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Overhauser Effect Spectroscopy (overhauser + effect_spectroscopy)
Kinds of Overhauser Effect Spectroscopy Selected AbstractsSemiautomatic sequence-specific assignment of proteins based on the tertiary structure,The program st2nmrJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2002Primo, Pristov Abstract The sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution NMR studies of proteins. In many cases a reliable three-dimensional (3D) structure of the protein is available, for example, from X-ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence-specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance-dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an ,-helical (cytochrome c) and ,-sheet (lipocalin) protein using homology models and/or X-ray structures; it succeeded in completely reproducing the correct sequence-specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 335,340, 2002 [source] 2,3-,-Epoxyjaeschkeanadiol 5-benzoate from Ferula hermonis BoissFLAVOUR AND FRAGRANCE JOURNAL, Issue 6 2001Youssef Diab Abstract The new 2,3-,-epoxyjaeschkeanadiol 5-benzoate has been isolated and its 1H- and 13C-NMR signals were completely assigned by the application of the modern NMR techniques. Its conformations are discussed on the basis of molecular modelling calculations and nuclear Overhauser effect spectroscopy (NOESY) spectra. Copyright © 2001 John Wiley & Sons, Ltd. [source] Synthesis of rhodium(III) complexes with tris/tetrakis-benzimidazoles and benzothiazoles,quick identification of cyclometallation by nuclear magnetic resonance spectroscopyMAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2009N. Chandrashekhar Abstract Reactions of rhodium(III) halides with multidentate N,S -heterocycles, (LH3) 1,3,5-tris(benzimidazolyl)benzene (L1H3; 1), 1,3,5-tris(N -methylbenzimidazolyl) benzene (L2H3; 2) and 1,3,5-tris(benzothiazolyl)benzene (L3H3; 3), in the molar ratio 1:1 in methanol,chloroform produced mononuclear cyclometallated products of the composition [RhX2(LH2)(H2O)] (X = Cl, Br, I; LH2 = L1H2, L2H2, L3H2). When the metal to ligand (1,3 or 1,2,4,5-tetrakis(benzothiazolyl)benzene [L4H2; 4]) molar ratio was 2:1, the reactions yielded binuclear complexes of the compositions [Rh2Cl5(LH2)(H2O)3] (LH2 = L1H2, L2H2, L3H2) and [Rh2X4(L4)(H2O)2] (X = Cl, Br, I). Elemental analysis, IR and 1H nuclear magnetic resonance (NMR) chemical shifts supported the binuclear nature of the complexes. Cyclometallation was detected by conventional 13C NMR spectra that showed a doublet around ,190 ppm. Cyclometallation was also detected by gradient-enhanced heteronuclear multiple bond correlation (g-HMBC) experiment that showed cross-peaks between the cyclometallated carbon and the central benzene ring protons of 1,3. Cyclometallation was substantiated by two-dimensional 1H1H correlated experiments (gradiant-correlation spectroscopy and rotating frame Overhauser effect spectroscopy) and 1H13C single bond correlated two-dimensional NMR experiments (gradient-enhanced heteronuclear single quantum coherence). The 1H15N g-HMBC experiment suggested the coordination of the heterocycles to the metal ion via tertiary nitrogen. Copyright © 2009 John Wiley & Sons, Ltd. [source] Complete assignments of 1H and 13C NMR spectral data for three new triterpenoid saponins from Ilex hainanensis Merr.MAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2009Xiao-Qing Chen Abstract Three new oleanane-type triterpenoid saponins, ilexhainanoside C, D and E, all with 24, 28-dioic acid groups, were isolated from the leaves of Ilex hainanensis. They were 3,-hydroxyolean-12-ene-24, 28-dioic acid-28- O -,- D -glucopyranoside(1), 3,, 19,-dihydroxyolean-12-ene-24, 28-dioic acid-28- O -,- D -glucopyranoside(2) and 3,, 29-dihydroxyolean-12-ene-24, 28-dioic acid-28- O -,- D -glucopyranoside(3). The structures of these three new compounds were elucidated and complete assignments of the 1H and 13C NMR spectroscopic data were achieved by 1D and 2D NMR experiments [heteronuclear single quantum coherence (HSQC), HMBC and rotational nuclear Overhauser effect spectroscopy (ROESY)]. Copyright © 2008 John Wiley & Sons, Ltd. [source] Assignments of 1H and 13C NMR spectral data for ondansetron and its two novel metabolites, 1-hydroxy-ondansetron diastereoisomersMAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2006Mingyu Duan Abstract Assignments of 1H and 13C NMR chemical shifts were made by means of heteronuclear single quantum coherence (HSQC) and heteronuclear multiple bond correlation (HMBC) experiments for ondansetron, and by means of 1H- 1H correlation spectroscopy (1H- 1H COSY) and two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments for two novel metabolites (M1 and M2) of ondansetron. These two metabolites were isolated for the first time from Mucor circinelloides. Copyright © 2006 John Wiley & Sons, Ltd. [source] The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze proteinPROTEIN SCIENCE, Issue 7 2003Margaret E. Daley AFP, antifreeze protein; DQF-COSY, double quantum filtered correlated spectroscopy; NMR, nuclear magnetic resonance; NOE, nuclear Overhauser enhancement; NOESY, nuclear Overhauser effect spectroscopy; 3J,,, 3-bond scalar coupling constant between spins H, and H, Abstract Two-dimensional nuclear magnetic resonance spectroscopy was used to investigate the flexibility of the threonine side chains in the ,-helical Tenebrio molitor antifreeze protein (TmAFP) at low temperatures. From measurement of the 3J,,1H- 1H scalar coupling constants, the ,1 angles and preferred rotamer populations can be calculated. It was determined that the threonines on the ice-binding face of the protein adopt a preferred rotameric conformation at near freezing temperatures, whereas the threonines not on the ice-binding face sample many rotameric states. This suggests that TmAFP maintains a preformed ice-binding conformation in solution, wherein the rigid array of threonines that form the AFP-ice interface matches the ice crystal lattice. A key factor in binding to the ice surface and inhibition of ice crystal growth appears to be the close surface-to-surface complementarity between the AFP and crystalline ice, and the lack of an entropic penalty associated with freezing out motions in a flexible ligand. [source] The role of ,-, 310 -, and ,-helix in helix,coil transitionsPROTEIN SCIENCE, Issue 6 2003Roger Armen Abstract The conformational equilibrium between 310 - and ,-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 310 -helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous ,N(i,i + 2) and ,N(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 310 - and ,-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 Å and a 10 Å force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the 3JHN, coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i , i + 3 hydrogen bonds (310 -helix); however, there was a large population of bifurcated i , i + 3 and i , i + 4 ,-helical hydrogen bonds. In addition, both simulations contained considerable populations of ,-helix (i , i + 5 hydrogen bonds). Individual turns formed over residues 1,9, which we predict contribute to the intensities of the experimentally observed ,N(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages. [source] NMR-derived model of interconverting conformations of an ICAM-1 inhibitory cyclic nonapeptideCHEMICAL BIOLOGY & DRUG DESIGN, Issue 3 2003L.O. Sillerud Abstract:, We have produced by phage-display a disulfide-linked cyclic nonapeptide (inhibitory peptide-01, IP01), CLLRMRSIC, that binds to intracellular adhesion molecule-1 (ICAM-1) and blocks binding to its counter-structure, leukocyte functional antigen-1 (LFA-1). As a first step towards improving its pharmacologic properties, we have performed a structural and functional analysis of this peptide inhibitor to determine the features relevant to ICAM-1 binding. We report here the solution model of our initial product, IP01, as derived from two-dimensional nuclear magnetic resonance (NMR) restraints and molecular modeling. Distance and dihedral angle restraints, generated from nuclear Overhauser effect spectroscopy (NOESY) and one-dimensional-NMR experiments respectively, were used to generate an ensemble of structures using distance geometry and simulated annealing. Molecular dynamic simulations produced three interconverting conformational families consistent with the NMR-derived constraints. We describe these conformations and their mechanism of interconversion. Furthermore, we have measured the IC50 s of a series of inhibitors generated from IP01 through alanine substitution of each residue. These results show that the L2-L3-R4-M5-R6 segment is functionally active, conformationally flexible, and contains a ,-turn involving residues R4-S7, while the C1-C9-I8-S7 segment is less functionally-active but adopts a more defined solution conformation, consistent with a scaffolding function. This model will be useful for designing nonpeptide-based organic inhibitors with improved pharmacologic properties. [source] Diffusion and NOE NMR Studies on Multicationic DAB-Organoruthenium Dendrimers: Size-Dependent Noncovalent Self-Assembly to Megamers and Ion Pairing,CHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2009Stefania Pettirossi Dr. Abstract Supra-mega ion pairing: Multicationic organoruthenium dendrimers show a notable tendency to self-aggregate when the concentration is increased, leading to megamers. This tendency increases with the generation. The self-aggregation of dendrimers to megamers is coupled with a decrease in the extent of ion pairing, as illustrated. New multicationic organoruthenium dendrimers (RuPF6 -Dabn, n=2, 4, 8, 16) have been synthesized by coupling of [Ru(,6 - p -cymene)(,3 -dpk-OCH2CH2OH)]X (1PF6, dpk=2,2,-dipyridyl ketone, X=PF6) with 1,4-diaminobutane (DAB) and polypropylenimine dendrimer DAB- dendr -(NH2)n {n=4, 8, 16} mediated by 1,1,-carbonyldiimidazole (CDI). The intermediate in the synthesis, [Ru(,6 - p -cymene)(,3 -dpk-OCH2CH2OC(O)Im]X (2PF6, Im=imidazole, X=PF6) has been isolated and characterized by single-crystal XRD. The intra- and supramolecular structures in a solution of RuPF6 -Dabn dendrimer have been investigated by multidimensional and multinuclear NMR techniques. Diffusion NMR experiments on dilute solutions indicated that the linear distance between two metal centers (14.9,22.1,Å depending on the dendrimer generation) is much greater than the diameter of 1PF6 (9.9,Å). 19F,1H-HOESY NMR experiments (HOESY= heteronuclear Overhauser effect spectroscopy) showed that the counterion is positioned on the surface of the dendrimers and assumes the same relative anion,cation orientation as in 2PF6. Diffusion NMR experiments on RuPF6 -Dabn dendrimers in CD2Cl2 at different concentrations revealed a process of supramolecular assembly of dendrimers to megamers that is strongly favored for the highest generations. Megamer formation is coupled with an increased fraction of free ions (,) and a consequent reduction in ion-paired ruthenium centers. Graphs of , versus CRu (the concentration of ruthenium centers) showed a minimum for RuPF6 -Dab4, RuPF6 -Dab8, and RuPF6 -Dab16 at a position coinciding with the significant presence of supramolecular dendritic dimers. The tendency to ion pairing decreases as the dendrimer generation increases. [source] Separation of propranolol enantiomers by CE using sulfated ,-CD derivatives in aqueous and non-aqueous electrolytes: Comparative CE and NMR study,ELECTROPHORESIS, Issue 9 2010Anne-Catherine Servais Abstract Separations using CE employing non-aqueous BGE are already as well established as separations in aqueous buffers. The separation mechanisms in achiral CE with non-aqueous BGEs are most likely similar to those in aqueous buffers. However, for the separation of enantiomers involving their interaction with chiral buffer additives, the interaction mechanisms might be very different in aqueous and non-aqueous BGEs. While the hypothesis regarding distinct mechanisms of enantiomer separations in aqueous and non-aqueous BGEs has been mentioned in several papers, no direct proof of this hypothesis has been reported to date. In the present study, the enantiomers of propranolol were resolved using CE in aqueous and non-aqueous methanolic BGEs with two single isomer sulfated derivatives of ,-CD, namely heptakis (2,3-diacetyl-6-sulfo)-,-CD and heptakis (2,3-dimethyl-6-sulfo)-,-CD. The enantiomer migration order of propranolol was inverted when an aqueous BGE was replaced with non-aqueous BGE in the case of heptakis (2,3-dimethyl-6-sulfo)-,-CD but remained the same in the case of heptakis (2,3-diacetyl-6-sulfo)-,-CD. The possible molecular mechanisms leading to this reversal of enantiomer migration order were studied by using nuclear overhauser effect spectroscopy in both aqueous and non-aqueous BGEs. [source] Structure of an Extracellular Polysaccharide from a Strain of Lactic Acid BacteriaCHINESE JOURNAL OF CHEMISTRY, Issue 12 2003Xiao-Mei Gu Abstract A new extracellular polysaccharide (EPS-I) isolated and purified from Z222, a strain of Lactic acid bacteria has been investigated. Sugar composition analysis, methylation analysis and 1H NMR and 13C NMR spectroscopy reveal that the EPS-I is composed of a pentasaccharide repeating unit. The sequence of sugar residue was determined by using two-dimensional NMR spectroscopy, including heteronuclear multiple-bond correlation (HMBC) and nuclear overhauser effect spectroscopy (NOESY). [source] | |||||||||||||||||||||||||