The Experts below are selected from a list of 261 Experts worldwide ranked by ideXlab platform
Angela M. Gronenborn - One of the best experts on this subject based on the ideXlab platform.
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Stereospecific assignment of β-methylene protons in larger proteins using 3D^15N-separated Hartmann-Hahn and^13C-separated rotating frame Overhauser Spectroscopy
Journal of Biomolecular NMR, 1991Co-Authors: G. Marius Clore, Angela M. GronenbornAbstract:^3J_ x β coupling constants and complementary nuclear Overhauser data on the intraresidue C^ x H−C^βH distances form an essential part of the data needed to obtain stereospecific assignments of β-methylene protons in proteins. In this paper we show that information regarding the magnitude of the^3J_ x β coupling constants can be extracted from a semi-quantitative interpretation of relative peak intensities in a 3D^15N-separated^1H−^1H Hartmann-Hahn^1H−^15N multiple quantum coherence (HOHAHA-HMQC) spectrum. In addition, we demonstrate that reliable information on the intraresidue C^ x H−C^βH distances, free of systematic errors arising from spin diffusion, can be obtained from a 3D^13C-separated^1H−^1H rotating frame Overhauser effect^1H−^13C multiple quantum coherence (ROESY-HMQC) spectrum. The applicability of these experiments to larger proteins is illustrated with respect to interleukin-1β, a protein of 153 residues and 17.4 kDa molecular weight.
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Stereospecific assignment of β-methylene protons in larger proteins using 3D15N-separated Hartmann-Hahn and13C-separated rotating frame Overhauser Spectroscopy
Journal of Biomolecular NMR, 1991Co-Authors: G. Marius Clore, Ad Bax, Angela M. GronenbornAbstract:3Jxβ coupling constants and complementary nuclear Overhauser data on the intraresidue C x H−CβH distances form an essential part of the data needed to obtain stereospecific assignments of β-methylene protons in proteins. In this paper we show that information regarding the magnitude of the3Jxβ coupling constants can be extracted from a semi-quantitative interpretation of relative peak intensities in a 3D15N-separated1H−1H Hartmann-Hahn1H−15N multiple quantum coherence (HOHAHA-HMQC) spectrum. In addition, we demonstrate that reliable information on the intraresidue C x H−CβH distances, free of systematic errors arising from spin diffusion, can be obtained from a 3D13C-separated1H−1H rotating frame Overhauser effect1H−13C multiple quantum coherence (ROESY-HMQC) spectrum. The applicability of these experiments to larger proteins is illustrated with respect to interleukin-1β, a protein of 153 residues and 17.4 kDa molecular weight.
G. Marius Clore - One of the best experts on this subject based on the ideXlab platform.
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Stereospecific assignment of β-methylene protons in larger proteins using 3D^15N-separated Hartmann-Hahn and^13C-separated rotating frame Overhauser Spectroscopy
Journal of Biomolecular NMR, 1991Co-Authors: G. Marius Clore, Angela M. GronenbornAbstract:^3J_ x β coupling constants and complementary nuclear Overhauser data on the intraresidue C^ x H−C^βH distances form an essential part of the data needed to obtain stereospecific assignments of β-methylene protons in proteins. In this paper we show that information regarding the magnitude of the^3J_ x β coupling constants can be extracted from a semi-quantitative interpretation of relative peak intensities in a 3D^15N-separated^1H−^1H Hartmann-Hahn^1H−^15N multiple quantum coherence (HOHAHA-HMQC) spectrum. In addition, we demonstrate that reliable information on the intraresidue C^ x H−C^βH distances, free of systematic errors arising from spin diffusion, can be obtained from a 3D^13C-separated^1H−^1H rotating frame Overhauser effect^1H−^13C multiple quantum coherence (ROESY-HMQC) spectrum. The applicability of these experiments to larger proteins is illustrated with respect to interleukin-1β, a protein of 153 residues and 17.4 kDa molecular weight.
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Stereospecific assignment of β-methylene protons in larger proteins using 3D15N-separated Hartmann-Hahn and13C-separated rotating frame Overhauser Spectroscopy
Journal of Biomolecular NMR, 1991Co-Authors: G. Marius Clore, Ad Bax, Angela M. GronenbornAbstract:3Jxβ coupling constants and complementary nuclear Overhauser data on the intraresidue C x H−CβH distances form an essential part of the data needed to obtain stereospecific assignments of β-methylene protons in proteins. In this paper we show that information regarding the magnitude of the3Jxβ coupling constants can be extracted from a semi-quantitative interpretation of relative peak intensities in a 3D15N-separated1H−1H Hartmann-Hahn1H−15N multiple quantum coherence (HOHAHA-HMQC) spectrum. In addition, we demonstrate that reliable information on the intraresidue C x H−CβH distances, free of systematic errors arising from spin diffusion, can be obtained from a 3D13C-separated1H−1H rotating frame Overhauser effect1H−13C multiple quantum coherence (ROESY-HMQC) spectrum. The applicability of these experiments to larger proteins is illustrated with respect to interleukin-1β, a protein of 153 residues and 17.4 kDa molecular weight.
Seunho Jung - One of the best experts on this subject based on the ideXlab platform.
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Solubility Enhancement of Atrazine by Complexation with Cyclosophoraose Isolated from Rhizobium leguminosarum biovar trifolii TA-1
Polymers, 2019Co-Authors: Yohan Kim, Vijay Vilas Shinde, Daham Jeong, Young-jin Choi, Seunho JungAbstract:Rhizobium leguminosarum biovar trifolii TA-1, a kind of soil bacteria, produces cyclosophoraoses (Cys). Cyclosophoraoses contain various ring sizes with degrees of polymerization ranging from 17 to 23. Atrazine is a hardly-soluble herbicide that contaminates soil and drinking water, and remains in soil for a long time. To remove this insoluble contaminant from aqueous solutions, we have enhanced the solubility of atrazine by complexation with Cys. The complex formation of Cys and atrazine was confirmed using 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) Spectroscopy, differential scanning calorimetry (DSC), field emission scanning electron microscopy (FE-SEM), rotating frame nuclear Overhauser Spectroscopy (ROESY), and molecular modeling studies. The aqueous solubility of atrazine was enhanced 3.69-fold according to the added concentrations (20 mM) of Cys, compared to the 1.78-fold enhancements by β-cyclodextrin (β-CD). Cyclosophoraoses as an excellent solubility enhancer with long glucose chains that can effectively capture insoluble materials showed a potential application of microbial polysaccharides in the removal of hazardous hardly-soluble materials from aqueous solutions in the fields of biological and environmental industry.
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Solubility Enhancement of Atrazine by Complexation with Cyclosophoraose Isolated from Rhizobium leguminosarum biovar trifolii TA-1
MDPI AG, 2019Co-Authors: Yohan Kim, Vijay Vilas Shinde, Daham Jeong, Young-jin Choi, Seunho JungAbstract:Rhizobium leguminosarum biovar trifolii TA-1, a kind of soil bacteria, produces cyclosophoraoses (Cys). Cyclosophoraoses contain various ring sizes with degrees of polymerization ranging from 17 to 23. Atrazine is a hardly-soluble herbicide that contaminates soil and drinking water, and remains in soil for a long time. To remove this insoluble contaminant from aqueous solutions, we have enhanced the solubility of atrazine by complexation with Cys. The complex formation of Cys and atrazine was confirmed using 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) Spectroscopy, differential scanning calorimetry (DSC), field emission scanning electron microscopy (FE-SEM), rotating frame nuclear Overhauser Spectroscopy (ROESY), and molecular modeling studies. The aqueous solubility of atrazine was enhanced 3.69-fold according to the added concentrations (20 mM) of Cys, compared to the 1.78-fold enhancements by β-cyclodextrin (β-CD). Cyclosophoraoses as an excellent solubility enhancer with long glucose chains that can effectively capture insoluble materials showed a potential application of microbial polysaccharides in the removal of hazardous hardly-soluble materials from aqueous solutions in the fields of biological and environmental industry
Fabien Ferrage - One of the best experts on this subject based on the ideXlab platform.
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Nuclear Overhauser Spectroscopy of chiral CHD methylene groups
Journal of Biomolecular NMR, 2016Co-Authors: Rafal Augustyniak, Jan Stanek, Henri Colaux, Geoffrey Bodenhausen, Wiktor Koźmiński, Torsten Herrmann, Fabien FerrageAbstract:Nuclear magnetic resonance Spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect Spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH_2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D_9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.
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Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density
Journal of Biomolecular NMR, 2010Co-Authors: Fabien Ferrage, Kaushik Dutta, Alexander Shekhtman, David CowburnAbstract:Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR Spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser Spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein–protein complexes.
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Single or triple gradients
Journal of Magnetic Resonance, 2008Co-Authors: Riddhiman Sarkar, Fabien Ferrage, Detlef Moskau, Paul R. Vasos, Geoffrey BodenhausenAbstract:Pulsed Field Gradients (PFGs) have become ubiquitous tools not only for Magnetic Resonance Imaging (MRI), but also for NMR experiments designed to study translational diffusion, for spatial encoding in ultra-fast Spectroscopy, for the selection of desirable coherence transfer pathways, for the suppression of solvent signals, and for the elimination of zero-quantum coherences. Some of these experiments can only be carried out if three orthogonal gradients are available, while others can also be implemented using a single gradient, albeit at some expense of performance. This paper discusses some of the advantages of triple- with respect to single-gradient probes. By way of examples we discuss (i) the measurement of small diffusion coefficients making use of the long spin-lattice relaxation times of nuclei with low gyromagnetic ratios γ such as nitrogen-15, and (ii) the elimination of zero-quantum coherences in Exchange or Nuclear Overhauser Spectroscopy (EXSY or NOESY) experiments, as well as in methods relying on long-lived (singlet) states to study very slow exchange or diffusion processes.
Bernard Ancian - One of the best experts on this subject based on the ideXlab platform.
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NMR Studies for Mapping Structure and Dynamics of Nucleosides in Water
Annual reports on NMR spectroscopy, 2010Co-Authors: Bernard AncianAbstract:Abstract An overview of the literature on structure of the nucleosides for the last 40 years is presented in order to gain a better understanding of their specific and non-specific interactions with water. The emphasis has been on NMR intermolecular interactions to probe the hydration of the compounds, especially homonuclear and heteronuclear Overhauser Spectroscopy. New aspects as given by well-designed diffusion experiments are investigated. Dynamics and microdynamics, e.g. lifetimes of the hydrates, structure of the first hydration shell and chemical exchange of the amide protons, are fully discussed on the example of uridine in water.
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Combined use of Overhauser Spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water.
Magnetic resonance in chemistry : MRC, 2006Co-Authors: H.b Seba, Bernard Ancian, Pierre Thureau, André ThévandAbstract:Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser Spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.
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Hydration structure of uracil as studied by 1D and 2D heteronuclear Overhauser Spectroscopy: evidence for the formation of a trihydrate in the first solvation shell
Chemical Physics Letters, 1998Co-Authors: M Chahinian, H.b Seba, Bernard AncianAbstract:Abstract The intermolecular heteronuclear Overhauser effect (HOE) between water and uracil has been measured. Steady-state 13 C, 1 H nuclear Overhauser effect (NOE) results show that the first solvation shell includes three water molecules. Transient 13 C, 1 H and 15 N, 1 H 2D HOESY experiments as well as 1 H NOESY experiments give further evidence for the formation of a cyclic trihydrate as obtained by three bridge hydrogen-bonding between the three water molecules and the two amide groups of the uracil. The trihydrate has only a very short life-time as compared to the rotational correlation time of the free uracil molecule which remains the tumbling species in the water–DMSO solution.
