazatetraasterane.

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

    PubMed

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

    2015-08-01

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

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

    PubMed Central

    Jang, Richard; Wang, Yan

    2015-01-01

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

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

    PubMed

    Singh, Kawarpal; Blümich, Bernhard

    2017-03-27

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

  14. Structural elucidation of dioxa-cage compounds from tetrahydroisobenzofuran-1(3H)-one: analysis of NMR data and GIAO chemical shifts calculations.

    PubMed

    da Costa Resende, Gabriela; Alvarenga, Elson Santiago

    2016-12-01

    The polycyclic compounds, especially the dioxa-cages, have attracted considerable attention in recent years. In our work, a series of 9β-substituted 3-oxo-4,11-dioxatetracyclo[5.2.1.1(5,8) .0(2,6) ]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3-hydroxy-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

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

  16. NMR methodologies in the analysis of blueberries.

    PubMed

    Capitani, Donatella; Sobolev, Anatoly P; Delfini, Maurizio; Vista, Silvia; Antiochia, Riccarda; Proietti, Noemi; Bubici, Salvatore; Ferrante, Gianni; Carradori, Simone; De Salvador, Flavio Roberto; Mannina, Luisa

    2014-06-01

    An NMR analytical protocol based on complementary high and low field measurements is proposed for blueberry characterization. Untargeted NMR metabolite profiling of blueberries aqueous and organic extracts as well as targeted NMR analysis focused on anthocyanins and other phenols are reported. Bligh-Dyer and microwave-assisted extractions were carried out and compared showing a better recovery of lipidic fraction in the case of microwave procedure. Water-soluble metabolites belonging to different classes such as sugars, amino acids, organic acids, and phenolic compounds, as well as metabolites soluble in organic solvent such as triglycerides, sterols, and fatty acids, were identified. Five anthocyanins (malvidin-3-glucoside, malvidin-3-galactoside, delphinidin-3-glucoside, delphinidin-3-galactoside, and petunidin-3-glucoside) and 3-O-α-l-rhamnopyranosyl quercetin were identified in solid phase extract. The water status of fresh and withered blueberries was monitored by portable NMR and fast-field cycling NMR. (1) H depth profiles, T2 transverse relaxation times and dispersion profiles were found to be sensitive to the withering.

  17. Native dynamics from diversity in NMR structures

    NASA Astrophysics Data System (ADS)

    Lammert, Heiko; Onuchic, Jose

    2015-03-01

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

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

    PubMed

    Patching, Simon G

    2015-01-01

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

  19. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1997-09-01

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

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

    PubMed

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

    2008-09-10

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

  1. Microgram-scale protein structure determination by NMR.

    PubMed

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

    2007-06-01

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

  2. Models of steroid binding based on the minimum deviation of structurally assigned 13C NMR spectra analysis (MiDSASA).

    PubMed

    Beger, Richard D; Harris, Stephen; Xie, Qian

    2004-01-01

    This paper develops a quantitative k-nearest neighbors modeling technique. The technique is used to demonstrate that a compound's biological binding activity to a receptor can be calculated from the minimum of the square root of the sum of squared deviations (SSSD) of a structurally assigned chemical shift on a template between the unknown compound to be predicted and a set of known compounds with known activities. When building models of biological activity, nonlinear relationships are built into the input training data. If a model is developed by selecting only compounds with minimum structurally assigned chemical shift deviations from the unknown compound, some of the nonlinear relationships can be removed. The smaller the total chemical shift deviation between a compound with known activity and another compound with unknown activity, the more likely it will have similar biological, chemical, and physical properties. This means that a model can be produced without rigorous statistics or neural networks. This technique is similar to structure-activity relationship (SAR) modeling, but instead of relying on substructure fragments to produce a model, this new model is based on minimum chemical shift differences on those substructure fragments. We refer to this method as minimum deviation of structurally assigned spectra analysis (MiDSASA) modeling. Modeling by the minimum deviation concept can be applied to other chemoinformatic data analyses such as metabolite concentrations in metabolic pathways for metabolomics research. A MiDSASA template model for 30 steroids binding the corticosterone binding globulin based on the activity factors of the two nearest compounds had a correlation of 0.88. A MiDSASA template model for 50 steroids binding the aromatse enzyme based on the average activity of the four nearest compounds had a correlation of 0.71.

  3. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 9, October 1, 1993--December 30, 1993

    SciTech Connect

    Smith, D.M.

    1993-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and dosed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and pore surface. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  4. Automatic analysis of quantitative NMR data of pharmaceutical compound libraries.

    PubMed

    Liu, Xuejun; Kolpak, Michael X; Wu, Jiejun; Leo, Gregory C

    2012-08-07

    In drug discovery, chemical library compounds are usually dissolved in DMSO at a certain concentration and then distributed to biologists for target screening. Quantitative (1)H NMR (qNMR) is the preferred method for the determination of the actual concentrations of compounds because the relative single proton peak areas of two chemical species represent the relative molar concentrations of the two compounds, that is, the compound of interest and a calibrant. Thus, an analyte concentration can be determined using a calibration compound at a known concentration. One particularly time-consuming step in the qNMR analysis of compound libraries is the manual integration of peaks. In this report is presented an automated method for performing this task without prior knowledge of compound structures and by using an external calibration spectrum. The script for automated integration is fast and adaptable to large-scale data sets, eliminating the need for manual integration in ~80% of the cases.

  5. NMR spectral analysis using prior knowledge

    NASA Astrophysics Data System (ADS)

    Kasai, Takuma; Nagata, Kenji; Okada, Masato; Kigawa, Takanori

    2016-03-01

    Signal assignment is a fundamental step for analyses of protein structure and dynamics with nuclear magnetic resonance (NMR). Main-chain signal assignment is achieved with a sequential assignment method and/or an amino-acid selective stable isotope labeling (AASIL) method. Combinatorial selective labeling (CSL) methods, as well as our labeling strategy, stable isotope encoding (SiCode), were developed to reduce the required number of labeled samples, since one of the drawbacks of AASIL is that many samples are needed. Signal overlapping in NMR spectra interferes with amino-acid determination by CSL and SiCode. Since spectral deconvolution by peak fitting with a gradient method cannot resolve closely overlapped signals, we developed a new method to perform both peak fitting and amino acid determination simultaneously, with a replica exchange Monte Carlo method, incorporating prior knowledge of stable-isotope labeling ratios and the amino-acid sequence of the protein.

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

    PubMed Central

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

    2013-01-01

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

  7. Molecular structure, vibrational, UV, NMR, HOMO-LUMO, MEP, NLO, NBO analysis of 3,5 di tert butyl 4 hydroxy benzoic acid

    NASA Astrophysics Data System (ADS)

    Mathammal, R.; Sangeetha, K.; Sangeetha, M.; Mekala, R.; Gadheeja, S.

    2016-09-01

    In this study, we report a combined experimental and theoretical study on molecular structure and vibrational spectra of 3,5 di tert butyl 4 hydroxy benzoic acid. The properties of title compound have been evaluated by quantum chemical calculation (DFT) using B3LYP functional and 6-31 + G (d, p) as basis set. IR Spectra has been recorded using Fourier transform infrared spectroscopy (FT-IR) in the region 4000-400 cm-1. The vibrational assignment of the calculated normal modes has been made on the basis set. The isotropic chemical shifts computed by 13C and 1H NMR (Nuclear Magnetic Resonance) analyses also show good agreement with experimental observations. The theoretical UV-Vis spectrum of the compound are used to study the visible absorption maxima (λ max). The structure activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug receptor interactions. The Mullikan charges, HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) energy are analyzed. HOMO-LUMO energy gap and other related molecular properties are also calculated. The Natural Bond Orbital (NBO) analysis is carried out to investigate the various intra and inter molecular interactions of molecular system. The Non-linear optical properties such as dipole moment (μ), polarizability (αtot) and molecular first order hyperpolarizability (β) of the title compound are computed with B3LYP/6-31 + G (d,p) level of theory.

  8. NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

    A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

  9. NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

    A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

  10. Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Alver, Özgür; Dikmen, Gökhan

    2016-03-01

    Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500-400 cm-1, and 3200-400 cm-1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.

  11. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Al-Hashimi, Hashim M; Patel, Dinshaw J

    2002-01-01

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

  14. Vibrational spectra, molecular structure, NBO, NMR, UV, first order hyperpolarizability, analysis of (S)-(-)-N-(5-Nitro-2-pyridyl) alaninol by Density functional theory.

    PubMed

    Govindarasu, K; Kavitha, E

    2014-06-05

    In this study, geometrical optimization, spectroscopic analysis, electronic structure and nuclear magnetic resonance studies of (S)-(-)-N-(5-Nitro-2-pyridyl) alaninol (abbreviated as SN5N2PLA) were investigated by utilizing HF and DFT/B3LYP with 6-31G(d,p) as basis set. The Fourier transform infrared (FT-IR) and FT-Raman spectra of SN5N2PLA were recorded in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. Complete vibrational assignments, analysis and correlation of the fundamental modes for the title compound were carried out. UV-Visible spectrum of the compound that dissolved in methanol were recorded in the region 200-800nm and the electronic properties HOMO and LUMO energies were measured by TD-DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The molecular stability and bond strength have been investigated by applying the Natural Bond Orbital (NBO) analysis. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of SN5N2PLA were calculated using the GIAO method in methanol solution and compared with the measured experimental data. The dipole moment, polarizability and first order hyperpolarizability values were also computed. The polarizability and first hyperpolarizability of the studied molecule indicate that the compound is a good candidate of nonlinear optical materials. The Chemical reactivity and Thermodynamic properties of SN5N2PLA at different temperature are calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs) analysis were investigated using theoretical calculations. Published by Elsevier B.V.

  15. Advances in NMR-based biofluid analysis and metabolite profiling.

    PubMed

    Zhang, Shucha; Nagana Gowda, G A; Ye, Tao; Raftery, Daniel

    2010-07-01

    Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.

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

    PubMed Central

    Hennig, Janosch; Sattler, Michael

    2014-01-01

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

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

    SciTech Connect

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

    2009-10-21

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

  18. Structural biology applications of solid state MAS DNP NMR

    NASA Astrophysics Data System (ADS)

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

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

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

    PubMed Central

    Konrat, Robert

    2014-01-01

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

  20. Solid-State NMR Studies of Amyloid Fibril Structure

    NASA Astrophysics Data System (ADS)

    Tycko, Robert

    2011-05-01

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

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

    PubMed Central

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

    2015-01-01

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [1H,1H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. PMID:26227870

  2. Multinuclear NMR analysis of the antitubercular drug ethionamide

    NASA Astrophysics Data System (ADS)

    Vale, Nuno; Correia, Alexandra; Figueiredo, Patrícia; Santos, Hélder A.

    2016-02-01

    Tuberculosis remains as the deadliest bacterial infection in developing countries, a situation that is particularly aggravated by the increasing spread of multidrug resistant mycobacteria (MDR-TB). In this view, not only new anti-tubercular drugs are urgently needed, but also a better understanding of the existing ones may aid in the future design of more efficient derivatives or surrogates. Ethionamide (ETA) is an anti-tubercular pro-drug used as second-line therapy against MDR-TB, being bio-activated by the mycobacterial monooxygenase EtA. ETA has been the focus of several research works, devoted either to the identification of ETA's metabolites or to the development of novel derivatives potentially useful to fight against tuberculosis. In either case, structural analysis of ETA and related structures is of undeniable relevance, while the presence of sulfur in ETA's structure brings about the possibility of including 33S-NMR in the toolbox of structural analysis techniques. In this work, we have engaged into a multinuclear NMR characterization of ETA, through the study of the drug's solubility in seven deuterated solvents, and of the chemical shifts for different nuclei in ETA. Results showed which are the best conditions to study ETA by NMR and provided some important evidence on the low reactivity of the drug's thioamide group, which may be of relevance for future drug derivatization approaches.

  3. Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy.

    PubMed

    Lundborg, Magnus; Fontana, Carolina; Widmalm, Göran

    2011-11-14

    The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (-)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic (1)H and (13)C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and implemented herein. The method is additionally advantageous in that reference data only have to be prepared once and from a user's point of view only the unknown sample has to be derivatized for use in CASPER.

  4. Microscopic structural analysis of fractured silk fibers from Bombyx mori and Samia cynthia ricini using 13C CP/MAS NMR with a 1mm microcoil MAS NMR probehead.

    PubMed

    Yamauchi, Kazuo; Yamasaki, Shizuo; Takahashi, Rui; Asakura, Tetsuo

    2010-07-01

    Conformational changes have been studied in silk fibers from the domestic silkworm Bombyx mori and a wild silkworm Samia cynthia ricini as a result of fractured by stretching. About 300 samples consisting of only the fractured regions of [1-13C]Ala or [1-13C]Gly labeled silk fibers were collected and observed by 13C CP/MAS NMR spectra. The total amount of these fractured fibers is only about 1mg and therefore we used a home-built 1mm microcoil MAS NMR probehead. A very small increase in the fraction of random coil was noted for the alanine regions of both silk fibroins and for the glycine region of B. mori silk fibroin. However, there is no difference in the spectra before and after fractured for the glycine region of S. c. ricini silk fibroin. Thus, the influence of fracture occurs exclusively at the Ala region for S. c. ricini. The relationship between sequence, fracture and structure is discussed.

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

    PubMed

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

    2012-01-01

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

  6. PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

    PubMed

    Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

    2013-08-01

    The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

  7. Structure and Metabolic-Flow Analysis of Molecular Complexity in a (13) C-Labeled Tree by 2D and 3D NMR.

    PubMed

    Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant.

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

    DOE PAGES

    Perras, Frederic A.

    2015-12-15

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

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

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

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

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

    PubMed

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

    2009-04-01

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

  11. Structural characterization of β-2'-pyridylaminocrotonoyl-2-pyridylamide by ESI-MS, NMR, single crystal X-ray analysis and ab initio methods

    NASA Astrophysics Data System (ADS)

    Ośmiałowski, Borys; Laihia, Katri; Virtanen, Elina; Nissinen, Maija; Kolehmainen, Erkki; Gawinecki, Ryszard

    2003-06-01

    In contradiction with earlier reports 1H, 13C and 15N NMR spectra show that β-2'-pyridylaminocrotonoyl-2-pyridylamide is the only form present in chloroform solution. According to the X-ray data the same tautomer exists also in the crystal state. The studied amide has a dimeric form where the monomer molecules are held together by two intermolecular hydrogen bonds. The NMR spectral data show that there is also an intramolecular hydrogen bond in each monomer subunit. The dilution experiments and variable-temperature 1H NMR runs show that β-2'-pyridylaminocrotonoyl-2-pyridylamide tends to form the dimers also in chloroform solution at higher concentrations. The ESI-TOF MS measurements at different concentrations confirm that there is a dimerization process taking place in solution. The calculated energetic effect of dimerization of β-2'-pyridylaminocrotonoyl-2-pyridylamide in vacuum is equal to -34 kJ/mol (exothermic process). X-ray analysis shows that the molecule in crystalline state is not planar. The ab initio RHF/6-31G** calculations approximate well the X-ray determined molecular geometry of β-2'-pyridylaminocrotonoyl-2-pyridyl-amide.

  12. Binding site identification and structure determination of protein-ligand complexes by NMR

    PubMed Central

    Ziarek, Joshua J.; Peterson, Francis C.; Lytle, Betsy L.; Volkman, Brian F.

    2013-01-01

    Over the last fifteen years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (Kd > 10-6 M) complexes, which often fail to crystallize. This article emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semi-automated NMR assignment methods, and structure determination of protein-ligand complexes by NMR. PMID:21371594

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  14. Automated NMR relaxation dispersion data analysis using NESSY.

    PubMed

    Bieri, Michael; Gooley, Paul R

    2011-10-27

    Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR) relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.

  15. Structure determination of membrane proteins by NMR spectroscopy

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2016-02-05

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

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

    PubMed Central

    2016-01-01

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

  18. Determination of a complex crystal structure in the absence of single crystals: analysis of powder X-ray diffraction data, guided by solid-state NMR and periodic DFT calculations, reveals a new 2'-deoxyguanosine structural motif.

    PubMed

    Hughes, Colan E; Reddy, G N Manjunatha; Masiero, Stefano; Brown, Steven P; Williams, P Andrew; Harris, Kenneth D M

    2017-05-01

    Derivatives of guanine exhibit diverse supramolecular chemistry, with a variety of distinct hydrogen-bonding motifs reported in the solid state, including ribbons and quartets, which resemble the G-quadruplex found in nucleic acids with sequences rich in guanine. Reflecting this diversity, the solid-state structural properties of 3',5'-bis-O-decanoyl-2'-deoxyguanosine, reported in this paper, reveal a hydrogen-bonded guanine ribbon motif that has not been observed previously for 2'-deoxyguanosine derivatives. In this case, structure determination was carried out directly from powder XRD data, representing one of the most challenging organic molecular structures (a 90-atom molecule) that has been solved to date by this technique. While specific challenges were encountered in the structure determination process, a successful outcome was achieved by augmenting the powder XRD analysis with information derived from solid-state NMR data and with dispersion-corrected periodic DFT calculations for structure optimization. The synergy of experimental and computational methodologies demonstrated in the present work is likely to be an essential feature of strategies to further expand the application of powder XRD as a technique for structure determination of organic molecular materials of even greater complexity in the future.

  19. Complete NMR analysis of oxytocin in phosphate buffer.

    PubMed

    Ohno, Akiko; Kawasaki, Nana; Fukuhara, Kiyoshi; Okuda, Haruhiro; Yamaguchi, Teruhide

    2010-02-01

    Complete NMR analysis of oxytocin (OXT) in phosphate buffer was elucidated by one-dimensional (1D)- and two-dimensional (2D)-NMR techniques, which involve the assignment of peptide amide NH protons and carbamoyl NH(2) protons. The (1)H-(15)N correlation of seven amide NH protons and three carbamoyl NH(2) protons were also shown by HSQC NMR of OXT without (15)N enrichment.

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

    PubMed

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

    2012-06-19

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

  1. Interplay between structure and dynamics in chitosan films investigated with solid-state NMR, dynamic mechanical analysis, and X-ray diffraction.

    PubMed

    Gartner, Carmiña; López, Betty Lucy; Sierra, Ligia; Graf, Robert; Spiess, Hans W; Gaborieau, Marianne

    2011-04-11

    Modern solid-state NMR techniques, combined with X-ray diffraction, revealed the molecular origin of the difference in mechanical properties of self-associated chitosan films. Films cast from acidic aqueous solutions were compared before and after neutralization, and the role of the counterion (acetate vs Cl(-)) was investigated. There is a competition between local structure and long-range order. Hydrogen bonding gives good mechanical strength to neutralized films, which lack long-range organization. The long-range structure is better defined in films cast from acidic solutions in which strong electrostatic interactions cause rotational distortion around the chitosan chains. Plasticization by acetate counterions enhances long-range molecular organization and film flexibility. In contrast, Cl(-) counterions act as a defect and impair the long-range organization by immobilizing hydration water. Molecular motion and proton exchange are restricted, resulting in brittle films despite the high moisture content.

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

    PubMed

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Fe57 NMR and spin structure of manganese ferrite

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  4. Dilute Bicellar Solutions for Structural NMR Work

    NASA Astrophysics Data System (ADS)

    Struppe, Jochem; Vold, Regitze R.

    1998-12-01

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

  5. NMR Structures of Membrane Proteins in Phospholipid Bilayers

    PubMed Central

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

    2014-01-01

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

  6. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene

    NASA Astrophysics Data System (ADS)

    Kose, E.; Atac, A.; Karabacak, M.; Nagabalasubramanian, P. B.; Asiri, A. M.; Periandy, S.

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, 1H and 13C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. 13C and 1H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule.

  7. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene.

    PubMed

    Kose, E; Atac, A; Karabacak, M; Nagabalasubramanian, P B; Asiri, A M; Periandy, S

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, (1)H and (13)C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. (13)C and (1)H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule.

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

    PubMed

    Korir, Albert K; Larive, Cynthia K

    2007-08-01

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

  9. SPINS: a laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations.

    PubMed

    Baran, Michael C; Moseley, Hunter N B; Aramini, James M; Bayro, Marvin J; Monleon, Daniel; Locke, Jessica Y; Montelione, Gaetano T

    2006-03-01

    Recent technological advances and experimental techniques have contributed to an increasing number and size of NMR datasets. In order to scale up productivity, laboratory information management systems for handling these extensive data need to be designed and implemented. The SPINS (Standardized ProteIn Nmr Storage) Laboratory Information Management System (LIMS) addresses these needs by providing an interface for archival of complete protein NMR structure determinations, together with functionality for depositing these data to the public BioMagResBank (BMRB). The software tracks intermediate files during each step of an NMR structure-determination process, including: data collection, data processing, resonance assignments, resonance assignment validation, structure calculation, and structure validation. The underlying SPINS data dictionary allows for the integration of various third party NMR data processing and analysis software, enabling users to launch programs they are accustomed to using for each step of the structure determination process directly out of the SPINS user interface.

  10. NMR analysis of compositional heterogeneity in polysaccharides

    USDA-ARS?s Scientific Manuscript database

    Many copolysaccharides are compositionally heterogeneous, and the composition determined by the usual analytical or spectroscopic methods provides only an average value. For some polysaccharides, the NMR data contain copolymer sequence information, such as diad, triad, and tetrad sequence intensiti...

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

    PubMed

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

    2016-01-01

    We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development. © 2015 The Protein Society.

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

    PubMed

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

    2002-03-01

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

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

    PubMed

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

    2017-09-01

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

  14. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 10, January 1, 1994--March 31, 1994

    SciTech Connect

    Smith, D.M.

    1994-06-01

    In the present quarter, results from {sup 129}Xe NMR experiments were made available that allowed the determination of the mean free path of a Xenon molecule within the pores of the material. The chemical shift at various loadings of Xenon was determined and the shift at zero loading was obtained by extrapolating the data to zero pressure. At zero loading, the collisions suffered by a Xenon molecule can be regarded as being entirely with the pore walls, since the concentration of Xenon molecules in the system is very low. Thus, the mean free path {lambda} is a measure of the distance travelled by a Xenon molecule before colliding with a wall, and hence is also a measure of the pore dimension. SAXS data reported in previous quarters gave the average radius of gyration R{sub g} which is also a measure of the average dimension of the pores of the material. In addition, application of the potential theory to the CO{sub 2} (274 K) adsorption data allowed the determination of a characteristic adsorption potential E, which is inversely proportional to the width of the pore. Thus, E should correlate inversely with the mean free path {lambda} as determined using {sup 129}Xe NMR. Also, E should correlate inversely with the radius of gyration R{sub g} from SAXS experiments. Another parameter obtained by analysis of the CO{sub 2} (274 K) adsorption data is the exponent n in the Dubinin-Astakhov equation. We had shown in previous quarters that this is a measure of the heterogeneity of the material.

  15. 1H-NMR analysis of CD3-epsilon reveals the presence of turn-helix structures around the ITAM motif in an otherwise random coil cytoplasmic tail.

    PubMed

    Borroto, A; Jiménez, M A; Alarcón, B; Rico, M

    1997-01-01

    The conformation adopted in solution by the cytoplasmic tail of CD3-epsilon has been analyzed by 1H-nmr. The cytoplasmic tail is mostly random coil expect for the amino acids conforming the immunoreceptor tyrosine-based activation motif (ITAM), YxxL/IxxxxxxxY xxL. Although the N-terminal Y xxL sequence of the motif is poorly folded, adopting 6-residue turn-like conformations with the Tyr side chain in two different orientations, the C-terminal Y xxL sequence is placed in a more complex structure involving a set of nonclassical alpha-helix turns and beta-turns that comprises 11 amino acids. This structure is not modified by phosphorylation of the tyrosine residue. The differences in the conformation adopted around the two tyrosines of the ITAM motif suggest that they may play different roles pertaining to either binding signal transducing proteins or, alternatively, proteins involved in other processes such as endoplasmic reticulum location.

  16. DNA Nanotubes for NMR Structure Determination of Membrane Proteins

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  18. In Depth Analysis on the Binding Sites of Adamantane Derivatives in HCV (Hepatitis C Virus) p7 Channel Based on the NMR Structure

    PubMed Central

    Du, Qi-Shi; Wang, Shu-Qing; Chen, Dong; Meng, Jian-Zong; Huang, Ri-Bo

    2014-01-01

    Background The recently solved solution structure of HCV (hepatitis C virus) p7 ion channel provides a solid structure basis for drug design against HCV infection. In the p7 channel the ligand amantadine (or rimantadine) was determined in a hydrophobic pocket. However the pharmocophore (−NH2) of the ligand was not assigned a specific binding site. Results The possible binding sites for amino group of adamantane derivatives is studied based on the NMR structure of p7 channel using QM calculation and molecular modeling. In the hydrophobic cavity and nearby three possible binding sites are proposed: His17, Phe20, and Trp21. The ligand binding energies at the three binding sites are studied using high level QM method CCSD(T)/6–311+G(d,p) and AutoDock calculations, and the interaction details are analyzed. The potential application of the binding sites for rational inhibitor design are discussed. Conclusions Some useful viewpoints are concluded as follows. (1) The amino group (−NH2) of adamantane derivatives is protonated (−NH3+), and the positively charged cation may form cation-π interactions with aromatic amino acids. (2) The aromatic amino acids (His17, Phe20, and Trp21) are the possible binding sites for the protonated amino group (−NH3+) of adamantane derivatives, and the cation-π bond energies are 3 to 5 times stronger than the energies of common hydrogen bonds. (3) The higher inhibition potent of rimantadine than amantadine probably because of its higher pKa value (pKa = 10.40) and the higher positive charge in the amino group. The potential application of p7 channel structure for inhibitor design is discussed. PMID:24714586

  19. Metabolite analysis of Cannabis sativa L. by NMR spectroscopy.

    PubMed

    Flores-Sanchez, Isvett Josefina; Choi, Young Hae; Verpoorte, Robert

    2012-01-01

    NMR-based metabolomics is an analytical platform, which has been used to classify and analyze Cannabis sativa L. cell suspension cultures and plants. Diverse groups of primary and secondary metabolites were identified by comparing NMR data with reference compounds and/or by structure elucidation using ¹H-NMR, J-resolved, ¹H-¹H COSY, and ¹H-¹³C HMBC spectroscopy. The direct extraction and the extraction by indirect fractionation are two suitable methods for the C. sativa sample preparation. Quantitative analyses could be performed without requiring fractionation or isolation procedures.

  20. Analysis of bacterial biofilms using NMR-based metabolomics.

    PubMed

    Zhang, Bo; Powers, Robert

    2012-06-01

    Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this 'social structure' of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms.

  1. NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    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.

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

    PubMed Central

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

    2001-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

  5. Broadband homonuclear correlation spectroscopy driven by combined R2(n)(v) sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids.

    PubMed

    Hou, Guangjin; Yan, Si; Trébosc, Julien; Amoureux, Jean-Paul; Polenova, Tatyana

    2013-07-01

    We recently described a family of experiments for R2n(v) Driven Spin Diffusion (RDSD) spectroscopy suitable for homonuclear correlation experiments under fast MAS conditions [G. Hou, S. Yan, S.J. Sun, Y. Han, I.J. Byeon, J. Ahn, J. Concel, A. Samoson, A.M. Gronenborn, T. Polenova, Spin diffusion drive by R-symmetry sequencs: applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids, J. Am. Chem. Soc. 133 (2011) 3943-3953]. In these RDSD experiments, since the broadened second-order rotational resonance conditions are dominated by the radio frequency field strength and the phase shifts, as well as the size of reintroduced dipolar couplings, the different R2n(v) sequences display unique polarization transfer behaviors and different recoupling frequency bandwidths. Herein, we present a series of modified R2n(v) sequences, dubbed COmbined R2n(v)-Driven (CORD), that yield broadband homonuclear dipolar recoupling and give rise to uniform distribution of cross peak intensities across the entire correlation spectrum. We report NMR experiments and numerical simulations demonstrating that these CORD spin diffusion sequences are suitable for broadband recoupling at a wide range of magnetic fields and MAS frequencies, including fast-MAS conditions (νr=40 kHz and above). Since these CORD sequences are largely insensitive to dipolar truncation, they are well suited for the determination of long-range distance constraints, which are indispensable for the structural characterization of a broad range of systems. Using U-(13)C,(15)N-alanine and U-(13)C,(15)N-histidine, we show that under fast-MAS conditions, the CORD sequences display polarization transfer efficiencies within broadband frequency regions that are generally higher than those offered by other existing spin diffusion pulse schemes. A 89-residue U-(13)C,(15)N-dynein light chain (LC8) protein has also been used to demonstrate that the CORD sequences exhibit uniformly high cross peak

  6. ADVANCED SOLIDS NMR STUDIES OF COAL STRUCTURE AND CHEMISTRY

    SciTech Connect

    1997-03-01

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

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

    PubMed

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

    2013-12-31

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

  8. Error analysis for NMR polymer microstructure measurement without calibration standards.

    PubMed

    Qiu, XiaoHua; Zhou, Zhe; Gobbi, Gian; Redwine, Oscar D

    2009-10-15

    We report an error analysis method for primary analytical methods in the absence of calibration standards. Quantitative (13)C NMR analysis of ethylene/1-octene (E/O) copolymers is given as an example. Because the method is based on a self-calibration scheme established by counting, it is a measure of accuracy rather than precision. We demonstrate it is self-consistent and neither underestimate nor excessively overestimate the experimental errors. We also show the method identified previously unknown systematic biases in a NMR instrument. The method can eliminate unnecessary data averaging to save valuable NMR resources. The accuracy estimate proposed is not unique to (13)C NMR spectroscopy of E/O but should be applicable to all other measurement systems where the accuracy of a subset of the measured responses can be established.

  9. A facile method for expression and purification of 15N isotope-labeled human Alzheimer's β-amyloid peptides from E. coli for NMR-based structural analysis

    PubMed Central

    Armand, Tara; Ball, K. Aurelia; Chen, Anna; Pelton, Jeffrey G.; Wemmer, David E.; Head-Gordon, Teresa

    2016-01-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disease affecting millions of people worldwide. AD is characterized by the presence of extracellular plaques composed of aggregated/oligomerized β-amyloid peptides with Aβ42 peptide representing a major isoform in the senile plaques. Given the pathological significance of Aβ42 in the progression of AD, there is considerable interest in understanding the structural ensembles for soluble monomer and oligomeric forms of Aβ42. This report describes an efficient method to express and purify high quality 15N isotope-labeled Aβ42 for structural studies by NMR. The protocol involves utilization of an auto induction system with 15N isotope labeled medium, for high-level expression of Aβ42 as a fusion with IFABP. After the over-expression of the 15N isotope-labeled IFABP-Aβ42 fusion protein in the inclusion bodies, pure 15N isotope-labeled Aβ42 peptide is obtained following a purification method that is streamlined and improved from the method originally developed for the isolation of unlabeled Aβ42 peptide (Garai et al., 2009). We obtain a final yield of ∼6 mg/L culture for 15N isotope-labeled Aβ42 peptide. Mass spectrometry and 1H–15N HSQC spectra of monomeric Aβ42 peptide validate the uniform incorporation of the isotopic label. The method described here is equally applicable for the uniform isotope labeling with 15N and 13C in Aβ42 peptide as well as its other variants including any Aβ42 peptide mutants. PMID:26231074

  10. NMR data visualization, processing, and analysis on mobile devices.

    PubMed

    Cobas, Carlos; Iglesias, Isaac; Seoane, Felipe

    2015-08-01

    Touch-screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR 'app' designed for hand-held and portable touch-controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non-uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand-alone tool or as a 'companion' to more advanced desktop applications such as Mnova NMR. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Deuterium incorporation in biomass cell wall components by NMR analysis

    SciTech Connect

    Foston, Marcus B; McGaughey, Joseph; O'Neill, Hugh Michael; Evans, Barbara R; Ragauskas, Arthur J

    2012-01-01

    A commercially available deuterated kale sample was analyzed for deuterium incorporation by ionic liquid solution 2H and 1H nuclear magnetic resonance (NMR). This protocol was found to effectively measure the percent deuterium incorporation at 33%, comparable to the 31% value determined by combustion. The solution NMR technique also suggested by a qualitative analysis that deuterium is preferentially incorporated into the carbohydrate components of the kale sample.

  12. Quantitative NMR Analysis of Partially Substituted Biodiesel Glycerols

    SciTech Connect

    Nagy, M.; Alleman, T. L.; Dyer, T.; Ragauskas, A. J.

    2009-01-01

    Phosphitylation of hydroxyl groups in biodiesel samples with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane followed by 31P-NMR analysis provides a rapid quantitative analytical technique for the determination of substitution patterns on partially esterified glycerols. The unique 31P-NMR chemical shift data was established with a series mono and di-substituted fatty acid esters of glycerol and then utilized to characterize an industrial sample of partially processed biodiesel.

  13. Protein NMR Structure Refinement based on Bayesian Inference

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2016-08-18

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

  15. Understanding NMR Multiplet Structure with WinDNMR

    NASA Astrophysics Data System (ADS)

    Bampos, N.; Vidal-Ferran, A.

    2000-01-01

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

  16. Analysis of bacterial biofilms using NMR-based metabolomics

    PubMed Central

    Zhang, Bo; Powers, Robert

    2013-01-01

    Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this ‘social structure’ of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms. PMID:22800371

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

    PubMed

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-05

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

  18. NMR and structural features of noble-metal fluorides

    SciTech Connect

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

    1987-11-01

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

  19. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

    NASA Astrophysics Data System (ADS)

    Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

  20. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

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

    PubMed

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

    2012-03-06

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

  2. Development and application of proton NMR methodology to lipoprotein analysis

    NASA Astrophysics Data System (ADS)

    Korhonen, Ari Juhani

    1998-11-01

    The present thesis describes the development of 1H NMR spectroscopy and its applications to lipoprotein analysis in vitro, utilizing biochemical prior knowledge and advanced lineshape fitting analysis in the frequency domain. A method for absolute quantification of lipoprotein lipids and proteins directly from the terminal methyl-CH3 resonance region of 1H NMR spectra of human blood plasma is described. Then the use of NMR methodology in time course studies of the oxidation process of LDL particles is presented. The function of the cholesteryl ester transfer protein (CETP) in lipoprotein mixtures was also assessed by 1H NMR, which allows for dynamic follow-up of the lipid transfer reactions between VLDL, LDL, and HDL particles. The results corroborated the suggestion that neutral lipid mass transfer among lipoproteins is not an equimolar heteroexchange. A novel method for studying lipoprotein particle fusion is also demonstrated. It is shown that the progression of proteolytically (α- chymotrypsin) induced fusion of LDL particles can be followed by 1H NMR spectroscopy and, moreover, that fusion can be distinguished from aggregation. In addition, NMR methodology was used to study the changes in HDL3 particles induced by phospholipid transfer protein (PLTP) in HDL3 + PLTP mixtures. The 1H NMR study revealed a gradual production of enlarged HDL particles, which demonstrated that PLTP-mediated remodeling of HDL involves fusion of the HDL particles. These applications demonstrated that the 1H NMR approach offers several advantages both in quantification and in time course studies of lipoprotein-lipoprotein interactions and of enzyme/lipid transfer protein function.

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

    PubMed

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

    2016-02-15

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

  4. Analysis of multiple pulse NMR in solids

    NASA Technical Reports Server (NTRS)

    Rhim, W.-K.; Elleman, D. D.; Vaughan, R. W.

    1973-01-01

    The general problems associated with the removal of the effects of dipolar broadening from solid-state NMR spectra are analyzed. The effects of finite pulse width and H sub 1 inhomogeneity are shown to have limited the resolution of previous pulse cycles, and a new eight-pulse cycle designed to minimize these problems is discussed. Spectra for F-19 in CaF2 taken with this cycle are presented which show residual linewidth near 10 Hz. The feasibility of measuring proton chemical shift tensors is discussed.

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

    PubMed

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

    2015-12-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    PubMed

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

    2017-01-23

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

  9. NMR analysis on microfluidic devices by remote detection.

    PubMed

    McDonnell, Erin E; Han, SongI; Hilty, Christian; Pierce, Kimberly L; Pines, Alexander

    2005-12-15

    We present a novel approach to perform high-sensitivity NMR imaging and spectroscopic analysis on microfluidic devices. The application of NMR, the most information-rich spectroscopic technique, to microfluidic devices remains a challenge because the inherently low sensitivity of NMR is aggravated by small fluid volumes leading to low NMR signal and geometric constraints resulting in poor efficiency for inductive detection. We address the latter by physically separating signal detection from encoding of information with remote detection. Thereby, we use a commercial imaging probe with sufficiently large diameter to encompass the entire device, enabling encoding of NMR information at any location on the chip. Because large-diameter coils are too insensitive for detection, we store the encoded information as longitudinal magnetization and flow it into the outlet capillary. There, we detect the signal with optimal sensitivity, using a solenoidal microcoil, and reconstruct the information encoded in the fluid. We present a generally applicable design for a detection-only microcoil probe that can be inserted into the bore of a commercial imaging probe. Using hyperpolarized 129Xe gas, we show that this probe enables sensitive reconstruction of NMR spectroscopic information encoded by the large imaging probe while keeping the flexibility of a large coil.

  10. Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

    PubMed

    Tang, Yuefeng; Schneider, William M; Shen, Yang; Raman, Srivatsan; Inouye, Masayori; Baker, David; Roth, Monica J; Montelione, Gaetano T

    2010-12-01

    Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using <4 days of data collection and fully automated data analysis methods together with CS-Rosetta. The resulting CspA structure is highly converged and in excellent agreement with the published crystal structure, with a backbone RMSD value of 0.5 Å, an all atom RMSD value of 1.2 Å to the crystal structure for well-defined regions, and RMSD value of 1.1 Å to crystal structure for core, non-solvent exposed sidechain atoms. Cross validation of the structure with (15)N- and (13)C-edited NOESY data obtained with a perdeuterated (15)N, (13)C-enriched (13)CH(3) methyl protonated CspA sample confirms that essentially all of these independently-interpreted NOE-based constraints are already satisfied in each of the 10 CS-Rosetta structures. By these criteria, the CS-Rosetta structure generated by fully automated analysis of data for a perdeuterated sample provides an accurate structure of CspA. This represents a general approach for rapid, automated structure determination of small proteins by NMR.

  11. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

    Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  14. NMR Metabolomics Analysis of Parkinson's Disease

    PubMed Central

    Lei, Shulei; Powers, Robert

    2015-01-01

    Parkinson's disease (PD) is a neurodegenerative disease, which is characterized by progressive death of dopaminergic neurons in the substantia nigra pars compacta. Although mitochondrial dysfunction and oxidative stress are linked to PD pathogenesis, its etiology and pathology remain to be elucidated. Metabolomics investigates metabolite changes in biofluids, cell lysates, tissues and tumors in order to correlate these metabolomic changes to a disease state. Thus, the application of metabolomics to investigate PD provides a systematic approach to understand the pathology of PD, to identify disease biomarkers, and to complement genomics, transcriptomics and proteomics studies. This review will examine current research into PD mechanisms with a focus on mitochondrial dysfunction and oxidative stress. Neurotoxin-based PD animal models and the rationale for metabolomics studies in PD will also be discussed. The review will also explore the potential of NMR metabolomics to address important issues related to PD treatment and diagnosis. PMID:26078917

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

    SciTech Connect

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy. NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance.

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

    PubMed

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

    1999-08-01

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

  17. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

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

    2011-01-01

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

  18. Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand-Receptor Complexes

    NASA Astrophysics Data System (ADS)

    Krishna, N. Rama; Jayalakshmi, V.

    We describe our work on the quantitative analysis of STD-NMR spectra of reversibly forming ligand-receptor complexes. This analysis is based on the theory of complete relaxation and conformational exchange matrix analysis of saturation transfer (CORCEMA-ST) effects. As part of this work, we have developed two separate versions of the CORCEMA-ST program. The first version predicts the expected STD intensities for a given model of a ligand-protein complex, and compares them quantitatively with the experimental data. This version is very useful for rapidly determining if a model for a given ligand-protein complex is compatible with the STD-NMR data obtained in solution. It is also useful in determining the optimal experimental conditions for undertaking the STD-NMR measurements on a given complex by computer simulations. In the second version of the CORCEMA-ST program, we have implemented a torsion angle refinement feature for the bound ligand within the protein binding pocket. In this approach, the global minimum for the bound ligand conformation is obtained by a hybrid structure refinement protocol involving CORCEMA-ST calculation of intensities and simulated annealing refinement of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints to minimize a pseudo-energy function. This procedure is useful in refining and improving the initial models based on crystallography, computer docking, or other procedures to generate models for the bound ligand within the protein binding pocket compatible with solution STD-NMR data. In this chapter we describe the properties of the STD-NMR spectra, including the dependence of the intensities on various parameters. We also describe the results of the CORCEMA-ST analyses of experimental STD-NMR data on some ligand-protein complexes to illustrate the quantitative analysis of the data using this method. This CORCEMA-ST program is likely to be useful in structure-based drug design efforts.

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

    PubMed

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

    2011-04-01

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

  20. Understanding the NMR properties and conformational behavior of indole vs. azaindole group in protoberberines: NICS and NCS analysis

    NASA Astrophysics Data System (ADS)

    Kadam, Shivaji S.; Toušek, Jaromír; Maier, Lukáš; Pipíška, Matej; Sklenář, Vladimír; Marek, Radek

    2012-11-01

    We report here the preparation and the structural investigation into a series of 8-(indol-1-yl)-7,8-dihydroprotoberberine derivatives derived from berberine, palmatine, and coptisine. Structures of these new compounds were characterized mainly by 2D NMR spectroscopy and the conformational behavior was investigated by using methods of density-functional theory (DFT). PBE0/6-311+G** calculated NMR chemical shifts for selected derivatives correlate excellently with the experimental NMR data and support the structural conclusions drawn from the NMR experiments. An interesting role of the nitrogen atom in position N7' of the indole moiety in 8-(7-azaindol-1-yl)-7,8-dihydroprotoberberines as compared to other 8-indolyl derivatives is investigated in detail. The experimentally observed trends in NMR chemical shifts are rationalized by DFT calculations and analysis based on the nucleus-independent chemical shifts (NICS) and natural localized molecular orbitals (NLMOs).

  1. NMR-based analysis of protein-ligand interactions.

    PubMed

    Cala, Olivier; Guillière, Florence; Krimm, Isabelle

    2014-02-01

    Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.

  2. sup 31 P NMR analysis of coal moieties bearing -OH, -NH and -SH functions

    SciTech Connect

    Verkade, J.G.

    1990-01-01

    Research continues on the structural analysis of coal. In attempting to derivatize solid coal for solid state NMR analysis, we observed {sup 31}P NMR shifts in an unexpected region; these interesting leads will be pursued on the chance that the reaction we have evoked holds potential for yielding new coal characterizational information. Two very gratifying results have emerged from our {sup 119}Sn chemical shift measurements of a limited set of model compounds in pyridine. Firstly, the chemical shift dispersion is very large for phenols, alcohols and amides. Secondly, unlike {sup 119}Sn chemical shifts in hexane or chloroform, the shifts in pyridine are concentration independent.

  3. Computer compensation for NMR quantitative analysis of trace components

    SciTech Connect

    Nakayama, T.; Fujiwara, Y.

    1981-07-22

    A computer program has been written that determines trace components and separates overlapping components in multicomponent NMR spectra. This program uses the Lorentzian curve as a theoretical curve of NMR spectra. The coefficients of the Lorentzian are determined by the method of least squares. Systematic errors such as baseline/phase distortion are compensated and random errors are smoothed by taking moving averages, so that there processes contribute substantially to decreasing the accumulation time of spectral data. The accuracy of quantitative analysis of trace components has been improved by two significant figures. This program was applied to determining the abundance of 13C and the saponification degree of PVA.

  4. Improved resolution and simplification of the spin-diffusion-based NMR method for the structural analysis of mixed-linker MOFs.

    PubMed

    Krajnc, Andraž; Bueken, Bart; De Vos, Dirk; Mali, Gregor

    2017-06-01

    Nuclear magnetic resonance spectroscopy combined with modeling represents a powerful tool for the structural analysis of heterogeneous materials. In this contribution we describe an upgraded method, particularly suited for the structural analysis of mixed-linker metal-organic framework materials, which is based on the measurement and modeling of proton spin diffusion among constituents. We tested the method on a UiO-66-type metal-organic material, in which the organic building units were 1,4-benzenedicarboxylate and trans-1,4-cyclohexanedicarboxylate anions distributed within the framework in an unknown manner. We showed that resolution of the signals of different building units could be significantly enhanced by the carbon-detected version of the proton spin-diffusion measurement. Because this kind of measurement is much more time consuming than the proton-detected measurement and because one has to carry out several two-dimensional measurements to extract spin-diffusion curves, we inspected the possibility of reducing the number of such measurements. This could be done by limiting the analysis to short mixing times, for which, as shown in this contribution, linear approximation is valid. When working in the linear regime, only a few experimental points are needed to determine the slope of spin-diffusion curves. Usage of short spin-diffusion mixing times significantly shortened the total measurement time and also markedly simplified the modeling of spin-diffusion curves. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Improved resolution and simplification of the spin-diffusion-based NMR method for the structural analysis of mixed-linker MOFs

    NASA Astrophysics Data System (ADS)

    Krajnc, Andraž; Bueken, Bart; De Vos, Dirk; Mali, Gregor

    2017-06-01

    Nuclear magnetic resonance spectroscopy combined with modeling represents a powerful tool for the structural analysis of heterogeneous materials. In this contribution we describe an upgraded method, particularly suited for the structural analysis of mixed-linker metal-organic framework materials, which is based on the measurement and modeling of proton spin diffusion among constituents. We tested the method on a UiO-66-type metal-organic material, in which the organic building units were 1,4-benzenedicarboxylate and trans-1,4-cyclohexanedicarboxylate anions distributed within the framework in an unknown manner. We showed that resolution of the signals of different building units could be significantly enhanced by the carbon-detected version of the proton spin-diffusion measurement. Because this kind of measurement is much more time consuming than the proton-detected measurement and because one has to carry out several two-dimensional measurements to extract spin-diffusion curves, we inspected the possibility of reducing the number of such measurements. This could be done by limiting the analysis to short mixing times, for which, as shown in this contribution, linear approximation is valid. When working in the linear regime, only a few experimental points are needed to determine the slope of spin-diffusion curves. Usage of short spin-diffusion mixing times significantly shortened the total measurement time and also markedly simplified the modeling of spin-diffusion curves.

  6. The elusive structure of Pd2(dba)3. Examination by isotopic labeling, NMR spectroscopy, and X-ray diffraction analysis: synthesis and characterization of Pd2(dba-Z)3 complexes.

    PubMed

    Kapdi, Anant R; Whitwood, Adrian C; Williamson, David C; Lynam, Jason M; Burns, Michael J; Williams, Thomas J; Reay, Alan J; Holmes, Jordan; Fairlamb, Ian J S

    2013-06-05

    Pd(0)2(dba)3 (dba = E,E-dibenzylidene acetone) is the most widely used Pd(0) source in Pd-mediated transformations. Pd(0)2(dba-Z)3 (Z = dba aryl substituents) complexes exhibit remarkable and differential catalytic performance in an eclectic array of cross-coupling reactions. The precise structure of these types of complexes has been confounding, since early studies in 1970s to the present day. In this study the solution and solid-state structures of Pd(0)2(dba)3 and Pd(0)2(dba-Z)3 have been determined. Isotopic labeling ((2)H and (13)C) has allowed the solution structures of the freely exchanging major and minor isomers of Pd(0)2(dba)3 to be determined at high field (700 MHz). DFT calculations support the experimentally determined major and minor isomeric structures, which show that the major isomer of Pd(0)2(dba)3 possesses bridging dba ligands found exclusively in a s-cis,s-trans conformation. For the minor isomer one of the dba ligands is found exclusively in a s-trans,s-trans conformation. Single crystal X-ray diffraction analysis of Pd(0)2(dba)3·CHCl3 (high-quality data) shows that all three dba ligands are found over two positions. NMR spectroscopic analysis of Pd(0)2(dba-Z)3 reveals that the aryl substituent has a profound effect on the rate of Pd-olefin exchange and the global stability of the complexes in solution. Complexes containing the aryl substituents, 4-CF3, 4-F, 4-t-Bu, 4-hexoxy, 4-OMe, exhibit well-resolved (1)H NMR spectra at 298 K, whereas those containing 3,5-OMe and 3,4,5-OMe exhibit broad spectra. The solid-state structures of three Pd(0)2(dba-Z)3 complexes (4-F, 4-OMe, 3,5-OMe) have been determined by single crystal X-ray diffraction methods, which have been compared with Goodson's X-ray structure of Pd(0)2(dba-4-OH)3.

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

    PubMed Central

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael; Pedrini, Bill; Herrmann, Torsten; Wüthrich, Kurt

    2014-01-01

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90% of the residues. For most proteins the APSY data acquisition was completed in less than 30 hours. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. PMID:25428764

  8. Synthesis and NMR Spectral Analysis of Amine Heterocycles: The Effect of Asymmetry on the [superscript 1]H and [superscript 13]C NMR Spectra of N,O-Acetals

    ERIC Educational Resources Information Center

    Saba, Shahrokh; Ciaccio, James A.; Espinal, Jennifer; Aman, Courtney E.

    2007-01-01

    The stereochemical investigation is conducted to give students the combined experience of chemical synthesis of amines and N-heterocycles and structural stereochemical analysis using NMR spectroscopy. Students are introduced to the concept of topicity-stereochemical relationships between ligands within a molecule by synthesizing N,O-acetals.

  9. Synthesis and NMR Spectral Analysis of Amine Heterocycles: The Effect of Asymmetry on the [superscript 1]H and [superscript 13]C NMR Spectra of N,O-Acetals

    ERIC Educational Resources Information Center

    Saba, Shahrokh; Ciaccio, James A.; Espinal, Jennifer; Aman, Courtney E.

    2007-01-01

    The stereochemical investigation is conducted to give students the combined experience of chemical synthesis of amines and N-heterocycles and structural stereochemical analysis using NMR spectroscopy. Students are introduced to the concept of topicity-stereochemical relationships between ligands within a molecule by synthesizing N,O-acetals.

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

    NASA Astrophysics Data System (ADS)

    Bossev, Dobrin; Matsumoto, Mustuo; Nakahara, Masaru

    2008-03-01

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

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

    PubMed

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

    2014-02-05

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

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2004-02-01

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

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

    PubMed

    Latosińska, J N

    2005-01-01

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

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

    PubMed

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

    2012-09-07

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

  16. Mapping allostery through the covariance analysis of NMR chemical shifts

    PubMed Central

    Selvaratnam, Rajeevan; Chowdhury, Somenath; VanSchouwen, Bryan; Melacini, Giuseppe

    2011-01-01

    Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical shift changes caused by a set of covalently modified analogs of the allosteric effector (i.e., agonists and antagonists) reveals extended networks of coupled residues. Unexpectedly, such networks reach not only sites subject to effector-dependent structural variations, but also regions that are controlled by dynamically driven allostery. In these regions the allosteric signal is propagated mainly by dynamic rather than structural modulations, which result in subtle but highly correlated chemical shift variations. The proposed chemical shift covariance analysis (CHESCA) identifies interresidue correlations based on the combination of agglomerative clustering (AC) and singular value decomposition (SVD). AC results in dendrograms that define functional clusters of coupled residues, while SVD generates score plots that provide a residue-specific dissection of the contributions to binding and allostery. The CHESCA approach was validated by applying it to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC) and the CHESCA results are in full agreement with independent mutational data on EPAC activation. Overall, CHESCA is a generally applicable method that utilizes a selected chemical library of effector analogs to quantitatively decode the binding and allosteric information content embedded in chemical shift changes. PMID:21444788

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

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

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

  18. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  19. Conformational analysis of small molecules: NMR and quantum mechanics calculations.

    PubMed

    Tormena, Cláudio F

    2016-08-01

    This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.

  20. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  1. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations.

    PubMed

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400cm(-1) and 3500-50cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The (1)H, (13)C and HMQC ((1)H-(13)C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  2. Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

    PubMed

    Jeannerat, Damien

    2017-01-01

    The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  3. Structural difference between group I and group II cobra cardiotoxins: X-ray, NMR, and CD analysis of the effect of cis-proline conformation on three-fingered toxins.

    PubMed

    Chen, Ting-Shou; Chung, Fong-Yu; Tjong, Siu-Cin; Goh, King-Siang; Huang, Wei-Ning; Chien, Kun-Yi; Wu, Po-Long; Lin, Hua-Ching; Chen, Chun-Jung; Wu, Wen-Guey

    2005-05-24

    Natural homologues of cobra cardiotoxins (CTXs) were classified into two structural subclasses of group I and II based on the amino acid sequence and circular dichroism analysis, but the exact differences in their three-dimensional structures and biological significance remain elusive. We show by circular dichroism, NMR spectroscopic, and X-ray crystallographic analyses of a newly purified group I CTX A6 from eastern Taiwan cobra (Naja atra) venoms that its loop I conformation adopts a type VIa turn with a cis peptide bond located between two proline residues of PPxY. A similar "banana-twisted" conformation can be observed in other group I CTXs and also in cyclolinopeptide A and its analogues. By binding to the membrane environment, group I CTX undergoes a conformational change to adopt a more extended hydrophobic domain with beta-sheet twisting closer to the one adopted by group II CTX. This result resolves a discrepancy in the CTX structural difference reported previously between solution as well as crystal state and shows that, in addition to the hydrophobicity, the exact loop I conformation also plays an important role in CTX-membrane interaction. Potential protein targets of group I CTXs after cell internalization are also discussed on the basis of the determined loop I conformation.

  4. Synthesis, structural, spectral (FT-IR, 1H and 13C NMR and UV-Vis), NBO and first order hyperpolarizability analysis of N-(4-nitrophenyl)-2, 2-dibenzoylacetamide by density functional theory

    NASA Astrophysics Data System (ADS)

    Yalçın, Şerife Pınar; Ceylan, Ümit; Sarıoğlu, Ahmet Oral; Sönmez, Mehmet; Aygün, Muhittin

    2015-10-01

    The title compound, C22H16N2O5, was synthesized and characterized by experimental techniques (FT-IR, 1H NMR, 13C NMR, UV-Vis and X-Ray single crystal determination) and theoretical calculations. The molecular geometry, vibrational frequencies, molecular electrostatic potential (MEP), thermodynamic properties, the dipole moments, HOMO-LUMO energy has been calculated by using the Density Functional Theory (DFT) method with 6-311G(d,p) and 6-311++G(d,p) basis sets. 1H and 13C NMR chemical shifts show good agreement with experimental values. According to calculated results, the 6-311G(d,p) and 6-311++G(d,p) basis sets have showed similar results. The optimized geometry can well reproduce the crystal structure parameters.

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

    PubMed Central

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

    2005-01-01

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

  6. Monomeric and dimeric structures analysis and spectroscopic characterization of 3,5-difluorophenylboronic acid with experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV) techniques and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Asiri, Abdullah M.; Kurt, Mustafa

    2014-01-01

    The spectroscopic properties of 3,5-difluorophenylboronic acid (3,5-DFPBA, C6H3F2B(OH)2) were investigated by FT-IR, FT-Raman UV-Vis, 1H and 13C NMR spectroscopic techniques. FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase and 1H and 13C NMR spectra in DMSO solution were recorded. The UV spectra that dissolved in ethanol and water were recorded in the range of 200-400 nm for each solution. The structural and spectroscopic data of the molecule have been obtained for possible three conformers from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Hydrogen-bonded dimer of title molecule, optimized by counterpoise correction, was also studied B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. 1H and 13C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. The effects due to the substitutions of boric acid group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), nonlinear optical properties (NLO) and thermodynamic features were performed.

  7. Quantitative produced water analysis using mobile 1H NMR

    NASA Astrophysics Data System (ADS)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

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

    PubMed Central

    Dammers, Christina; Gremer, Lothar; Neudecker, Philipp; Demuth, Hans-Ulrich; Schwarten, Melanie; Willbold, Dieter

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

  10. NMR structural studies of PECVD amorphous silicon films

    NASA Astrophysics Data System (ADS)

    Cull, Thomas Sidley, Jr.

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

  11. NMR Structure Note: PHD Domain from Human SHPRH

    PubMed Central

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

    2013-01-01

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

  12. MQ NMR and SPME analysis of nonlinearity in the degradation of a filled silicone elastomer

    SciTech Connect

    Chinn, S C; Alviso, C T; Berman, E S; Harvey, C A; Maxwell, R S; Wilson, T S; Cohenour, R; Saalwachter, K; Chasse, W

    2008-10-10

    Radiation induced degradation of polymeric materials occurs via numerous, simultaneous, competing chemical reactions. Though degradation is typically found to be linear in adsorbed dose, some silicone materials exhibit non-linear dose dependence due to dose dependent dominant degradation pathways. We have characterized the effects of radiative and thermal degradation on a model filled-PDMS system, Sylgard 184 (commonly used as an electronic encapsulant and in biomedical applications), using traditional mechanical testing, NMR spectroscopy, and sample headspace analysis using Solid Phase Micro-Extraction (SPME) followed by Gas Chromatography/Mass Spectrometry (GC/MS). The mechanical data and {sup 1}H spin-echo NMR indicated that radiation exposure leads to predominantly crosslinking over the cumulative dose range studies (0 to 250 kGray) with a rate roughly linear with dose. {sup 1}H Multiple Quantum NMR detected a bimodal distribution in the network structure, as expected by the proposed structure of Sylgard 184. The MQ-NMR further indicated that the radiation induced structural changes were not linear in adsorbed dose and competing chain scission mechanisms contribute more largely to the overall degradation process in the range of 50 -100 kGray (though crosslinking still dominates). The SPME-GC/MS data were analyzed using Principal Component Analysis (PCA), which identified subtle changes in the distributions of degradation products (the cyclic siloxanes and other components of the material) as a function of age that provide insight into the dominant degradation pathways at low and high adsorbed dose.

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

    PubMed

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

    2002-01-22

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

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

    NASA Astrophysics Data System (ADS)

    Salgado, Gilmar Fernandes De Jesus

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

  15. Factor analysis of 27Al MAS NMR spectra for identifying nanocrystalline phases in amorphous geopolymers.

    PubMed

    Urbanova, Martina; Kobera, Libor; Brus, Jiri

    2013-11-01

    Nanostructured materials offer enhanced physicochemical properties because of the large interfacial area. Typically, geopolymers with specifically synthesized nanosized zeolites are a promising material for the sorption of pollutants. The structural characterization of these aluminosilicates, however, continues to be a challenge. To circumvent complications resulting from the amorphous character of the aluminosilicate matrix and from the low concentrations of nanosized crystallites, we have proposed a procedure based on factor analysis of (27)Al MAS NMR spectra. The capability of the proposed method was tested on geopolymers that exhibited various tendencies to crystallize (i) completely amorphous systems, (ii) X-ray amorphous systems with nanocrystalline phases, and (iii) highly crystalline systems. Although the recorded (27)Al MAS NMR spectra did not show visible differences between the amorphous systems (i) and the geopolymers with the nanocrystalline phase (ii), the applied factor analysis unambiguously distinguished these materials. The samples were separated into the well-defined clusters, and the systems with the evolving crystalline phase were identified even before any crystalline fraction was detected by X-ray powder diffraction. Reliability of the proposed procedure was verified by comparing it with (29)Si MAS NMR spectra. Factor analysis of (27)Al MAS NMR spectra thus has the ability to reveal spectroscopic features corresponding to the nanocrystalline phases. Because the measurement time of (27)Al MAS NMR spectra is significantly shorter than that of (29)Si MAS NMR data, the proposed procedure is particularly suitable for the analysis of large sets of specifically synthesized geopolymers in which the formation of the limited fractions of nanocrystalline phases is desired.

  16. NMR solution structures of actin depolymerizing factor homology domains

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2017-04-01

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

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

    NASA Astrophysics Data System (ADS)

    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

  19. NMR relaxometry analysis of lubricant oils degradation

    NASA Astrophysics Data System (ADS)

    Ballari, M.; Bonetto, F.; Anoardo, E.

    2005-10-01

    The present work was undertaken in order to investigate lubricant oil degradation at the molecular level. Ageing effects, as reflected on the proton spin-lattice relaxation rate (T_1^{-1}) dispersion, were studied in two different lubricant engine oils. The proton field cycling technique was used to scan relaxation of new and aged samples of monograde and multigrade oils. Relaxation dispersions were interpreted in terms of self-diffusion and molecular rotations. Our study shows that proton T_1^{-1} could be very sensitive to degradation processes, especially at low Larmor frequencies. The analysis reveals a noticeable sensitivity of the involved correlation times. The pros and cons of the technique are also discussed.

  20. Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline.

    PubMed

    Pathak, S K; Srivastava, R; Sachan, A K; Prasad, O; Sinha, L; Asiri, A M; Karabacak, M

    2015-01-25

    Comprehensive investigation of geometrical and electronic structure in ground as well as the first excited state of 3,5-Difluoroaniline (C6H5NF2) was carried out. The experimentally observed spectral data (FT-TR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were measured by TD-DFT approach. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. Global and local reactivity descriptors were computed to predict reactivity and reactive sites on the molecule. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data obtained. Moreover, the thermodynamic properties were evaluated.

  1. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

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

    2007-08-17

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

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

    PubMed

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

    2015-04-30

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

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

    PubMed

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

    2001-07-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-05-28

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

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

    PubMed

    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.

  7. NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen αC-Domain Fragment†

    PubMed Central

    Burton, Robert A.; Tsurupa, Galina; Hantgan, Roy R.; Tjandra, Nico; Medved, Leonid

    2008-01-01

    According to the current hypothesis, in fibrinogen, the COOH-terminal portions of two Aα chains are folded into compact αC-domains that interact intramolecularly with each other and with the central region of the molecule; in fibrin, the αC-domains switch to an intermolecular interaction resulting in αC polymers. In agreement, our recent NMR study identified within the bovine fibrinogen Aα374-538 αC-domain fragment an ordered compact structure including a β-hairpin restricted at the base by a 423–453 disulfide linkage. To establish the complete structure of the αC-domain and to further test the hypothesis, we expressed a shorter αC-fragment, Aα406-483, and performed detailed analysis of its structure, stability, and interactions. NMR experiments on the Aα406-483 fragment identified a second loose β-hairpin formed by residues 459–476, yielding a structure consisting of an intrinsically unstable mixed parallel/anti-parallel β-sheet. Size-exclusion chromatography and sedimentation velocity experiments revealed that the Aα406-483 fragment forms soluble oligomers whose fraction increases with increasing concentration. This was confirmed by sedimentation equilibrium analysis, which also revealed that the addition of each monomer to an assembling αC oligomer substantially increases its stabilizing free energy. In agreement, unfolding experiments monitored by CD established that oligomerization of Aα406-483 results in increased thermal stability. Altogether, these experiments establish the complete NMR solution structure of the Aα406-483 αC-domain fragment, provide direct evidence for the intra- and intermolecular interactions between the αC-domains, and confirm that these interactions are thermodynamically driven. PMID:17590019

  8. NMR apparatus for in situ analysis of fuel cells

    SciTech Connect

    Gerald, II, Rex E; Rathke, Jerome W

    2012-11-13

    The subject apparatus is a fuel cell toroid cavity detector for in situ analysis of samples through the use of nuclear magnetic resonance. The toroid cavity detector comprises a gas-tight housing forming a toroid cavity where the housing is exposed to an externally applied magnetic field B.sub.0 and contains fuel cell component samples to be analyzed. An NMR spectrometer is electrically coupled and applies a radiofrequency excitation signal pulse to the detector to produce a radiofrequency magnetic field B.sub.1 in the samples and in the toroid cavity. Embedded coils modulate the static external magnetic field to provide a means for spatial selection of the recorded NMR signals.

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

    PubMed

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

    2015-08-01

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

  10. Use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal

    SciTech Connect

    Netzel, D.A.

    1991-01-01

    The overall objectives of this study are to develop an NMR method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, and to determine the mechanism by which water may enhance coal reactivity toward liquefaction. Different methods of drying will be investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction, thereby making coal drying an attractive and economical method for coal pretreatment. Coal drying methods will include thermal drying under different atmospheres and temperatures, drying with microwave radiation, and low-temperature chemical dehydration. The objective for this quarterly report were (1) to determine the limit of detection of water by NMR, (2) to determine the reproducibility of the NMR integration method using the Lab Cal {sup {trademark}} PC software, (3) to determine the amount of water in standard solutions, and (4) to determine the amount of water in a coal sample. The studies performed this last quarter have shown that the {sup 1}H NMR method for determining water in a coal sample via the reaction with 2,2-dimethoxypropane will be suitable for determining the water content in coals. The method should be most suitable for coals having low moisture content; that is, those coals which have been subjected to other drying techniques. 9 refs., 1 tab.

  11. Use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, December 1, 1991--February 29, 1992

    SciTech Connect

    Netzel, D.A.

    1991-12-31

    The overall objectives of this study are to develop an NMR method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, and to determine the mechanism by which water may enhance coal reactivity toward liquefaction. Different methods of drying will be investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction, thereby making coal drying an attractive and economical method for coal pretreatment. Coal drying methods will include thermal drying under different atmospheres and temperatures, drying with microwave radiation, and low-temperature chemical dehydration. The objective for this quarterly report were (1) to determine the limit of detection of water by NMR, (2) to determine the reproducibility of the NMR integration method using the Lab Cal {sup {trademark}} PC software, (3) to determine the amount of water in standard solutions, and (4) to determine the amount of water in a coal sample. The studies performed this last quarter have shown that the {sup 1}H NMR method for determining water in a coal sample via the reaction with 2,2-dimethoxypropane will be suitable for determining the water content in coals. The method should be most suitable for coals having low moisture content; that is, those coals which have been subjected to other drying techniques. 9 refs., 1 tab.

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

    PubMed

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

    2014-01-01

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

  13. Structural analysis of glucans

    PubMed Central

    Novak, Miroslav

    2014-01-01

    Glucans are most widespread polysaccharides in the nature. There is a large diversity in their molecular weight and configuration depending on the original source. According to the anomeric structure of glucose units it is possible to distinguish linear and branched α-, β- as well as mixed α,β-glucans with various glycoside bond positions and molecular masses. Isolation of glucans from raw sources needs removal of ballast compounds including proteins, lipids, polyphenols and other polysaccharides. Purity control of glucan fractions is necessary to evaluate the isolation and purification steps; more rigorous structural analyses of purified polysaccharides are required to clarify their structure. A set of spectroscopic, chemical and separation methods are used for this purpose. Among them, NMR spectroscopy is known as a powerful tool in structural analysis of glucans both in solution and in solid state. Along with chemolytic methods [methylation analysis (MA), periodate oxidation, partial chemical or enzymatic hydrolysis, etc.], correlation NMR experiments are able to determine the exact structure of tested polysaccharides. Vibration spectroscopic methods (FTIR, Raman) are sensitive to anomeric structure of glucans and can be used for purity control as well. Molecular weight distribution, homogeneity and branching of glucans can be estimated by size-exclusion chromatography (SEC), laser light scattering (LLS) and viscometry. PMID:25332993

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

    PubMed

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

    PubMed

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

    2013-01-01

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

  16. Multivariate analysis relating oil shale geochemical properties to NMR relaxometry

    USGS Publications Warehouse

    Birdwell, Justin E.; Washburn, Kathryn E.

    2015-01-01

    Low-field nuclear magnetic resonance (NMR) relaxometry has been used to provide insight into shale composition by separating relaxation responses from the various hydrogen-bearing phases present in shales in a noninvasive way. Previous low-field NMR work using solid-echo methods provided qualitative information on organic constituents associated with raw and pyrolyzed oil shale samples, but uncertainty in the interpretation of longitudinal-transverse (T1–T2) relaxometry correlation results indicated further study was required. Qualitative confirmation of peaks attributed to kerogen in oil shale was achieved by comparing T1–T2 correlation measurements made on oil shale samples to measurements made on kerogen isolated from those shales. Quantitative relationships between T1–T2 correlation data and organic geochemical properties of raw and pyrolyzed oil shales were determined using partial least-squares regression (PLSR). Relaxometry results were also compared to infrared spectra, and the results not only provided further confidence in the organic matter peak interpretations but also confirmed attribution of T1–T2 peaks to clay hydroxyls. In addition, PLSR analysis was applied to correlate relaxometry data to trace element concentrations with good success. The results of this work show that NMR relaxometry measurements using the solid-echo approach produce T1–T2 peak distributions that correlate well with geochemical properties of raw and pyrolyzed oil shales.

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  18. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

    PubMed Central

    Shen, Yang; Bax, Ad

    2015-01-01

    Summary 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 sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 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 13Cβ 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. PMID:25502373

  19. Automated structure determination of proteins with the SAIL-FLYA NMR method.

    PubMed

    Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

    2007-01-01

    The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

  20. Elucidation of the structures of residual and dissolved pine kraft lignins using an HMQC NMR technique.

    PubMed

    Balakshin, Mikhail Yu; Capanema, Ewellyn A; Chen, Chen-Loung; Gracz, Hanna S

    2003-10-08

    Comparative studies on the structures of residual and dissolved lignins isolated from pine kraft pulp and pulping liquor have been undertaken using the (1)H-(13)C HMQC NMR technique, GPC, and sugar analysis to elucidate the reaction mechanisms in kraft pulping and the lignin reactivity. A modified procedure for the isolation of enzymatic residual lignins has resulted in an appreciable decrease in protein contaminants in the residual lignin preparations (N content < 0.2%). The very high dispersion of HMQC spectra allows identification of different lignin moieties, which signals appear overlapped in 1D (13)C NMR spectra. Elucidation of the role of condensation reactions indicates that an increase in the degree of lignin condensation during pulping results from accumulation of original condensed lignin moieties rather than from the formation of new alkyl-aryl structures. Among aryl-vinyl type moieties, only stilbene structures are accumulated in lignin in appreciable amounts. Benzyl ether lignin-carbohydrate bonds involving primary hydroxyl groups of carbohydrates have been detected in residual and dissolved lignin preparations. Structures of the alpha-hydroxyacid type have been postulated to be among the important lignin degradation products in kraft pulping. The effect of the isolation method on the lignin structure and differences between the residual and dissolved lignins are discussed.

  1. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR.

    PubMed

    van der Wel, Patrick C A; Lewandowski, Józef R; Griffin, Robert G

    2010-11-09

    Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance, on the peptide fragment GNNQQNY7−13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. On the basis of additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these coexisting conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clearly increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation.

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  4. NMR analysis of base-pair opening kinetics in DNA.

    PubMed

    Szulik, Marta W; Voehler, Markus; Stone, Michael P

    2014-12-12

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.

  5. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    PubMed

    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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    Simpson, A.

    2009-04-01

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

  8. A new laboratory approach to shale analysis using NMR relaxometry

    USGS Publications Warehouse

    Washburn, Kathryn E.; Birdwell, Justin E.; Baez, Luis; Beeney, Ken; Sonnenberg, Steve

    2013-01-01

    kerogen, thermally degraded kerogen, and char. Integrated peak areas from the LF-NMR results representative of kerogen and bitumen were found to be well correlated with S1 and S2 parameters from Rock-Eval programmed pyrolysis. This study demonstrates that LFNMR relaxometry can provide a wide range of information on shales and other reservoir rocks that goes well beyond porosity and pore-fluid analysis.

  9. [NMR structure and dynamics of the chimeric protein SH3-F2].

    PubMed

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

    2010-01-01

    For the further elucidation of structural and dynamic principles of protein self-organization and protein-ligand interactions the design of new chimeric protein SH3-F2 was made and genetically engineered construct was created. The SH3-F2 amino acid sequence consists of polyproline ligand mgAPPLPPYSA, GG linker and the sequence of spectrin SH3 domain circular permutant S19-P20s. Structural and dynamics properties of the protein were studied by high-resolution NMR. According to NMR data the tertiary structure of the chimeric protein SH3-F2 has the topology which is typical of SH3 domains in the complex with the ligand, forming polyproline type II helix, located in the conservative region of binding in the orientation II. The polyproline ligand closely adjoins with the protein globule and is stabilized by hydrophobic interactions. However the interaction of ligand and the part of globule relative to SH3 domain is not too large because the analysis of protein dynamic characteristics points to the low amplitude, high-frequency ligand tumbling in relation to the slow intramolecular motions of the main globule. The constructed chimera permits to carry out further structural and thermodynamic investigations of polyproline helix properties and its interaction with regulatory domains.

  10. Carbon-dot organic surface modifier analysis by solution-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Philippidis, Aggelos; Spyros, Apostolos; Anglos, Demetrios; Bourlinos, Athanasios B.; Zbořil, Radek; Giannelis, Emmanuel P.

    2013-07-01

    Carbon dots (C-dots) represent a new class of carbon-based materials that were discovered recently and have drawn the interest of the scientific community, particularly because of their attractive optical properties and their potential as fluorescent sensors. Investigation of the chemical structure of C-dots is extremely important for correlating the surface modifier composition with C-dot optical properties and allow for structure-properties fine tuning. In this article, we report the structural analysis of the surface modifiers of three different types of C-dot nanoparticles (Cwax, Cws, and Csalt) by use of 1D- and 2D-high-resolution NMR spectroscopy in solution. We unambiguously verify that the structure of the modifier chains remains chemically unchanged during the passivation procedure, and confirm the covalent attachment of the modifiers to the nanoparticle core, which contributes no signal to the solution-state NMR spectra. To our knowledge, this is the first study confirming the full structural assignment of C-dot organic surface modifiers by use of solution NMR spectroscopy.

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

    PubMed

    Saheb, Vahid; Sheikhshoaie, Iran

    2011-10-15

    The Schiff base compound, N,N'-(2,2-dimetylpropane)-bis(dihydroxylacetophenone) (NDHA) is synthesized through the condensation of 2-hydroxylacetophenone and 2,2-dimethyl 1,3-amino propane in methanol at ambient temperature. The yellow crystalline precipitate is used for X-ray single-crystal determination and measuring Fourier transform infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP, PBEPBE and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the FTIR, (1)H NMR and (13)C NMR spectra of the compound. Time-dependent density functional theory (TDDFT) method is used to calculate the UV-visible spectrum of NDHA. Vibrational frequencies are determined experimentally and compared with those obtained theoretically. Vibrational assignments and analysis of the fundamental modes of the compound are also performed. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR and (13)C NMR chemical shifts calculated by all DFT methods are consistent with the experimental data. However, the NMR shielding tensors computed at the B3LYP/6-31+G(d,p) level of theory are in better agreement with experimental (1)H NMR and (13)C NMR spectra. The electronic absorption spectrum calculated at the B3LYP/6-31+G(d,p) level by using TD-DFT method is in accordance with the observed UV-visible spectrum of NDHA. In addition, some quantum descriptors of the molecule are calculated and conformational analysis is performed and the results were compared with the crystallographic data. Copyright © 2011 Elsevier B.V. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

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

  13. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

    PubMed

    Gottstein, Daniel; Kirchner, Donata K; Güntert, Peter

    2012-04-01

    A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative 'regmean structure' is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordinates than the alternatives while maintaining the same quality as individual conformers. The method is thus suitable to generate representative single structure representations of protein structure ensembles in torsion angle space. Since in the case of NMR structure calculations with CYANA the single structure is calculated in the same way as the individual conformers except that weak positional and torsion angle restraints are added, we propose to represent new NMR structures by a 'regmean bundle' consisting of the single representative structure as the first conformer and all but one original individual conformers (the original conformer with the highest target function value is discarded in order to keep the number of conformers in the

  14. Functional Analysis of the Nitrogen Metabolite Repression Regulator Gene nmrA in Aspergillus flavus.

    PubMed

    Han, Xiaoyun; Qiu, Mengguang; Wang, Bin; Yin, Wen-Bing; Nie, Xinyi; Qin, Qiuping; Ren, Silin; Yang, Kunlong; Zhang, Feng; Zhuang, Zhenhong; Wang, Shihua

    2016-01-01

    In Aspergillus nidulans, the nitrogen metabolite repression (NMR) regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in A. flavus has not been previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif. Deletion of nmrA slowed the growth of A. flavus but significantly increased conidiation and sclerotia production. Moreover, seed infection experiments indicated that nmrA is required for the invasive virulence of A. flavus. In addition, the ΔnmrA mutant showed increased sensitivity to rapamycin and methyl methanesulfonate, suggesting that nmrA could be responsive to target of rapamycin signaling and DNA damage. Furthermore, quantitative real-time reverse transcription polymerase chain reaction analysis suggested that nmrA might interact with other nitrogen regulatory and catabolic genes. Our study provides a better understanding of NMR and the nitrogen metabolism network in fungi.

  15. Functional Analysis of the Nitrogen Metabolite Repression Regulator Gene nmrA in Aspergillus flavus

    PubMed Central

    Han, Xiaoyun; Qiu, Mengguang; Wang, Bin; Yin, Wen-Bing; Nie, Xinyi; Qin, Qiuping; Ren, Silin; Yang, Kunlong; Zhang, Feng; Zhuang, Zhenhong; Wang, Shihua

    2016-01-01

    In Aspergillus nidulans, the nitrogen metabolite repression (NMR) regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in A. flavus has not been previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif. Deletion of nmrA slowed the growth of A. flavus but significantly increased conidiation and sclerotia production. Moreover, seed infection experiments indicated that nmrA is required for the invasive virulence of A. flavus. In addition, the ΔnmrA mutant showed increased sensitivity to rapamycin and methyl methanesulfonate, suggesting that nmrA could be responsive to target of rapamycin signaling and DNA damage. Furthermore, quantitative real-time reverse transcription polymerase chain reaction analysis suggested that nmrA might interact with other nitrogen regulatory and catabolic genes. Our study provides a better understanding of NMR and the nitrogen metabolism network in fungi. PMID:27933036

  16. NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization.

    PubMed

    Lusin, Jacqueline D; Vanarotti, Murugendra; Li, Congmin; Valiveti, Aswani; Ames, James B

    2008-02-26

    DREAM (calsenilin/KChIP3) is an EF-hand calcium-binding protein that binds to specific DNA sequences and regulates Ca2+-induced transcription of prodynorphin and c-fos genes. Here, we present the atomic-resolution structure of Ca2+-bound DREAM in solution determined by nuclear magnetic resonance (NMR) spectroscopy. Pulsed-field gradient NMR diffusion experiments and 15N NMR relaxation analysis indicate that Ca2+-bound DREAM forms a stable dimer in solution. The structure of the first 77 residues from the N-terminus could not be determined by our NMR analysis. The C-terminal DREAM structure (residues 78-256) contains four EF-hand motifs arranged in a tandem linear array, similar to that seen in KChIP1, recoverin, and other structures of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily. Mg2+ is bound at the second EF-hand, whereas Ca2+ is bound functionally at the third and fourth sites. The first and second EF-hands form an exposed hydrophobic groove on the protein surface lined by side-chain atoms of L96, F100, F114, I117, Y118, F121, F122, Y151, L155, L158, and L159 that are highly conserved in all NCS proteins. An exposed leucine near the C-terminus (L251) is suggested to form intermolecular contacts with leucine residues in the hydrophobic groove (L155, L158, and L159). Positively charged side chains of Arg and Lys (Lys87, Lys90, Lys91, Arg98, Lys101, Arg160, and Lys166) are clustered on one side of the protein surface and may mediate electrostatic contacts with DNA targets. We propose that Ca2+-induced dimerization of DREAM may partially block the putative DNA-binding site, which may suggest as to how Ca2+ abolishes DREAM binding to DNA to activate the transcription of prodynorphin and other downstream genes in pain control.

  17. Compositional analysis of multi-element magnetic nanoparticles with a combined NMR and TEM approach

    NASA Astrophysics Data System (ADS)

    Gellesch, Markus; Hammerath, Franziska; Süß, Vicky; Haft, Marcel; Hampel, Silke; Wurmehl, Sabine; Büchner, Bernd

    2017-09-01

    The increasing interest in nanoscale materials goes hand in hand with the challenge to reliably characterize the chemical compositions and structural features of nanosized objects in order to relate those to their physical properties. Despite efforts, the analysis of the chemical composition of individual multi-element nanoparticles remains challenging—from the technical point of view as well as from the point of view of measurement statistics. Here, we demonstrate that zero-field solid-state nuclear magnetic resonance (NMR) complements local, single particle transmission electron microscopy (TEM) studies with information on a large assembly of chemically complex nanoparticles. The combination of both experimental techniques gives information on the local composition and structure and provides an excellent measurement statistic through the corresponding NMR ensemble measurement. This analytical approach is applicable to many kinds of magnetic materials and therefore may prove very versatile in the future research of particulate magnetic nanomaterials.

  18. Structure elucidation and NMR assignments of an unusual triterpene saponin derivative from Ilex kudincha.

    PubMed

    Zuo, Wenjian; Wang, Qinghu; Li, Wen; Sha, Yi; Li, Xian; Wang, Jinhui

    2012-04-01

    One unusual triterpenoid derivative, ilekudinchoside E (1), was isolated from the leaves of Ilex kudincha. The structure was established by various spectroscopic techniques, including one- and two-dimensional NMR, HRTOFMS and CD spectra.

  19. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.

    PubMed

    Wang, Shenlin; Ing, Christopher; Emami, Sanaz; Jiang, Yunjiang; Liang, Hongjun; Pomès, Régis; Brown, Leonid S; Ladizhansky, Vladimir

    2016-09-22

    Multiple moderate-resolution crystal structures of human aquaporin-1 have provided a foundation for understanding the molecular mechanism of selective water translocation in human cells. To gain insight into the interfacial structure and dynamics of human aquaporin-1 in a lipid environment, we performed nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations. Using magic angle spinning solid-state NMR, we report a near complete resonance assignment of the human aquaporin-1. Chemical shift analysis of the secondary structure identified pronounced deviations from crystallographic structures in extracellular loops A and C, including the cis Y37-P38 bond in loop A, as well as ordering and immobilization of loop C. Site-specific H/D exchange measurements identify a number of protected nitrogen-bearing side chains and backbone amide groups, involved in stabilizing the loops. A combination of molecular dynamics simulations with NMR-derived restraints and filtering based on solvent accessibility allowed for the determination of a structural model of extracellular loops largely consistent with NMR results. The simulations reveal loop stabilizing interactions that alter the extracellular surface of human AQP1, with possible implications for water transport regulation through the channel. Modulation of water permeation may occur as a result of rearrangement of side chains from loop C in the extracellular vestibule of hAQP1, affecting the aromatic arginine selectivity filter.

  20. Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

    NASA Astrophysics Data System (ADS)

    Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

    2017-10-01

    Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

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

    PubMed

    Hee Kim, Nam; Lim, Ae Ran

    2015-09-01

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

  2. Synthesis, molecular structure and vibrational analysis of D-D-A based carbazole decorated phenothiazine-3-carbaldehyde: Experimental (FT-IR, UV and NMR) and density functional theory (DFT) calculations

    NASA Astrophysics Data System (ADS)

    Karuppasamy, Ayyanar; Gokula Krishnan, Kannan; Pillai Velayutham Pillai, Muthiah; Ramalingan, Chennan

    2017-01-01

    A novel molecule, 10-(9-hexyl-9H-carbazol-3yl)-10H-phenothiazine-3-carbaldehyde (CZPTZA) has been synthesized and characterized through FT-IR, UV-Vis, NMR spectroscopic studies and molecular orbital calculations. Optimized geometrical structure, harmonic vibrational frequencies and NMR are computed with B3LYP method using 6-311++G (d,p) basis set. The geometrical parameters of the title compound obtained from Single Crystal XRD studies have been found in accord with the calculated (DFT) values. The experimentally observed vibrational frequencies are compared with the calculated ones, which were found to be in good agreement with each other. UV-Vis spectra of the title compound have also been recorded and the electronic properties, viz. excitation energies, calculated energies, oscillator strengths, frontier orbital energies and band gap energies are computed with TD-DFT/CAM-B3LYP method using 6-311++G (d,p) as the basis set. The 1H and 13C NMR chemical shifts of the molecule have been calculated by the Gauge Independent Atomic Orbital (GIAO) method and compared with the experimental outcome. Also, the values of dipole moment, polarizabilities and first order hyperpolarizabilities have been computed.

  3. Separation and analysis of trace degradants in a pharmaceutical formulation using on-line capillary isotachophoresis-NMR.

    PubMed

    Eldridge, Stacie L; Almeida, Valentino K; Korir, Albert K; Larive, Cynthia K

    2007-11-15

    NMR spectroscopy is widely used in the pharmaceutical industry for the structure elucidation of pharmaceutical impurities, especially when coupled to a separation method, such as HPLC. However, NMR has relatively poor sensitivity compared with other techniques such as mass spectrometry, limiting its applicability in impurity analyses. This limitation is addressed here through the on-line coupling of microcoil NMR with capillary isotachophoresis (cITP), a separation method that can concentrate dilute components by 2-3 orders of magnitude. With this approach, 1H NMR spectra can be acquired for microgram (nanomole) quantities of trace impurities in a complex sample matrix. cITP-NMR was used in this work to isolate and detect 4-aminophenol (PAP) in an acetaminophen sample spiked at the 0.1% level, with no interference from the parent compound. Analysis of an acetaminophen thermal degradation sample revealed resonances of several degradation products in addition to PAP, confirming the effectiveness of on-line cITP-NMR for trace analyses of pharmaceutical formulations. Subsequent LC-MS/MS analysis provided complementary information for the structure elucidation of the unknown degradation products, which were dimers formed during the degradation process.

  4. The molecular structure and vibrational, 1H and 13C NMR spectra of lidocaine hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

    2016-01-01

    The structure, vibrational and NMR spectra of the local anesthetic drug lidocaine hydrochloride monohydrate salt were investigated by B3LYP/6-311G∗∗ calculations. The lidocaine·HCl·H2O salt is predicted to have the gauche structure as the predominant form at ambient temperature with NCCN and CNCC torsional angles of 110° and -123° as compared to 10° and -64°, respectively in the base lidocaine. The repulsive interaction between the two N-H bonds destabilized the gauche structure of lidocaine·HCl·H2O salt. The analysis of the observed vibrational spectra is consistent with the presence of the lidocaine salt in only one gauche conformation at room temperature. The 1H and 13C NMR spectra of lidocaine·HCl·H2O were interpreted by experimental and DFT calculated chemical shifts of the lidocaine salt. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine·HCl·H2O is 2.32 and 8.21 ppm, respectively.

  5. The molecular structure and vibrational, (1)H and (13)C NMR spectra of lidocaine hydrochloride monohydrate.

    PubMed

    Badawi, Hassan M; Förner, Wolfgang; Ali, Shaikh A

    2016-01-05

    The structure, vibrational and NMR spectra of the local anesthetic drug lidocaine hydrochloride monohydrate salt were investigated by B3LYP/6-311G(∗∗) calculations. The lidocaine·HCl·H2O salt is predicted to have the gauche structure as the predominant form at ambient temperature with NCCN and CNCC torsional angles of 110° and -123° as compared to 10° and -64°, respectively in the base lidocaine. The repulsive interaction between the two N-H bonds destabilized the gauche structure of lidocaine·HCl·H2O salt. The analysis of the observed vibrational spectra is consistent with the presence of the lidocaine salt in only one gauche conformation at room temperature. The (1)H and (13)C NMR spectra of lidocaine·HCl·H2O were interpreted by experimental and DFT calculated chemical shifts of the lidocaine salt. The RMSD between experimental and theoretical (1)H and (13)C chemical shifts for lidocaine·HCl·H2O is 2.32 and 8.21ppm, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    PubMed

    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.

  7. Solid-state 19F-NMR analysis of 19F-labeled tryptophan in gramicidin A in oriented membranes.

    PubMed Central

    Grage, Stephan L; Wang, Junfeng; Cross, Timothy A; Ulrich, Anne S

    2002-01-01

    The response of membrane-associated peptides toward the lipid environment or other binding partners can be monitored by solid-state NMR of suitably labeled side chains. Tryptophan is a prominent amino acid in transmembrane helices, and its (19)F-labeled analogues are generally biocompatible and cause little structural perturbation. Hence, we use 5F-Trp as a highly sensitive NMR probe to monitor the conformation and dynamics of the indole ring. To establish this (19)F-NMR strategy, gramicidin A was labeled with 5F-Trp in position 13 or 15, whose chi(1)/chi(2) torsion angles are known from previous (2)H-NMR studies. First, the alignment of the (19)F chemical shift anisotropy tensor within the membrane was deduced by lineshape analysis of oriented samples. Next, the three principal axes of the (19)F chemical shift anisotropy tensor were assigned within the molecular frame of the indole ring. Finally, determination of chi(1)/chi(2) for 5F-Trp in the lipid gel phase showed that the side chain alignment differs by up to 20 degrees from its known conformation in the liquid crystalline state. The sensitivity gain of (19)F-NMR and the reduction in the amount of material was at least 10-fold compared with previous (2)H-NMR studies on the same system and 100-fold compared with (15)N-NMR. PMID:12496101

  8. In vivo NMR for ¹³C Metabolic Flux Analysis.

    PubMed

    Roscher, Albrecht; Troufflard, Stéphanie; Taghki, Abdelghani Idrissi

    2014-01-01

    The use of in vivo NMR within the framework of Metabolic Flux Analysis in plants is presented. In vivo NMR allows to visualize the active metabolic network, to determine metabolic and isotopic steady state and to measure metabolic fluxes which are not necessarily accessible by isotopic steady state (stationary) Metabolic Flux Analysis. The kinetic data can be used as input for dynamic (nonstationary) Metabolic Flux Analysis. Both 1D and 2D NMR methods are employed.

  9. Structural Analysis

    NASA Technical Reports Server (NTRS)

    1991-01-01

    After an 800-foot-tall offshore oil recovery platform collapsed, the engineers at Engineering Dynamics, Inc., Kenner, LA, needed to learn the cause of the collapse, and analyze the proposed repairs. They used STAGSC-1, a NASA structural analysis program with geometric and nonlinear buckling analysis. The program allowed engineers to determine the deflected and buckling shapes of the structural elements. They could then view the proposed repairs under the pressure that caused the original collapse.

  10. High resolution magic angle spinning NMR applied to the analysis of organic compounds bound to solid supports.

    PubMed

    Espinosa, Juan F

    2011-01-01

    In situ structural characterization of organic compounds attached to solid supports can be achieved by high-resolution magic angle spinning NMR (HRMAS NMR), a technique that provides solution-like spectra for resin-bound molecules. This review outlines the principles of the technique, the influence of the solid support on data quality, and NMR experiments that are useful for obtaining valuable information. The review describes, with multiple examples mainly from the last 7 years, how HRMAS NMR has been applied to monitor solid-phase reactions, elucidate reaction products and quantify compound loading on a solid support. Other applications, such as conformational analysis of immobilized compounds and investigation of molecular interactions with compounds in solution, are also discussed.

  11. 19F NMR analysis of the antimicrobial peptide PGLa bound to native cell membranes from bacterial protoplasts and human erythrocytes.

    PubMed

    Ieronimo, Marco; Afonin, Sergii; Koch, Katja; Berditsch, Marina; Wadhwani, Parvesh; Ulrich, Anne S

    2010-07-07

    (19)F NMR is a unique tool to examine the structure of fluorine-labeled peptides in their native cellular environment, due to an exquisite sensitivity and lack of natural abundance background. For solid-state NMR analysis, we isolated native membranes from erythrocyte ghosts and bacterial protoplasts and prepared them as macroscopically oriented samples. They showed a high purity and quality of alignment according to (31)P NMR, and the membrane-bound antimicrobial peptide PGLa could be detected by (19)F NMR. The characteristic fingerprint splitting of its (19)F reporter group indicated that the peptide helix binds to the native membranes in a surface alignment, albeit with a higher affinity in the prokaryotic than the eukaryotic system.

  12. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

    PubMed

    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

  13. Micellar solubilization of tributylphosphate in aqueous solutions of Pluronic block copolymers. Part II. Structural characterization inferred by 1H NMR.

    PubMed

    Causse, J; Lagerge, S; de Menorval, L C; Faure, S

    2006-08-15

    The solubilization of tributylphosphate (TBP), a polar oil, in various micellar solutions of Pluronic has been investigated by (1)H NMR spectroscopy. Partial phase diagrams of the three components systems (Pluronic-TBP-water) have shown two characteristic temperatures, called CPT and SMT, which control the phase behavior (see Part I); Both temperature depend on the copolymer structure and, interestingly, are directly related to the TBP concentration in the medium. Monophasic microemulsions are observed only when the temperature ranges between the SMT and the CPT. Moreover, the evolution of the CPT with the TBP content clearly indicated the occurrence of a structural change of the microemulsions which allows higher quantities of TBP to be solubilized. In this second part, (1)H NMR studies of TPB/micellar systems have essentially focused on elucidating the nature of the interactions between TBP and micelle, or on the location of the solubilized species, mainly from the dependence of chemical shifts or linewidths on TBP concentration. Especially, the NMR spectra of the microemulsions before and after the structural change have been compared with those obtained for pure solution of Pluronic in D(2)O at different temperatures and in CDCl(3). The analysis of the (1)H NMR chemical shifts suggests a structural transformation of the TBP-Pluronic micelles in the sense of an hydrophobic TBP-PPO core becoming more and more dense as the TBP concentration increases. Especially, (1)H NMR data evidence an evolution of the hydration state of the hydrophobic core following addition of TBP in the micellar solutions. During the addition of TBP, the microemulsion structure turns from spherical swelled micelles to nanodroplets of pure TBP stabilized by the Pluronic (pure nanophase of TBP stabilized by the copolymer). It is shown that the structural change strongly depends on the temperatures (CPT and SMT, see Part I) and on the copolymer structure.

  14. Glycerol and glycerol carbonate as ultraviscous solvents for mixture analysis by NMR.

    PubMed

    Lameiras, Pedro; Boudesocque, Leslie; Mouloungui, Zéphirin; Renault, Jean-Hugues; Wieruszeski, Jean-Michel; Lippens, Guy; Nuzillard, Jean-Marc

    2011-09-01

    NMR of weakly polar analytes in an apolar ultraviscous solvent has recently been proposed for mixture analysis as a pertinent alternative to the DOSY experiment. The present article reports the first use of glycerol and glycerol carbonate as polar solvents for the NMR analysis of a model mixture of dipeptides. This work demonstrates the high potentiality of these solvents for the analysis of mixtures made of polar and potentially bioactive compounds. Medium-sized molecules slowly reorient in glycerol and glycerol carbonate under particular temperature conditions, so that solute resonances may show spin diffusion in NOESY spectra, thus opening the way to mixture analysis. Glycerol and glycerol carbonate have turned out to be ultraviscous solvents of choice for the individualization of four structurally close mixed dipeptides: Leu-Val, Leu-Tyr, Gly-Tyr and Ala-Tyr by means of 1D and 2D NOESY experiments. Selective sample excitation and signal detection were implemented to eliminate the intense proton signals of the non-deuterated solvents. Moreover, the recording of a multiplet selective 2D NOESY-TOCSY has shown that the analytical power of NMR in highly viscous solvents is not limited to the extraction of mixture component 1D subspectra but may also yield some supplementary information about atom connectivity within components. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Glass Structure by Scattering Methods and Spectroscopy — D. SOLID STATE NMR AS A STRUCTURAL TOOL IN GLASS SCIENCE

    NASA Astrophysics Data System (ADS)

    Eckert, Hellmut

    The following sections are included: * Introduction * Fundamentals of Solid State NMR * Nuclear magnetism and resonance * Spectroscopic technique * Internal interactions * Chemical shielding interaction * Direct magnetic dipole-dipole coupling * Nuclear electric quadrupolar interaction * Experimental separation strategies * Magic-angle spinning * Multi-dimensional NMR * Structural Issues in Non-crystalline Solids and Glasses * Short-Range Order in Oxide Glasses * Local coordination number and symmetry * Bond angle distribution functions * Spatial distribution of modifier cations and structural implications of the mixed-alkali effect * Short-Range Order in Non-Oxide Glasses * Chemical bond distribution and intermediate range order * Chemical equilibria and kinetics in glassforming liquids * Future Perspectives * Towards higher resolution for quadrupolar nuclei * Recovery of dipolar interactions in MAS-NMR: site connectivities * Double resonance NMR in heteronuclear systems * Zero- and double quantum NMR in homonuclear systems * Acknowledgments * References

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

    PubMed

    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.

  17. Assessment of (1)H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

    PubMed

    Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

    2017-01-01

    Proton nuclear magnetic resonance ((1)H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R(2)=0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R(2)=0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO2(L)(H2O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H2L) and MoO2(acac)2. The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, 1H NMR and 13C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, 1H NMR and 13C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The 1H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental 1H NMR spectra. However, the 13C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6 - 31 + G(2df,p) for other atoms, are in better agreement with experimental 13C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound.

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

    PubMed

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

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. The efficient structure elucidation of minor components in heparin digests using microcoil NMR.

    PubMed

    Limtiaco, John F K; Beni, Szabolcs; Jones, Christopher J; Langeslay, Derek J; Larive, Cynthia K

    2011-10-18

    The structural complexity and microheterogeneity of the glycosaminoglycans heparin and heparan sulfate make their characterization a daunting task. The methodology described herein utilizes a combination of enzymatic digestion, size-exclusion chromatography, strong anion-exchange HPLC, reverse-phase ion-pair ultrahigh performance liquid chromatography-mass spectrometry, and microcoil NMR for the efficient sequencing of heparin-derived tetrasaccharides. The high mass sensitivity of microcoil NMR makes this technique well suited for the characterization of mass-limited samples removing a bottleneck in the analysis workflow and permitting structural characterization of minor components isolated from a heparin enzymatic digestion. Complete characterization of one tetrasulfonated, five pentasulfonated isomers and two hexasulfonated tetrasaccharide sequences is described. To our knowledge, two of the identified minor tetrasaccharides are unique, and have not been previously reported: IdoA(2S)-GlcNS(6S)-IdoA(2S)-GlcNS(6S) and ΔUA(2S)-GlcNS(6S)-IdoA-GlcNS(6S).

  1. 13C NMR study of halogen bonding of haloarenes: measurements of solvent effects and theoretical analysis.

    PubMed

    Glaser, Rainer; Chen, Naijun; Wu, Hong; Knotts, Nathan; Kaupp, Martin

    2004-04-07

    Solvent effects on the NMR spectra of symmetrical (X = F (1), X = Cl (2), X = Br (3), X = I (4), X = NO2 (5), X = CN (6)) and unsymmetrical (X = I, Y = MeO (7), Y = PhO (8)) para-disubstituted acetophenone azines X-C6H4-CMe=N-N=CMe-C6H4-Y and of models X-C6H4-CMe=N-Z (X = I, Z = H (9), Z = NH2 (10)), 4-iodoacetophenone (11), and iodobenzene (12) were measured in CDCl(3), DMSO, THF, pyridine, and benzene to address one intramolecular and one intermolecular issue. Solvent effects on the (13)C NMR spectra are generally small, and this finding firmly establishes that the azine bridge indeed functions as a "conjugation stopper," an important design concept in our polar materials research. Since intermolecular halogen bonding of haloarenes do occur in polar organic crystalline materials, the NMR solution data pose the question as to whether the absence of solvent shifts indicates the absence of strong halogen bonding in solution. This question was studied by the theoretical analysis of the DMSO complexes of iodoarenes 4, 9-12, and of iodoacetylene. DFT and MP2 computations show iodine bonding, and characteristic structural and electronic features are described. The nonrelativistic complexation shifts and the change in the spin-orbit induced heavy atom effect of iodine compensate each other, and iodine bonding thus has no apparent effect on Ci in the iodoarenes. For iodides, complexation by DMSO occurs and may or may not manifest itself in the NMR spectra. The absence of complexation shifts in the NMR spectra of halides does not exclude the occurrence of halogen bonding in solution.

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

    PubMed

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

    1991-04-01

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

  3. Watching protein structure at work in living cells using NMR spectroscopy.

    PubMed

    Tochio, Hidehito

    2012-12-01

    Isotope-assisted multi-dimensional NMR spectroscopy can now be applied to proteins inside living cells. The technique, called in-cell NMR, aims to investigate the structures, interactions and dynamics of proteins under their native conditions, ideally at an atomic resolution. The application has begun with bacterial cells but has now expanded to mammalian cultured cells, such as HeLa cells. The importance of the realization of such 'in-mammalian cell' NMR should be stressed, as these are the cells most often employed in cell biology. Hence, a substantially wide range of application would be possible in the near future once the technique has been well developed.

  4. FT-IR, UV-vis, 1H and 13C NMR spectra and the equilibrium structure of organic dye molecule disperse red 1 acrylate: a combined experimental and theoretical analysis.

    PubMed

    Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet

    2011-12-01

    This study reports the characterization of disperse red 1 acrylate compound by spectral techniques and quantum chemical calculations. The spectroscopic properties were analyzed by FT-IR, UV-vis, (1)H NMR and (13)C NMR techniques. FT-IR spectrum in solid state was recorded in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound that dissolved in methanol was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP exchange correlation and the 6-311++G(d,p) basis set. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. A satisfactory consistency between the experimental and theoretical spectra was obtained and it shows that the hybrid DFT method is very useful in predicting accurate vibrational structure, especially for high-frequency region. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. A study on the electronic properties were performed by timedependent DFT (TD-DFT) and CIS(D) approach. To investigate non linear optical properties, the electric dipole moment μ, polarizability α, anisotropy of polarizability Δα and molecular first hyperpolarizability β were computed. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the compound can be a good candidate of nonlinear optical materials.

  5. Structure of the light-harvesting bacteriochlorophyll c assembly in chlorosomes from Chlorobium limicola determined by solid-state NMR

    PubMed Central

    Egawa, Ayako; Fujiwara, Toshimichi; Mizoguchi, Tadashi; Kakitani, Yoshinori; Koyama, Yasushi; Akutsu, Hideo

    2007-01-01

    We have determined the atomic structure of the bacteriochlorophyll c (BChl c) assembly in a huge light-harvesting organelle, the chlorosome of green photosynthetic bacteria, by solid-state NMR. Previous electron microscopic and spectroscopic studies indicated that chlorosomes have a cylindrical architecture with a diameter of ≈10 nm consisting of layered BChl molecules. Assembly structures in huge noncrystalline chlorosomes have been proposed based mainly on structure-dependent chemical shifts and a few distances acquired by solid-state NMR, but those studies did not provide a definite structure. Our approach is based on 13C dipolar spin-diffusion solid-state NMR of uniformly 13C-labeled chlorosomes under magic-angle spinning. Approximately 90 intermolecular CC distances were obtained by simultaneous assignment of distance correlations and structure optimization preceded by polarization-transfer matrix analysis. It was determined from the ≈90 intermolecular distances that BChl c molecules form piggyback-dimer-based parallel layers. This finding rules out the well known monomer-based structures. A molecular model of the cylinder in the chlorosome was built by using this structure. It provided insights into the mechanisms of efficient light harvesting and excitation transfer to the reaction centers. This work constitutes an important advance in the structure determination of huge intact systems that cannot be crystallized. PMID:17215361

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

    NASA Astrophysics Data System (ADS)

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

    2005-07-01

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

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

    PubMed

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

    2015-06-02

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

  8. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR.

    PubMed

    Peti, Wolfgang; Page, Rebecca; Moy, Kin; O'Neil-Johnson, Mark; Wilson, Ian A; Stevens, Raymond C; Wüthrich, Kurt

    2005-12-01

    In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D 1H NMR spectra or 2D [1H,15N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D 1H NMR and/or 2D [1H,15N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the "macro-scale" Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.

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

    PubMed

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

    2017-03-21

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2002-01-01

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

  12. The use of NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Final report

    SciTech Connect

    Netzel, D.A.; Miknis, F.P.; Wallace, J.C. Jr.; Butcher, C.H.; Mitzel, J.M.; Turner, T.F.; Hurtubise, R.J.

    1995-02-01

    Western Research Institute has conducted a study of different methods of coal drying as pretreatment steps before liquefaction. The objectives of this study were to develop a combined chemical dehydration/nuclear magnetic resonance (NMR) method for measuring the moisture content of coal, to measure the changes in coal structure that occur during drying, and to determine the effects of different drying methods on liquefaction reactivity of coals. Different methods of drying were investigated to determine whether coal drying can be accomplished without reducing the reactivity of coals toward liquefaction. Drying methods included thermal, microwave, and chemical dehydration. Coals of rank lignite to high volatile bituminous were studied. Coals that were dried or partially dried thermally and with microwaves had lower liquefaction conversions than coals containing equilibrium moisture contents. However, chemically dried coals had conversions equal to or greater than the premoisturized coals. The conversion behavior is consistent with changes in the physical structure and cross linking reactions because of drying. Thermal and microwave drying appear to cause a collapse in the pore structure, thus preventing donor solvents such as tetralin from contacting reactive sites inside the coals. Chemical dehydration does not appear to collapse the pore structure. These results are supported by the solvent swelling measurements in which the swelling ratios of thermally dried and microwave-dried coals were lower than those of premoisturized coals, indicating a greater degree of cross linking in the dried coals. The swelling ratios of the chemically dried coals were greater than those of the premoisturized coals because the pore structure remaining unchanged or increased when water was removed. These results are consistent with the NMR results, which did not show significant changes in coal chemical structure.

  13. Protein structure determination by conformational space annealing using NMR geometric restraints.

    PubMed

    Joo, Keehyoung; Joung, InSuk; Lee, Jinhyuk; Lee, Jinwoo; Lee, Weontae; Brooks, Bernard; Lee, Sung Jong; Lee, Jooyoung

    2015-12-01

    We have carried out numerical experiments to investigate the applicability of the global optimization method of conformational space annealing (CSA) to the enhanced NMR protein structure determination over existing PDB structures. The NMR protein structure determination is driven by the optimization of collective multiple restraints arising from experimental data and the basic stereochemical properties of a protein-like molecule. By rigorous and straightforward application of CSA to the identical NMR experimental data used to generate existing PDB structures, we redetermined 56 recent PDB protein structures starting from fully randomized structures. The quality of CSA-generated structures and existing PDB structures were assessed by multiobjective functions in terms of their consistencies with experimental data and the requirements of protein-like stereochemistry. In 54 out of 56 cases, CSA-generated structures were better than existing PDB structures in the Pareto-dominant manner, while in the remaining two cases, it was a tie with mixed results. As a whole, all structural features tested improved in a statistically meaningful manner. The most improved feature was the Ramachandran favored portion of backbone torsion angles with about 8.6% improvement from 88.9% to 97.5% (P-value <10(-17)). We show that by straightforward application of CSA to the efficient global optimization of an energy function, NMR structures will be of better quality than existing PDB structures. © 2015 Wiley Periodicals, Inc.

  14. Structure elucidation and complete NMR spectral assignments of four new diterpenoids from Smallantus sonchifolius.

    PubMed

    Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Kang, Ting-Guo; Dong, Feng

    2008-08-01

    Four new diterpenoids, named smaditerpenic acid A-D, together with five known compounds, were isolated from the H(2)O extract of the leaves of Smallantus sonchifolius (yacon) cultivated in Liaoning, China and their structures were elucidated on the basis of one- and two-dimensional NMR (including (1)H, (13)C-NMR, (1)H-(1)H COSY, HSQC, TOCSY, HMBC, and ROESY), electrospray ionization mass spectrometry (ESI-MS), and chemical methods.

  15. Synthesis, crystal structure analysis, spectral IR, NMR UV-Vis investigations, NBO and NLO of 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide with use of X-ray diffractions studies along with DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Sarioğlu, Ahmet Oral; Güler, Semih; Dege, Necmi; Sönmez, Mehmet

    2016-08-01

    The title compound, 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide compound (C22H16NO3Cl) has been synthesized and characterized by X-ray diffraction, IR, 1H and 13C NMR and UV-Vis spectra. Optimized geometrical structure, harmonic vibrational frequencies and chemical shifts were computed using hybrid-DFT (B3LYP and B3PW91) methods and 6-311G(d,p) as the basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The calculated optimized geometries, vibrational frequencies and 1H NMR chemical shift values are in strong agreement with experimentally measured values. UV-Vis spectrum of the title compound, was also recorded and the electronic properties, such as calculated energies, excitation energies, oscillator strengths, dipole moments and frontier orbital energies and band gap energies were computed with TDDFT-B3LYP methodolgy and using 6-311G(d,p) as the basis set. Furthermore, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), natural bond orbital (NBO) and non linear optical (NLO) properties were performed by using B3LYP/6-311G(d,p) level for the title compound.

  16. 1H NMR Metabolomics Analysis of Glioblastoma Subtypes

    PubMed Central

    Cuperlovic-Culf, Miroslava; Ferguson, Dean; Culf, Adrian; Morin, Pier; Touaibia, Mohamed

    2012-01-01

    Glioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by unpredictable clinical behaviors that suggest distinct molecular subtypes. With the tumor metabolic phenotype being one of the hallmarks of cancer, we have set upon to investigate whether GBMs show differences in their metabolic profiles. 1H NMR analysis was performed on metabolite extracts from a selection of nine glioblastoma cell lines. Analysis was performed directly on spectral data and on relative concentrations of metabolites obtained from spectra using a multivariate regression method developed in this work. Both qualitative and quantitative sample clustering have shown that cell lines can be divided into four groups for which the most significantly different metabolites have been determined. Analysis shows that some of the major cancer metabolic markers (such as choline, lactate, and glutamine) have significantly dissimilar concentrations in different GBM groups. The obtained lists of metabolic markers for subgroups were correlated with gene expression data for the same cell lines. Metabolic analysis generally agrees with gene expression measurements, and in several cases, we have shown in detail how the metabolic results can be correlated with the analysis of gene expression. Combined gene expression and metabolomics analysis have shown differential expression of transporters of metabolic markers in these cells as well as some of the major metabolic pathways leading to accumulation of metabolites. Obtained lists of marker metabolites can be leveraged for subtype determination in glioblastomas. PMID:22528487

  17. Extraction, Purification, and NMR Analysis of Terpenes from Brown Algae.

    PubMed

    Gaysinski, Marc; Ortalo-Magné, Annick; Thomas, Olivier P; Culioli, Gérald

    2015-01-01

    Algal terpenes constitute a wide and well-documented group of marine natural products with structures differing from their terrestrial plant biosynthetic analogues. Amongst macroalgae, brown seaweeds are considered as one of the richest source of biologically and ecologically relevant terpenoids. These metabolites, mostly encountered in algae of the class Phaeophyceae, are mainly diterpenes and meroditerpenes (metabolites of mixed biogenesis characterized by a toluquinol or a toluquinone nucleus linked to a diterpene moiety).In this chapter, we describe analytical processes commonly employed for the isolation and structural characterization of the main terpenoid constituents obtained from organic extracts of brown algae. The successive steps include (1) extraction of lipidic content from algal samples; (2) purification of terpenes by column chromatography and semi-preparative high-performance liquid chromatography; and (3) structure elucidation of the isolated terpenes by means of 1D and 2D nuclear magnetic resonance (NMR). More precisely, we propose a representative methodology which allows the isolation and structural determination of the monocyclic meroditerpene methoxybifurcarenone (MBFC) from the Mediterranean brown alga Cystoseira amentacea var. stricta. This methodology has a large field of applications and can then be extended to terpenes isolated from other species of the family Sargassaceae.

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

    PubMed

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

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Nanostructural analysis of water distribution in hydrated multicomponent gels using thermal analysis and NMR relaxometry.

    PubMed

    Codoni, Doroty; Belton, Peter; Qi, Sheng

    2015-06-01

    Highly complex, multicomponent gels and water-containing soft materials have varied applications in biomedical, pharmaceutical, and food sciences, but the characterization of these nanostructured materials is extremely challenging. The aim of this study was to use stearoyl macrogol-32 glycerides (Gelucire 50/13) gels containing seven different species of glycerides, PEG, and PEG-esters, as model, complex, multicomponent gels, to investigate the effect of water content on the micro- and nanoarchitecture of the gel interior. Thermal analysis and NMR relaxometry were used to probe the thermal and diffusional behavior of water molecules within the gel network. For the highly concentrated gels (low water content), the water activity was significantly lowered due to entrapment in the dense gel network. For the gels with intermediate water content, multiple populations of water molecules with different thermal responses and diffusion behavior were detected, indicating the presence of water in different microenvironments. This correlated with the network architecture of the freeze-dried gels observed using SEM. For the gels with high water content, increased quantities of water with similar diffusion characteristics as free water could be detected, indicating the presence of large water pockets in these gels. The results of this study provide new insights into structure of Gelucire gels, which have not been reported before because of the complexity of the material. They also demonstrate that the combination of thermal analysis and NMR relaxometry offers insights into the structure of soft materials not available by the use of each technique alone. However, we also note that in some instances the results of these measurements are overinterpreted and we suggest limitations of the methods that must be considered when using them.

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    PubMed

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

    2015-05-27

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

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

    SciTech Connect

    Lee, D.

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  5. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.

    PubMed

    Kassem, Maher M; Wang, Yong; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2016-06-07

    Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.

  6. Determination of the Structural Basis of Antibody Diversity Using NMR

    DTIC Science & Technology

    1988-09-15

    1): 290. "Distances of tyruzsnc residues from a spin-label hapten in the combining site of a specific monoclonal antibody," Jacob Anglister, Tom Frey...anti-spin-label antibody," Tom Frey, Jacob Anglister and Harden M. McConnell, Biochemistry 23, 6470-6473 (1984). 298. "NMR technique for assessing...contributions of heavy and light chains to an antibody combining site," Jacob Anglister, Tom Frey and Harden M. McConnell, Nature 315, 65-67 (1985). 305

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

    PubMed

    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

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

    PubMed

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

    PubMed Central

    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

    2016-01-01

    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 1H-1H 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. PMID:27489348

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

    SciTech Connect

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

    1987-12-29

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

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

    SciTech Connect

    Nohaile, Michael James

    1996-05-01

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

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

    PubMed

    Tugarinov, Vitali

    2014-02-01

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

  13. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, March 1, 1994--May 31, 1994

    SciTech Connect

    Netzel, D.A.

    1994-08-01

    One area for improvement in the economics of coal liquefaction is coal drying, particularly for the lower rank coals. However, there is considerable evidence to show that drying has a detrimental effect on the liquefaction behavior of coals. Regarding the liquefaction of coal, there does not appear to have been any systematic study of the methods of coal drying on coal structure and the role water plays in enhancing or lessening coal reactivity toward liquefaction. For the research program reported here, different methods of drying are being investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction. In an effort to understand the mechanism of water for enhancing coal liquefaction yield, the reactions of D{sub 2}O with the molecular constituents of coal during coal liquefaction are being investigated. This study involves the use of solution-state deuterium NMR, as well as, conventional solution-state {sup 1}H and {sup 13}C NMR analyses of the coal, and the coal liquids and residue from a coal liquefaction process. These D{sub 2}O transfer reactions will be conducted on coals which have been dried by various methods and rehydrated using D{sub 2}O and by successive exchange of H{sub 2}O associated with the coals with D{sub 2}O. The drying methods include thermal, microwave, and chemical dehydration of the coal.

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

    SciTech Connect

    Gronenborn, A.M.; Clore, G.M.

    1994-12-01

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

  15. A Unique Tool for Cellular Structural Biology: In-cell NMR*

    PubMed Central

    Luchinat, Enrico; Banci, Lucia

    2016-01-01

    Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When this is done, important structural and functional features of macromolecules, which depend on their native network of interactions within the cell, may be lost. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that allows macromolecules to be analyzed in living cells, at the atomic level. In-cell NMR can be applied to several cellular systems to obtain biologically relevant structural and functional information. Here we summarize the existing approaches and focus on the applications to protein folding, interactions, and post-translational modifications. PMID:26677229

  16. GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.

    PubMed

    Kleckner, Ian R; Foster, Mark P

    2012-01-01

    Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data ( http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ (2)-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.

  17. GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data

    PubMed Central

    2013-01-01

    Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial µs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data (http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ2-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community. PMID:22160811

  18. Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization.

    PubMed

    Tong, Yan; Ji, Chang G; Mei, Ye; Zhang, John Z H

    2009-06-24

    Molecular dynamics simulations of NMR backbone relaxation order parameters have been carried out to investigate the polarization effect on the protein's local structure and dynamics for five benchmark proteins (bovine pancreatic trypsin inhibitor, immunoglobulin-binding domain (B1) of streptococcal protein G, bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and hen egg white lysozyme). In order to isolate the polarization effect from other interaction effects, our study employed both the standard AMBER force field (AMBER03) and polarized protein-specific charges (PPCs) in the MD simulations. The simulated order parameters, employing both the standard nonpolarizable and polarized force fields, are directly compared with experimental data. Our results show that residue-specific order parameters at some specific loop and turn regions are significantly underestimated by the MD simulations using the standard AMBER force field, indicating hyperflexibility of these local structures. Detailed analysis of the structures and dynamic motions of individual residues reveals that the hyperflexibility of these local structures is largely related to the breaking or weakening of relevant hydrogen bonds. In contrast, the agreement with the experimental results is significantly improved and more stable local structures are observed in the MD simulations using the polarized force field. The comparison between theory and experiment provides convincing evidence that intraprotein hydrogen bonds in these regions are stabilized by electronic polarization, which is critical to the dynamical stability of these local structures in proteins.

  19. NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.

    PubMed

    Helmling, Christina; Wacker, Anna; Wolfinger, Michael T; Hofacker, Ivo L; Hengesbach, Martin; Fürtig, Boris; Schwalbe, Harald

    2017-02-22

    Gene repression induced by the formation of transcriptional terminators represents a prime example for the coupling of RNA synthesis, folding, and regulation. In this context, mapping the changes in available conformational space of transcription intermediates during RNA synthesis is important to understand riboswitch function. A majority of riboswitches, an important class of small metabolite-sensing regulatory RNAs, act as transcriptional regulators, but the dependence of ligand binding and the subsequent allosteric conformational switch on mRNA transcript length has not yet been investigated. We show a strict fine-tuning of binding and sequence-dependent alterations of conformational space by structural analysis of all relevant transcription intermediates at single-nucleotide resolution for the I-A type 2'dG-sensing riboswitch from Mesoplasma florum by NMR spectroscopy. Our results provide a general framework to dissect the coupling of synthesis and folding essential for riboswitch function, revealing the importance of metastable states for RNA-based gene regulation.

  20. Structure Determination Using 19-F NMR: A Simple Fluorination Experiment of Cinnamyl Alcohol

    NASA Astrophysics Data System (ADS)

    Demendonca, Daniel J.; Digits, Cheryl A.; Navin, Erin W.; Sander, Tanya C.; Hammond, Gerald B.

    1995-08-01

    Described here is the nucleophilic substitution of a hydroxyl group, in cinnamyl alcohol, by fluorine, and analysis of the product using 19-F NMR spectroscopy. This experiment brings important innovations to the teaching of experimental organic chemistry at the undergraduate level. The fluorination of cinnamyl alcohol requires only a mild fluorinating agent and so it provides the student with a direct contact with organofluorine, chemistry. The allylic nucleophilic substitution typified by our experiment will enhance the instruction of nucleophilic substitution in the laboratory, traditionally limited to SN1 or SN2 substitutions. Because the ratio of SN2 to SN2' derived products cannot be determined directly using 1-H NMR spectroscopy but it can be measured easily using 19-F NMR spectroscopy. The experiment gives the student a firsthand experience of the usefulness of NMR spectra of different nuclei.

  1. Structure determination of a partially ordered layered silicate material with an NMR crystallography approach.

    PubMed

    Brouwer, Darren Henry; Cadars, Sylvian; Hotke, Kathryn; Van Huizen, Jared; Van Huizen, Nicholas

    2017-03-01

    Structure determination of layered materials can present challenges for conventional diffraction methods due to the fact that such materials often lack full three-dimensional periodicity since adjacent layers may not stack in an orderly and regular fashion. In such cases, NMR crystallography strategies involving a combination of solid-state NMR spectroscopy, powder X-ray diffraction, and computational chemistry methods can often reveal structural details that cannot be acquired from diffraction alone. We present here the structure determination of a surfactant-templated layered silicate material that lacks full three-dimensional crystallinity using such an NMR crystallography approach. Through a combination of powder X-ray diffraction and advanced (29)Si solid-state NMR spectroscopy, it is revealed that the structure of the silicate layer of this layered silicate material templated with cetyltrimethylammonium surfactant cations is isostructural with the silicate layer of a previously reported material referred to as ilerite, octosilicate, or RUB-18. High-field (1)H NMR spectroscopy reveals differences between the materials in terms of the ordering of silanol groups on the surfaces of the layers, as well as the contents of the inter-layer space.

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

    PubMed Central

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

    2010-01-01

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

  3. DFT molecular modeling and NMR conformational analysis of a new longipinenetriolone diester

    NASA Astrophysics Data System (ADS)

    Cerda-García-Rojas, Carlos M.; Guerra-Ramírez, Diana; Román-Marín, Luisa U.; Hernández-Hernández, Juan D.; Joseph-Nathan, Pedro

    2006-05-01

    The structure and conformational behavior of the new natural compound (4 R,5 S,7 S,8 R,9 S,10 R,11 R)-longipin-2-en-7,8,9-triol-1-one 7-angelate-9-isovalerate (1) isolated from Stevia eupatoria, were studied by molecular modeling and NMR spectroscopy. A Monte Carlo search followed by DFT calculations at the B3LYP/6-31G* level provided the theoretical conformations of the sesquiterpene framework, which were in full agreement with results derived from the 1H- 1H coupling constant analysis.

  4. 2D NMR Barcoding and Differential Analysis of Complex Mixtures for Chemical Identification: The Actaea Triterpenes

    PubMed Central

    2015-01-01

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ−δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

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

    PubMed

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

    2013-06-01

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

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

    PubMed

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

    2010-12-08

    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. Comprehensive non-targeted analysis of contaminated groundwater of a former ammunition destruction site using 1H-NMR and HPLC-SPE-NMR/TOF-MS.

    PubMed

    Godejohann, Markus; Heintz, Lea; Daolio, Cristina; Berset, Jean-Daniel; Muff, Daniel

    2009-09-15

    The aim of the present study was to explore the capabilities of the combination of 1H NMR (proton nuclear magnetic resonance) mixture analysis and HPLC-SPE-NMR/TOF-MS (high-performance liquid chromatography coupled to solid-phase extraction and nuclear magnetic resonance and time-of-flight mass spectrometry) for the characterization of xenobiotic contaminants in groundwater samples. As an example, solid-phase extracts of two groundwater samples taken from a former ammunition destruction site in Switzerland were investigated. 1H NMR spectra of postcolumn SPE enriched compounds, together with accurate mass measurements, allowed the structural elucidation of unknowns. This untargeted approach allowed us to identify expected residues of explosives such as 2,4,6-trinitrotoluene (2,4,6-TNT), Hexogen (RDX) and Octogen (HMX), degradation products of TNT (1,3,5-trinitrobenzene (1,3,5-TNB), 2-amino-4,6-dinitrotoluene (2-A-4,6-DNT), 3,5-dinitrophenol (3,5-DNP), 3,5-dinitroaniline (3,5-DNA), 2,6-dinitroanthranite, and 2-Hydroxy-4,6-dinitrobenzonitrile), benzoic acid, Bisphenol A (a known endocrine disruptor compound), and some toxicologically relevant additives for propelling charges: Centralite I (1,3-diethyl-1,3-diphenylurea), DPU (N,N-diphenylurethane), N,N-diphenylcarbamate (Acardite II), and N-methyl-N-phenylurethane. To our knowledge, this is the first report of the presence of these additives in environmental samples. Extraction recoveries for Centralite I and DPU have been determined. Contaminants identified by our techniques were quantified based on HPLC-UV (HPLC-ultraviolet detection) and 1H NMR mixture analysis. The concentrations of the contaminants ranged between 0.1 and 48 microg/L assuming 100% recovery for the SPE step.

  8. Molecular structures, spectroscopic (FT-IR, NMR, UV) studies, NBO analysis and NLO properties for tautomeric forms of 1,3-dimethyl-5-(phenylazo)-6-aminouracil by density functional method.

    PubMed

    Eşme, Aslı; Sağdınç, Seda Güneşdoğdu

    2018-01-05

    The equilibrium geometry, nuclear magnetic resonance (NMR) and UV-Vis analysis, and vibrational frequencies for the azo and hydrazone isomers of 1,3-dimethyl-5-(phenylazo)-6-aminouracil have been performed using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. A detailed interpretation of the vibrational spectra has been made on the basis of the calculated potential energy distribution (PED) obtained from the Vibrational Energy Distribution Analysis (VEDA4) program. The (1)H NMR chemical shifts with respect to TMS were calculated by the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Using the TD-DFT method, electronic absorption spectra in CHCl3 solvent of the title compound have been predicted, and good agreement is determined with the experimental one. The NLO properties such as mean polarizability (⟨α⟩), the anisotropy of the polarizability (⟨Δα⟩) and the mean first-order hyperpolarizability (⟨β⟩) were computed by using finite field method. The computed values of μ, α and β for the azo and hydrazone forms of the title molecule are 5.4717 and 3.8905 D, 2.7773×10(-23) and 2.7598×10(-23)esu, and 3.4499×10-(30) and 6.8504×10-(30)esu, respectively. The high β values and non-zero values of μ indicate that the title compound might be a good candidate for NLO material. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2012-01-01

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C 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 Cu2+ (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 1H-1H 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. PMID:22723345

  10. Isolation and structure elucidation of tetrameric procyanidins from unripe apples (Malus pumila cv. Fuji) by NMR spectroscopy.

    PubMed

    Nakashima, Shohei; Oda, Chihiro; Masuda, Susumu; Tagashira, Motoyuki; Kanda, Tomomasa

    2012-11-01

    Procyanidins are plant secondary metabolites widely consumed and known to have various physiological functions, but their bioavailability and mechanism of action are still unclear especially for larger oligomers. One of the reasons is scarce information about the detailed structure of oligomeric procyanidins. As for apple, structures of procyanidin components larger than trimers are scarcely known. In this study, 11 tetrameric procyanidins including two known compounds were isolated from unripe apples (Malus pumila cv. Fuji) and identified by NMR spectroscopic analysis and phloroglucinol degradation. As a result, the detailed structural diversity of tetrameric procyanidins in apple was established. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. NMR solution structure of ATTp, an Arabidopsis thaliana trypsin inhibitor.

    PubMed

    Zhao, Qin; Chae, Young Kee; Markley, John L

    2002-10-15

    The three-dimensional structure of the precursor form of the Arabidopsis thaliana trypsin inhibitor (ATT(p), GenBank entry Z46816), a 68-residue (approximately 7.5 kDa) rapeseed class proteinase inhibitor, has been determined in solution at pH 5.0 and 25 degrees C by multinuclear magnetic resonance spectroscopy. The protein contains one alpha-helix and two strands of antiparallel beta-sheet, with a type IV beta-turn connecting the two strands. The alpha-helix and the inhibitory loop are connected to the beta-sheet through three disulfide bridges; a fourth disulfide bridge connects the N- and C-termini. The overall structural topology of ATT(p) is similar to those of the sweet tasting protein brazzein (rmsd of 3.0 A) and the antifungal protein Rs-Afp1 [a knottin protein from radish (Raphanus sativus), rmsd of 2.7 A]. The precursor segment in ATT(p) is disordered, as visualized by the final 20-conformer ensemble and as confirmed by (15)N heteronuclear NOE analysis. The overall fold of ATT(p) is distinct from those of other classes of serine proteinase inhibitors except in the inhibitor loop; therefore, it represents a new inhibitor fold.

  12. (27)Al-(27)Al double-quantum single-quantum MAS NMR: Applications to the structural characterization of microporous materials.

    PubMed

    Martineau-Corcos, Charlotte; Dědeček, Jiri; Taulelle, Francis

    In this paper, we review and illustrate applications, reported in the literature or used in our group, of (27)Al-(27)Al double-quantum single-quantum (DQ-SQ) MAS NMR experiments for the structural characterization of Al-containing microporous solids, namely zeolites, aluminophosphates and metal-organic frameworks. Information regarding the periodic frameworks or the localization of the various aluminum species in the materials are obtained from the analysis of the two-dimensional NMR spectra, which allows getting local structural details sometimes inaccessible from other characterization technique. An application of (27)Al-(27)Al of the DQ-SQ experiment for the detection of aluminum pairing in zeolite is shown. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed

    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.

  14. An Analysis of a Commercial Furniture Refinisher: A Comprehensive Introductory NMR Experiment.

    ERIC Educational Resources Information Center

    Markow, Peter G.; Cramer, John A.

    1983-01-01

    Describes a comprehensive nuclear magnetic resonance (NMR) experiment designed to introduce undergraduate organic chemistry students to measurement/interpretation of NMR parameters. Students investigate chemical shift analysis, spin-spin coupling, peak integrations, effect of deuterium oxide extraction, and comparisons with literature spectra;…

  15. Reliability of ^1^H NMR analysis for assessment of lipid oxidation at frying temperatures

    USDA-ARS?s Scientific Manuscript database

    The reliability of a method using ^1^H NMR analysis for assessment of oil oxidation at a frying temperature was examined. During heating and frying at 180 °C, changes of soybean oil signals in the ^1^H NMR spectrum including olefinic (5.16-5.30 ppm), bisallylic (2.70-2.88 ppm), and allylic (1.94-2.1...

  16. Analysis of Radiation Induced Degradation in FPC-461 Fluoropolymers by Variable Temperature Multinuclear NMR

    SciTech Connect

    Chinn, S C; Wilson, T S; Maxwell, R S

    2004-10-27

    Solid state nuclear magnetic resonance techniques have been used to investigate aging mechanisms in a vinyl chloride:chlorotrifluoroethylene copolymer, FPC-461, due to exposure to {gamma}-radiation. Solid state {sup 1}H MAS NMR spectra revealed structural changes of the polymer upon irradiation under both air and nitrogen atmospheres. Considerable degradation is seen with {sup 1}H NMR in the vinyl chloride region of the polymer, particularly in the samples irradiated in air. {sup 19}F MAS NMR was used to investigate speciation in the chlorotrifluoroethylene blocks, though negligible changes were seen. {sup 1}H and {sup 19}F NMR at elevated temperature revealed increased segmental mobility and decreased structural heterogeneity within the polymer, yielding significant resolution enhancement over room temperature solid state detection. The effects of multi-site exchange are manifest in both the {sup 1}H and {sup 19}F NMR spectra as a line broadening and change in peak position as a function of temperature.

  17. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

    PubMed Central

    Hafsa, Noor E.; Arndt, David; Wishart, David S.

    2015-01-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

  18. Structural comparison of Gilsonite and Trinidad Lake Asphalt using 13C-NMR technique

    NASA Astrophysics Data System (ADS)

    Nciri, Nader; Cho, Namjun

    2017-04-01

    The recent increased importance of natural asphalt as an alternative binder for sustainable road pavement has dictated that more knowledge should be acquired about its structure and properties. Earlier, Carbon-13 NMR spectroscopy has been applied to very few natural bituminous materials. In this work, two types of raw binders namely Gilsonite and Trinidad Lake asphalt (TLA) have been subjected to an extensive investigation by using 13C-NMR technique. Results have shown that valuable chemical data can be readily withdrawn on aromatic ring structures and ring substituents in natural asphalts derived from different sources. The chemical significance of these findings will be discussed.

  19. Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

    PubMed

    Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

    2017-01-31

    Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level.

  20. Spectral analysis, vibrational assignments, NBO analysis, NMR, UV-Vis, hyperpolarizability analysis of 2-aminofluorene by density functional theory.

    PubMed

    Jone Pradeepa, S; Sundaraganesan, N

    2014-05-05

    In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated.

  1. 15N NMR study of nitrate ion structure and dynamics in hydrotalcite-like compounds

    USGS Publications Warehouse

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

    2000-01-01

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

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

    SciTech Connect

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

    1996-04-01

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

  3. Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

    PubMed Central

    Horst, Reto; Wider, Gerhard; Fiaux, Jocelyne; Bertelsen, Eric B.; Horwich, Arthur L.; Wüthrich, Kurt

    2006-01-01

    The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution. PMID:17032756

  4. NMR determination of an incommensurate helical antiferromagnetic structure in EuCo2As2

    DOE PAGES

    Ding, Q. -P.; Higa, N.; Sangeetha, N. S.; ...

    2017-05-05

    In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo2As2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature TN = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo2As2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter. Finally, the incommensurate helical AFMmore » state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

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

    PubMed

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

    2011-05-01

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

  6. Structure and dynamics of Pin1 during catalysis by NMR

    PubMed Central

    Labeikovsky, Wladimir; Eisenmesser, Elan Z.; Bosco, Daryl A.; Kern, Dorothee

    2009-01-01

    The link between internal enzyme motions and catalysis is poorly understood. Correlated motions in the us-ms timescale may be critical for enzyme function. We have characterized the backbone dynamics of the peptidyl-prolyl isomerase Pin1 catalytic domain in the free state and during catalysis. Pin1 is a prolyl isomerase of the parvulin family and specifically catalyzes the isomerization of phosphorylated Ser/Thr-Pro peptide bonds. Pin1 has been shown to be essential for cell-cycle progression and to interact with the neuronal tau protein inhibiting its aggregation into fibrillar tangles as found in Alzheimer’s disease. 15N relaxation dispersion measurements performed on Pin1 during catalysis reveal conformational exchange processes in the microsecond timescale. A subset of active site residues undergo kinetically similar exchange processes even in the absence of substrate, suggesting that this area is already “primed” for catalysis. Furthermore, structural data of the turning-over enzyme were obtained through inter- and intra-molecular NOEs. This analysis together with a characterization of the substrate concentration dependence of the conformational exchange allowed distinguishing of regions of the enzyme active site that are affected primarily by substrate binding versus substrate isomerization. Together these data suggest a model for the reaction trajectory of Pin1 catalysis. PMID:17316687

  7. Total lineshape analysis of high-resolution NMR spectra powered by simulated annealing.

    PubMed

    Cheshkov, D A; Sinitsyn, D O; Sheberstov, K F; Chertkov, V A

    2016-11-01

    The novel algorithm for a total lineshape analysis of high-resolution NMR spectra has been developed. A global optimization by simulated annealing has been applied that has allowed to overcome the main trouble of common approaches which had frequently returned solutions for local minima rather than for global ones. The algorithm has been verified for the four-spin test systems ABCD, and has been successfully used for analysis of experimental NMR spectra of proline. The approach has allowed to avoid a sophisticated manual setup of initial parameters and to conduct the analysis of complicated high-resolution NMR spectra nearly automatically. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2012-06-06

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

  9. Whole-core analysis by sup 13 C NMR

    SciTech Connect

    Vinegar, H.J.; Tutunjian, P.N. ); Edelstein, W.A.; Roemer, P.B. )

    1991-06-01

    This paper reports on a whole-core nuclear magnetic resonance (NMR) system that was used to obtain natural abundance {sup 13}C spectra. The system enables rapid, nondestructive measurements of bulk volume of movable oil, aliphatic/aromatic ratio, oil viscosity, and organic vs. carbonate carbon. {sup 13}C NMR can be used in cores where the {sup 1}H NMR spectrum is too broad to resolve oil and water resonances separately. A 5 1/4-in. {sup 13}C/{sup 1}H NMR coil was installed on a General Electric (GE) CSI-2T NMR imager/spectrometer. With a 4-in.-OD whole core, good {sup 13}C signal/noise ratio (SNR) is obtained within minutes, while {sup 1}H spectra are obtained in seconds. NMR measurements have been made of the {sup 13}C and {sup 1}H density of crude oils with a wide range of API gravities. For light- and medium-gravity oils, the {sup 13}C and {sup 1}H signal per unit volume is constant within about 3.5%. For heavy crudes, the {sup 13}C and {sup 1}H density measured by NMR is reduced by the shortening of spin-spin relaxation time. {sup 13}C and {sup 1}H NMR spin-lattice relaxation times were measured on a suite of Cannon viscosity standards, crude oils (4 to 60{degrees} API), and alkanes (C{sub 5} through C{sub 16}) with viscosities at 77{degrees}F ranging from 0.5 cp to 2.5 {times} 10{sup 7} cp. The {sup 13}C and {sup 1}H relaxation times show a similar correlation with viscosity from which oil viscosity can be estimated accurately for viscosities up to 100 cp. The {sup 13}C surface relaxation rate for oils on water-wet rocks is very low. Nonproton decoupled {sup 13}C NMR is shown to be insensitive to kerogen; thus, {sup 13}C NMR measures only the movable hydrocarbon content of the cores. In carbonates, the {sup 13}C spectrum also contains a carbonate powder pattern useful in quantifying inorganic carbon and distinguishing organic from carbonate carbon.

  10. Molecular structure, spectroscopic (FTIR, FT-Raman, 13C and 1H NMR, UV), polarizability and first-order hyperpolarizability, HOMO-LUMO analysis of 2,4-difluoroacetophenone

    NASA Astrophysics Data System (ADS)

    Jeyavijayan, S.

    2015-02-01

    The FTIR and FT-Raman spectra of 2,4-difluoroacetophenone (DFAP) have been recorded in the regions 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of DFAP is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atom as well as the positive potential sites are around the hydrogen atoms. The UV-Vis spectral analysis of DFAP has also been done which confirms the charge transfer of DFAP. The chemical shifts of H atoms and C atoms were calculated using NMR analysis. Furthermore, the polarizability, the first hyperpolarizability and total dipole moment of the molecule have been calculated.

  11. Molecular structure, spectroscopic (FTIR, FT-Raman, 13C and 1H NMR, UV), polarizability and first-order hyperpolarizability, HOMO-LUMO analysis of 2,4-difluoroacetophenone.

    PubMed

    Jeyavijayan, S

    2015-02-05

    The FTIR and FT-Raman spectra of 2,4-difluoroacetophenone (DFAP) have been recorded in the regions 4000-400 cm(-1) and 3500-50 cm(-1), respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of DFAP is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atom as well as the positive potential sites are around the hydrogen atoms. The UV-Vis spectral analysis of DFAP has also been done which confirms the charge transfer of DFAP. The chemical shifts of H atoms and C atoms were calculated using NMR analysis. Furthermore, the polarizability, the first hyperpolarizability and total dipole moment of the molecule have been calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-10-22

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

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

    PubMed

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

    2015-11-01

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

  15. Nanogram-scale preparation and NMR analysis for mass-limited small volatile compounds.

    PubMed

    Nojima, Satoshi; Kiemle, David J; Webster, Francis X; Apperson, Charles S; Schal, Coby

    2011-03-28

    Semiochemicals are often produced in infinitesimally small quantities, so their isolation requires large amounts of starting material, not only requiring significant effort in sample preparation, but also resulting in a complex mixture of compounds from which the bioactive compound needs to be purified and identified. Often, compounds cannot be unambiguously identified by their mass spectra alone, and NMR analysis is required for absolute chemical identification, further exacerbating the situation because NMR is relatively insensitive and requires large amounts of pure analyte, generally more than several micrograms. We developed an integrated approach for purification and NMR analysis of <1 µg of material. Collections from high performance preparative gas-chromatography are directly eluted with minimal NMR solvent into capillary NMR tubes. With this technique, (1)H-NMR spectra were obtained on 50 ng of geranyl acetate, which served as a model compound, and reasonable H-H COSY NMR spectra were obtained from 250 ng of geranyl acetate. This simple off-line integration of preparative GC and NMR will facilitate the purification and chemical identification of novel volatile compounds, such as insect pheromones and other semiochemicals, which occur in minute (sub-nanogram), and often limited, quantities.

  16. Nanogram-Scale Preparation and NMR Analysis for Mass-Limited Small Volatile Compounds

    PubMed Central

    Nojima, Satoshi; Kiemle, David J.; Webster, Francis X.; Apperson, Charles S.; Schal, Coby

    2011-01-01

    Semiochemicals are often produced in infinitesimally small quantities, so their isolation requires large amounts of starting material, not only requiring significant effort in sample preparation, but also resulting in a complex mixture of compounds from which the bioactive compound needs to be purified and identified. Often, compounds cannot be unambiguously identified by their mass spectra alone, and NMR analysis is required for absolute chemical identification, further exacerbating the situation because NMR is relatively insensitive and requires large amounts of pure analyte, generally more than several micrograms. We developed an integrated approach for purification and NMR analysis of <1 µg of material. Collections from high performance preparative gas-chromatography are directly eluted with minimal NMR solvent into capillary NMR tubes. With this technique, 1H-NMR spectra were obtained on 50 ng of geranyl acetate, which served as a model compound, and reasonable H-H COSY NMR spectra were obtained from 250 ng of geranyl acetate. This simple off-line integration of preparative GC and NMR will facilitate the purification and chemical identification of novel volatile compounds, such as insect pheromones and other semiochemicals, which occur in minute (sub-nanogram), and often limited, quantities. PMID:21464906

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

    PubMed

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

    1987-12-29

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

  18. Crystallinity and compositional changes in carbonated apatites: Evidence from {sup 31}P solid-state NMR, Raman, and AFM analysis

    SciTech Connect

    McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M.Banaszak; Tecklenburg, Mary M.J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

    2013-10-15

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and {sup 31}P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse {sup 31}P NMR linewidth and inverse Raman PO{sub 4}{sup 3−}ν{sub 1} bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3–10.3 wt% CO{sub 3}{sup 2−} range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the {sup 31}P NMR chemical shift frequency and the Raman phosphate ν{sub 1} band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals. - Graphical abstract: Carbonated apatite shows an abrupt change in spectral (NMR, Raman) and morphological (AFM) properties at a composition of about one carbonate substitution per unit cell. Display Omitted - Highlights: • Crystallinity (XRD), particle size (AFM) of carbonated apatites and bone mineral. • Linear relationships among crystallinity, {sup 31}P NMR and Raman inverse bandwidths. • Low and high carbonated apatites use different charge-balancing ion-loss mechanism.

  19. Structure and Dynamics of the Aβ21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations

    PubMed Central

    Fawzi, Nicolas L.; Phillips, Aaron H.; Ruscio, Jory Z.; Doucleff, Michaeleen; Wemmer, David E.; Head-Gordon, Teresa

    2012-01-01

    We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Aβ21–30 peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer’s disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants (3JHNHα), chemical-shift values, 13C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Aβ21–30. We find robust prediction of the 13C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Aβ21–30 peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Aβ21–30 conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Aβ21–30 peptide involves a majority population (~60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a β-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Aβ1–40 and Aβ1–42, for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high

  20. Which kind of aromatic structures are produced during biomass charring? New insights provided by modern solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Knicker, Heike; Paneque-Carmona, Marina; Velasco-Molina, Marta; de la Rosa, José Maria; León-Ovelar, Laura Regina; Fernandez-Boy, Elena

    2017-04-01

    Intense research on biochar and charcoal of the last years has revealed that depending on the production conditions, the chemical and physical characteristics of their aromatic network can greatly vary. Since such variations are determining the behavior and stability of charred material in soils, a better understanding of the structural changes occurring during their heating and the impact of those changes on their function is needed. One method to characterize pyrogenic organic matter (PyOM) represents solid-state 13C NMR spectroscopy applying the cross polarization (CP) magic angle spinning technique (MAS). A drawback of this technique is that the quantification of NMR spectra of samples with highly condensed and proton-depleted structures is assumed to be bias. Typical samples with such attributes are charcoals produced at temperatures above 700°C under pyrolytic conditions. Commonly their high condensation degree leads to graphenic structures that are not only reducing the CP efficiency but create also a conductive lattice which acts as a shield and prevents the entering of the excitation pulse into the sample during the NMR experiments. Since the latter can damage the NMR probe and in the most cases the obtained NMR spectra show only one broad signal assignable to aromatic C, this technique is rarely applied for characterizing high temperature chars or soot. As a consequence, a more detailed knowledge of the nature of the aromatic ring systems is still missing. The latter is also true for the aromatic domains of PyOM produced at lower temperatures, since older NMR instruments operating at low magnetic fields deliver solid-state 13C NMR spectra with low resolution which turns a more detailed analysis of the aromatic chemical shift region into a challenging task. In order to overcome this disadvantages, modern NMR spectroscopy offers not only instruments with greatly improved resolution but also special pulse sequences for NMR experiments which allow a more

  1. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.

    PubMed

    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.

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

    PubMed Central

    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.

    2016-01-01

    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 13C-13C 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. PMID:26365800

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

    PubMed

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

    2015-10-06

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

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

    PubMed

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

    2011-12-14

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

  5. Structural Isomer Identification via NMR: A Nuclear Magnetic Resonance Experiment for Organic, Analytical, or Physical Chemistry.

    ERIC Educational Resources Information Center

    Szafran, Zvi

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment that examines the ability of nuclear magnetic resonance (NMR) to distinguish between structural isomers via resonance multiplicities and chemical shifts. Reasons for incorporating the experiment into organic, analytical, or physical chemistry…

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

    PubMed

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

    2009-10-12

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

  7. Structural Isomer Identification via NMR: A Nuclear Magnetic Resonance Experiment for Organic, Analytical, or Physical Chemistry.

    ERIC Educational Resources Information Center

    Szafran, Zvi

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment that examines the ability of nuclear magnetic resonance (NMR) to distinguish between structural isomers via resonance multiplicities and chemical shifts. Reasons for incorporating the experiment into organic, analytical, or physical chemistry…

  8. Structure elucidation and NMR assignments of two unusual monoterpene indole alkaloids from Psychotria stachyoides.

    PubMed

    Pimenta, Antonia Torres Avila; Braz-Filho, Raimundo; Delprete, Piero Giuseppe; de Souza, Elnatan Bezerra; Silveira, Edilberto Rocha; Lima, Mary Anne Sousa

    2010-09-01

    Two unusual monoterpene indole alkaloids, stachyoside (1) and nor-methyl-23-oxo-correantoside (2), have been isolated from the aerial parts of Psychotria stachyoides. The structural elucidation of both compounds was performed by the aid of HRESIMS, FT-IR, and 1D- and 2D-NMR techniques including COSY, HSQC, HMBC, and NOESY.

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

    SciTech Connect

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

    2016-09-20

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

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

    DOE PAGES

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

    2016-09-20

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

  11. Crystallinity and compositional changes in carbonated apatites: Evidence from (31)P solid-state NMR, Raman, and AFM analysis.

    PubMed

    McElderry, John-David P; Zhu, Peizhi; Mroue, Kamal H; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H; Franceschi, Renny T; Holl, Mark M Banaszak; Tecklenburg, Mary M J; Ramamoorthy, Ayyalusamy; Morris, Michael D

    2013-10-01

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and (31)P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse (31)P NMR linewidth and inverse Raman PO4(3-) ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO3(2-) range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the (31)P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

  12. Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

    PubMed Central

    McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M.J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

    2013-01-01

    Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43− ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3–10.3 wt% CO32− range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals. PMID:24273344

  13. An NMR Strategy for Unraveling Structures of Bioactive Sponge-derived Oxy-polyhalogenated Diphenyl Ethers⊥

    PubMed Central

    Calcul, Laurent; Chow, Raymond; Oliver, Allen G.; Tenney, Karen; White, Kimberly N.; Wood, Alexander W.; Fiorilla, Catherine; Crews, Phillip

    2009-01-01

    The over-expression of the Mcl-1 protein in cancerous cells results in the sequestering of Bak, a key component in the regulation of normal cell apoptosis. Our investigation of the ability of marine-derived small molecule natural products to inhibit this protein-protein interaction led to the isolation of several bioactive oxy-polyhalogenated diphenyl ethers. A semi-pure extract, previously obtained from Dysidea (Lamellodysidea) herbacea and preserved in our repository, along with an untouched Dysidea granulosa marine sponge afforded 13 distinct oxy-polyhalogenated diphenyl ethers. Among these isolates were four new compounds, 5, 6, 10, and 12. The structure elucidation of these molecules was complicated by the plethora of structural variants that exist in the literature. During dereplication, we established a systematic method for analyzing this class of compounds. The strategy is governed by trends in the 1H and 13C NMR shifts of the aromatic rings and the success of the strategy was checked by X-ray crystal structure analysis. PMID:19323567

  14. NMR strategy for unraveling structures of bioactive sponge-derived oxy-polyhalogenated diphenyl ethers.

    PubMed

    Calcul, Laurent; Chow, Raymond; Oliver, Allen G; Tenney, Karen; White, Kimberly N; Wood, Alexander W; Fiorilla, Catherine; Crews, Phillip

    2009-03-27

    The overexpression of the Mcl-1 protein in cancerous cells results in the sequestering of Bak, a key component in the regulation of normal cell apoptosis. Our investigation of the ability of marine-derived small-molecule natural products to inhibit this protein-protein interaction led to the isolation of several bioactive oxy-polyhalogenated diphenyl ethers. A semipure extract, previously obtained from Dysidea (Lamellodysidea) herbacea and preserved in our repository, along with an untouched Dysidea granulosa marine sponge afforded 13 distinct oxy-polyhalogenated diphenyl ethers. Among these isolates were four new compounds, 5, 6, 10, and 12. The structure elucidation of these molecules was complicated by the plethora of structural variants that exist in the literature. During dereplication, we established a systematic method for analyzing this class of compounds. The strategy is governed by trends in the (1)H and (13)C NMR shifts of the aromatic rings, and the success of the strategy was checked by X-ray crystal structure analysis.

  15. Combined Analysis of Stable Isotope, (1)H NMR, and Fatty Acid To Verify Sesame Oil Authenticity.

    PubMed

    Kim, Jeongeun; Jin, Gyungsu; Lee, Yunhee; Chun, Hyang Sook; Ahn, Sangdoo; Kim, Byung Hee

    2015-10-14

    The aim of this study was to verify the authenticity of sesame oils using combined analysis of stable isotope ratio, (1)H NMR spectroscopy, and fatty acid profiles of the oils. Analytical data were obtained from 35 samples of authentic sesame oils and 29 samples of adulterated sesame oils currently distributed in Korea. The orthogonal projection to latent structure discriminant analysis technique was used to select variables that most effectively verify the sesame oil authenticity. The variables include δ(13)C value, integration values of NMR peaks that signify the CH3 of n-3 fatty acids, CH2 between two C═C, protons from sesamin/sesamolin, and 18:1n-9, 18:3n-3, 18:2t, and 18:3t content values. The authenticity of 65 of 70 blind samples was correctly verified by applying the range of the eight variables found in the authentic sesame oil samples, suggesting that triple analysis is a useful approach to verify sesame oil authenticity.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2011-09-08

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

  18. NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

    PubMed

    Ryu, Shoraku; Furihata, Kazuo; Koda, Masanori; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2016-03-01

    Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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

    PubMed

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

    2016-07-15

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

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

    SciTech Connect

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

    1990-07-06

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

  1. Structural water in carbonated hydroxylapatite and fluorapatite: confirmation by solid state (2)H NMR.

    PubMed

    Yoder, Claude H; Pasteris, Jill D; Worcester, Kimberly N; Schermerhorn, Demetra V

    2012-01-01

    Water is well recognized as an important component in bone, typically regarded as a constituent of collagen, a pore-filling fluid in bone, and an adsorbed species on the surface of bone crystallites. The possible siting and role of water within the structure of the apatite crystallites have not been fully explored. In our experiments, carbonated hydroxyl- and fluorapatites were prepared in D(2)O and characterized by elemental analysis, thermal gravimetric analysis, powder X-ray diffraction, and infrared and Raman spectroscopy. Two hydroxylapatites and two fluorapatites, with widely different amounts of carbonate were analyzed by solid state (2)H NMR spectroscopy using the quadrupole echo pulse sequence, and each spectrum showed one single line as well as a low-intensity powder pattern. The relaxation time of 7.1 ms for 5.9 wt% carbonated hydroxylapatite indicates that the single line is likely due to rapid, high-symmetry jumps in translationally rigid D(2)O molecules, indicative of structural incorporation within the lattice. Discrimination between structurally incorporated and adsorbed water is enhanced by the rapid exchange of surface D(2)O with atmospheric H(2)O. Moreover, a (2)H resonance was observed for samples dried under a variety of conditions, including in vacuo heating to 150°C. In contrast, a sample heated to 500°C produced no deuterium resonance, indicating that structural water had been released by that temperature. We propose that water is located in the c-axis channels. Because structural water is observed even for apatites with very low carbonate content, some of the water molecules must lie between the monovalent ions.

  2. Analysis of mass-limited mixtures using supercritical-fluid chromatography and microcoil NMR.

    PubMed

    Tayler, Michael C D; van Meerten, S Bas G J; Kentgens, Arno P M; van Bentum, P Jan M

    2015-09-21

    A protocol is presented for offline microfluidic NMR analysis hyphenated with supercritical chromatographic separation. The method demonstrates quantitative detection with good sensitivity. Typical sample amounts of 10 nanomoles can be detected in a fast and cost-effective manner.

  3. NMR structure of hypothetical protein MG354 from Mycoplasmagenitalium

    SciTech Connect

    Pelton, Jeffrey G.; Shi, Jianxia; Yokotoa, Hisao; Kim, Rosalind; Wemmer, David E.

    2005-04-12

    Mycoplasma genitalium (Mg) and M. pneumoniae (Mp) are human pathogens with two of the smallest genomes sequenced to date ({approx} 480 and 680 genes, respectively). The Berkeley Structural Genomics Center is determining representative structures for gene products in these organisms, helping to understand the set of protein folds needed to sustain this minimal organism. The protein coded by gene MG354 (gi3844938) from M. genitalium has a relatively unique sequence, related only to MPN530 from M. pneumoniae (68% identity, coverage 99%) and MGA{_}0870 from the avian pathogen M. gallisepticum (23% identity, coverage 94%), has no homologue with a determined structure, and no functional annotations.

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

    PubMed Central

    Horst, Reto; Wüthrich, Kurt

    2016-01-01

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [2H, 15N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al., 2013). 2D [15N, 1H]-correlation maps are used as “fingerprints” to assess the foldedness of the IMP in solution. For promising samples, these “inexpensive” data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer. PMID:27077076

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

    PubMed

    Horst, Reto; Wüthrich, Kurt

    2015-07-20

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

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

    PubMed

    Rogawski, Rivkah; McDermott, Ann E

    2017-08-15

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

  7. NMR solution structure of Ole e 6, a major allergen from olive tree pollen.

    PubMed

    Treviño, Miguel Angel; García-Mayoral, María Flor; Barral, Patricia; Villalba, Mayte; Santoro, Jorge; Rico, Manuel; Rodríguez, Rosalía; Bruix, Marta

    2004-09-10

    Ole e 6 is a pollen protein from the olive tree (Olea europaea) that exhibits allergenic activity with a high prevalence among olive-allergic individuals. The three-dimensional structure of Ole e 6 has been determined in solution by NMR methods. This is the first experimentally determined structure of an olive tree pollen allergen. The structure of this 50-residue protein is based on 486 upper limit distance constraints derived from nuclear Overhauser effects and 24 torsion angle restraints. The global fold of Ole e 6 consists of two nearly antiparallel alpha-helices, spanning residues 3-19 and 23-33, that are connected by a short loop and followed by a long, unstructured C-terminal tail. Viewed edge-on, the structured N terminus has a dumbbell-like shape with the two helices on the outside and with the hydrophobic core, mainly composed of 3 aromatic and 6 cysteine residues, on the inside. All the aromatic rings lie on top of and pack against the three disulfide bonds. The lack of thermal unfolding, even at 85 degrees C, indicates a high conformational stability. Based on the analysis of the molecular surface, we propose five plausible epitopes for IgE recognition. The results presented here provide the structural foundation for future experiments to verify the antigenicity of the proposed epitopes, as well as to design novel hypoallergenic forms of the protein suitable for diagnosis and treatment of type-I allergies. In addition, three-dimensional structure features of Ole e 6 are discussed to provide a basis for future functional studies.

  8. Facile backbone structure determination of human membrane proteins by NMR spectroscopy

    PubMed Central

    Klammt, Christian; Maslennikov, Innokentiy; Bayrhuber, Monika; Eichmann, Cédric; Vajpai, Navratna; Chiu, Ellis Jeremy Chua; Blain, Katherine Y; Esquivies, Luis; Kwon, June Hyun Jung; Balana, Bartosz; Pieper, Ursula; Sali, Andrej; Slesinger, Paul A; Kwiatkowski, Witek; Riek, Roland; Choe, Senyon

    2013-01-01

    Although nearly half of today’s major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization. PMID:22609626

  9. Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra.

    PubMed

    Meiler, Jens; Will, Martin

    2002-03-06

    The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.

  10. Solid phase synthesis, NMR structure determination of α-KTx3.8, its in silico docking to Kv1.x potassium channels, and electrophysiological analysis provide insights into toxin-channel selectivity.

    PubMed

    Kohl, Bastian; Rothenberg, Ina; Ali, Syed Abid; Alam, Mehtab; Seebohm, Guiscard; Kalbacher, Hubert; Voelter, Wolfgang; Stoll, Raphael

    2015-07-01

    Animal venoms, such as those from scorpions, are a potent source for new pharmacological substances. In this study we have determined the structure of the α-KTx3.8 (named as Bs6) scorpion toxin by multidimensional (1)H homonuclear NMR spectroscopy and investigated its function by molecular dynamics (MD) simulations and electrophysiological measurements. Bs6 is a potent inhibitor of the Kv1.3 channel which plays an important role during the activation and proliferation of memory T-cells (TEM), which play an important role in autoimmune diseases. Therefore, it could be an interesting target for treatment of autoimmune diseases. In this study, Bs6 was synthesised by solid phase synthesis and its three-dimensional (3D) structure has been determined. To gain a deeper insight into the interaction of Bs6 with different potassium channels like hKv1.1 and hKv1.3, the protein-protein complex was modelled based on known toxin-channel structures and tested for stability in MD simulations using GROMACS. The toxin-channel interaction was further analysed by electrophysiological measurements of different potassium channels like hKv1.3 and hKv7.1. As potassium channel inhibitors could play an important role to overcome autoimmune diseases like multiple sclerosis and type-1 diabetes mellitus, our data contributes to the understanding of the molecular mechanism of action and will ultimately help to develop new potent inhibitors in future. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Vibrational analysis, NBO analysis, NMR, UV-VIS, hyperpolarizability analysis of Trimethadione by density functional theory

    NASA Astrophysics Data System (ADS)

    Vijayachamundeeswari, S. P.; Yagna Narayana, B.; Jone Pradeepa, S.; Sundaraganesan, N.

    2015-11-01

    Trimethadione (TMD) is an anticonvulsant drug widely used against absences seizures. We have characterised the TMD by various spectra including UV-VIS, IR, Raman, GC-MS and NMR. In this work, we made use of Density Functional Theory (DFT) B3LYP method with 6-31G (d, p) basis set, to calculate the molecular structure of TMD, and predicted its infrared, Raman and ultraviolet spectra for the first time. FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. The vibrational frequencies were calculated and scaled values were compared with the experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes. The optimized geometry parameters were calculated. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The predicted first hyperpolarizibility also shows that the molecule might have convincingly good nonlinear optical (NLO) activities. The calculated HOMO-LUMO energy gap discloses that charge transfer occurs within the molecule.

  12. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal

    SciTech Connect

    Netzel, D.A.

    1992-01-01

    The results of measuring the change in moisture content of the Eagle Butte and Usebelli coals as a function of time are shown in Figure 1. As expected, the measured moisture content increases with time and reaches a maximum after about 8 hours. Two different types of sorbed water are removed sequentially. Free or surface sorbed water is rapidly removed followed by the water in the micropores of the coal as the reagents migrate into the pore structure. There appears to be an induction period of about 4 hours for the Eagle Butte coal before the moisture content increases more rapidly with time due to the reactions of the more tightly bound or pore'' water with the reagents. The chemical drying experiment was repeated twice for the Usebelli coal. In the first experiment, aliquots of the reaction mixture were removed sequentially, and in the second experiment separate coal samples were prepared and allowed to stand until the appropriate time for the NMR spectrum to be acquired. Excellent reproducibility was obtained. Both cools were thermally dried by heating to 110[degrees]C for 1 hour. The moisture content was determined by weight loss. Using the thermal drying method, the Eagle Butte coal had a moisture content of 16.6 wt % and the Usebelli coal a moisture content of 14.1 wt %. These values are near the moisture content of coal as determined by chemical drying.

  13. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, June 1, 1992--August 31, 1992

    SciTech Connect

    Netzel, D.A.

    1992-12-01

    The results of measuring the change in moisture content of the Eagle Butte and Usebelli coals as a function of time are shown in Figure 1. As expected, the measured moisture content increases with time and reaches a maximum after about 8 hours. Two different types of sorbed water are removed sequentially. Free or surface sorbed water is rapidly removed followed by the water in the micropores of the coal as the reagents migrate into the pore structure. There appears to be an induction period of about 4 hours for the Eagle Butte coal before the moisture content increases more rapidly with time due to the reactions of the more ``tightly bound or ``pore`` water with the reagents. The chemical drying experiment was repeated twice for the Usebelli coal. In the first experiment, aliquots of the reaction mixture were removed sequentially, and in the second experiment separate coal samples were prepared and allowed to stand until the appropriate time for the NMR spectrum to be acquired. Excellent reproducibility was obtained. Both cools were thermally dried by heating to 110{degrees}C for 1 hour. The moisture content was determined by weight loss. Using the thermal drying method, the Eagle Butte coal had a moisture content of 16.6 wt % and the Usebelli coal a moisture content of 14.1 wt %. These values are near the moisture content of coal as determined by chemical drying.

  14. Intensity and mosaic spread analysis from PISEMA tensors in solid-state NMR

    NASA Astrophysics Data System (ADS)

    Quine, J. R.; Achuthan, S.; Asbury, T.; Bertram, R.; Chapman, M. S.; Hu, J.; Cross, T. A.

    2006-04-01

    The solid-state NMR experiment PISEMA, is a technique for determining structures of proteins, especially membrane proteins, from oriented samples. One method for determining the structure is to find orientations of local molecular frames (peptide planes) with respect to the unit magnetic field direction, B0. This is done using equations that compute the coordinates of this vector in the frames. This requires an analysis of the PISEMA function and its degeneracies. As a measure of the sensitivity of peptide plane orientations to the data, we use these equations to derive a formula for the intensity function in the powder pattern. With this function and other measures, we investigate the effect of small changes in peptide plane orientations depending on the location of the resonances in the powder pattern spectrum. This gives us an indication of the change in lineshape due to mosaic spread and a way to interpret these in terms of an orientational error bar.

  15. Intensity and mosaic spread analysis from PISEMA tensors in solid-state NMR.

    PubMed

    Quine, J R; Achuthan, S; Asbury, T; Bertram, R; Chapman, M S; Hu, J; Cross, T A

    2006-04-01

    The solid-state NMR experiment PISEMA, is a technique for determining structures of proteins, especially membrane proteins, from oriented samples. One method for determining the structure is to find orientations of local molecular frames (peptide planes) with respect to the unit magnetic field direction, B0. This is done using equations that compute the coordinates of this vector in the frames. This requires an analysis of the PISEMA function and its degeneracies. As a measure of the sensitivity of peptide plane orientations to the data, we use these equations to derive a formula for the intensity function in the powder pattern. With this function and other measures, we investigate the effect of small changes in peptide plane orientations depending on the location of the resonances in the powder pattern spectrum. This gives us an indication of the change in lineshape due to mosaic spread and a way to interpret these in terms of an orientational error bar.

  16. Synthesis, fine structure of 19F NMR and fluorescence of novel amorphous TPA derivatives having perfluorinated cyclopentenyl and benzo[b]thiophene unit

    NASA Astrophysics Data System (ADS)

    Wu, Bian-Peng; Pang, Mei-Li; Tan, Ting-Feng; Meng, Ji-ben

    2013-04-01

    Three novel triphenylamine (TPA) derivatives having perfluorinated cyclopentenyl and benzo[b]thiophene unit are obtained from 4-bromo-N,N-diphenyl-2-methylbenzo[b]thiophen-5-amine. The new compounds are expected to find their use in thin film devices as charge transport materials and host organic light-emitting materials. It is found that the new compounds show relatively strong fluorescence either in solution or in solid state, and are amorphous due to a special conformation which is elucidated by the fine structure of 19F NMR. Molecular structure and properties of these compounds is characterized by 1H NMR, 13C NMR (broadband decoupled), ESI-HRMS, elemental analysis and thermal analysis (DSC). Fluorescent quantum yield in solution is measured using 9,10-diphenylanthrancene (DPA) as standard fluorescent substance.

  17. Quality evaluation and prediction of Citrullus lanatus by 1H NMR-based metabolomics and multivariate analysis.

    PubMed

    Tarachiwin, Lucksanaporn; Masako, Osawa; Fukusaki, Eiichiro

    2008-07-23

    (1)H NMR spectrometry in combination with multivariate analysis was considered to provide greater information on quality assessment over an ordinary sensory testing method due to its high reliability and high accuracy. The sensory quality evaluation of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) was carried out by means of (1)H NMR-based metabolomics. Multivariate analyses by partial least-squares projections to latent structures-discrimination analysis (PLS-DA) and PLS-regression offered extensive information for quality differentiation and quality evaluation, respectively. The impact of watermelon and rootstock cultivars on the sensory qualities of watermelon was determined on the basis of (1)H NMR metabolic fingerprinting and profiling. The significant metabolites contributing to the discrimination were also identified. A multivariate calibration model was successfully constructed by PLS-regression with extremely high reliability and accuracy. Thus, (1)H NMR-based metabolomics with multivariate analysis was considered to be one of the most suitable complementary techniques that could be applied to assess and predict the sensory quality of watermelons and other horticultural plants.

  18. Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone-Pair and Bond Orbital Contributions.

    PubMed

    Sutter, Kiplangat; Aucar, Gustavo A; Autschbach, Jochen

    2015-12-07

    NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance-assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero-point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J-coupling is performed in terms of "chemist's orbitals", that is, localized molecular orbitals (LMOs) representing lone-pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de-shielding of the protons in resonance-assisted hydrogen bonds with delocalization involving the π-backbone. Resonance is also shown to be an important factor causing de-shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J-couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra- and intermolecular resonance. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

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

    2015-02-01

    We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Structural changes of lipoprotein lipids by 1H NMR

    NASA Astrophysics Data System (ADS)

    Ala-Korpela, M.; Oja, J.; Lounila, J.; Jokisaari, J.; Savolainen, M. J.; Kesäniemi, Y. A.

    1995-08-01

    A new procedure for detecting structural changes of lipoprotein lipids is introduced and applied to study native low (LDL) and high density lipoprotein (HDL) particles. The method involves lineshape fitting analyses of specific resonances in proton nuclear magnetic resonance spectra together with numerical derivation of the obtained intensity curves with respect to temperature. In addition to the well-known phase transition of the LDL core cholesterol esters, a novel structural change was revealed in the phospholipid monolayer of both native LDL and HDL particles. The attributes of this phenomenon are discussed.

  1. Structural dynamics of a single-stranded RNA–helix junction using NMR

    PubMed Central

    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. Quantitative 2D HSQC NMR determination of polymer structures by selecting suitable internal standard references.

    PubMed

    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.

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

    PubMed

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

    2015-11-11

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

  4. NMR structure of the integral membrane protein OmpX.

    PubMed

    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.

  5. NMR structural determination of unique invertebrate glycosaminoglycans endowed with medical properties.

    PubMed

    Pomin, Vitor H

    2015-09-02

    Glycosaminoglycans (GAGs) are sulfated polysaccharides of complex structure endowed with numerous biomedical functions. Although ubiquitously distributed in vertebrates, GAGs can also occur in certain terrestrial or marine invertebrates. Solution nuclear magnetic resonance (NMR) spectroscopy has been the analytical technique mostly employed in structural characterization of GAGs from any source. This review aims at illustrating the application of NMR in structural determination of few representative invertebrate GAG examples of unique structures and endowed with therapeutic actions. They are the holothurian fucosylated chondroitin sulfate, the acharan sulfate isolated from the snail Achatina fulica, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei. These invertebrate GAGs exhibit distinct structures when compared to those extracted from mammalian GAGs. The distinct structures of the invertebrate GAGs lead also to different mechanisms of actions as compared to the mammalian GAG standards. Invertebrate GAGs comprise promising therapeutic candidates in fights against diseases. Solution NMR has been playing a pivotal role in this carbohydrate-based drug research, discovery and development.

  6. Stereospecific assignment of 1H resonances through chemical shift calculation and their use in structure determination by NMR

    NASA Astrophysics Data System (ADS)

    Harvey, Timothy S.; van Gunsteren, Wilfred F.; Ikura, Mitsuhiko

    1995-04-01

    Understanding of the factors which influence proton chemical shifts in nuclear magnetic resonance (NMR) spectra of proteins has advanced steadily as the number of proteins, for which assignments in conjunction with high resolution structures have been obtained, has increased. Progress has been made in both the calculation of chemical shifts from given coordinates, both empirically for 1H (Williamson & Asakura J. Magn. Reson. (1991) 94, 557) and using ab initio approaches for calculation of 13C (De Dios et al. Science (1993) 260, 1491). Concomitantly Wishart et al. (J. Mol. Biol. (1992) 222, 311), using statistical methods have clarified the relationship between Hα chemical shift and regular secondary structure in proteins to a high degree of accuracy. We recently demonstrated the significant amount of structural information present in the Hα chemical shift through the use of chemical shift restrained molecular dynamics simulations (Harvey & van Gunsteren Techniques in Protein Chemistry IV (1993) 615, Academic Press). Here we apply a similar methodology to the stereospecific assignment of methylene and methyl proton resonances in proteins. Stereospecific assignment of such 1H resonances dramatically increases the degree of precision of ensembles of structures derived from NMR data. However, this is often a cumbersome process, requiring detailed analysis of large amounts of data. Furthermore, experimental considerations such as poor signal-to-noise ratios, spectral overlap and spin diffusion combine to make this process somewhat unreliable. We present calculations of the chemical shifts for the known structures of bovine pancreatic trypsin inhibitor (Mw 6.5 kDa) and the α-amylase inhibitor tendamistat (Mw 8 kDa), for which stereospecific assignments and high resolution structures from both NMR and crystallographic studies are available. The methods described are also applied to the ensemble of structures obtained for protein S (Mw 19 kDa) for both structure

  7. Recommendations of the wwPDB NMR Validation Task Force

    PubMed Central

    Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

    2013-01-01

    As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

  8. Synthesis and structural analysis using 2-D NMR of Sialyl Lewis X (SLe{sup x}) and Lewis X (Le{sup x}) oligosaccharides: Ligands related to E-selectin [ELAM-1] binding

    SciTech Connect

    Ball, G.E.; Nagy, J.O.; Brown, E.G.

    1992-06-17

    The sialyl Lewis X (SLe{sup x}) determinant (NeuAc-{alpha}-2,3-Gal-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), compound 1, is a ligand for E-selectin (endothelial leucocyte adhesion molecule 1, or ELAM-1), a member of the selectin family of cell adhesion molecules. Interactions between E-selectin and leucocyte-bound SLe{sup x} or closely related oligosaccharides are thought to be important early events in the inflammation process. Binding analysis has shown that the sialic acid (NeuAc) and the fucose (Fuc) moieties are essential for high affinity. The related desialylated trisaccharide Le{sup x} (Gas-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), for example, is not a high-affinity ligand for E-selectin. In this communication, the authors describe the syntheses of SLe{sup x} 1 and the {beta}-O-allyl glycoside of Le{sup x} 2 using a cloned fucosyltransferase and their complete NMR spectral assignments including ROESY and NOESY experiments in order to investigate the conformation of these compounds in solution. 25 refs., 2 figs.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2005-03-04

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

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

    USGS Publications Warehouse

    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.

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

    SciTech Connect

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

    1988-04-19

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

  14. NMR structure of human apolipoprotein C-II in the presence of sodium dodecyl sulfate.

    PubMed

    MacRaild, C A; Hatters, D M; Howlett, G J; Gooley, P R

    2001-05-08

    The structure and protein-detergent interactions of apolipoprotein C-II (apoC-II) in the presence of SDS micelles have been investigated using circular dichroism and heteronuclear NMR techniques applied to (15)N-labeled protein. Micellar SDS, a commonly used mimetic of the lipoprotein surface, inhibits the aggregation of apoC-II and induces a stable structure containing approximately 60% alpha-helix as determined by circular dichroism. NMR reveals the first 12 residues of apoC-II to be structurally heterogeneous and largely disordered, with the rest of the protein forming a predominantly helical structure. Three regions of helical conformation, residues 16-36, 50-56, and 63-77, are well-defined by NMR-derived constraints, with the intervening regions showing more loosely defined helical conformation. The structure of apoC-II is compared to that determined for other apolipoproteins in a similar environment. Our results shed light on the lipid interactions of apoC-II and its mechanism of lipoprotein lipase activation.

  15. Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters.

    PubMed

    Mali, Gregor

    2017-03-01

    Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS2, exhibiting a modified rocksalt structure, in which S(2-) anions were replaced by S2(2-) dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, (25)Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined (25)Mg NMR parameters of magnesium sulfide species.

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

    NASA Astrophysics Data System (ADS)

    He, Chao; Smith, Mark A.

    2014-11-01

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

  17. Determination of the Structural Basis of Antibody Diversity Using NMR

    DTIC Science & Technology

    1990-12-14

    22. Perkins, S.J. and Dwek, R.A. (1980). Comparison of Ring-Current Shifts Calculated from the Crystal Structure of Egg White Lysozyme 27 of Hen with...the first and second kind with modulus k = 2 J (4) + p) 2 + z 2 Values for the parameters a and i are giver, in Table I. The separation of the current...the sp 2 plane of the two doublely bonded nuclei. The current loops were separated from this plane by 0.638 A. Each ring was given one electron. The

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

    USDA-ARS?s Scientific Manuscript database

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

  19. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  20. The application of high resolution diffusion NMR to the analysis of manuka honey.

    PubMed

    Gresley, Adam Le; Kenny, Jackie; Cassar, Claire; Kelly, Alison; Sinclair, Alex; Fielder, Mark D

    2012-12-15

    The application of DOSY (Diffusion Ordered SpectroscopY) NMR as a technique for the virtual separation of key components of manuka honey and the implications for future discriminatory analysis of honey types is reported for the first time. The scope and the limitations of DOSY NMR are considered using the recently conceived DOSY Tool Box processing software and preliminary anti-bacterial data for the different honey types is reported.

  1. Baseline correction for NMR spectroscopic metabolomics data analysis.

    PubMed

    Xi, Yuanxin; Rocke, David M

    2008-07-29

    We propose a statistically principled baseline correction method, derived from a parametric smoothing model. It uses a score function to describe the key features of baseline distortion and constructs an optimal baseline curve to maximize it. The parameters are determined automatically by using LOWESS (locally weighted scatterplot smoothing) regression to estimate the noise variance. We tested this method on 1D NMR spectra with different forms of baseline distortions, and demonstrated that it is effective for both regular 1D NMR spectra and metabolomics spectra with over-crowded peaks. Compared with the automatic baseline correction function in XWINNMR 3.5, the penalized smoothing method provides more accurate baseline correction for high-signal density metabolomics spectra.

  2. Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis

    PubMed Central

    Xi, Yuanxin; Rocke, David M

    2008-01-01

    Background We propose a statistically principled baseline correction method, derived from a parametric smoothing model. It uses a score function to describe the key features of baseline distortion and constructs an optimal baseline curve to maximize it. The parameters are determined automatically by using LOWESS (locally weighted scatterplot smoothing) regression to estimate the noise variance. Results We tested this method on 1D NMR spectra with different forms of baseline distortions, and demonstrated that it is effective for both regular 1D NMR spectra and metabolomics spectra with over-crowded peaks. Conclusion Compared with the automatic baseline correction function in XWINNMR 3.5, the penalized smoothing method provides more accurate baseline correction for high-signal density metabolomics spectra. PMID:18664284

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

    PubMed Central

    Yang, Yunhuang; Ramelot, Theresa A.; Cort, John R.; Garcia, Maite; Yee, Adelinda; Arrowsmith, Cheryl H.; Kennedy, Michael A.

    2012-01-01

    CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum. PMID:22837698

  4. Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum.

    PubMed

    Yang, Yunhuang; Ramelot, Theresa A; Cort, John R; Garcia, Maite; Yee, Adelinda; Arrowsmith, Cheryl H; Kennedy, Michael A

    2012-01-01

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

  5. An investigation into the structure and reactivity of calcium-zinc-silicate ionomer glasses using MAS-NMR spectroscopy.

    PubMed

    Boyd, D; Towler, M R; Law, R V; Hill, R G

    2006-05-01

    The suitability of Glass Polyalkenoate Cements (GPCs) for orthopaedic applications is retarded by the presence in the glass phase of aluminium, a neurotoxin. Unfortunately, the aluminium ion plays an integral role in the setting process of GPCs and its absence is likely to hinder cement formation. However, the authors have previously shown that aluminium-free GPCs may be formulated based on calcium zinc silicate glasses and these novel materials exhibit significant potential as hard tissue biomaterials. However there is no data available on the structure of these glasses. (29)Si MAS-NMR, differential thermal analysis (DTA), X-ray diffraction (XRD), and network crosslink density (CLD) calculations were used to characterize the structure of five calcium zinc silicate glasses and relate glass structure to reactivity. The results indicate that glasses capable of forming Zn-GPCs are predominantly Q(2)/Q(3) in structure with corresponding network crosslink densities greater than 2. The correlation of CLD and MAS-NMR results indicate the primary role of zinc in these simple glass networks is as a network modifier and not an intermediate oxide; this fact will allow for more refined glass compositions, with less reactive structures, to be formulated in the future.

  6. NMR analysis, protonation equilibria and decomposition kinetics of tolperisone.

    PubMed

    Orgován, Gábor; Tihanyi, Károly; Noszál, Béla

    2009-12-05

    The rate constants of spontaneous and hydroxide-catalyzed decomposition and the tautomer-specific protonation constants of tolperisone, a classical muscle relaxant were determined. A solution NMR method without any separation techniques was elaborated to quantitate the progress of decomposition. All the rate and equilibrium constants were determined at four different temperatures and the activation parameters were calculated. The molecular mechanism of decomposition is proposed.

  7. 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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed Central

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

    2008-01-01

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

  9. Kinetic fragility and structure of lithium borophosphate glasses analysed by 1D/2D NMR.

    PubMed

    Muñoz-Senovilla, Laura; Tricot, Gregory; Muñoz, Francisco

    2017-08-30

    The macroscopic and high temperature properties of lithium borophosphate glasses were determined in this contribution. Our data, obtained on 50Li2O-xB2O3-(50-x)P2O5 glasses, confirm a continuous and linear increase of the glass transition temperature with the B/P substitution but show a two-domain evolution of the kinetic fragility with a steep decrease in the low B2O3 region (0 ≤ x ≤ 10) followed by a moderate increase for higher B2O3 contents. In order to understand this different behaviour, the glass structure was investigated in detail using 1D and 2D (11)B/(31)P correlation solid state nuclear magnetic resonance. The local and medium orders of borate units were determined by 1D MAS-NMR, 2D (11)B DQSQ- and (11)B((31)P) D-HMQC NMR experiments. The latter NMR technique was also used to deeply interpret the 1D (31)P MAS-NMR spectra. Altogether the data allow (i) highlighting of the presence of four borate and seven phosphate units, (ii) evaluation of the number of homopolar POP and mixed POB linkages, and (iii) contribute to a better understanding of the Tg and kinetic fragility evolution.

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

    SciTech Connect

    Mao, Degen.

    1991-01-01

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

  11. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    PubMed Central

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-01-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues. PMID:24284435

  12. Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

    PubMed

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

    2015-08-05

    The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained.

  13. Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R2 = 0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the 1H- and 13C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained.

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

    SciTech Connect

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

    1988-03-08

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

  15. A revisited structure for nitrosoprodenafil from NMR, mass spectrometry, X-ray and hydrolysis data.

    PubMed

    Martino, Robert; Menendez, Christophe; Balayssac, Stéphane; Martins-Froment, Nathalie; Lherbet, Christian; Couderc, François; Gilard, Véronique; Malet-Martino, Myriam

    2017-02-20

    The sildenafil analogue adulterant previously identified as a nitroso derivative (nitrosoprodenafil) in a dietary supplement (DS) marketed to increase sexual performance and sold in Europe in the early 2010s is the same as that found in the same type of DS available in Japan whose structure was established as a nitro derivative (mutaprodenafil or nitroprodenafil). Indeed, the compound isolated from the Man Power DS has identical UV, IR, NMR and MS spectroscopic characteristics and hydrolysis behavior than nitrosoprode-nafil. By revisiting its NMR assignments and MS and MS/MS data interpretation, it is demonstrated that the compound is actually a nitrothioimidazole-methisosildenafil hybrid, i.e. nitroprodenafil, whose structure is unequivocally confirmed by X-ray crystallography and synthesis experiments. Because the product is converted to methisosildenafil by hydrolysis, it is named nitropromethisosildenafil. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2006-05-17

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

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

    PubMed Central

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

    2008-01-01

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

  18. Structure of (KIAGKIA)3 aggregates in phospholipid bilayers by solid-state NMR.

    PubMed

    Toke, Orsolya; O'Connor, R D; Weldeghiorghis, Thomas K; Maloy, W Lee; Glaser, Ralf W; Ulrich, Anne S; Schaefer, Jacob

    2004-07-01

    The interchain (13)C-(19)F dipolar coupling measured in a rotational-echo double-resonance (REDOR) experiment performed on mixtures of differently labeled KIAGKIA-KIAGKIA-KIAGKIA (K3) peptides (one specifically (13)C labeled, and the other specifically (19)F labeled) in multilamellar vesicles of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol (1:1) shows that K3 forms close-packed clusters, primarily dimers, in bilayers at a lipid/peptide molar ratio (L/P) of 20. Dipolar coupling to additional peptides is weaker than that within the dimers, consistent with aggregates of monomers and dimers. Analysis of the sideband dephasing rates indicates a preferred orientation between the peptide chains of the dimers. The combination of the distance and orientation information from REDOR is consistent with a parallel (N-N) dimer structure in which two K3 helices intersect at a cross-angle of approximately 20 degrees. Static (19)F NMR experiments performed on K3 in oriented lipid bilayers show that between L/P = 200 and L/P = 20, K3 chains change their absolute orientation with respect to the membrane normal. This result suggests that the K3 dimers detected by REDOR at L/P = 20 are not on the surface of the bilayer but are in a membrane pore.

  19. Homodecoupled 1,1- and 1,n-ADEQUATE: Pivotal NMR Experiments for the Structure Revision of Cryptospirolepine.

    PubMed

    Saurí, Josep; Bermel, Wolfgang; Buevich, Alexei V; Sherer, Edward C; Joyce, Leo A; Sharaf, Maged H M; Schiff, Paul L; Parella, Teodor; Williamson, R Thomas; Martin, Gary E

    2015-08-24

    Cryptospirolepine is the most structurally complex alkaloid discovered and characterized thus far from any Cryptolepis specie. Characterization of several degradants of the original, sealed NMR sample a decade after the initial report called the validity of the originally proposed structure in question. We now report the development of improved, homodecoupled variants of the 1,1- and 1,n-ADEQUATE (HD-ADEQUATE) NMR experiments; utilization of these techniques was critical to successfully resolving long-standing structural questions associated with crytospirolepine.

  20. Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics

    SciTech Connect

    Spielmann, H.P.; Dwyer, T.J.; Hearst, J.E. |

    1995-10-10

    We have used two-dimensional {sup 1}H NMR spectroscopy to determine the solution structures of the 4,5{prime}, 8-trimethylpsoralen (HMT) furanside monoadducted (MAf) and the photoisomeric HMT interstrand cross-linked (XL) DNA oligonucleotide d(t{prime}-GCGTACGC-3{prime}){sub 2}. The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental {open_quotes}noise{close_quotes} in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for both the MAf and XL from both A-form and B-form dsDNA starting structures. 80 refs., 7 figs., 6 tabs.

  1. 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.

    PubMed

    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.

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

    SciTech Connect

    Popa, Karin; Raison, Philippe E.; Martel, Laura; Martin, Philippe M.; Solari, Pier L.; Bouëxière, Daniel; Konings, Rudy J.M.; Somers, Joseph

    2015-10-15

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

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

    SciTech Connect

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

    1995-12-31

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

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

    PubMed

    El Eter, Mohamad; Hamzaoui, Bilel; Abou-Hamad, Edy; Pelletier, Jérémie D A; Basset, Jean-Marie

    2013-05-21

    Grafting of Zr(NMe2)4 on mesoporous silica SBA-15 afforded selectively well-defined surface species [triple bond, length as m-dash]SiOZr(NMe2)(η2NMeCH2). 2D solid-state NMR ((1)H-(13)C HETCOR, Multiple Quantum) experiments have shown a unique structural rearrangement occurring on the immobilised zirconium bis methylamido ligand.

  5. Independent component analysis (ICA) algorithms for improved spectral deconvolution of overlapped signals in 1H NMR analysis: application to foods and related products.

    PubMed

    Monakhova, Yulia B; Tsikin, Alexey M; Kuballa, Thomas; Lachenmeier, Dirk W; Mushtakova, Svetlana P

    2014-05-01

    The major challenge facing NMR spectroscopic mixture analysis is the overlapping of signals and the arising impossibility to easily recover the structures for identification of the individual components and to integrate separated signals for quantification. In this paper, various independent component analysis (ICA) algorithms [mutual information least dependent component analysis (MILCA); stochastic non-negative ICA (SNICA); joint approximate diagonalization of eigenmatrices (JADE); and robust, accurate, direct ICA algorithm (RADICAL)] as well as deconvolution methods [simple-to-use-interactive self-modeling mixture analysis (SIMPLISMA) and multivariate curve resolution-alternating least squares (MCR-ALS)] are applied for simultaneous (1)H NMR spectroscopic determination of organic substances in complex mixtures. Among others, we studied constituents of the following matrices: honey, soft drinks, and liquids used in electronic cigarettes. Good quality spectral resolution of up to eight-component mixtures was achieved (correlation coefficients between resolved and experimental spectra were not less than 0.90). In general, the relative errors in the recovered concentrations were below 12%. SIMPLISMA and MILCA algorithms were found to be preferable for NMR spectra deconvolution and showed similar performance. The proposed method was used for analysis of authentic samples. The resolved ICA concentrations match well with the results of reference gas chromatography-mass spectrometry as well as the MCR-ALS algorithm used for comparison. ICA deconvolution considerably improves the application range of direct NMR spectroscopy for analysis of complex mixtures. Copyright © 2014 John Wiley & Sons, Ltd.

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

    PubMed

    Mareuil, Fabien; Malliavin, Thérèse E; Nilges, Michael; Bardiaux, Benjamin

    2015-08-01

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

  7. XPS and NMR analysis on 12CaO•7Al2O3

    NASA Astrophysics Data System (ADS)

    Pan, R. K.; Feng, S.; Tao, H. Z.

    2017-01-01

    12CaO·7Al2O3 (C12A7) glass was prepared by the melt quenching method. The glass transition temperature (T g) and the crystallization temperature (T c) of C12A7 glass are about 1050 K and 1194 K, respectively, measured by the differential scanning calorimetry (DSC). The structure of C12A7 glass was investigated by X-ray photoelectron spectroscopy (XPS) as well as magic angle spinning-nuclear magnetic resonance spectroscopy (MAS-NMR). Analysis shows that Al coordination number is about four in C12A7 glass, in which AlO4 tetrahedrons and bridging oxygens (BO) constitute the glass network. Ca2+ produces a few of non-bridging oxygens (NBO), which become neighbours of Al.

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

    DOE PAGES

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

    2016-04-26

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

  9. Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy.

    PubMed

    Ragavan, Mukundan; Iconaru, Luigi I; Park, Cheon-Gil; Kriwacki, Richard W; Hilty, Christian

    2017-06-12

    The kinase inhibitory domain of the cell cycle regulatory protein p27(Kip1) (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of (13) C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Micro-spectrometer for NMR: analysis of small quantities in vitro

    NASA Astrophysics Data System (ADS)

    Sorli, B.; Chateaux, J. F.; Pitaval, M.; Chahboune, H.; Favre, B.; Briguet, A.; Morin, P.

    2004-05-01

    This paper reports the design, fabrication and preliminary tests of planar microcoils associated with a micromachined channel in silicon. These microcoils are used as nuclear magnetic resonance (NMR) radio frequency detection coils. They allow in vitro NMR analysis of small quantities introduced into the microchannel. It is a real challenging task to develop microsystems for NMR spectrum extraction for smaller and smaller sample volumes. Moreover, it is advantageous that these microsystems could be integrated in a micro total analysing system (µ-TAS) as an analysing stage. In this paper the description, fabrication process and electrical characterization of planar microcoil receivers are described. Results obtained on NMR microspectroscopy experiments have been performed in water and ethanol, using a 500 µm × 500 µm planar microcoil tuned and matched at 85.13 MHz (proton frequency at 2 T).

  11. NMR Structure and Action on Nicotinic Acetylcholine Receptors of Water-soluble Domain of Human LYNX1*

    PubMed Central

    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

  12. NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1.

    PubMed

    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.

  13. NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein

    PubMed Central

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

    2013-01-01

    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 WIPC, 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 WIPC and the high occurrence (25%) of proline residues, we employed 5D-NMR13C-detected NMR experiments with nonuniform sampling to accomplish full resonance assignment. Secondary chemical-shift analysis, 15N 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 13C-detected approach allows chemical-shift assignment in the WIPC 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 WIPC. Thus, we conclude that the disordered WIPC fragment is comprised of regions with latent structure connected by flexible loops, an architecture with implications for binding affinity and function. PMID:23870269

  14. Structural characterization of lignins isolated from Caragana sinica using FT-IR and NMR spectroscopy.

    PubMed

    Xiao, Ling-Ping; Shi, Zheng-Jun; Xu, Feng; Sun, Run-Cang; Mohanty, Amar K

    2011-09-01

    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 1H and 13C NMR demonstrated that the lignin fraction L2, isolated with 70% ethanol containing 1% NaOH, was mainly composed of beta-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 beta-O-4' aryl ether linkages (61% of total side chains), and a low abundance of condensed carbon-carbon linked structures (such as beta-beta', beta-1', and beta-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 gamma-carbon.

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

    PubMed

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

    2015-12-01

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

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

    PubMed

    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.

  17. Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

    PubMed Central

    Helmus, Jonathan J.; Jaroniec, Christopher P.

    2013-01-01

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file for