Structure and dynamics of porcine submaxillary mucin as determined by natural abundance carbon-13 NMR spectroscopy

Nearly all of the resonances in the 13C NMR spectrum of porcine submaxillary mucin glycoprotein (PSM) have been assigned to the peptide core carbons and to the carbons in the eight different oligosaccharide side chains that arise from the incomplete biosynthesis of the sialylated A blood group pentasaccharide (alpha-GalNAc(1-3) [alpha-Fuc(1-2)]-beta-Gal(1-3) [alpha-NeuNGl(2-6)]- alpha-GalNAc-O-Ser/Thr). By use of these assignments, a nearly complete structural analysis of intact PSM has been performed without resorting to degradative chemical methods. Considerable structural variability in the carbohydrate side chains was observed between mucins obtained from different animals, while no variability was observed between glands in a single animal. The dynamics of the PSM core and carbohydrate side chains were examined by using the carbon-13 nuclear magnetic resonance relaxation times and nuclear Overhauser enhancements of each assigned carbon resonance. The peptide core of PSM exhibits internal segmental flexibility that is virtually identical with that of ovine submaxillary mucin (OSM), whose carbohydrate side chain consists of the alpha-NeuNAc(2-6)alpha-GalNAc disaccharide. The longer oligosaccharide side chains of PSM, therefore, have no significant effect on peptide core mobility compared to the shorter side chains of native OSM or asialo-OSM. Although the dynamics of the shorter carbohydrate side chains shared by both OSM and PSM appear to be identical, the A and H blood group structures in PSM have reduced mobilities, indicating that the glycosidic linkages of the terminal sugars in these determinants are relatively inflexible. These results differ from most reports of glycoprotein dynamics, which typically find the terminal carbohydrate residues to be undergoing rapid internal rotation about their terminal glycosidic bonds. The results reported here are consistent with previous studies on the conformations of the A and H determinants derived from model oligosaccharides and further indicate that the conformations of these determinants are unchanged when covalently bound to the mucin peptide core. In spite of their carbohydrate side-chain heterogeneity, mucins appear to be ideal glycoproteins for the study of O-linked oligosaccharide conformation and dynamics and for the study of the effects of glycosylation on polypeptide conformation and dynamics.     

Natural abundance carbon-13 nuclear magnetic resonance studies of histone and DNA dynamics in nucleosome cores

Natural abundance carbon-13 nuclear magnetic resonance spectra (67.9 MHz) were obtained for native nucleosome cores: cores dissociated in 2 M NaCl and 2 M NaCl, 6 M urea; and cores degraded with DNase I plus proteinase K. Phosphorus-31 NMR spectra of native and dissociated cores and core length DNA were also obtained at 60.7 MHz. The 31P resonance and spin-lattice relaxation time (T1) of DNA were only slightly affected by packaging in nucleosome cores, in agreement with other reports, but 13C resonances of DNA were essentially unobservable. The loss of DNA spectral intensity suggests that rapid internal motions of DNA sugar carbons in protein-free DNA previously demonstrated by 13C NMR methods are partly restricted in nucleosomes. The 13C spectrum of native cores contains many narrow intense resonances assigned to lysine side chain and alpha-carbons, glycine alpha-carbons, alanine alpha- and beta- carbons, and arginine side chain carbons. Several weaker resonances were also assigned. The narrow line widths, short T1 values, and non-minimal nuclear Overhauser enhancements of these resonances, including alpha- and beta-carbons, show that some terminal chain segments of histones in nucleosomes are as mobile as small random coil polypeptides. The mobile segments include about 9% of all histone residues and 25% of all lysines, but only 10% of all arginines. The compositions of these segments indicate that mobile regions are located in amino- or carboxyl-terminal sequences of two or more histones. In addition, high mobility was observed for side chain carbons of 45-50% of all lysines (delta and epsilon carbons) and about 25% of all arginines (zeta carbon) in histones (including those in mobile segments), suggesting that basic residues in terminal histone sequences are not strongly involved in nucleosome structure and may instead help stabilize higher order chromatin structure.     

Spinach plastocyanin: Comparison of reduced and oxidized forms by natural abundance carbon-13 nuclear magnetic resonance spectroscopy

Differences between the reduced Cu(I) and oxidized Cu(II) forms of spinach plastocyanin were investigated by natural abundance carbon-13 nuclear magnetic resonance spectroscopy at 67.9 MHz using proton noise decoupling. The spectra confirm that histidines 38 and 91 are copper ligands and demonstrate that coordination is by the N^o1 of both imidazole rings. Spectra of reduced plastocyanin yielded 128 separately resolved carbon resonances. Upon oxidation, 16 of these were observed to disappear; yet there was little change in the positions or intensities of other peaks. Those peaks which disappear are assigned to carbons near the metal. The protein evidently does not undergo a substantial change in conformation upon change of redox state.     

Carbon-13 NMR studies of chloroplast membranes: carbon-13 enrichment without 13C-13C couplings

A novel approach to carbon-13 (13C) enrichment of chloroplast membranes (and plant materials in general) is presented for 13C-nuclear magnetic resonance (13C-NMR) studies. The method minimizes the occurrence of spectral complications arising from 13C-13C couplings resulting from a statistical distribution of 13C within the molecule with low probability of encountering two 13C atoms adjacent to each other. This is achieved by growing the plants in light surrounded by an atmosphere containing 1/3rd 12CO2 and 2/3rd 13CO2, liberated by weak acid-treatment of a mixture of corresponding barium carbonate salts.     

Characterization of the wound-induced material in Citrus paradisi fruit peel by carbon-13 CP-MAS solid state NMR spectroscopy

Grapefruit, Citrus paradisi, were injured, inoculated with Penicillium digitatum and incubated under conditions favourable for the accumulation of defence related material. Histochemical examination revealed that tissues adjacent to inoculated injuries contained phloroglucinol-HCl (PG-HCl) reactive material. Solvent washed cell wall preparations of intact and injured-inoculated peel were further purified using a mixture of cell wall degrading enzymes. Samples from injured inoculated tissue contained PG-HCl reactive globular material in addition to the fragments of xylem and cuticle found in controls. The principal chemical moieties of the material that accumulates in grapefruit injuries during wound-healing were studied by solid state 13C cross-polarization magic angle spinning NMR. A complete assignment of the NMR signals was made. From the analysis evidence was found that cellulose and hemicellulose are the biopolymers present in the intact peel samples, in addition, relevant quantities of cutin were found in the residues of enzyme digest. The NMR difference spectrum intact- wounded peels showed resonances which were attributed to all major functional groups of the aromatic-aliphatic suberin polyester of new material produced by the wounds. Information on the latter polyester was obtained by analyzing the T(1)rho (1H) relaxation.     

Changes in the natural abundance 13C NMR spectra of intact frog muscle upon storage and caffeine contracture

The carbons of phospholipids have limited mobility in fresh, resting, gastrocnemius frog muscle, but a population of phospholipids gains considerable mobility upon storage in the muscle or in contracture induced by caffeine. In parallel with the appearance of sharp phospholipid resonances, lactic acid also appears in the 13C NMR spectra. There is a correlation between the mobility of phospholipids and the depletion of phosphocreatine and ATP in muscle.     

Wheat bran biodegradation by Pleurotus ostreatus: a solid-state carbon-13 NMR study

Solid-state (13)C nuclear magnetic resonance (NMR) and elemental analysis techniques were used to monitor the degradation of wheat bran by the white-rot fungus Pleurotus ostreatus during a 62-day cultivation period. The weight loss and in vitro organic matter digestibility of the substrate were also evaluated after fungal treatment. The (13)C NMR spectra of degraded wheat bran samples showed a lower content in carbohydrates and a higher content in aliphatic and carboxylic groups than the untreated control sample. In parallel, changes in the wheat bran elemental composition evidenced a decrease in carbon content and a concomitant increase in nitrogen and oxygen content during mycelium growth. These results clearly indicate the occurrence of progressive changes in the composition of wheat bran during fungal treatment and are interpreted in terms of preferential degradation of amorphous vs. crystalline polysaccharides by the fungal mycelium and accumulation of proteins in the substrate. At the end of the cultivation period, the treated samples experienced an average weight loss of 20% and an increase in organic matter digestibility of 17%.     

Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy

The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance (13)C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the [(1)H]-(13)C NOE were determined in this study. The C alpha H relaxation measurements were compared to the previously measured (15)N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the chi(1) dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than +/-25 degrees.     

The fermentation of xylose: studies by carbon-13 nuclear magnetic resonance spectroscopy

Summary The fermentation ofd-xylose byPachysolen tannophilus, Candida shehatae, andPichia stipitis has been investigated by¹³C-nuclear magnetic resonance spectroscopy of both whole cells and extracts. The spectra of whole cells metabolizingd-xylose with natural isotopic abundance had significant resonance signals corresponding only to xylitol, ethanol and xylose. The spectra of whole cells in the presence of [1-¹³C]xylose or [2-¹³C]xylose had resonance signals corresponding to the C-1 or C-2, respectively, of xylose, the C-1 or C-2, respectively, of xylitol, and the C-2 or C-1, respectively, of ethanol. Xylitol was metabolized only in the presence of an electron acceptor (acetone) and the only identifiable product was ethanol. The fact that the amount of ethanol was insufficient to account for the xylitol metabolized indicates that an additional fate of xylitol carbon must exist, probably carbon dioxide. The rapid metabolism of xylulose to ethanol, xylitol and arabinitol indicates that xylulose is a true intermediate and that xylitol dehydrogenase catalyzes the reduction (or oxidation) with different stereochemical specificity from that which interconverts xylitol andd-xylulose. The amino acidl-alanine was identified by the resonance position of the C-3 carbon and by enzymatic analysis of incubation mixtures containing yeast and [1-¹³C]xylose or [1-¹³C]glucose. The position of the label from both substrates and the identification of isotope also in C-1 of alamine indicates flux through the transketolase/transaldolase pathway in the metabolism. The identification of a resonance signal corresponding to the C-1 of ethanol in spectra of yeast in the presence of [1-¹³C]xylose and fluoroacetate (but not arsenite) indicates the existence of equilibration of some precursor of ethanol (e.g. pyruvate) with a symmetric intermediate (e.g. fumarate or succinate) under these conditions.     

One-dimensional 13C NMR and HPLC-1H NMR techniques for observing carbon-13 and deuterium labelling in biosynthetic studies

For several decades isotope labelling techniques have been the indispensable tools used to unravel pathways of secondary product biosynthesis. NMR spectroscopy, together with mass spectrometry, is the most effective measuring technique used in the analysis of metabolites enriched with stable isotopes. ²H and ¹³C are the NMR-detectable nuclides which have been most frequently employed in plant secondary metabolite synthesis. Examples from the biosynthesis of phenylpropanoids, phenylphenalenones, and glucosinolates are used when discussing some aspects of one-dimensional NMR analysis of metabolites selectively labelled with ²H and ¹³C. Besides direct NMR detection of ¹³C-enriched metabolites, special emphasis is placed on indirect detection of ¹³C and ²H, especially by HPLC-¹H NMR coupling, to analyse the isotopomer pattern of compounds in low concentration. The examples discussed in this paper were obtained from studies with Anigozanthos preissii (root cultures) (Haemodoraceae) and Eruca sativa (Brassicaceae).     

Short-term mineralization of maize residues in soils as determined by carbon-13 natural abundance

Studies of soil organic matter equilibria must include estimates of C turnover. The objective of this study was to provide data on how the natural ¹³C abundance method can be used to determine the flow of C from C₄ residues and soil organic matter (C₃-source) in a short-term incubation. Corn residue was added at a rate of 5.7 mg C g⁻¹ soil to two soils, a clay and a sandy clay loam. During the course of a 35-day incubation in a CO₂-free system, CO₂-C and ¹³C natural abundance of the respired CO₂ were measured. About 20% of the corn residue-C added was mineralized in both soils as determined from the CO₂ respired and the ¹³C natural abundance of the respired CO₂. Mineralization of the added residues was also calculated as the difference of the total amount of the respired CO₂-C between the control and the corn residue-treated soils divided by the total amount of corn residue-C. Values were 35% for the clay soil, and 30% for the sandy clay loam soil. The difference in values calculated from the ¹³ C natural abundance and the difference method was due to mineralization of the indigenous soil organic C resulting from the addition of corn residues. Use of the natural ¹³C abundance method could determine the degree of ‘priming effect’ in soils amended with C₄-C residues. This revised version was published online in June 2006 with corrections to the Cover Date.     

The influence of fertilizer nitrogen and season on the carbon-13 abundance of wheat straw

Carbon-13 abundance, expressed as δ¹³C in ‰, was measured in wheat straw grown between 1984 and 1989 on the Broadbalk Continuous Wheat Experiment at Rothamsted. In all six years, straw grown without fertilizer N contained less carbon-13 (i.e.δ¹³C was more negative) than straw grown with fertilizer, although the magnitude of this difference varied with year. In a dry year, when dry matter response to fertilizer N was relatively small, there was a large difference between the δ¹³C of straw grown with and without N. Conversely, in a wet year, when there was a marked response to N, there was little difference in the isotopic composition of N-fertilized and unfertilized straw. Over the six years, the difference between the δ¹³C value of straw grown with and without nitrogen (D ¹³C, in ‰) was related to drought, measured as the calculated soil water deficit on 15 July (W_j, in mm), by the equation D ¹³C=−0.299+0.01034 W_j (r=0.87). H Lambers Section editor     

Supramolecular aggregation and organization in peripheral nerve myelin

Under certain preparative conditions the lipid bilayers of glutaraldehyde-fixed, PNS myelin demonstrate a marked compartmentalization, which can be augmented by lipid extraction following sectioning. The results are interpreted as indicating a supramolecular domain pattern of arrangement centered upon the transmembrane protein (P0) molecules. The latter are thought to be surrounded by annuli of substantially immobilized phospholipids. In the lamellar planes particular lipids are considered to have a nonrandom distribution. The visualization of bilayer compartmentalization was seen only in negatively stained sections obtained from unembedded or glutaraldehyde-urea-embedded myelin. Lipids were unextracted in the basic preparations except in so far as some unfixed, amphipathic molecules escaped at the trough-fluid interface at the time of sectioning, an observed phenomenon which probably aided in the visualization of the compartmentalization. Visualization was also augmented by surface tension expanding section fragments as they floated on the trough fluid. All stages of transition between well-ordered myelin and dispersed globular units were commonly to be found. Deliberately delipidated myelin exposed more sharply defined and smaller globular units in bilayer regions, but even these are regarded as being supramolecular aggregates including residual lipid annuli around the transmembrane proteins. The addition of cadmium ions as a "fixative" for lecithin seemed to improve the preservation of glutaraldehyde-urea-embedded myelin but was not strictly necessary to reveal its domain structure. A secondary tannic acid fixation was required to process unembedded myelin so as to reveal the fundamental compartmentalization of its lipid bilayers.     

Natural abundance carbon-13 nuclear magnetic resonance study of anthopleurin-A, a cardiac stimulant from the sea anemone Anthopleura xanthogrammica.

Natural-abundance 13C NMR spectra (at 15.04 MHz) of the polypeptide cardiac stimulant Anthopleurin-A are presented. The spectra contain many resolved one- and two-carbon resonances from carbonyl and aromatic carbons and a few resolved resonances from aliphatic carbons. Most of these have been assigned to individual carbons in the protein. The effect of pH on the 13C spectrum has been investigated. In conjunction with the resonance assignments, this yields estimates for the pK alpha values of the COOH-terminal and NH2-terminal residues, the side chain carboxylate of 1 of the 2 aspartic acid residues, and the imidazolium groups of the 2 histidine residues. The effects of the lanthanides La3+ and Gd3+ on the spectrum have also been studied. The results suggest that there are at least two binding sites, and further studies will be required to characterize these before they can be utilized as an aid in structural mapping. Finally, the results are discussed in relation to a postulated model for the mode of action of Anthopleurin-A.