Structural investigation of Klebsiella serotype K36 polysaccharide

Klebsiella K36 capsular polysaccharide has been investigated by methylation, Smith-periodate oxidation and partial hydrolysis techniques. The structure was found to consist of a hexasaccharide repeating unit as shown. The anomeric configurations of the sugar were determined by ¹H and ¹³C n.m.r. spectroscopy on isolated oligomers obtained during the degradative studies and on the intact polysaccharide.     

Investigation of labeled amino acid side-chain motion in collagen using 13C nuclear magnetic resonance

¹³C¹H double magnetic resonance was used to study the interactions and mobility of certain amino acid side-chains of collagen. Samples of collagen, labeled with [3-¹³C]alanine (a small hydrophobic amino acid), [methyl-¹³C]-methionine (a large hydrophobic), [6-¹³C]lysine (positively charged at physiological pH), and [5-¹³C]glutamic acid (negatively charged), were prepared via chick calvaria culture. ¹³C linewidths, lineshapes, NOE² values, and T₁ values were measured for each sample as fibrils and as native (helical) material in solution.The measured T₁ and NOE values for [3-¹³C]alanine-labeled collagen in solution, in conjunction with an ellipsoid model for collagen, indicate that the methyl rotation rate is 2 × 10¹⁰ s^?1 and that the overall rate of diffusion about the long axis is 4× 10⁶ s^?1. These values agree with values for model compounds which undergo internal methyl rotation (Lyerla & Horikawa, 1976) and with previous n.m.r. measurements of the rate of rotational diffusion of backbone ([1-¹³C]- and [2-¹³C]glycine)-labeled collagen (Jelinski & Torchia, 1979). In addition, the n.m.r. data indicate that the terminal carbons of lysine, methionine and glutamic acid in labeled collagen (both in solution and as fibrils) are characterized by reorientation rates of approximately 10⁹ to 10¹⁰ s^?1.Taken together, the n.m.r. data provide strong evidence that the contact regions between the helices in collagen fibrils are fluid and that there is not a unique set of interactions between amino acid side-chains. In this respect, these n.m.r. results support current concepts of globular protein structure which suggest that a variety of conformations, in dynamic equilibrium, are responsible for the structure and function of proteins.     

13C-N.M.R.-spectroscopic investigation of agarose oligomers

A complete, unambiguous assignment of all of the ¹³C-n.m.r.-spectral signals of agarose oligomers produced by enzymic hydrolysis has been achieved. The ¹J¹³C-H coupling constants are reported, and the chemical shifts and coupling constants of both the agarose polymer and oligomers are compared.     

Reassignment of the methine resonances of D-fructose based on the carbon-13 n.m.r. spectrum of 3-O-methyl-D-fructose

Several disagreements in the ¹³C n.m.r. assignments of the methine carbons of D-fructose exist in the literature. In order to settle these inconsistencies, we examined the ¹³C n.m.r. spectrum of 3-O-methyl-D-fructose. By following the methyl induced shift in this spectrum, as compared to the parent sugar, we identified the alkylated C-3 resonance of all four tautomeric forms of D-fructose. This information, together with our previous identification of the C-5 resonances of the α- and β-forms of D-fructofuranose 6-phosphate, allow the unambiguous identification of all methine carbons of D-fructose in its ¹³C n.m.r. spectrum. The tautomeric composition of 3-O-methyl-D-fructose at 16.5°, in aqueous solution, was found to be as follows: α-pyranose 18%, β-pyranose 37%, α-furanose 11% and β-furanose 34%.     

Secondary structure of peptidese: 13. 15N and 13C n.m.r. spectroscopic investigation of the helix stability of poly(l-alanine) in acidic solutions

¹⁵N-enriched poly(l-alanines) of various molecular weights were prepared from $\text{l}\text{-alanine}\text{-N-}\text{carboxyanhydride}$ (l-Ala-NCA) and their helix/coil equilibrium in trifluoroacetic acid (TFA) investigated by means of 40.5 MHz ¹⁵N nuclear magneic resonance (n.m.r.), 22.3 MHz ¹³C n.m.r. and circular dichroism (c.d.) spectra. The ¹⁵N n.m.r. spectra exhibit at least three peaks, and the dependence of their intensities on molecular weight, molecular weight distribution and temperature, as well as dynamic nuclear Overhauser effect (NOE) measurements, indicate that the high-field peak represents the helix fraction. All three spectroscopic methods agree that a helix→coil transition takes place with decreasing concentration. Furthermore, poly(l-alanines) containing d-alanine or glycine in various mole ratios were synthesizsed by copolymerizations of N-carboxyanhydrides (NCAs). The ¹⁵N n.m.r. spetra demonstrate that one d-Ala unit per 100 l-Ala units suffices to affect significantly the helix/coil equilibrium in TFA. In other words, the helix content under equilibrium conditions is highly sensitive to racemization. Furthermore, ¹³ C n.m.r. cross-polarization/magic angle spinning (CP/MAS) spectra demonstrate that the presence of d-Ala units also affects the α-helix content in the solid state.     

Secondary structure of peptides: 8. 13C n.m.r. CP/MAS investigation of solid poly(l-leucines) and poly(d-norvalines) prepared from N-carboxyanhydrides

¹³C n.m.r. CP/MAS spectra (50.3 and 75.4 MHz) of solid poly(l-lleucines) and poly(d-norvalines) measured with suitable acquisition parameters allow quantification of the composition of the secondary structure. The optimum acquisition parameters were found by systematic variation of the contact time by means of samples containing 5?0% α-helix structure. The polypeptides were prepared by primary or tertiary amine-initiated polymerizations of the corresponding amino acid NCAs and the average degrees of polymerization ($\text{DP}$) were determined by ¹H n.m.r. endgroup analysis. The mole fraction of α-helices increases with increasing $\text{DP}$; it depends on the nature of the solvent and to a lesser degree on the polymerization temperature. When prepared under identical conditions, poly(d-norvaline) samples contain more β-sheet structure than poly(l-leucine. Reprecipitation increases the α-helix content, demonstrating that a part of the original β-sheet structure is thermodynamically unstable. The presence of oligomers of $\text{DP}$ ?10 is mainly responsible for the thermodynamically stable part of the β-sheet structure. The chain growth mechanism is discussed.     

13C-n.m.r. studies of the conformational changes in proline oligomers brought about by lithium and calcium salts

A detailed ¹³C-n.m.r. investigation has been carried out on the conformational changes in proline oligomers brought about by interaction with lithium and calcium perchlorates. Interaction of lithium and calcium salts with Piv-(Pro)_n-OMe, n = 2, 4 and 5 results in trans-cis isomerization. In the case of pentaproline, metal salts also give rise to other trans-isomers caused by the rotation about the C^αC(O) bond (Ψ, cis). Calcium salts seem to stabilize cis'-isomers and produce effects somewhat different from those of lithium salts.     

Dicarboxyamylose and dicarboxycellulose,stereoregular polyelectrolytes: physicochemical characterization and interaction with divalent cations

2,3-Dicarboxyamylose (DCA) and 2,3-dicarboxycellulose (DCC) have been obtained by splitting with periodate of all the C(2)C(3) bonds of amylose and cellulose, and further oxidation (with chlorite) of the corresponding polydialdehydes. Small, but reproducible, differences of ¹³C chemical shifts in dicate that DCA and DCC retained the different configuration at C-1 of the original polysaccharides, therefore being stereoisomers. The potentiometric and conductimetric titration curves of DCA and DCC and the pH-dependence of their ¹H n.m.r. spectra are those of typical polydicarboxylates. Interaction of DCA and DCC (Na salts) with divalent cations is clearly indicated by inflexions in conductimetric titration curves with Ca²⁺, Mg²⁺, Cu²⁺ and Fe²⁺, and by variation in specific optical rotation.     

A physico-chemical study of heparin: Evidence for a calcium-induced co-operative conformational transition

The conformations of heparin in aqueous solution in the presence of sodium, potassium, magnesium and calcium cations were studied using circular dichroism, optical rotation, nuclear magnetic resonance and equilibrium dialysis. Potassium and magnesium cations, when added to sodium heparinate solutions, cause small chiroptical changes. Binding of calcium ions gives rise to large changes in both optical rotation and circular dichroism. This is indicative of a major change in chain conformation, which is also manifest in ¹³C and ¹H n.m.r.⁴Equilibrium dialysis suggests one mole of calcium bound per mole of tetrasaccharide, which n.m.r. indicates to be appropriately sulphated iduronateglucosamine-iduronate-glucosamine. The calcium is chelated by two iduronate carboxyl groups. Proton-proton coupling constants, determined by convolution difference spectroscopy and Carr-Purcell sequences, indicate that, over the temperature range 285 to 353 K, the iduronate ring is best described as ¹C₄(l) and the glucosamine residue as ⁴C₁(d) for both sodium and calcium forms.The conformational change induced by calcium is ascribed to rotation around the glycosidic linkages. The binding process is co-operative and the binding constant of 10³ to 10⁴m^?1 is biologically significant. The findings are consistent with intramolecular binding. Hence, this study represents the first report of a polysaccharide undergoing a cation-induced intramolecular disorder-order process. The authors postulate that a function of the post-polymerization epimerization of d-glucuronate to l-iduronate is the attainment of the precise geometry required for co-operative calcium binding with consequent modulation of the flexibility of the tetrasaccharide units.     

13C/1H high power double magnetic resonance investigation of collagen backbone motion in fibrils and in solution

${}^{13}\text{C}{}^1\text{H}$ high power double magnetic resonance spectroscopy was used to investigate the mobility of the collagen peptide backbone. [1-¹³C]- and [2-¹³C]-glycine-labeled collagen samples (with >50% enrichment in ¹³C) were prepared via chick calvaria culture. ¹³C n.m.r.² spectra of labeled reconstituted collagen fibrils, of labeled helical collagen in solution, and of unlabeled bovine Achilles tendon collagen were obtained with scalar decoupling and with dipolar decoupling of protons. Proton-enhanced spectra were also obtained using cross-polarization techniques. n.m.r. parameters (linewidths, lineshapes, T₁ values, nuclear Overhauser enhancements, and cross polarization enhancements) were measured for the labeled samples and for collagen in natural abundance. Comparison of ¹³C n.m.r. parameters for bovine Achilles tendon fibrils and for reconstituted chick calvaria collagen fibrils established that chick calvaria collagen is a good model for the molecular dynamics of collagen in vivo.Spin-lattice relaxation times and nuclear Overhauser enhancements for [1-¹³C]- and [2-¹³C]glycine-labeled collagen indicated that R₁ ~2 × 10⁷s^?1 in solution, where R₁ is the diffusion constant for reorientation about the long axis of the molecule. A substantially smaller value for R₁ (2.6 × 10⁶s^?1) was calculated for an axially symmetric ellipsoid of revolution having dimensions appropriate to the collagen helix. The discrepancy between the rigid ellipsoid and n.m.r. values of R₁ suggests that the collagen molecule undergoes torsional reorientation, as well as rod-like reorientation, about its long axis.The T₁ and NOE values measured in the glycine-labeled fibrils show that rapid axial motion (R₁ ~ 10⁷s^?1) persists in the fibrillar state. In the collagen fibril the full width of the glycyl carbonyl powder pattern is 103 p.p.m. This value is substantially smaller than the rigid lattice value, 144 p.p.m., which provides further evidence for motion in the fibril. The observed powder pattern is axially asymmetric, which shows that certain azimuthal orientations are energetically preferred in the fibril. Taken together, the n.m.r. data provide strong evidence that rapid reorientation of the helix backbone occurs in the fibrils. This result shows that formation of a fibrillar structure does not require the existence of a unique set of intermolecular interactions at the helical surfaces.     

Scope and limitations of the simple 13C-n.m.r. method of structural analysis of carbohydrates: glucodisaccharides

The scope and limitations of the SIMPLE n.m.r. method (secondary isotope multiplet n.m.r. spectroscopy of partially labelled entities) has been investigated for a series of glucodisaccharies. ¹³C-SIMPLE n.m.r. measurements have been made on solutions of (1→1)- (α,α-trehalose), (1→2)- (sophorose and kojibiose), (1→3)- (laminaribiose), and (1→6)-linked (gentiobiose and isomaltose) glucodisaccharides in (CD₃)₂SO and the results combined with those previously published for (1→4)-linked analogues (maltose and cellobiose). Each linkage (and substitution) type gives rise to a unique pattern of ¹³C isotopomers which, in principle, may be used for complete assignment of the spectra and structural analysis of the molecule. The glucodisaccharides are difficult to analyse, compared with other disaccharides, because the presence of two glucose moieties leads to degeneracies of a few isotopic multiplets which cannot be differentiated by the magnitudes of the isotope effects. Assignments in aqueous solutions were obtained by using the DIS (differential isotope shift) n.m.r. method in conjunction with the results from SIMPLE n.m.r. In practice, nearly all of the signals can be assigned unequivocally and the remaining signals are choices between two possible assignments.     

Sodium-transport NADH-quinone reductase of a marineVibrio alginolyticus

The respiratory chain of a marine bacterium,Vibrio alginolyticus, required Na⁺ for maximum activity, and the site of Na⁺-dependent activation was localized on the NADH-quinone reductase segment. The Na⁺-dependent NADH-quinone reductase extruded Na⁺ as a direct result of redox reaction. It was composed of three subunits, , , and , with apparentMr of 52, 46, and 32 KDa, respectively. The reduction of ubiquinone-1 to ubiquinol proceeded via ubisemiquinone radicals. The former reaction was catalyzed by the FAD-containing subunit. This reaction showed no specific requirement for Na⁺. For the formation of ubiquinol, the presence of the subunit and the FMN-containing subunit was essential. The latter reaction specifically required Na⁺ for activity and was strongly inhibited by 2-n-heptyl-4-hydroxyquinolineN-oxide. It was assigned to the coupling site for Na⁺ transport. The mode of energy coupling of redox-driven Na⁺ pump was compared with those of decarboxylase- and ATP-driven Na⁺ pumps found in other bacteria.     

Synthesis of 7-(tetrahydropyran-2-yl)- and 7-(4-acetoxytetrahydropyran-2-yl)-ε-rhodomycinone and 7-(tetrahydropyran-2-yl)-ε-pyrromycinone

The ¹³C.n.m.r spectra of water-soluble and -insoluble glucans synthesized by enzymes isolated from six strains of Streptococcus mutans are interpreted. The glucans are shown to be composed primarily of α(1→3)- and α-(1→6)-linked glucosyl residues, and the relative abundance of each linkage is estimated from peak areas. Treatment of water-insoluble glucans with dextranase is found to result in water-soluble and -insoluble products, the former enriched in α-(1→6)-linkages and the latter in α-(1→3)-linkages. The structural conclusions arrived at by ¹³C-n.m.r. spectroscopy are consistent with data from methylation analysis and ¹H-n.m.r. spectroscopy.     

Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags

Using currently available MS-based methods, accurate mass measurements are essential for the characterization of DNA oligomers. However, there is a lack of specificity in mass peaks when the characterization of individual DNA species in a mass spectrum is dependent solely upon the mass-to-charge ratio (m/z). Here, we utilize nucleotide-specific tagging with stable isotopes to provide internal signatures that quantitatively display the nucleotide content of oligomer peaks in MS spectra. The characteristic mass-split patterns induced by the partially ¹³C/¹⁵N-enriched dNTPs in DNA oligomers indicate the number of labeled precursors and in turn the base substitution in each mass peak, and provide for efficient SNP detection. Signals in mass spectra not only reflect the masses of particular DNA oligomers, but also their specific composition of particular nucleotides. The measurements of mass tags are relative in the mass-split pattern and, hence, the accuracy of the determination of nucleotide substitution is indirectly increased. For high sample throughput, ¹³C/¹⁵N-labeled sequences of interest have been generated, excised in solution and purified for MS analysis in a single-tube format. This method can substantially improve the specificity, accuracy and efficiency of mass spectrometry in the characterization of DNA oligomers and genetic variations.     

Studies of glucose metabolism in Hymenolepis diminuta using 13C nuclear magnetic resonance

The metabolism in vitro of U-¹³C-glucose and NaH¹³CO₃ by two strains of adult Hymenolepis diminuta, the ANU and UT strains, was examined using ¹³C n.m.r. spectroscopy. The incubation medium and perchlorate extracts from worms incubated in vitro with U-¹³C-glucose showed incorporation of significant quantities of label into the end products succinate, lactate and acetate, and also into glycogen. Similar experiments with NaH¹³CO₃ showed incorporation principally into succinate C-1,4, plus significant labelling also in lactate C-1. This shows that nutochondrial malate or pyruvate contributes to the cytosolic pyruvate pool in H. diminuta. The metabolism of U-¹³C-glucose was followed directly by incubating live worms directly in the spectrometer. Worms from 24 h-fasted hosts metabolised the added glucose completely during an experimental period of 2 h and incorporation of label was evident in the time course spectra. Parasites from fed hosts metabolised the added glucose more slowly. This work confirms the accepted routes of glucose metabolism in H. diminuta and demonstrates the utility of the n.m.r. technique in investigating the metabolism of parasites.     

13C- and 1H-N.M.R. spectroscopy of permethylated α- and β-D-galactopyranoses

The complete assignment of the ¹³C- and ¹H-n.m.r. spectra of the permethylated α- and β-D-galactopyranoses was performed with the aid of specific trideuteriomethylation, heteronuclear spin-decoupling, and spectrum simulation. The n.m.r. data are discussed and compared with those of the permethylated glucopyranoses. Identification of partially methylated galactoses, e.g., as obtained in the methylation analysis of carbohydrates, can be carried out by conversion of the free hydroxyl functions into ²H- or ¹³C-labelled methoxyl groups, and comparison of the n.m.r. spectra of the resulting permethyl ethers with those of reference compounds.     

Methyl β-lactoside: 600-MHz H- and 75-MHz C-n.m.r. studies of H- and C-enriched compounds

Using UDP-d-galactose : 2-acetamido-2-deoxy-d-glucose 4-β-d-galactosyltransferase (EC 2.4.1.22), several methyl β-lactosides have been prepared with ²H- and/or ¹³C-enrichment at specific sites to facilitate study by ¹³C (75 MHz) and ¹H (600 MHz) n.m.r. spectroscopy. ¹³C-Chemical shift assignments were verified and the ¹H-spectrum of β-lactoside was fully assigned. Sites of enrichment were selected to permit all of the potential three-bond C-C and C-H couplings through the glycosidic bond to be obtained. Replacement of H-3 of the d-glucose residue of methyl β-lactoside with ²H allowed resolution of C-1–H-4′ coupling in the 600-MHz ¹H-spectrum. Single or multiple ¹³C-enrichment at C-1, C-2, C-3, C-1′, C-3′, and/or C-4′ in the disaccharide allowed observation of intra- and inter-residue couplings. ¹³C-Spin-lattice relaxation-times (T₁) are interpreted in terms of molecular motion in solution. The data suggest that methyl β-lactoside has an extended conformation with little rotation about the glycosidic bond. Inter-residue couplings are best explained by tortion angles of φ ~ 40° and ψ ~ 15°, indicating that the conformations of β-lactoside in solution and in the crystal are similar.     

Determination of the 13C chemical-shift tensors in a single crystal of methyl α-d-glucopyranoside.

The chemical shielding tensors and their direction cosines of the ¹³C nuclei in a single crystal of methyl α-d-glucopyranoside were determined by the high-resolution solid state n.m.r. technique. The results were used to assign the ¹³C cross-polarization, magic angle spinning (c.p.-m.a.s.) spectrum of a polycrystalline sample of that compound. The differences between the ¹³C chemical shifts observed in the c.p.-m.a.s. spectrum of the solid and of solutions of methyl α-d-glucopyranoside are discussed in terms of the different types of hydrogen bonds formed in the crystalline state and in solution.     

Stereospecificity of peptide synthesis by means of phosphorus derivatives: a model of peptide synthesis in molecular evolution

A hypothesis is presented to explain the prebiotic formation of optically pure oligo- and polypeptides from racemic amino acids. Stereospecific condensation reactions favouring the formation of isotactic stereosequences (l-l and d-d blocks) are a basic requirement of this hypothesis. Since phosphorus derivatives such as polyphosphates or nucleic acid imidazolides were postulated to be prebiotic condensing reagents, a variety of peptide syntheses by means of phosphorus derivatives was investigated. Dipeptides and tripeptides were prepared from N-protected d,l-amino acids or d,l-amino acid esters, and d,l-leucine and d,l-valine were subjected to condensation polymerizations. The stereosequences were analysed by means of ¹³C n.m.r. spectroscopy. More than 80% of all condensations were more or less stereospecific and in all cases isotactic sequences were predominant. In the case of poly(d,l-leucines), ¹³C n.m.r. cross-polarization/magic angle spinning (CP/MAS) spectra revealed the formation of α-helical blocks.     

Carbon-13 and proton nuclear magnetic resonance studies on methyl aldofuranosides and their O-alkyl derivatives

The effect of O-alkylation on the carbon-13 n.m.r. spectra of methyl pentofuranosides has been determined. O-Alkylation of an OH group displaced the signal of the appended.¹³C nucleus downfield, whereas the adjacent ¹³C nuclei were, in most instances, shifted upfield to a smaller extent. The effect of O-methylation was appreciably larger than O-isopropylation or O-glycosylation, but either O-methyl or O-isopropyl derivatives may be used as models for interpreting the spectra of furanoid oligo- and poly-saccharides, including the galactomannan of Penicillium charlesii. The signal displacements are, to a large extent, comparable to those observed in the conformationally more stable mannopyranose series, so that they are insensitive to effects of steric distortion and population (or both). These effects occurred on 3-O-alkylation of methyl pentofuranosides, as appreciable changes in J_1,2 values in their p.m.r. spectra were observed.