共查询到20条相似文献,搜索用时 15 毫秒
1.
Rustem A. Shaykhutdinov Glen D. MacInnis Reza Dowlatabadi Aalim M. Weljie Hans J. Vogel 《Metabolomics : Official journal of the Metabolomic Society》2009,5(3):307-317
Targeted profiling is a library-based method of using mathematically modeled reference spectra for quantification of metabolite
concentrations in NMR mixture analysis. Metabolomics studies of biofluids, such as urine, represent a highly complex problem
in this area, and for this reason targeted profiling of 1H NMR spectra can be hampered. A number of the issues relating to 1H NMR spectroscopy can be overcome using 13C{1H} NMR spectroscopy. In this work, a 13C{1H} NMR database was created using Chenomx NMR Suite, incorporating 120 metabolites. The 13C{1H} NMR database was standardized through the analysis of a series of metabolite solutions containing varying concentrations
of 19 distinct metabolites, where the metabolite concentrations were varied across a range of values including biological
ranges. Subsequently, the NMR spectra of urine samples were collected using 13C{1H} NMR spectroscopy and profiled using the 13C{1H} NMR library. In total, about 30 metabolites were conclusively identified and quantified in the urine samples using 13C{1H} NMR targeted profiling. The proton decoupling and larger spectral window provided easier identification and more accurate
quantification for specific classes of metabolites, such as sugars and amino acids with overlap in the aliphatic region of
the 1H NMR spectrum. We discuss potential application areas in which 13C{1H} NMR targeted profiling may be superior to 1H NMR targeted profiling. 相似文献
2.
The analysis of primary and secondary nitrogen metabolism in plants by nuclear magnetic resonance (NMR) spectroscopy is comprehensively reviewed. NMR is a versatile analytical tool, and the combined use of 1H, 2H, 13C, 14N and 15N NMR allows detailed investigation of the acquisition, assimilation and metabolism of nitrogen. The analysis of tissue extracts can be complemented by the in vivo NMR analysis of functioning tissues and cell suspensions, and by the application of solid state NMR techniques. Moreover stable isotope labelling with 2H-, 13C- and 15N-labelled precursors provides direct insight into specific pathways, with the option of both time-course and steady state analysis increasing the potential value of the approach. The scope of the NMR method, and its contribution to studies of plant nitrogen metabolism, are illustrated with a wide range of examples. These include studies of the GS/GOGAT pathway of ammonium assimilation, investigations of the metabolism of glutamate, glycine and other amino acids, and applications to tropane alkaloid metabolism. The continuing development of the NMR technique, together with potential applications in the emerging fields of metabolomics and metabolic flux analysis, leads to the conclusion that NMR will play an increasingly valuable role in the analysis of plant nitrogen metabolism. 相似文献
3.
Mattias U. Roslund Elin Säwén Jens Landström Jerk Rönnols K.Hanna M. Jonsson Magnus Lundborg Mona V. Svensson Göran Widmalm 《Carbohydrate research》2011,(11):1311
The computer program casper uses 1H and 13C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the 1H and 13C, as well as 31P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 1H and 13C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D 1H,13C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t1 incremented 1H,13C-HSQC experiment and a 1D 1H,1H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3 Hz apart. The 1H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental 1H and 13C NMR chemical shifts. 相似文献
4.
《Inorganica chimica acta》1986,121(2):113-117
1H and 2H NMR spectra of the title copper(II) complexes and its derivatives have been measured. In contrast with their 1H NMR spectra, 2H NMR spectra gave well resolved sharp signals, and demonstrated that two diastereomers attributable to two asymmetric ligand nitrogens are readily resolved. The remarkable linewidth-narrowing was found in the peripheral methyl groups, which make 2H NMR spectra very useful even for copper(II) complexes with a long electron spin relaxation time. By using 2H NMR spectra, meso-racemate equilibrium was pursued and examined in aqueous and acetonitrile solutions. 相似文献
5.
《Phytochemistry》1986,25(6):1411-1413
A diterpene lactone was isolated from the cold petrol (60−80°) extract of rhizomes of Euphorbia acaulis, a plant material used by a tribe of central India for curing various inflammatory disorder. The diterpene, which was observed to be identical to caudicifolin on the basis of its physical constants, was subjected to high resolution NMR spectroscopy and X-ray crystallography examination. This paper reports the salient features of the 2D 1H NMR, 13C NMR and X-ray crystallography data of the compound. 13C NMR assignments were made by the use of proton noise decoupling, SFORD, APT and automatic spectral editing techniques. 1H NMR assignments were made with the aid of a COSY experiment for long range couplings and NOE correlated 2D-experiments. The 1H and 13C NMR spectral assignments have been further corroborated by H/C correlation experimental results. 相似文献
6.
Toru Shimizu Masahiro Hatano 《Biochemical and biophysical research communications》1982,104(4):1356-1362
43Ca NMR spectroscopy of Ca2+-thermolysin complexes reveals that the structure and/or exchange rate of Ca2+ bound to the regulative-site of the enzyme are not essentially changed by adding Zn2+ or an inhibitor, L-leucine hydroxamate, both of which may be bound to the active-site of the enzyme. It is shown that the chemical exchange mechanism dominates the 43Ca NMR of Ca2+ bound to the enzyme on the basis of temperature-dependences of the NMR. In contrast with the 43Ca NMR findings, first application of 67Zn NMR to the Zn2+-thermolysin complexes offers convincing evidences that the structure and/or exchange rate of Zn2+ bound to the active-site of the enzyme are remarkably changed by adding Ca2+ or the inhibitor, L-leucine hydroxamate. 相似文献
7.
Natural Abundance Fourier Transform of <Superscript>13</Superscript>C Nuclear Magnetic Resonance Spectra of Lysozyme 总被引:1,自引:0,他引:1
NUCLEAR magnetic resonance (NMR) studies of biopolymers have so far been limited to proton resonances. On the other hand, 13C NMR analysis is potentially a more powerful technique because of the larger range of chemical shifts (300 p.p.m. compared with 10 p.p.m. for XH NMR) and because the chemical shift of 13C NMR is more sensitive to the nature of the chemical bonds. The chief limitations of 13C NMR are low natural abundance (1·1%), low relative sensitivity (1·59% of proton) and long relaxation times (?1 min). These can be largely overcome, however, by the combined techniques of nuclear Overhauser enhancement and fourier transform spectroscopy. Thus, Gibbons et al.1 obtained a simple and elegant spectral analysis of ‘Gramicidin S-A’, a decapeptide. We report here the first natural abundance 13C NMR spectrum of an enzyme. Lysozyme was chosen because its primary structure is known2,3 and because its 1H NMR spectrum has already been described4. 相似文献
8.
Freeman W. Cope 《The Journal of general physiology》1967,50(5):1353-1375
The nuclear magnetic resonance (NMR) spectrum of Na+ is suitable for qualitative and quantitative analysis of Na+ in tissues. The width of the NMR spectrum is dependent upon the environment surrounding the individual Na+ ion. NMR spectra of fresh muscle compared with spectra of the same samples after ashing show that approximately 70% of total muscle Na+ gives no detectable NMR spectrum. This is probably due to complexation of Na+ with macromolecules, which causes the NMR spectrum to be broadened beyond detection. A similar effect has been observed when Na+ interacts with ion exchange resin. NMR also indicates that about 60% of Na+ of kidney and brain is complexed. Destruction of cell structure of muscle by homogenization little alters the per cent complexing of Na+. NMR studies show that Na+ is complexed by actomyosin, which may be the molecular site of complexation of some Na+ in muscle. The same studies indicate that the solubility of Na+ in the interstitial water of actomyosin gel is markedly reduced compared with its solubility in liquid water, which suggests that the water in the gel is organized into an icelike state by the nearby actomyosin molecules. If a major fraction of intracellular Na+ exists in a complexed state, then major revisions in most theoretical treatments of equilibria, diffusion, and transport of cellular Na+ become appropriate. 相似文献
9.
Coxon B 《Carbohydrate research》2005,340(10):1714-1721
Complete 1H and 13C NMR chemical shift assignments have been generated from a series of acetamidodeoxy and aminodeoxy sugar derivatives. For free sugars, the enhanced sensitivity of an NMR cryoprobe allowed simple 1D and 2D NMR spectra to be obtained from essentially single anomers, before significant mutarotation had occurred. The NMR assignments have been used to characterize deuterium isotope effects on 13C chemical shifts measured under conditions of slow NH to ND exchange in single solutions. Within a range of 0 to −0.138 ppm, β, γ, δ, and ζ deuterium isotope effects have been observed, thus providing additional reference data for assignment of the 13C NMR spectra of nitrogenous saccharides. 相似文献
10.
Sandra Ward 《Carbohydrate research》2009,344(6):808-3921
Tetratritylation of α-cyclodextrin (CD) and subsequent peracetylation of the partially tritylated mixture allowed the preparation and isolation of the symmetrical 6A,6B,6D,6E-tetratritylated α-CD in pure form. The 1H NMR spectra of the compound showed abnormal behaviour with the anomeric proton of one of the glycopyranosyl systems resonating below 3.0 ppm, which is exceptionally unusual. To understand this anomaly in the 1H NMR data, we performed a complete NMR analysis and using molecular modelling as a tool, we were able to obtain a conformation that can explain the observed NMR phenomenon. 相似文献
11.
Marise Ouellet 《生物化学与生物物理学报:生物膜》2010,1798(2):235-1094
We have investigated the membrane interactions and dynamics of a 21-mer cytotoxic model peptide that acts as an ion channel by solid-state NMR spectroscopy. To shed light on its mechanism of membrane perturbation, 31P and 2H NMR experiments were performed on 21-mer peptide-containing bicelles. 31P NMR results indicate that the 21-mer peptide stabilizes the bicelle structure and orientation in the magnetic field and perturbs the lipid polar head group conformation. On the other hand, 2H NMR spectra reveal that the 21-mer peptide orders the lipid acyl chains upon binding. 15N NMR experiments performed in DMPC bilayers stacked between glass plates also reveal that the 21-mer peptide remains at the bilayer surface. 15N NMR experiments in perpendicular DMPC bicelles indicate that the 21-mer peptide does not show a circular orientational distribution in the bicelle planar region. Finally, 13C NMR experiments were used to study the 21-mer peptide dynamics in DMPC multilamellar vesicles. By analyzing the 13CO spinning sidebands, the results show that the 21-mer peptide is immobilized upon membrane binding. In light of these results, we propose a model of membrane interaction for the 21-mer peptide where it lies at the bilayer surface and perturbs the lipid head group conformation. 相似文献
12.
Juan Carlos FuentesMonteverde Stefan Becker Nasrollah RezaeiGhaleh 《Protein science : a publication of the Protein Society》2021,30(7):1315
Phase separation is a fundamental physicochemical process underlying the spatial arrangement and coordination of cellular events. Detailed characterization of biomolecular phase separation requires experimental access to the internal environment of dilute and especially condensed phases at high resolution. In this study, we take advantage from the ubiquitous presence of sodium ions in biomolecular samples and present the potentials of 23Na NMR as a proxy to report the internal fluidity of biomolecular condensed phases. After establishing the temperature and viscosity dependence of 23Na NMR relaxation rates and translational diffusion coefficient, we demonstrate that 23Na NMR probes of rotational and translational mobility of sodium ions are capable of capturing the increasing levels of confinement in agarose gels in dependence of agarose concentration. The 23Na NMR approach is then applied to a gel‐forming phenylalanine‐glycine (FG)‐containing peptide, part of the nuclear pore complex involved in controlling the traffic between cytoplasm and cell nucleus. It is shown that the 23Na NMR together with the 17O NMR provide a detailed picture of the sodium ion and water mobility within the interior of the FG peptide hydrogel. As another example, we study phase separation in water‐triethylamine (TEA) mixture and provide evidence for the presence of multiple microscopic environments within the TEA‐rich phase. Our results highlight the potentials of 23Na NMR in combination with 17O NMR in studying biological phase separation, in particular with regards to the molecular properties of biomolecular condensates and their regulation through various physico‐ and biochemical factors. 相似文献
13.
NMR studies of plastocyanin have centered on the ligands to the copper atom at the active site, particularly histidines-37 and -87. Heteronuclear (13C, 1H) J-connectivity spectroscopy has enabled cross assignment of 1H and 13C NMR resonances from the two copper-ligated histidines. In addition to providing assignments of the 13C resonances, the two-dimensional Fourier transform NMR results require the reversal of the original 1H NMR assignments to the ring protons of histidine-37. The line widths of the ring protons of histidine-87 are field-dependent leading to determination of the reduced lifetime of the proton on the Nδ atom (about 400 μs). 相似文献
14.
《Phytochemistry》1986,25(3):751-752
Structure elucidation and total assignment of the 13C NMR spectrum of 12-(S)-hydroxygeranylgeraniol, a new acyclic diterpene from the grown alga Bifurcaria bifurcata, was accomplished through the use of 1HNMR, 13C NMR and 2D NMR spectroscope including 2D long range 1H-13C chemical shift correlations. 相似文献
15.
Peti W Page R Moy K O'Neil-Johnson M Wilson IA Stevens RC Wüthrich K 《Journal of structural and functional genomics》2005,6(4):259-267
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. 相似文献
16.
Yoshikazu Hattori David Heidenreich Yuki Ono Toshihiko Sugiki Kei-ichi Yokoyama Ei-ichiro Suzuki Toshimichi Fujiwara Chojiro Kojima 《Journal of biomolecular NMR》2017,68(4):271-279
The preparation of stable isotope-labeled proteins is important for NMR studies, however, it is often hampered in the case of eukaryotic proteins which are not readily expressed in Escherichia coli. Such proteins are often conveniently investigated following post-expression chemical isotope tagging. Enzymatic 15N-labeling of glutamine side chains using transglutaminase (TGase) has been applied to several proteins for NMR studies. 19F-labeling is useful for interaction studies due to its high NMR sensitivity and susceptibility. Here, 19F-labeling of glutamine side chains using TGase and 2,2,2-trifluoroethylamine hydrochloride was established for use in an NMR study. This enzymatic 19F-labeling readily provided NMR detection of protein-drug and protein–protein interactions with complexes of about 100 kDa since the surface residues provided a good substrate for TGase. The 19F-labeling method was 3.5-fold more sensitive than 15N-labeling, and could be combined with other chemical modification techniques such as lysine 13C-methylation. 13C-dimethylated-19F-labeled FKBP12 provided more accurate information concerning the FK506 binding site. 相似文献
17.
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19.
2D [13C,1H] COSY NMR is used by the metabolic engineering community for determining 13C–13C connectivities in intracellular compounds that contain information regarding the steady-state fluxes in cellular metabolism. This paper proposes innovations in the generation and analysis of these specific NMR spectra. These include a computer tool that allows accurate determination of the relative peak areas and their complete covariance matrices even in very complex spectra. Additionally, a method is introduced for correcting the results for isotopic non-steady-state conditions. The proposed methods were applied to measured 2D [13C,1H] COSY NMR spectra. Peak intensities in a one-dimensional section of the spectrum are frequently not representative for relative peak volumes in the two-dimensional spectrum. It is shown that for some spectra a significant amount of additional information can be gained from long-range 13C–13C scalar couplings in 2D [13C,1H] COSY NMR spectra. Finally, the NMR resolution enhancement by dissolving amino acid derivatives in a nonpolar solvent is demonstrated. 相似文献
20.
Bing Wang Mark Miskolzie George Kotovych Peter Pulay 《Journal of biomolecular structure & dynamics》2013,31(1):71-79
Abstract Calculated and experimental 1H, 13C and 19F chemical shifts were compared in BKM-824, a cyclic bradykinin antagonist mimic, c[Ava1-Igl2-Ser3-DF5F4-Oic5-Arg6] (Ava=5-amino- valeric acid, Igl=α-(2-indanyl)glycine, DF5F=pentafluorophenylalanine, Oic=(2S,3aS,7aS)- octahydroindole-2-carboxylic acid). The conformation of BKM-824 has been studied earlier by NMR spectroscopy (M. Miskolzie et al., J. Biomolec. Struct. Dyn. 17, 947–955 (2000)). All NMR structures have qualitatively the same backbone structure but there is considerable variation in the side chain conformations. We have carried out quantum mechanical optimization for three representative NMR structures at the B3LYP/6–31G* level, constraining the backbone dihedral angles at their NMR structure values, followed by NMR chemical shift calculations at the optimized structures with the 6–311G** basis set. There is an intramolecular hydrogen bond at Ser3 in the optimized structures. The experimental 13C chemical shifts at five Cα positions as well as at the Cβ, Cγ and Cδ position of Ava1, which forms part of the backbone, are well reproduced by the calculations, confirming the NMR backbone structure. A comparison between the calculated and experimental Hβ chemical shifts in Igl2 shows that the dominant conformation at this residue is gauche. Changes of proton chemical shifts with the scan of the χ1 angle in DF5F4 suggest that χ1 ≈180°. The calculated 1H and 13C chemical shifts are in good agreement with experiment at the rigid residue Oic5. None of the models gives accurate results for Arg6, presumably because of its positive charge. Our study indicates that calculated NMR shifts can be used as additional constraints in conjunction with NMR data to determine protein conformations. However, to be computationally effective, a database of chemical shifts in small peptide fragments should be precalculated. 相似文献