Use Of NMR Data Research Articles

Treasures from the Deep: Characellides as Anti-Inflammatory Lipoglycotripeptides from the Sponge Characella pachastrelloides.

The chemical investigation of marine invertebrates from the deep Northeastern Atlantic revealed new lipoglycotripeptides named characellides isolated from the tetractinellid sponge Characella pachastrelloides. This new family of natural products features a central tripeptide linked to a rare sugar unit and a long alkyl chain ending with a 2,3-dimethyltetrahydropyran. The configurations of all 13 chiral centers were determined by extensive use of NMR data and circular dichroism spectra combined with calculations.

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

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 experience, and work in groups to assign names and structures to unknown compounds. This laboratory can be successfully run at a number of experimental levels, from students preparing their own NMR samples for analysis to running this as a dry laboratory with spectra provided by the instructor.

NMR crystallography driven structure determination: nanoporous materials

A summary of the recent results obtained in the field of NMR crystallography of nanoporous materials is proposed, and new original methods and strategies to perform NMR crystallography driven structure determination are presented. Although the work to reach structure resolution of a powder is much more difficult than for a single crystal, the use of NMR data associated with diffraction methods and modelling has provided significant successes in this domain. However, a general method to combine the different measurements, and overcome their respective limitations, has been only recently proposed. The structure search can therefore be organized to converge to possible structure models. This is of utmost importance for the structure determination of complex nanoporous crystals.

NMR relaxation data for quality characterization of Balsamic vinegar of Modena

In this paper, 22 samples consisting of Balsamic vinegar of Modena and two Traditional Balsamic vinegar of Modena samples have been analyzed by means of 1H NMR spectroscopy. Some selected resonances have been used for quantification and for T1 (spin–lattice relaxation time) measurements. Statistical protocols applied to NMR data for quantification of selected resonances revealed the possibility to differentiate the samples according to their ageing process. Additionally, T1 measurements revealed a strong correlation with the ageing process and these new data were added for improving the statistical model, which was used to predict T1 relaxation time of selected compounds for Balsamic vinegar samples. Our results indicate that the use of NMR data and statistical methods is a valid approach that can be successfully used for ageing characterization of Balsamic vinegar of Modena samples.

Conformational study of the complementary peptide to a B-cell epitope of the La/SSB autoantigen

Starting from the 20-mer peptide 289–308, one of the experimentally characterized B-cell epitopes of the La/SSB autoantigen, the complementary peptide cpl(289–308), encoded by the complementary RNA was designed. The conformational properties of the cpl(289–308) were investigated in DMSO solution with the combined use of NMR data (vicinal coupling constants, NOE effects and temperature coefficient values), molecular modelling calculations of energy minimization and molecular dynamics. MD calculations led to a folded structure in which a βI-turn, stabilized by the H8 amide proton to the F5 carbonyl hydrogen bond, was found for the F5P6S7H8 sequence, whereas two γ-turns, centred around the E15 and I18 residues respectively, were found in the C-terminal part of the peptide. In the whole crown folded structure of the peptide, the Y4, F5, H8, F9 and F10 aromatic side chains are situated on one side with the E13, E15, T17 and C20 side chains on the other. This 3D structure resembles and could mimic the binding site of an antibody. Nous avons synthétisé le peptide cpl(289-308), qui est un fragment peptidique de 20 résidus codé par la séquence ARN complémentaire de celle codant lˈépitope (289-308), lui-même autoantigène des lymphocytes B. Lˈétude conformationnelle du peptide cpl(289-308), en solution dans le DMSO, a été réalisée à partir de données RMN (constantes de couplage vicinal, effets NOE et coefficients de gradient de température des protons NH) couplées à des calculs de modélisation moléculaire par minimisation énergétique et par simulation des dynamiques moléculaires (MD). Les calculs MD conduisent à une structure globalement repliée en forme de couronne, incluant, dˈune part, un coude βI au niveau de la séquence F5P6S7H8, stabilisé par une liaison hydrogène entre le NH du résidu H8 et le CO du résidu F5 et, dˈautre part, deux repliements γ, centrés autour des résidus E15 et I18, dans la partie C-terminale du peptide. Les chaînes latérales aromatiques Y4, F5, H8, F9 et F10 se situent sur le même côté de cette structure repliée en forme de couronne, alors que les chaînes latérales E13, E15, T17 et C20 se trouvent de lˈautre côté. Cette structure 3D ressemble au site de liaison dˈun anticorps et pourrait ainsi le mimer.

Structural analysis of peptide substrates for mucin-type O-glycosylation.

The structures of three nine-residue peptide substrates that show differential kinetics of O-linked glycosylation catalyzed by distinct recombinant uridine diphosphate-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases (GalNAc transferases) were investigated by NMR spectroscopy. A combined use of NMR data, molecular modeling techniques, and kinetic data may explain some structural features required for O-glycosylation of these substrates by two GalNAc transferases, GalNAc-T1 and GalNAc-T3. In the proposed model, the formation of an extended backbone structure at the threonine residue to be glycosylated is likely to enhance the O-glycosylation process. The segment of extended structure includes the reactive residue in a beta-like or an inverse gamma-turn conformation and flanking residues in a beta-strand conformation. The hydroxyl group of the threonine to be glycosylated is exposed to solvent, and both the amide proton and carbonyl oxygen of the peptide backbone are exposed to solvent. The exchange rate of the amide proton for the reactive threonine correlated well with substrate efficiency, leading us to hypothesize that this proton may serve as a donor for hydrogen bonding with the active site of the enzyme. The oxygens of the residue to be glycosylated and several flanking residues may also be involved in a set of hydrogen bonds with the GalNAc-T1 and -T3 transferases.

Proton Nuclear Magnetic Resonance Studies of the Structure of Neuropeptide V and its Analogs

NPY is regarded as the most common peptide in the central and peripheral nervous systems and heart of many mammalian species including man. It has been found to perform critical regulatory functions in behavior, control of the cardiovascular system, memory processing etc. Development of highly selective and potent antagonists will allow better understanding of the pathological and physiological roles of NPY. In the process of designing potent receptor antagonists, which are essential in detailed studies of structure function relationships, NMR has played a major role in determining the solution structure of NPY and its analogs. Sequential proton NMR assignments have been made using several two dimensional techniques, COSY, DQFCOSY, HOHAHA, NOESY and ROESY. NMR has served as a complementary technique to X-ray since solid state studies do not necessarily always provide the correct picture of molecular conformation in solution, particularly for small flexible peptides. NPY consists of an a-helix domain (residues 15-35) with a hinge at position 27 and a polyproline stretch (residues 1--10) connected by a tight hairpin (residues 11-14). NMR has provided critical information in demonstrating formation of NPY dimers in aqueous media. Based on these results, recent designs have shown that high affinity analogs can be developed through C-terminal analogs dimerized with disulfide or lactam bridges. This review surveys NMR studies of NPY and its analogs with particular reference to the use of NMR data in molecular modeling of the solution structure.

Solution structure of an SRYD-containing sequence (250?257) of the fibronectin-like Leishmania gp63 protein by restrained molecular dynamics

The IASRYDQL synthetic octapeptide (250–257) of the Leishmania major surface glycoprotein gp63 efficiently inhibits parasite attachment to the macrophage receptors in in vitro experiments, and the SRYD-containing tetrapeptide mimics antigenically and functionally the RGDS sequence of fibronectin. The conformational properties of the octapeptide were investigated in dimethylsulfoxide (DMSO) with the combined use of NMR data (vicinal coupling constants, nuclear Overhauser effects (NOEs) and temperature coefficient values), molecular modeling by energy minimization and molecular dynamics. The structure is characterized by the high occurrence, exceeding 95%, of the Arg-Asp side-chain-side-chain ionic interaction, which plays a key role in the backbone folding through a distorted type-I β-turn involving the Gln256-NH to Arg253-CO hydrogen bond.

Structure and Mobility Pattern of Proton-Containing Groups in Hydrates of Titanium, Zirconium and Tin Acid Phosphates; Their Conducting and Ion Exchanging Properties

Abstract Phosphates of tetravalent elements are practically important for ion exchange, catalysis and conductivity. This study deals with a number of hydrates of titanium, tin and zirconium phosphates. PMR data show that the structure of water molecules in hydrates is slightly distorted, and at temperatures higher than 160 K water has high translation mobility. NMR 31P proves HPO2 4 dissociation to be growing with increase of temperature. Energetic parameters of this process are determined. Close values of anion dissociation enthalpy (0, 16/2/Ev) and obtained activation energy of conductivity for di- and monohydrates (0,17/2/Ev) show tunnel pattern of proton transfer along H-bond direction, This type of correlation was not observed in anhydrous compounds. That can be explained by impossibility of anion proton tunneling because of H-bond weakening. Proton conductivity of acid phosphates was studied. Ten-fold decrease of conductivity at room temperature with the loss of each water molecule proves H2O participation in proton transport. Mechanism of this process is discussed with the use of NMR data. Dependence of water mobility and conductivity level on the degree of crystallinity is also discussed. With the help of NMR-data processes of ion exchange in tin and zirconium acid phosphates, as well as the state of developed salt forms were studied. Presence of lithium with high mobility in Li2Sn(PO4)2 ·nF2O was established.

Ultrasonic absorption evidence for enhanced volume fluctuations in the tobacco mosaic virus protein helical aggregate

The increased ultrasonic absorption brought about by self-assembly of biomolecules is analyzed for the assembly process from the 20S aggregate to the helical rod of tobacco mosaic virus protein in solution, designated here as the 20S --> P-helix transition. The analysis is based on theoretical developments in ultrasonic relaxation spectrometry presented previously and illustrates the possibility that this technique can be used for characterizing fluctuations. The analysis makes use of NMR data for the system in solution and of x-ray diffraction data for the closely related transition from the two-ring disk to the virion. These x-ray data comprise the high-resolution structures and the Debye-Waller temperature factors of the main chain atoms of both the two-ring disk in crystals and the virion in oriented gel form. First, reduced ultrasonic spectra are obtained for the 4S, 20S, and helical rod aggregates. The fluctuation-enhancement factor for the helical rod is determined independently of any deconvolution into normal modes of relaxation and is shown not to depend on the particular procedure of reduction employed. The increase of ultrasonic absorption in the 20S --> P-helix transition primarily reveals enhancement of the relaxing system's normal-mode volume fluctuations. The observed relaxations probably involve one conformational process per subunit. The normal-mode volume fluctuations are then estimated from a bimodal least-squares best fit to the data, and a lower bound for the reaction volume associated with the fast steps is obtained. Two mechanisms are considered as follows: (i) a destabilization process in which the free-energy difference between two states is reduced and (ii) an increase in reaction volumes of local conformation changes in the helical aggregate, resulting from the formation of a "carboxyl cage-like" structure and from the change in environment produced inside the cage. Increased reaction volumes would not be detected with x-ray diffraction. The possible occurrence of fluctuations at the RNA binding site raises the question of whether a quaternary structure that exhibits significant conformational fluctuations must be present for the binding of the nucleic acid.

Estimates of the Stoner enhancement factor from NMR-data for noble metals

The magnitudes of electron interactions in noble and alkali metals are estimated by the use of NMR-data and compared with existing values. The values in noble metals are in contrast to the results from the band calculation by Janak.

A Refinement of the Hg2F2Structure by the Use of NMR Data

Abstract The crystal structure of Hg2F2 was studied in works.1,2 The Hg2F2elementary cell of the tetragonal syngony with a=3.66 A and c=10.89 A contains two formula units, the space-group being 14/mmm. Hg2F2 belongs to those types of structures which possess one non-fixed coordinate (zF and zHg); hence, the position of the fluorine nuclei may be determined from the value of the second moment of the NMR spectrum of 19F for powder sample.3 In this case it is ostensibly important, inasmuch as determining the positions of fluorine nuclei near the heavy mercury atoms presents a difficulty for X-ray analysis.

A Refinement of the InF3.3H2O Structure by the Use of NMR Data

Abstract Bokij and Khodashova' derived from X-ray diffraction study and coordination considerations that InF.3H2O is pseudotetragonal with a=7.90, c=4.14 8, 2=2, space group PII2/n. each indium atom is surrounded by six ligands (F and H2O) to form nearly are gular octahedron. The adjacent octahedra have common a pices forming in finitechains along the c-axis. Since the F and O scattering factors are much the same, the identification of F atoms and H2O molecules was performed on the basis of coordination considerations. The bridges between In atoms were unambiguously identif iedas fluorine atoms (F). The fouro the rligands of each octahedron are two fluorine atoms (F) and two water molecules (H2O equatorial plane of the octahedra (fluorines under fluorines in order to retain 2=2). estimated as oxygens of H2OI molecules due to the irspecifictetrahedral surrounding by FII and H2OI In such a lamellar structure, the layers of H2OI and H2OII molecules interchange with the layers of F atoms. The existence of H2O layersin the InF3.3H2structure, claimed by B. and K., is notin agreement with the factth that the crystals of this fluoride have needle-like habitus and do not exhibit excellent cleavage in the plane (110). In order toresolve this contradiction and find out the proton position sin the InF.3H 2o structure, we have applied the NMR method