NMR structure analysis of uniformly 13C-labeled carbohydrates

In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of ¹³C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly ¹³C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-¹³C)-sucrose, 342 Da] and one compound of medium molecular weight (¹³C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The ¹³C resonances are traced using ¹³C–¹³C correlations from homonuclear experiments, such as (H)CC–CT–COSY, (H)CC–NOESY, CC–CT–TOCSY and/or virtually decoupled (H)CC–TOCSY. Based on the assignment of the ¹³C resonances, the ¹H chemical shifts are derived in a straightforward manner using one-bond ¹H–¹³C correlations from heteronuclear experiments (HC–CT–HSQC). In order to avoid the ¹ J _CC splitting of the ¹³C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either ¹³C or ¹H detected experiments, namely CC–CT–COSY, band-selective (H)CC–TOCSY, HC–CT–HSQC–NOESY or long-range HC–CT–HSQC. However, due to the short T₂ relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the ¹H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the ¹³C-enriched polysaccharide were assigned by using HC–H2BC spectra. The assignment of the N-acetyl groups with ¹⁵N at natural abundance was completed by using HN–SOFAST–HMQC, HNCA, HNCO and ¹³C-detected (H)CACO spectra.     

Synthesis of 13C-labeled steroid hormones

The synthesis of 13C-labeled steroid hormones is reviewed. Two general approaches are highlighted: partial synthesis in which part of the steroid nucleus is replaced with 13C-labeled synthons, and total synthesis. Examples from both approaches, leading to (3-(3)C)-, (4-(13)C)-, (3,4-(13)C2)-, and (1,2,3,4-(13)C4)- labeled steroid hormones (e.g., testosterone, estradiol, progesterone, and cortisol), are presented.     

Synthesis and NMR experiments of (4,5,6-13C)-deoxymannojirimycin. A new entry to 13C-labeled glycosidase inhibitors

The synthesis of (4,5,6-13C)-deoxymannojirimycin is described. The route employed is based on Sharpless asymmetric epoxidation of (1,2,3-13C)(E)-2,4-pentadien-1-ol and uses ring-closing metathesis as a key step. The labeled compound may be easily used for protein-binding experiments using NMR spectroscopic methods.     

Synthesis of multiply 13C-labeled furofuran lignans using 13C-labeled cinnamyl alcohols as building blocks

Plant lignans are currently being widely studied for their potential benefits for human health as their consumption has been correlated with lower risks for developing chronic diseases, such as breast cancer and coronary heart disease. However, studies of some classes of lignans, in particular the furofurans, are hampered by the lack of suitable standards to allow accurate analysis. Herein, we report the syntheses of two racemic (13)C-labeled furofuran lignans [7,8,9-(13)C(3)]medioresinol and [7,8,9-(13)C(3)]sesamin as internal standards for LC-MS analysis. The labeled furofuran lignans were constructed from triply labeled cinnamyl alcohols, using a radical cyclization method.     

13C NMR or coenzyme A and its constituent moieties.

Natural abundance 13C nuclear magnetic resonance spectra, in D2O, were obtained for the following: pantoyl lactone, beta-alanine, cysteamine hydrochloride, cystamine dihydrochloride, calcium pantothenate, beta-aletheine oxalate, pantetheine, pantethine, pantetheine 4'-phosphate, oxypantetheine 4'-phosphate, desulfopantetheine 4'-phosphate, N-acetyl-aminodesthiopantetheine 4'-phosphate, adenosine 2',5'-diphosphate, adenosine 3',5'-diphosphate, and coenzyme A. A complete assignment of the 13C chemical shifts in the NMR spectrum of CoA is reported. Comparison of spectra indicates that CoA most likely exists in an extended conformation.     

Synthesis of single- and double-13C-labeled cholesterol oleate

Cholesterol oleate with the 13C-label in oleic acid at the carbonyl and/or in the sterol ring at position 4 was synthesized by two methods: (1) cholesterol was condensed with oleic anhydride, prepared from [1-13C] oleic acid, in the presence of dimethylaminopyridine (DMAP) in anhydrous chloroform at room temperature for 4--5 h; (2) cholesterol or 13C-enriched cholesterol at position 4 were reacted with 90% [1-13C]-oleic acid in the presence of dicyclohexylcarbodiimide (DCC) and DMAP at room temperature in anhydrous chloroform for 1.25 h. The single-13C and double-13C-labeled cholesterol oleate were obtained in 90% yields after purification by silicic acid column chromatography. Their purity was assessed by thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC) and 13C-NMR spectroscopy. Tritium-labeled cholesterol oleate was also synthesized by method 1 using the fatty acid anhydride.     

Carbon-13 NMR spectra of carbon-13 enriched chlorophylls a and b

The proton decoupled ¹³C NMR (CMR) spectra of chlorophylls a and b enriched to 90% ¹³C have been obtained at 25.2 MHz and, despite the complexity of the spectra, many of the assignments of the ¹³C resonances have been made.     

Solid-state NMR determination of sugar ring pucker in (13)C-labeled 2'-deoxynucleosides

The H3'-C3'-C4'-H4' torsional angles of two microcrystalline 2'-deoxynucleosides, thymidine and 2'-deoxycytidine.HCl, doubly (13)C-labeled at the C3' and C4' positions of the sugar ring, have been measured by solid-state magic-angle-spinning nuclear magnetic resonance (NMR). A double-quantum heteronuclear local field experiment with frequency-switched Lee-Goldberg homonuclear decoupling was used. The H3'-C3'-C4'-H4' torsional angles were obtained by comparing the experimental curves with numerical simulations, including the two (13)C nuclei, the directly bonded (1)H nuclei, and five remote protons. The H3'-C3'-C4'-H4' angles were converted into sugar pucker angles and compared with crystallographic data. The delta torsional angles determined by solid-state NMR and x-ray crystallography agree within experimental error. Evidence is also obtained that the proton positions may be unreliable in the x-ray structures. This work confirms that double-quantum solid-state NMR is a feasible tool for studying sugar pucker conformations in macromolecular complexes that are unsuitable for solution NMR or crystallography.     

The 13C NMR spectra of some rosane diterpenoids

The ¹³C NMR signals of rosenonolactone have been assigned utilizing the ¹³C-¹³C couplings in material obtained biosynthetically from sodium [1,2-¹³C₂] acetate.     

Synthesis of 13C-labeled and functionalized Hyaluronan derivatives for biophysical studies and surface modifications

A convergent synthesis of a tetrasaccharide partial sequence of ¹³C-labeled Hyaluronan is presented. This tetrasaccharide can be used for biophysical studies as well as for surface modifications. Furthermore, tetrasaccharide 7 can be employed for the synthesis of additionally labeled higher oligomers of Hyaluronan on the basis of the presented methodology.     

Helix-helix interconversion rates of short 13C-labeled helical peptides as measured by dynamic NMR spectroscopy

The rates at which a peptide hexamer and a peptide octamer interconvert between left- and right-handed helical forms in CD2Cl2 solution have been characterized by 13C dynamic NMR (DNMR) spectroscopy. The peptide esters studied are Fmoc-(Aib)n-OtBu (n = 6 and 8), where Fmoc is 9-fluorenylmethyoxycarbonyl and Aib is the strongly helix-forming residue alpha-aminoisobutyric acid. Because the Aib residue is itself achiral, homooligomers of this residue form a 50/50 mixture of enantiomeric 3(10)-helices in solution. It has been demonstrated (R.-P. Hummel, C. Toniolo, and G. Jung, Angewandte Chemie International Edition, 1987, Vol. 26, pp. 1150-1152) that oligomers of Aib interconvert on the millisecond timescale. We have performed lineshape analysis of 13C-NMR spectra collected for our peptides enriched with 13C at a single residue. Rate constants for the octamer range from 6 s(-1) at 196 K to about 56,500 s(-1) at 320 K. At all temperatures, the hexamer interconverts about three times faster than the octamer. Eyring plots of the data reveal experimentally indistinguishable DeltaH++ values for the hexamer and octamer of 37.8 +/- 0.6 and 37.6 +/- 0.4 kJ mol(-1) respectively. The difference in the rates of interconversion is dictated by entropic factors. The hexamer and octamer exhibit negative DeltaS++ values of -29.0(-1) +/- 2.5 and -37.3 +/- 1.7 J K(-1) mol(-1), respectively. A mechanism for the helix-helix interconversion is proposed. and calculated DeltaG++ values are compared to the estimate for a decamer undergoing a helix-helix interconversion.     

The biosynthesis of tabtoxinine-beta-lactam. Use of specifically 13C-labeled glucose and 13C NMR spectroscopy to identify its biosynthetic precursors

Tabtoxinine-beta-lactam, an irreversible inhibitor of glutamine synthetase is produced by several pathovars of Pseudomonas syringae. We have examined tabtoxinine-beta-lactam biosynthesis, an important and poorly characterized step in pathogenesis caused by this organism. We have identified the biosynthetic precursors of tabtoxinine-beta-lactam by incorporating 13C from specifically 13C-labeled D-glucose precursors and determining the labeling pattern using 13C NMR spectroscopy. Tabtoxinine-beta-lactam is generated by combining a 4-carbon fragment, a 2-carbon fragment, and a single carbon. The 4-carbon fragment arises from aspartic acid, and the 2-carbon unit is donated from carbons 2 and 3 of pyruvate. The 6-carbon backbone of tabtoxinine-beta-lactam arises from the condensation of fragments from aspartate and pyruvate, probably using reactions analogous to the initial steps in the pathway of lysine biosynthesis.     

Application of 2D-TOCSY NMR to the measurement of specific(13C-enrichments in complex mixtures of 13C-labeled metabolites

A 2D-NMR method based on zero-quantum filtered (ZQF-) TOtal Correlation SpectroscopY (TOCSY) was applied to measure 13C-enrichments in complex mixtures of 13C-labeled metabolites generated in carbon-labeling experiments. Using ZQF-TOCSY, more than 30 13C-enrichments could be potentially measured from the analysis of a biomass hydrolyzate prepared from Escherichia coli cells grown on a mixture of 20% [U-13C]-glucose and 80% [1-13C]-glucose, without need for separation of metabolites. The method is applicable to biomass hydrolyzates, cell extracts, and other complex biological samples. It is also applicable to any combination of labeled substrates and provides a basis for examining non-steady-state conditions.     

Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein-RNA complexes

We report an optimized synthesis of all canonical 2'-O-TOM protected ribonucleoside phosphoramidites and solid supports containing [13C5]-labeled ribose moieties, their sequence-specific introduction into very short RNA sequences and their use for the structure determination of two protein-RNA complexes. These specifically labeled sequences facilitate RNA resonance assignments and are essential to assign a high number of sugar-sugar and intermolecular NOEs, which ultimately improve the precision and accuracy of the resulting structures. This labeling strategy is particularly useful for the study of protein-RNA complexes with single-stranded RNA in solution, which is rapidly an increasingly relevant research area in biology.     

Synthesis and mass spectra of esters of branched chain fatty acids

The Wittig reaction between alkylidene triphenylphosphoranes [R — CH = P(C₆H₅)₃, where R varied from H to n — C₁₇H₃₅] and methyl 12-oxooctadecanoate or methyl 10-oxohexadecanoate in dimethylformamide (DMF) has been employed in the synthesis of a partial homologous series of esters of branched chain fatty acids in high yields. The effect of various ratios of reactants in both DMF and dimethylsulfoxide (DMSO) was investigated. Purification from triphenylphosphine oxide was readily accomplished by chromatography on a column of silicic acid-Celite impregnated with silver nitrate.     

Contribution of exogenous substrates to acetyl coenzyme A: measurement by 13C NMR under non-steady-state conditions

A method is presented for the rapid determination of substrate selection in a manner that is not restricted to conditions of metabolic and isotopic steady state. Competition between several substrates can be assessed directly and continuously in a single experiment, allowing the effect of interventions to be studied. It is shown that a single proton-decoupled 13C NMR spectrum of glutamate provides a direct measure of the contribution of exogenous 13C-labeled substrates to acetyl-CoA without measurement of oxygen consumption and that steady-state conditions need not apply. Two sets of experiments were performed: one in which a metabolic steady state but a non-steady-state 13C distribution was achieved and another in which both metabolism and labeling were not at steady state. In the first group, isolated rat hearts were supplied with [1,2-13C]acetate, [3-13C]lactate, and unlabeled glucose. 13C NMR spectra of extracts from hearts perfused under identical conditions for 5 or 30 min were compared. In spite of significant differences in the spectra, the measured contributions of acetate, lactate, and unlabeled sources to acetyl-CoA were the same. In the second set of experiments, the same group of labeled substrates was used in a regional ischemia model in isolated rabbit hearts to show regional differences in substrate utilization under both metabolic and isotopic non steady state. This sensitive probe of substrate selection was also demonstrated in intact hearts where excellent time resolution (3 min) of substrate selection was feasible.(ABSTRACT TRUNCATED AT 250 WORDS)     

Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers

Actinobacillus succinogenes is a promising candidate for industrial succinate production. However, in addition to producing succinate, it also produces formate and acetate. To understand carbon flux distribution to succinate and alternative products we fed A. succinogenes [1-(13)C]glucose and analyzed the resulting isotopomers of excreted organic acids, proteinaceous amino acids, and glycogen monomers by gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy. The isotopomer data, together with the glucose consumption and product formation rates and the A. succinogenes biomass composition, were supplied to a metabolic flux model. Oxidative pentose phosphate pathway flux supplied, at most, 20% of the estimated NADPH requirement for cell growth. The model indicated that NADPH was instead produced primarily by the conversion of NADH to NADPH by transhydrogenase and/or by NADP-dependent malic enzyme. Transhydrogenase activity was detected in A. succinogenes cell extracts, as were formate and pyruvate dehydrogenases, which the model suggested were contributing to NADH production. Malic enzyme activity was also detected in cell extracts, consistent with the flux analysis results. Labeling patterns in amino acids and organic acids showed that oxaloacetate and malate were being decarboxylated to pyruvate. These are the first in vivo experiments to show that the partitioning of flux between succinate and alternative fermentation products can occur at multiple nodes in A. succinogenes. The implications for designing effective metabolic engineering strategies to increase A. succinogenes succinate production are discussed.     

13C NMR spectra of some naturally occurring binaphthoquinones and related compounds

¹³C NMR chemical shift assignments have been shown to be diagnostic for the establishment of the dimeric linkage of some naturally occurring binaphthoquinones. The unsymmetric ¹³C and ¹H spin-spin coupled pattern observed in the ¹H coupled ¹³C NMR spectrum of plumbagin for C-6 has also been noticed earlier with the related compound juglone. The nature of these effects has been substantiated for the first time using benzene induced solvent shifts and D₂O exchange. ¹³C chemical shift assignments of plumbagin reported earlier for C-6 and C-8 have been revised.