86,374 research outputs found

    A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions

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    <p>Abstract</p> <p>Background</p> <p>Stable isotope tracing is a powerful technique for following the fate of individual atoms through metabolic pathways. Measuring isotopic enrichment in metabolites provides quantitative insights into the biosynthetic network and enables flux analysis as a function of external perturbations. NMR and mass spectrometry are the techniques of choice for global profiling of stable isotope labeling patterns in cellular metabolites. However, meaningful biochemical interpretation of the labeling data requires both quantitative analysis and complex modeling. Here, we demonstrate a novel approach that involved acquiring and modeling the timecourses of <sup>13</sup>C isotopologue data for UDP-<it>N</it>-acetyl-<smcaps>D</smcaps>-glucosamine (UDP-GlcNAc) synthesized from [U-<sup>13</sup>C]-glucose in human prostate cancer LnCaP-LN3 cells. UDP-GlcNAc is an activated building block for protein glycosylation, which is an important regulatory mechanism in the development of many prominent human diseases including cancer and diabetes.</p> <p>Results</p> <p>We utilized a stable isotope resolved metabolomics (SIRM) approach to determine the timecourse of <sup>13</sup>C incorporation from [U-<sup>13</sup>C]-glucose into UDP-GlcNAc in LnCaP-LN3 cells. <sup>13</sup>C Positional isotopomers and isotopologues of UDP-GlcNAc were determined by high resolution NMR and Fourier transform-ion cyclotron resonance-mass spectrometry. A novel simulated annealing/genetic algorithm, called 'Genetic Algorithm for Isotopologues in Metabolic Systems' (GAIMS) was developed to find the optimal solutions to a set of simultaneous equations that represent the isotopologue compositions, which is a mixture of isotopomer species. The best model was selected based on information theory. The output comprises the timecourse of the individual labeled species, which was deconvoluted into labeled metabolic units, namely glucose, ribose, acetyl and uracil. The performance of the algorithm was demonstrated by validating the computed fractional <sup>13</sup>C enrichment in these subunits against experimental data. The reproducibility and robustness of the deconvolution were verified by replicate experiments, extensive statistical analyses, and cross-validation against NMR data.</p> <p>Conclusions</p> <p>This computational approach revealed the relative fluxes through the different biosynthetic pathways of UDP-GlcNAc, which comprises simultaneous sequential and parallel reactions, providing new insight into the regulation of UDP-GlcNAc levels and <it>O</it>-linked protein glycosylation. This is the first such analysis of UDP-GlcNAc dynamics, and the approach is generally applicable to other complex metabolites comprising distinct metabolic subunits, where sufficient numbers of isotopologues can be unambiguously resolved and accurately measured.</p

    NMR-Based Structural Modeling of Graphite Oxide Using Multidimensional 13C Solid-State NMR and ab Initio Chemical Shift Calculations

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    Chemically modified graphenes and other graphite-based materials have attracted growing interest for their unique potential as lightweight electronic and structural nanomaterials. It is an important challenge to construct structural models of noncrystalline graphite-based materials on the basis of NMR or other spectroscopic data. To address this challenge, a solid-state NMR (SSNMR)-based structural modeling approach is presented on graphite oxide (GO), which is a prominent precursor and interesting benchmark system of modified graphene. An experimental 2D C-13 double-quantum/single-quantum correlation SSNMR spectrum of C-13-labeled GO was compared with spectra simulated for different structural models using ab initio geometry optimization and chemical shift calculations. The results show that the spectral features of the GO sample are best reproduced by a geometry-optimized structural model that is based on the Lerf-Klinowski model (Lerf, A. et al. Phys. Chem. B 1998, 102, 4477); this model is composed of interconnected sp(2), 1,2-epoxide, and COH carbons. This study also convincingly excludes the possibility of other previously proposed models, including the highly oxidized structures involving 1,3-epoxide carbons (Szabo, I. et al. Chem. Mater. 2006, 18, 2740). C-13 chemical shift anisotropy (CSA) patterns measured by a 2D C-13 CSA/isotropic shift correlation SSNMR were well reproduced by the chemical shift tensor obtained by the ab initio calculation for the former model. The approach presented here is likely to be applicable to other chemically modified graphenes and graphite-based systems

    Exploration of new 3α-pregnenolone ester analogues via Mitsunobu reaction, their anti-HIV activity and molecular modeling study

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    A new series of (5-pregnen-20-on-3α-yl)-substituted-benzoate analogues (10-13), (5-pregnene-20-on-3α-yl)-3-(substituted)acrylate derivatives (17-19) as well as the (17-(2-acetoxyacetyl)pregen-3α-yl)-3,4,5-trihydroxybenzoate (21) were synthesized from the ÎČ-pregenenolone scaffolds, by applying Mitsunobu reaction. All new compounds were characterized by 1H, 13C and 2D NMR spectroscopy. The inversion in configuration at C-3 during the formation of α-ester analogues was confirmed by NOESY NMR spectroscopy. The new compounds were evaluated for their in vitro antiviral activity against the replication of HIV-1 and HIV-2 in MT-4 cells. Compounds 18 showed an EC50 value of >1.95 mg/mL. In addition, preliminary structure-activity relationship and molecular modeling of compound 18 has been studied

    Sub-minute kinetics of human red cell fumarase: H-1 spin-echo NMR spectroscopy and C-13 rapid-dissolution dynamic nuclear polarization

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    Fumarate is an important probe of metabolism in hyperpolarized magnetic resonance imaging and spectroscopy. It is used to detect the release of fumarase in cancer tissues, which is associated with necrosis and drug treatment. Nevertheless, there are limited reports describing the detailed kinetic studies of this enzyme in various cells and tissues. Thus, we aimed to evaluate the sub-minute kinetics of human red blood cell fumarase using nuclear magnetic resonance (NMR) spectroscopy, and to provide a quantitative description of the enzyme that is relevant to the use of fumarate as a probe of cell rupture. The fumarase reaction was studied using time courses of H-1 spin-echo and C-13-NMR spectra. H-1-NMR experiments showed that the fumarase reaction in hemolysates is sufficiently rapid to make its kinetics amenable to study in a period of approximately 3 min, a timescale characteristic of hyperpolarized C-13-NMR spectroscopy. The rapid-dissolution dynamic nuclear polarization (RD-DNP) technique was used to hyperpolarize [1,4-C-13]fumarate, which was injected into concentrated hemolysates. The kinetic data were analyzed using recently developed FmR analysis and modeling of the enzymatic reaction using Michaelis-Menten equations. In RD-DNP experiments, the decline in the C-13-NMR signal from fumarate, and the concurrent rise and fall of that from malate, were captured with high spectral resolution and signal-to-noise ratio, which allowed the robust quantification of fumarase kinetics. The kinetic parameters obtained indicate the potential contribution of hemolysis to the overall rate of the fumarase reaction when C-13-NMR RD-DNP is used to detect necrosis in animal models of implanted tumors. The analytical procedures developed will be applicable to studies of other rapid enzymatic reactions using conventional and hyperpolarized substrate NMR spectroscopy.Cancer Research UK‐Engineering and Physical Sciences Research Council (CRUK/EPSRC) Imaging Centre in Cambridge and Manchester, Grant/Award Number: 16465; Cancer Research UK Programme, Grant/Award Number: 17242; European Research Council (ERC); Australian Research Council, Grant/Award Number: DP14010259

    Synthesis, structural elucidation and antimicrobial effectiveness of coordination entities of cobalt (II) and nickel (II) derived from 9,17-diaza-2,6,11,15-tetrathia-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene

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    9,17-Diaza-2,6,11,15-tetrathia-1,7,10,16-(1,2)-tetrabenzenacyclooctadecaphan-8,17-diene, macrocycle was synthesized, thereafter formulation and designing strategies applied for the preparation of coordination entities of Co(II) and Ni(II). Coordination behaviour of N2S4 donor macrocycle towards metal ion(s) was assessed by physiochemical measurements and spectral investigations viz. elemental analysis, molar conductance, magnetic susceptibility measurements, infrared, UV-Vis, 1H and 13 C NMR, mass spectroscopy, electron paramagnetic resonance (EPR), cyclic voltammetry and molecular modeling. Side-by-side comparison of the spectral findings exposed different geometrical aspects of macrocycle and coordination entities. Cyclic voltammogram showed fully oxidized and reduced species in one unified experiment. Macrocycle and coordination entities were screened for antimicrobial effectiveness (antifungal properties against Aspergillus-niger)

    Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

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    Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. (2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. (3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. (4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. (5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. (6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. (7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas

    Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by 13C NMR Spin Relaxation and Stochastic Modeling

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    Among biomolecules, carbohydrates are unique in that not only can linkages be formed through different positions but the structures may also be branched. The trisaccharide \uf062-D-Glcp-(1\uf0ae3)[\uf062-D-Glcp-(1\uf0ae2)]-\uf061-D-Manp-OMe represents a model of a branched vicinally disubstituted structure. A 13C site-specific isotopologue with labeling in each of the two terminal glucosyl residues enabled acquisition of high-quality 13C NMR relaxation parameters T1, T2 and heteronuclear NOE, with standard deviations of \uf0a3 0.5%. For interpretation of the experimental NMR data a diffusive chain model was used in which the dynamics of the glycosidic linkages is coupled to the global reorientation motion of the trisaccharide. Brownian dynamics simulations relying on the potential of mean force at the glycosidic linkages were employed to evaluate spectral densities of the spin probes. Calculated NMR relaxation parameters showed very good agreement with experimental data, deviating < 3%. The resulting dynamics is described by correlation times of 196 ps and 174 ps for the \uf062-(1\uf0ae2)- and \uf062-(1\uf0ae3)-linked glucosyl residues, respectively, i.e., different and linkage dependent. Notably, the devised computational protocol was performed without any fitting of parameters