1H-NMR study of GM2 ganglioside: evidence that an interresidue amide-carboxyl hydrogen bond contributes to stabilization of a preferred conformation

Several properties of the exchangeable amide protons of the ganglioside G_M2 were studied in detail by¹H-NMR spectroscopy in fully deuterated dimethylsulfoxide [²H₆]DMSO/2% H₂O, and compared with data obtained for the simpler constituent glycosphingolipids G_A2 and G_M3. In addition to chemical shifts,³ J _2,HN coupling constants, and temperature shift coefficients, the kinetics of NH/²H chemical exchange were examined by following the disappearance of the amide resonances in [²H₆]DMSO/2%²H₂O. The results included observation of an increase in half-life of theN-acetylgalactosamine acetamido HN by more than an order of magnitude in G_M2 compared to G_A2, attributable to the presence of the additionalN-acetylneuraminic acid residue. Additional one-dimensional dipolar cross relaxation experiments were also performed on nonexchangeable protons of G_M2. The results of all of these experiments support a three-dimensional model for the terminal trisaccharide in which a hydrogen bond is formed between theN-acetylgalactosamine acetamido NH and theN-acetylneuraminic acid carboxyl group. The interaction is proposed to be of the -acceptor type, a possibility which has not yet been explored in the literature on carbohydrates. The proposed model is discussed in comparison with that of Sabesanet al. (1984,Can J Chem 62: 1034–45), and the models of G_M1 proposed more recently by Acquottiet al. (1990,J Am Chem Soc 112:7772–8) and Scarsdaleet al. (1990,Biochemistry 29:9843–55).     

A study on human urine in a high-selenium area of China by 1H-NMR spectroscopy

In this study, high-resolution 600-MHz ¹H-NMR (nuclear magnetic resonance) spectroscopies were used to compare the urinary metabolic profiles of healthy humans and humans in a high-selenium area of China. NMR biomarkers for renal and liver lesions were observed by comparing the urine ¹H-NMR spectra. In urinary excretion, the concentrations in human urine samples of formate, lactate, acetate, hippurate, and alanine in overexposure to selenium were increased, whereas citrate, creatine, and TMAO excretion were decreased compared with that of the healthy human—some of them even disappeared. An interesting result was the appearance of formate in urine, which has previously been shown to lead to acidosis and chronic renal failure and interfere with the lumen and proximal tubular cells. The level of creatine was associated with the seminal activity. The changes of acetate and citrate may explain the disorder of the cellular energy metabolism caused by selenium, and the changes of other amino acids were a result of the reuptake of these compounds that had been blocked in the glomerulus and proximal tubule. The results elucidate the renal/liver lesion in humans in high-selenium area by ¹H-NMR spectroscopy and offer the molecular basic of selenium toxicity.     

A 500-MHz1H-NMR study on theN-linked carbohydrate chain of bromelain

The 500-MHz¹H-NMR characteristics of theN-linked carbohydrate chain Man1-6[Xyl1-2]Man1-4GlcNAc1-4[Fuc1-3]GlcNAc1-NAsn of the proteolytic enzyme bromelain (EC 3.4.22.4) from pineapple stem were determined for the oligosaccharide-alditol and the glycopeptide, obtained by hydrazinolysis and Pronase digestion, respectively. The¹H-NMR structural-reporter-groups of the (1–3)-linked fucose residue form unique sets of data for the alditol as well as for the glycopeptide.     

1H-NMR metabolite profiles of different strains of Plasmodium falciparum

Although efforts to understand the basis for inter-strain phenotypic variation in the most virulent malaria species, Plasmodium falciparum, have benefited from advances in genomic technologies, there have to date been few metabolomic studies of this parasite. Using ¹H-NMR spectroscopy, we have compared the metabolite profiles of red blood cells infected with different P. falciparum strains. These included both chloroquine-sensitive and chloroquine-resistant strains, as well as transfectant lines engineered to express different isoforms of the chloroquine-resistance-conferring pfcrt (P. falciparum chloroquine resistance transporter). Our analyses revealed strain-specific differences in a range of metabolites. There was marked variation in the levels of the membrane precursors choline and phosphocholine, with some strains having >30-fold higher choline levels and >5-fold higher phosphocholine levels than others. Chloroquine-resistant strains showed elevated levels of a number of amino acids relative to chloroquine-sensitive strains, including an approximately 2-fold increase in aspartate levels. The elevation in amino acid levels was attributable to mutations in pfcrt. Pfcrt-linked differences in amino acid abundance were confirmed using alternate extraction and detection (HPLC) methods. Mutations acquired to withstand chloroquine exposure therefore give rise to significant biochemical alterations in the parasite.     

Conversion of Major Ginsenoside Rb1 to Ginsenoside F2 by Caulobacter leidyia

Ginsenoside Rb₁ is the most predominant ginsenoside in Panax species (ginseng) and the hydrolysis of this ginsenoside produces pharmaceutically active compounds. Caulobacter leidyia GP45, one of the isolates having strong β-glucosidase-producing activity, converted ginsenoside Rb₁ to the active metabolites by 91%. The structures of the resultant metabolites were identified by NMR. Ginsenoside Rb₁ had been consecutively converted to ginsenoside Rd (1), F₂ (2) and compound K (3) via the hydrolyses of 20-C β-(1→6)-glucoside, 3-C β-(1→2)-glucoside, and 3-C β-glucose of ginsenoside Rb₁.     

Components and fractions for differently bound water molecules of dipalmitoylphosphatidylcholine-water system as studied by DSC and H-NMR spectroscopy

Differently bound water molecules of dipalmitoylphosphatidylcholine (DPPC)-H₂O system were investigated with differential scanning calorimetry (DSC). According to a method previously reported by us, the ice-melting DSC curves of the DPPC-H₂O samples of varying water contents were deconvoluted into multiple components, and the ice-melting enthalpies for the individual deconvoluted components were used to estimate average molar ice-melting enthalpies for freezable interlamellar and bulk waters, respectively. With these average molar ice-melting enthalpies, the numbers of differently bound water molecules of the DPPC-H₂O system were calculated at varying water contents and were used to construct a water distribution diagram of this system. Furthermore, to evaluate the reliability of the present DSC deconvolution method, ²H-NMR T₁ measurements of DPPC-²H₂O system were carried out at 5 °C of the gel phase temperature, and components and fractions for differently bound water (²H₂O) molecules were estimated from the analysis of nonexponential magnetization recovery curves.     

<Superscript>1</Superscript>H-NMR metabonomics analysis of sera differentiates between mammary tumor-bearing mice and healthy controls

Global analysis of ¹H-NMR spectra of serum is an appealing approach for the rapid detection of cancer. To evaluate the usefulness of this method in distinguishing between mammary tumor-bearing mice and healthy controls, we conducted ¹H-NMR metabonomic analyses on serum samples obtained from the following: 10 mice inoculated with a highly-metastatic mammary carcinoma cell line, 10 mice inoculated with a “normally” metastatic mammary carcinoma cell line, and 10 healthy controls. Following standard spectral processing and subsequent data reduction, we applied unsupervised Principal Component Analysis (PCA) to determine if unique metabolic fingerprints for different categories of metastatic breast cancer in serum exist. The PCA method correctly separated sera of tumor-bearing mice from that of normal healthy controls, as shown using the scores plot which indicated that sera classes from tumor-bearing mice did not share multivariate space with that from healthy controls. In addition, this technique was capable of distinguishing between classes of varying metastatic ability in this system. Metabolites apparently responsible for separation between diseased and healthy mice include lactate, taurine, choline, and sugar moieties. Results of this study suggest that ¹H-NMR spectra of mouse serum analyzed using PCA statistical methods indicate separation of tumor-bearing mice from healthy normal controls, justifying further study of the use of ¹H-NMR metabonomics for cancer detection using serum.     

Qualitative high field <Superscript>1</Superscript>H-NMR spectroscopy for the characterization of endogenous metabolites in earthworms with biochemical biomarker potential

This study was designed to provide a database of the endogenous metabolites in earthworm extracts of the species, Eisenia veneta and Lumbricus terrestris by high resolution ¹H-NMR spectroscopy in view of identifying biomarkers of toxicity or stress in environmental metabolomics studies. 1D and 2D NMR spectroscopic techniques enabled the identification and confirmation of the organic components in the tissue extracts of whole and segmented earthworms, dissected organs, and coelomic fluid. The extracts gave rise to characteristic ¹H-NMR spectral fingerprints of the low MW metabolites contained, specific to the species of earthworm, and to the specific regions or dissected organs of the earthworms under investigation. Distinct changes in the normal biochemistry were observed upon starvation and cooling, such as markedly decreased glucose and maltose, but increased lactate, acetate, succinate, formate and acetone. Additionally, slightly decreased threonine, arginine, lysine, leucine, citrate, asparagine and glycine were observed. Furthermore, lactate could be identified as a biomarker of acute toxic stress in expressed coelomic fluid following exposure to a model ecotoxin (3-trifluoromethylaniline). This work supports the application of ¹H-NMR spectroscopy for the study of changes in the normal invertebrate biochemistry in order to allow for the reliable assessment of biomarker responses following toxicity testing.     

In situ localization of PCR-amplified DNA and cDNA

Combining the high sensitivity of PCR with the cell localizing ability ofin situ hybridization allows for the reproducible detection of low copy targets in intact cells. This article describes several key variables that include fixation, protease digestion, the hot start maneuver, stringency, and, for RNA analysis, DNase digestion that are important to successfulin situ PCR. Also stressed is the importance of performing and interpreting controls with each experiment. Important controls include omission of key components, use of samples known either to contain or lack the target of interest and, most importantly, the in-built controls invariably present in the heterogeneous component of any given tissue type.     

Interaction of amphotericin B with membrane lipids as viewed by H-NMR

The effects of amphotericin B upon the organization and dynamics of multibilayer membranes of dimyristoylphosphatidylcholine (DMPC) were investigated by means of ²H-NMR. At high amphotericin B concentrations (30 mol% with respect to the lipid) and at temperatures above 25°C, DMPC experiences two different environments which are in slow exchange on the ²H-NMR time scale. In one of these, the lipid is immobilized by the antibiotic, in a molar ratio of approximately 1:1, whereas the lipid unsequestered by amphotericin B is more ordered than in its pure state. This ordering effect is perceived at relatively low antibiotic doses (4%). The local lipid order, and the relative percentage, of sequestered DMPC, are temperature-independent (up to 65°C), whereas the ordering of the unsequestered lipid domain is not. The perturbation induced by amphotericin B is manifest similarly at the edges as well as in the center of the bilayer. Antibiotic addition leads to large decreases in the transverse relaxation time, T₂, of the labelled lipid, but not in the spin-lattice relaxation time, T₁. This indicates an increased density of slow motional modes and little change in rapid motions.     

Farnesol-DMPC phase behaviour: a H-NMR study

Involved in a number of diverse metabolic and functional contexts, farnesol is a central component of the mevalonate pathway, post-translationally attaches to proteins, and affects a number of other membrane-associated events. Despite farnesol's biological implications, a detailed analysis of how farnesol affects the physical properties and phase behaviour of lipid membranes is lacking. As ²H-NMR spectra are sensitive to molecular motions and acyl chain orientation, they can be used to measure the degree of molecular order present in the system. Also, since the ²H-NMR spectra of fluid and gel phase lipids are very different, they are sensitive probes of membrane phase equilibrium and can be used to determine fluid-gel phase boundaries. In this study, dimyristoyl phosphatidylcholine-d₅₄ (DMPC-d₅₄) bilayers containing varying concentrations of trans-trans farnesol (2.5-20.0 mol%) are investigated over a range of temperatures (8-30 °C). Analysis of these spectra has led to the construction of a farnesol-DMPC-d₅₄ temperature-composition plot. We show that increasing concentrations of farnesol induce a decrease in the fluid-gel phase transition temperature and promote fluid-gel coexistence. Interestingly, farnesol does not seem to affect the quadrupolar splittings (Δv_Q) in the fluid phase, i.e., the organization of farnesol within the bilayer and its interaction with phospholipids does not appreciably influence acyl chain order in the fluid phase.     

1H-NMR spectroscopic characterization of dansyl glyco-asparagines derived from hen egg white clycoproteins

Dansyl glyco-asparagines were prepared from a partially fractionated mixture of hen egg white glycoproteins. Reverse-phase high performance liquid chromatography (HPLC) on a silica-based octadecyl column yielded ten such derivatives in a virtually pure state. The detailed structures of the glyco-asparagines were identified by 500-MHz¹H nuclear magnetic resonance (NMR) spectroscopy. Two of them were found to be of the oligomannosideN-type, four were of the intersected-hybridN-type and another four were of the intersected multi-antennaryN-type. In monogalactosylated, intersected structures the galactose residue was proved by¹H-NMR to be attached in (1–4)-linkage to the GlcNAc1-4Man1–3 branch.Dansyl glyco-asparagines turned out to be suitable derivatives for¹H-NMR spectroscopic analysis. The combination of HPLC and high-resolution NMR spectroscopy of such derivatives proved to be a powerful technique in studying the (micro-)heterogeneity of sugar chains in glycoproteins.Abbreviations dns dansyl (5-dimethylaminonaphthalene-1-sulfonyl) - ODS octadecyl-silica - WEFT water-eliminating Fourier transform - DSS sodium 4,4-dimethyl-4-silapentane-1-sulfonate - OVA ovalbumin - OVM ovomucoid - OVT ovotransferrin     

Evidence of Metyrapone Reduction by two Mycobacterium strains shown by 1H NMR

In situ 1H NMR monitoring of metyrapone incubations with resting-cells of two strains of Mycobacterium, Mycobacterium aurum MO1 and Mycobacterium sp. RP1, showed the biotransformation of this compound, and more precisely the carbonyl-reduction of metyrapone into the corresponding alcohol, metyrapol. This reduction produced both enantiomers. The use of inhibitors allowed us to show the multiple enzymatic activities involved in this biotransformation including carbonyl reductase (EC 1.1.1.1.84) from the short-chain dehydrogenase superfamily and aldehyde reductase (EC 1.1.1.2) from the aldo-keto reductase superfamily.     

A study of gramicidin using deuterium oxide

The single channel conductivity of the gramicidin channel has been measured for all the alkali ions using both H₂O and ²H₂O as a medium. Significant changes in conductivity with medium have been observed in all cases except lithium.     

Energy production and growth of Pseudomonas oxalaticus OX1 on oxalate and formate

The efficiency of oxidative phosphorylation in Pseudomonas oxalaticus during growth on oxalate and formate was estimated by two methods. In the first method the amount of ATP required to synthesize cell material of standard composition was calculated during growth of the organism on either of the two substrates. The [Y _ATP ^max ] theor. values thus obtained were 12.5 and 6.5 for oxalate and formate respectively, if the assumption were made that no energy is required for transport of oxalate or carbon dioxide. When active transport of oxalate requiring an energy input equivalent to 1 mole of ATP per mole of oxalate was taken into account, [Y _ATP ^max ]theor. for oxalate was 9.4. True Y _ATP ^max values were derived from these data on the assumption that the energy produced in the catabolism of Pseudomonas oxalaticus is used with approximately the same efficiency as in a range of other chemoorganotrophs. P/O ratios were calculated using the equation P/O=Y _O/Y _ATP. The data for Y _O and m _e required for these calculations were obtained from cultures of Pseudomonas oxalaticus growing on oxalate or formate in carbon-limited continuous cultures. The P/O ratios calculated by this method were, for oxalate, 1.3 (or 1.0 if active transport were ignored), and for formate, 1.7.In the second method the stoicheiometries of the respiration-linked proton translocations with oxalate and formate were measured in washed suspensions of cells grown on the two substrates. The H⁺/O ratios obtained were 4.3 with oxalate and 3.9 with formate. These data indicate the presence of two functional phosphorylation sites in the electron transport chain of Pseudomonas oxalaticus during growth on both substrates. A comparison of the P/O ratio on oxalate obtained with the two methods indicated that the energy requirement for active transport of oxalate has a major effect on the energy budget of the cell; about 50% of the potentially available energy in oxalate is required for its active transport across the cell membrane. Translocation of formate requires approximately 25% of the energy potentially available in the substrate. These results offer an explanation for the fact that molar growth yields of Pseudomonas oxalaticus on oxalate and formate are not very different.Abbreviations PMS phenazinemethosulphate - DCPIP 2,6-dichlorophenolindophenol - TMPD N,N,N,N-tetramethyl-1,4-phenylene-diamine dihydrochloride - SD standard deviation - PEP Phosphoenol-pyruvate     

1H-NMR study on ganglioside amide protons: evidence that the deuterium exchange kinetics are affected by the preparation of samples

The kinetics of H/²H chemical exchange of the amide proton has been suggested as one of the tools available for investigating hydrogenbond stabilizing interactions in gangliosides.The amide proton/deuterium (NH/²H) exchange rates in GM2 ganglioside were studied by¹H-NMR spectroscopy on 12 samples prepared following different procedures. In samples passed through a sodium salt Chelex-100 cation exchange resin column prior to being analysed theN-acetylneuraminic acid NH exchange occurred in less than 10 min and that of ceramide NH in 30 min. TheN-acetylgalactosamine acetamido NH exchange was slower, the half-life of the signal ranging from 15 min to 3.5 h. Contact of the Chelex-treated GM2 samples with water, through a dialysis process, modified the NH/²H exchange rate values, theN-acetylgalactosamine acetamido NH exchange becoming faster than that of ceramide NH and similar to that ofN-acetylneuraminic acid NH. Our results indicate that the deuterium/proton exchange rate strongly depends on sample preparation (ion content and minor contaminants present in water). The three-dimensional model involving theN-acetylgalactosamine acetamido NH and theN-acetylneuraminic acid carboxyl group hydrogen-bonding, which is supported by experimental evidence, cannot be confirmed by NH-exchange measurement.     

人单拷贝及重复DNA序列的原位PCR

在培养的人小肠癌转移腹水细胞系细胞中进行了Y染色体特异的重复序列及单拷贝序列的原位扩增与检测.结果显示原位PCR法的灵敏度比直接的原位杂交法明显提高.     

核磁共振氢谱法在芹亚科植物化学分类中的简便应用

用核磁共振红谱（1H－NMR）方法对芹亚科14种植物的香豆素类成分进行了检测,然后用常规植物化学方法加以验证。结果表明,1H-NMR方法可以简便应用于芹亚科植物的化学分类。