Experimental determination of the three-dimensional structure of oligosaccharides

Incremented alkyl derivatives enhance collision induced glycosidic bond cleavage in mass spectrometry of disaccharides

Electrospray ionization and collision induced dissociation on a triple quadrupole mass spectrometer were used to determine the effect of spatial crowding of incremented alkyl groups of two anomeric pairs of peralkylated (methyl to pentyl) disaccharides (maltose/cellobiose and isomaltose/gentiobiose). Protonated molecules were generated which underwent extensive fragmentation under low energy conditions. For both the 1 --> 4 and 1 --> 6 alpha and beta isomers, at comparable collision energies the methyl derivative exhibited the least fragmentation followed by ethyl, propyl, butyl, and pentyl. Collision energy is converted to rotational-vibrational modes in competition with bond cleavage, as represented by the slope of product/parent ion (D/P) ratio versus offset energy. Variable rotational freedom at the glycosidic linkage with incremented alkyl groups is hypothesized to be responsible for this effect. Discrimination of anomeric configuration was also assessed for these stereoiosmeric disaccharides. A systematic study showed that an increasing discrimination was attained for the 1 --> 4 isomeric pair as the size of the derivative increased from methyl to pentyl. No anomeric discrimination was attained for the 1 --> 6 isomeric pair. Parent and product ion scans confirmed the consistency of fragmentation pathways among derivatives. Chem-X and MM3 molecular modeling programs were used to obtain minimum energy structures and freedom of motion volumes for the permethylated disaccharides. The modeling results correlated with the fragmentation ratios obtained in the mass spectrometer giving strong indication that the collision induced spectra are dependent on the freedom of rotational motion around the glycosidic bond.

Structure and conformation of complex carbohydrates of glycoproteins, glycolipids, and bacterial polysaccharides

For nuclear magnetic resonance determinations of the conformation of oligosaccharides in solution, simple molecular mechanics calculations and nuclear Overhauser enhancement measurements are adequate for small oligosaccharides that adopt single, relatively rigid conformations. Polysaccharides and larger or more flexible oligosaccharides generally require additional types of data, such as scalar and dipolar coupling constants, which are most conveniently measured in 13C-enriched samples. Nuclear magnetic resonance relaxation data provide information on the dynamics of oligosaccharides, which involves several different types of internal motion. Oligosaccharides complexed with lectins and antibodies have been successfully studied both by X-ray crystallography and by nuclear magnetic resonance spectroscopy. The complexes have been shown to be stabilized by a combination of polar hydrogen bonding interactions and van der Waals attractions. Although theoretical calculations of the conformation and stability of free oligosaccharides and of complexes with proteins can be carried out by molecular mechanics methods, the role of solvent water for these highly polar molecules continues to present computational problems.

Molecular dynamics simulation of glycoprotein-glycans of immunoglobulin G and immunoglobulin M

Glycoprotein-glycans have recently been implicated to play a variety of functional roles. The same glycan chain have been found complexed with proteins of diverse functions. In this article two such glycan chains found attached to Fc regions of immunoglobulin G and immunoglobulin M have been studied. An extensive simulated annealing procedure have been adopted to arrive at a low-energy minimum of the two oligosaccharides. Molecular dynamics simulations have been performed to study the flexibility of the glycosidic linkages. It was found that both glycan chains can undergo conformational transitions and adopt folded and extended conformations. The two beta (1-2) linkages of complex-type glycan had been found to prefer different conformational regime and the terminal fucose linked to the GlcNAc residue drastically modifies the GlcNAc beta (1-4) GlcNAc linkage conformation. In the high-mannose type glycan chain alpha (1-3) linkages can induce flexibility in addition to the alpha (1-6) linkages. The results have been compared with recent experimental nmr and fluorescence energy transfer data.

Measurement of long-range carbon-carbon coupling constants in a uniformly enriched complex polysaccharide

A quantitative coherence transfer scheme for 1H-detected measurement of long-range carbon-carbon coupling constants in NMR spectra of complex carbohydrates is described. It is applied to a uniformly highly 13C-enriched monosaccharide and to a complex cell wall polysaccharide from Streptococcus mitis J22 having seven distinct sugars in the repeating subunit. Coupling values within the ring were compared to published values for monosaccharides to demonstrate the validity of the method. An attempt was made to relate coupling constants between carbon atoms across the glycosidic linkage to the dihedral angles of a recently published flexible model for the polysaccharide which is based on 3JCH data. The experimental coupling constants do not agree with any single conformation demonstrating that the repeating subunit of the polysaccharide must be flexible. This conclusion is in accord with results of molecular modeling nuclear Overhauser effect and 3JCH data.

Studies on the structure and the solution conformation of an acidic extracellular polysaccharide isolated from Bradyrhizobium

The structure of an acidic extracellular polysaccharide isolated from Bradyrhizobium (Chamaecytisus proliferus) has been elucidated by hydrolysis, methylation analysis, and 1D and 2D 1H- and 13C-NMR spectroscopy of the complete polysaccharide. The NMR spectrum showed that microheterogeneity was present due to the minor existence of a variety of O-acetyl groups. Thus, a deacetylated sample was prepared by alkaline treatment which was then fully analysed. The deacetylated polysaccharide has the following sequence: -->3)-[alpha-D-Galp-(1-->6)-alpha-D-Glcp-(1-->3)-beta-D-Glcp-(1-->3)- alpha-D-GalpA-(1-->3)-alpha-D-Manp-(1--> The sample is partially O-methylated at position 4 of the alpha-D-Galp-(1-->6) unit. In addition, the same moiety of the native sample is also partially and heterogeneously O-acetylated. The conformational features of the deacetylated sample have been evaluated by molecular mechanics and dynamics calculations and NOE spectroscopy. The results indicate that the polysaccharide may adopt a variety of three dimensional shapes, and that there is a fair agreement between the NMR-derived distances and those provided by the calculations

Solution conformation and dynamics of an extracellular polysaccharide isolated from Bradyrhyzobium as deduced from 1H-NMR off resonance ROESY and 13C-NMR relaxation measurements

The conformational and dynamical features of an extracellular branched deacetylated polysaccharide isolated from Bradyrhizobium (Chamaecytisus proliferus) have been investigated by homo and heteronuclear NMR methods. 1H-NMR cross relaxation rates have been obtained for this polysaccharide through regular NOESY and ROESY spectra as well as by modern off resonance ROESY techniques. Local proton-proton correlation times as well as interproton distances have been obtained. 13C-NMR relaxation parameters (T1, T2, NOE) have also been measured at two different magnetic fields and interpreted using different approximations based on the Lipari and Szabo model free approach. The analysis of the data indicates the existence of important flexibility for the different linkages of the polysaccharide. Motions in the range of several ns contribute to the relaxation of the macromolecule, although faster internal motions in the 600-800 ps time scales are also present. These time scales indicate that segmental motions as well as internal motions around the glycosidic linkages are the major sources of relaxation for this molecule at 299 K.

Solution conformation and dynamics of a tetrasaccharide related to the Lewix(X) antigen deduced by 1H NMR NOESY, ROESY, and T-ROESY measurements

The conformational and dynamical features of a Le(X) tetrasaccharide analogue GalNAc (alpha 1-3)Gal(beta 1-4)[Fuc(alpha 1-3)]Glc(beta OMe) 1 have been studied through 1H NMR relaxation measurements. The results indicate that the different glycosidic linkages of 1 present distinct conformational flexibility in solution. In addition, the use of T-ROESY experiments in conformational analysis of oligosaccharides is explored emphasizing its scope and limitations.

A flexible model for the cell wall polysaccharide of Streptococcus mitis J22 determined by three-dimensional 13C edited nuclear overhauser effect spectroscopy and 13C-1H long-range coupling constants combined with molecular modeling

We report on the conformation of a tetrasaccharide fragment in the repeating subunit of the cell wall polysaccharide of Streptococcus mitis J22, a receptor for the lectin of Actinomyces viscosus T14V in a bacterial coaggregation that is important in the ecological interactions of oral bacteria. Although there is considerable overlap of the 1H-nmr signals, some cross peaks can be extracted from conventional two-dimensional nuclear Overhauser effect spectroscopy (NOESY) data on the polysaccharide. These data cannot be fit to a single conformation of the tetrasaccharide fragment. Therefore we have prepared a polysaccharide sample fully enriched in 13C from which we have determined accurate NOESY cross-peak volumes in a three-dimensional heteronuclear-resolved spectrum that allows accurate determination of many more NOESY cross peaks than does conventional two-dimensional spectroscopy. We have also used the 13C enriched polysaccharide to measure accurate values of long-range 13C-1H coupling constants that can be correlated with glycosidic dihedral angles. Molecular modeling calculations on the polysaccharide fragment, including molecular dynamics simulations, identify multiple low-energy conformations. This result is to be contrasted with previous calculations on blood group oligosaccharides in our laboratory using similar methods that showed relatively rigid conformations with little flexibility of the glycosidic linkages. The present NOESY and 3JCH data can be reconciled with a model for the antigenic tetrasaccharide in which three distinct conformations are in fast exchange. We propose that some carbohydrate epitopes such as those of the blood group oligosaccharides are relatively rigid while others such as the tetrasaccharide fragment in these studies exhibit much greater flexibility.

Solution conformations of a biantennary glycopeptide and a series of its exoglycosidase products from sequential trimming of sugar residues

Linkages between sugar residues in branched oligosaccharides exhibit various degrees of flexibility. This flexibility, together with other forces, determines the overall solution conformation of oligosaccharides. We used the method of time-resolved resonance energy transfer to study the solution conformations of a biantennary glycopeptide and its partially trimmed products by exoglycosidases. The N-terminal of the glycopeptide was labeled with 2-naphthyl acetic acid as a fluorescent donor. Either terminal sugar residue, Gal6', on the branch bearing 6-linked Man (antenna 6'), or Neu5Ac on the branch bearing 3-linked Man (antenna 6) was labeled with 5-dimethylaminophthalene-1-sulfonyl as an acceptor. The distance and distance distributions between the terminals were measured. In the intact biantennary glycopeptide, the donor-acceptor distance distribution of antenna 6' is bimodal with a majority of the population in the extended conformation and that of antenna 6 in one very broad population. The Neu5Ac on antenna 6 is oriented toward the N-terminal at low temperature and adopts a more extended form at high temperature. The removal of individual sugar residues along one of the two antenna in the biantennary oligosaccharide has a small effect on the distance distribution of the remaining antenna for both antennae 6 and 6'. Together with previous studies of the triantennary glycopeptides (Rice, K. G., Wu, P. G., Brand, L., and Lee, Y.C. (1993) Biochemistry 32, 7264-7270), our results suggest that both steric hindrance and inter-residue hydrogen bonding are very important in the folding pattern in oligosaccharide structures.

Studies of the bound conformations of methyl alpha-lactoside and methyl beta-allolactoside to ricin B chain using transferred NOE experiments in the laboratory and rotating frames, assisted by molecular mechanics and dynamics calculations

The conformation in solution of methyl beta-galactopyranosyl-(1-->4)-alpha-glucopyranoside (methyl alpha-lactoside) and methyl beta-galactopyranosyl-(1-->6)-beta-glucopyranoside (methyl beta-allolactoside) has been studied through NMR spectroscopy and molecular mechanics calculations. NOE measurements both in the laboratory and rotating frames, have been interpreted in terms of an ensemble average distribution of conformers. Molecular mechanics calculations have been performed to estimate the probability distribution of conformers from the steric energy maps. The experimental results indicate that methyl alpha-lactoside spends about 90% of its time in a broad low-energy region close to the global minimum, while methyl beta-allolactoside presents much higher flexibility. The conformational changes that occur when both disaccharides are bound to the ricin B chain in aqueous solution have been studied using transferred NOE experiments at several protein/ligand ratios. The observed data indicate that the protein causes a conformational variation in the torsion angles of methyl alpha-lactoside changing towards smaller angle values (phi/psi approximately -20/-20), although the recognized conformer is still within the lowest energy region. In particular, the torsional changes separate Gal H1 from Glc H3 and Glc H6 protons, with a noticeable decrease in the intensities of the corresponding NOE cross-peaks, which were clearly observed for the free disaccharide. On the other hand, different conformations around the phi, psi, and omega glycosidic bonds of methyl beta-allolactoside are recognized by the lectin. In fact, for the methyl-beta-allolactoside-ricin-B complex, only the NOESY cross-peaks corresponding to the protons of the galactose residue are negative, as expected for a molecule in the slow motion regime. In contrast, the corresponding cross peaks for the glucose residue were about zero, as expected for a molecule whose motion is practically independent of the protein. However, for the methyl-alpha-lactoside-ricin-B complex, all the NOESY cross-peaks for both the galactose and glucose moieties were clearly negative. From the NMR experimental point of view, it is demonstrated that the comparison of longitudinal and transversal transferred NOEs allows one to clearly differentiate direct enhancements from spin diffusion effects, which are of major concern when analysing NOE spectra of macromolecules.(ABSTRACT TRUNCATED AT 250 WORDS)

The use of CVFF and CFF91 force fields in conformational analysis of carbohydrate molecules. Comparison with AMBER molecular mechanics and dynamics calculations for methyl alpha-lactoside

The solution conformation of methyl alpha-lactoside has been studied through molecular mechanics calculations using the AMBER/Homans, CVFF and CFF91 force fields, and compared to NMR nuclear Overhauser data. Steady-state and transient nuclear Overhauser effects (NOEs) have been interpreted in terms of the ensemble average distribution of conformers. The NOEs have been analysed using the complete relaxation matrix approach for a rigid and isotropic motion model. The molecular mechanics calculations have been performed at two dielectric constants (i.e. epsilon = 1 and 80 debyes, or epsilon = r and 80 debyes) in an exhaustive way, and, in some cases, have been complemented by specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. Our results indicate that the beta-(1-->4) glycosidic linkage shows some fluctuations between three low-energy regions, although it spends about 90% of its time in the region close to the global minimum. The observed conformation of methyl alpha-lactoside seems to be closer to that predicted by CVFF, although the AMBER/Homans results are also in qualitative agreement with the experimental data.

Conformational features of galacturonans. I. Structure and energy minimization of charged and uncharged galacturonan dimeric units

Structural parameters (e.g. the geometry, partial charges and dipole moment) of the alpha-D-galacturonic residue have been calculated by using semi-empirical quantum mechanical methods on several combinations of either the uncharged or charged forms, GalAH and GalA-, respectively. Three residue types have been explored: (i) the isolated residue, termed GEO1 and GEO1C for GalAH and GalA-, respectively; (ii) the residue with a methyl group attached to the O4 and O1 positions (GEO2 and GEO2C); and (iii) the internal residue in a trimer, e.g. GalAH-GalAH-GalAH or the corresponding fully charged version (GEO3 and GEO3C). The presence of a charged group in the galacturonate residue and the distribution of the excess negative charge on the molecule lead to significant differences in the structural parameters in comparison with those of the uncharged galacturonic residue. These perceptible differences in internal coordinates of GalAH and GalA- residues appear to play a major role in the delimitation of the conformational space that is accessible to the dimers, as clearly seen by inspection of the conformational maps. Although the overall features seem alike, the maps show that the position of the minimum and the shape of the lower energy region significantly change if one or both residues in the dimer are charged. The relevance of these results for the conformational properties of polygalacturonate chains is discussed elsewhere (Ruggiero et al. Int. J. Biol. Macromol. 1995, 17, 213-218).

The solution conformation of hyaluronan: a combined NMR and molecular dynamics study

Hyaluronan (HA) is a negatively charged glycosaminoglycan that exhibits a wide variety of biological effects mediated by binding to cell-surface and extracellular matrix proteins (hyaladherins). Short HA oligosaccharides have been shown to retain the specific interactions and biological effects of high molecular weight HA. Although it has a simple disaccharide repeating unit, the aqueous solution conformation of HA has been very difficult to determine because of strong coupling and overlapping resonances. In this study, we propose aqueous solution conformations for an octasaccharide of HA, derived from proton-proton NOE data and restrained molecular dynamics. To overcome spectral overlap and strong coupling, alternate methods for extracting distance restraints were employed. Restrained molecular dynamics calculations yielded one set of interglycosidic angle values for the beta (1,3) linkage (phi 13 = 46 degrees, psi 13 = 24 degrees). In contrast, two sets of values for the beta (1,4) linkage were consistent with the NOE restraints (phi 14 = 24 degrees, psi 14 = -53 degrees or phi 14 = 48 degrees, psi 14 = 8 degrees). The potential difference in flexibility for the two linkages is consistent with unrestrained as well as the restrained molecular dynamics trajectories described here. The conformational parameters obtained from restrained molecular dynamics are used to predict helical parameters of high molecular weight HA and will provide a basis for studies of HA binding to proteins.

Measurement of long-range2 13C-1H coupling constants of 95% uniformly 13C-labeled polysaccharide from Streptococcus mitis J22

The coaggregation of Streptococcus mitis strain J22 in the early stages of dental plaque formation has been shown to result from interaction of cell wall polysaccharides with lectins on the surface of other oral bacterial species. This bacterium was grown in a medium containing 13C as the sole carbon source. We have isolated the lectin receptor polysaccharide from this strain with full enrichment in 13C and have determined a number of two-bond and three-bond 13C-1H coupling constants from measurements of the offsets in two-dimensional homonuclear nmr spectra [exclusive correlated spectroscopy (E-COSY) method]. A scheme for reliable extraction of these coupling constants from homonuclear Hartmann-Hahn and nuclear Overhauser effect spectroscopy spectra is tested in model compounds. We interpret the three-bond coupling across the glycosidic linkage in terms of dihedral angles in order to provide conformational information to supplement molecular modeling and nuclear Overhauser effect data. We show that the E-COSY method works well even for coupling constants smaller than the nmr line width and that a number of the 3JCH across the glycosidic linkage are in the range of 1-2 Hz, which is much smaller than many previously reported values.

13C NMR studies of wheat germ agglutinin interactions with N-acetylglucosamine at a magnetically oriented bilayer surface

The orientation of synthetic 13C-labeled glycolipid receptors and their interaction with the plant lectin wheat germ agglutinin have been studied in an oriented membrane system using NMR spectroscopy. A series of 2-[1,2-13C2]acetamido-2-deoxy-beta-D-glucopyranosides were synthesized with between zero and four hydrophilic ethoxy units between the headgroup and an alkyl chain which anchors the receptors in the bilayers. The chemical shift anisotropy of the 13C carbonyl and a 13C-13C dipolar coupling between the labeled carbons provide information about the orientation and dynamics of the receptor headgroup in oriented membrane systems. It was found that the headgroups of the receptors with two, three, or four ethoxy units appeared isotropic when incorporated in the oriented bilayers, but those of the receptors with zero or one ethoxy units were significantly ordered by the bilayers. The average orientations consistent with measured spectral parameters were determined for the receptors with zero and one ethoxy units and were found to coincide with low-energy conformations from molecular modeling. When the plant lectin wheat germ agglutinin was added to the sample, only the receptors with two, three, or four ethoxy units separating the headgroup from the alkyl chain showed evidence of binding by the lectin. Although the 13C-labeled resonances broadened when the protein bound, no changes in dipolar couplings or chemical shift anisotropies could be detected, suggesting that the motion of the headgroup was slowed by protein binding, but average orientation and overall order changed little. Competition studies demonstrated that none of the lectin/receptor complexes are more stable than the complex of the lectin and N-acetylglucosamine in solution. These results suggest that the membrane does not stabilize the interactions of wheat germ agglutinin with these cell-surface receptors. Furthermore, molecular modeling demonstrates that the zero- and one-spacer receptors may not bind wheat germ agglutinin because the orientations of the N-acetyl groups in these receptors would result in significant steric contacts between the lectin/receptor complex and the membrane.

Conformational equilibria of 4-thiomaltose and nitrogen analogues of maltose in aqueous solutions

The 1H and 13C NMR data at neutral pH are presented for methyl 4-thio-beta- and alpha-maltoside (1 and 2) together with methyl 1-thio-alpha-D-glucopyranoside (3) and methyl 4-thio-alpha-D-glucopyranoside (4) as reference compounds. Furthermore, the NMR data at high and low pH are presented for the 4-amino-4-deoxy analogues of methyl alpha-maltoside (5 and 6) and the 5-amino-5-deoxy analogue (8) together with reference compounds methyl 4-amino-4-deoxy-alpha-D-glucopyranoside (7) and 1-deoxynojirimycin (9). The experimental NMR data are assigned by 1- and 2-dimensional spectroscopy at 500 and 600 MHz. The conformational preferences of the maltose analogues 1, 2, 5, 6 and 8 are evaluated by difference NOE experiments, 13C-1H long-range coupling constants, chemical-shift comparison with model compounds and hard-sphere force field calculations for 1 using Monte Carlo simulations. Additionally, the results are compared with extensive experimental NOE data for methyl alpha- and beta-maltoside and the results discussed in light of earlier studies.

An NMR spectroscopic and conformational study of 12 pseudo-disaccharides (D-glucopyranosyl-5a-carba-D- and -L-glucopyranoses)

NMR spectroscopic data for 12 pseudo-disaccharides of the general structure: (alpha or beta)-D-glucopyranosyl-(1-->chi)-5a-carba-(D or L)-glucopyranose, representing analogues of laminaribiose (beta-D-Glc p, chi = 3), cellobiose (beta-D-Glc p, chi = 4), and maltose (alpha-D-Glc p, chi = 4) are presented. The assigned NMR chemical shifts together with NOE difference measurements in association with calculations applying the HSEA force field combined with Monte Carlo simulations have been used to assess the conformational preferences of the investigated compounds. The results are correlated with general structural features involved in the interactions between monosaccharide units of oligosaccharides.

Carbohydrates and drug discovery--the role of computer simulation

Recent advances in the molecular modelling of carbohydrates have brought this technique to a level comparable with that of protein and nucleic acid simulations. After a brief introduction to the techniques used in the computer simulation of carbohydrates and carbohydrate interactions, an overview of applications in the field of carbohydrate-related drug discovery is presented.

Conformation of the oligosaccharide receptor for E-selectin

A tetrasaccharide related to the blood group oligosaccharides, known as sialyl LewisX, has been proposed as the receptor for the lectin responsible for leukocyte adhesion named alternatively as E-selectin or ELAM-1. The 13C- and 1H-nmr spectra have been completely assigned for a tetrasaccharide model of this receptor, Neu5Ac alpha-(2-->3)-Gal beta-(1-->4)-[Fuc alpha-(1-->3)-]GlcNAc beta-NHAc. Quantitative nuclear Overhauser data (NOESY) have been recorded and analyzed by a complete spin matrix simulation method. Conformational space was exhaustively searched and all conformational models whose simulated NOESY spectra matched the experiment were found. Molecular mechanics and molecular dynamics calculations were carried out to test whether the experimental conformations are low energy and thus likely to represent true single conformations for the tetrasaccharide. It was concluded that while the LewisX trisaccharide portion of the compound adopts a single conformation, there is likely to be some flexibility about the Neu5Ac alpha-(2-->3)-linkage. A model featuring fast exchange between two different conformations of this linkage is found to be consistent with both the nmr experiments and the molecular dynamics simulations.

Protein glycosylation. Structural and functional aspects

During the last decade, there have been enormous advances in our knowledge of glycoproteins and the stage has been set for the biotechnological production of many of them for therapeutic use. These advances are reviewed, with special emphasis on the structure and function of the glycoproteins (excluding the proteoglycans). Current methods for structural analysis of glycoproteins are surveyed, as are novel carbohydrate-peptide linking groups, and mono- and oligo-saccharide constituents found in these macromolecules. The possible roles of the carbohydrate units in modulating the physicochemical and biological properties of the parent proteins are discussed, and evidence is presented on their roles as recognition determinants between molecules and cells, or cell and cells. Finally, examples are given of changes that occur in the carbohydrates of soluble and cell-surface glycoproteins during differentiation, growth and malignancy, which further highlight the important role of these substances in health and disease.

Carbohydrate analysis

Carbohydrate analysis is an active field that is expanding rapidly. Hundreds of new structures are reported each year and methods for screening glycopolymers for known structures are now becoming accessible to the nonspecialist. Detailed structure analysis of recombinant glycoproteins has become relatively routine in specialist laboratories. Rapid advances are being made in the understanding of structure and function of biologically active carbohydrates that are of interest to the pharmaceutical industry.