Conformation Of Glycosidic Linkage Research Articles

Methyl α-D-galactopyranosyl-(1→3)-β-D-galactopyranoside and methyl β-D-galactopyranosyl-(1→3)-β-D-galactopyranoside: Glycosidic linkage conformation determined from MA'AT analysis.

MA'AT analysis has been applied to two biologically-important O-glycosidic linkages in two disaccharides, α-D-Galp-(1→3)-β-D-GalpOMe (3) and β-D-Galp-(1→3)-β-D-GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans-O-glycosidic NMR spin-couplings to either phi (ϕ') or psi (ψ'), and experimental 3 JCOCH , 2 JCOC , and 3 JCOCC spin-couplings measured in aqueous solution in 13 C-labeled isotopomers, probability distributions of ϕ' and ψ' in each linkage were determined and compared to those determined by aqueous 1-μs molecular dynamics (MD) simulation. Good agreement was found between the MA'AT and single-state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values of ϕ' and ψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger for ϕ' determined from MA'AT analysis than from MD for both linkages. The MA'AT model of the α-Galp-(1→3)-β-Galp linkage agrees well with those determined previously using conventional NMR methods (3 JCOCH values and/or 1 H-1 H NOEs), but some discrepancy was observed for the β-Galp-(1→3)-β-Galp linkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X-ray crystal structures show ranges of ϕ' and ψ' for both linkages that include the mean angles determined from MA'AT analyses, although both angles adopt a wide range of values in the crystalline state, with ϕ' in β-Galp-(1→3)-β-Galp linkages showing greater-than-expected conformational variability.

Synthesis and interaction with growth factors of sulfated oligosaccharides containing an anomeric fluorinated tail

Compounds that mimic the biological properties of glycosaminoglycans (GAGs) and can be more easily prepared than the native GAG oligosaccharides are highly demanded. Here, we present the synthesis of sulfated oligosaccharides displaying a perfluorinated aliphatic tag at the reducing end as GAG mimetics. The preparation of these molecules was greatly facilitated by the presence of the fluorinated tail since the reaction intermediates were isolated by simple fluorous solid-phase extraction. Fluorescence polarization competition assays indicated that the synthesized oligosaccharides interacted with two heparin-binding growth factors, midkine (MK) and FGF-2, showing higher binding affinities than the natural oligosaccharides, and can be therefore considered as useful GAG mimetics. Moreover, NMR experiments showed that the 3D structure of these compounds is similar to that of the native sequences, in terms of sugar ring and glycosidic linkage conformations. Finally, we also demonstrated that these derivatives are able to block the MK-stimulating effect on NIH3T3 cells growth.

Molecular dynamics study of sucrose aqueous solutions: From solution structure to transport coefficients

In this work, we study the applicability of the equilibrium molecular dynamics methods for the prediction of solution structure, equation of state and transport properties of sucrose aqueous solution for various concentrations and temperatures. The OPLS-AA force field with 1.14*CM1A charge corrections is used to describe the interactions in the model. We analyze the prediction power of the model against the experimental data and simulation results, obtained previously in CHARMM, OPLS-AA, GLYCAM06 and their modifications. The glycosidic linkage conformations of sucrose in solution are found. Their independence from the sugar concentration and the appearance of the conformation region at temperatures from 283 K to 308 K are observed. Sucrose solution densities are calculated for different sugar concentrations and temperatures. The obtained viscosities and sucrose diffusion coefficients match the experimental data at low sucrose concentrations, and diverge within 41% from the experiment as the concentration increases. The change of boundary condition in Stokes–Einstein formula is observed with an increase of the sucrose concentration above 40%.

Conformational Properties of Glycosaminoglycan Disaccharides: A Molecular Dynamics Study.

The structure and conformation of glycosaminoglycans (GAGs) are of central importance to understand the mechanisms behind their functions in biological systems. Due to the inherent chemical and structural heterogeneity of GAGs, focusing on longer, naturally existing GAG chains hinders drawing conclusions on the influence of the chemical functionalization on the basic conformational degree of freedom, that is, the dynamic shape of glycosidic linkage present in the particular disaccharide repeating unit. In the present study, we have considered the complete set of 106 GAG-related disaccharides, being potential building blocks for longer GAG chains (including hyaluronan, chondroitin, keratan, dermatan, and heparan). Both the unfunctionalized units and all possible combinations of either partially or fully sulfated derivatives contribute to this number. The unbiased and enhanced sampling molecular dynamics simulations provide a link to understand the influence of sulfation on the conformational properties of GAG glycosidic linkages. Residue-residue hydrogen bonding is not significant for either the glycosidic linkage conformation or its flexibility. It was found that in the majority of cases, the dominating conformation of the linkage is weakly affected by sulfation and the main role is played by the steric and stereoelectronic effects. However, there exist numerous cases where sulfation increases the contribution of alternative conformations to a nonnegligible extent and, in some rare cases (restricted to disaccharides building heparan), leads to the reorientation of the glycosidic linkage. The identified sulfation sites, being the most important in this context, are C6 and C3 at the GlcNAc residue. Finally, the full set of free energy maps relying on the glycosidic dihedral angle values for diverse GAG disaccharides are provided; they may be used for further studies, focused on longer GAG chains.

Physicochemical, Structural, and Biological Properties of Polysaccharides from Dandelion.

The edible and medicinal perennial herb dandelion is known to have antitumor, antioxidant, and anticomplement properties. However, the structural characterization and biological effects of its polysaccharides are not well understood. Here, we aimed to extract and investigate a novel polysaccharide from dandelion. A water-soluble polysaccharide, PD1-1, was successfully obtained from dandelion through ultrasonic-assisted extraction and purification using diethylaminoethyl (DEAE)–Sepharose fast flow and Sephadex G-75 columns. The results showed that PD1-1 is an inulin-type polysaccharide with a molecular weight of 2.6 kDa and is composed of glucose (52.39%), and mannose (45.41%). Glycosidic linkage analysis demonstrated that PD1-1 contains terminal α-d-Man/Glcp-(1→ and →1)-β-d-Man/Glcf-(2→ glycosidic linkage conformations. A physicochemical analysis indicated that PD1-1 has a triple helix structure and exhibits important properties, including good swelling, water-holding, and oil-holding capacities. Furthermore, PD1-1 showed good antioxidant activities in DPPH and hydroxyl free radical scavenging abilities, with IC50 values of 0.23 mg/mL and 0.25 mg/mL, respectively, and good hypoglycemic activities in α-amylase and α-glucosidase inhibition, with IC50 values of 0.53 mg/mL and 0.40 mg/mL, respectively, in a concentration-dependent manner. Results suggest that PD1-1 possesses efficacious antioxidant and hypoglycemic properties and has potential applications as a functional food ingredient.

Extension of the GROMOS 56a6CARBO/CARBO_R Force Field for Charged, Protonated, and Esterified Uronates.

An extension of the GROMOS 56a6CARBO/CARBO_R force field for hexopyranose-based carbohydrates is presented. The additional parameters describe the conformational properties of uronate residues. The three distinct chemical states of the carboxyl group are considered: deprotonated (negatively charged), protonated (neutral), and esterified (neutral). The parametrization procedure was based on quantum-chemical calculations, and the resulting parameters were tested in the context of (i) flexibility of the pyranose rings under different pH conditions, (ii) conformation of the glycosidic linkage of the (1 → 4)-type for uronates with different chemical states of carboxyl moieties, (iii) conformation of the exocyclic (i.e., carboxylate and lactol) moieties, and (iv) structure of the Ca2+-linked chain-chain complexes of uronates. The presently proposed parameters in combination with the 56a6CARBO/CARBO_R set can be used to describe the naturally occurring polyuronates, composed either of homogeneous (e.g., glucuronans) or heterogeneous (e.g., pectins, alginates) segments. The results of simulations relying on the new set of parameters indicate that the conformation of glycosidic linkage is nearly unaffected by the chemical state of the carboxyl group, in contrary to the ring conformational equilibria. The calculations for the poly(α-d-galacturonate)-Ca2+ and poly(α-l-guluronate)-Ca2+ complexes show that both parallel and anitiparallel arrangements of uronate chains are possible but differ in several structural aspects.

Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.

Exploration of the conformational spaces of flexible oligosaccharides is essential to gain deeper insights into their functional mechanisms. Here we characterised dynamic conformation of a high-mannose-type dodecasaccharide with a terminal glucose residue, a critical determinant recognised by molecular chaperones. The dodecasaccharide was prepared by our developed chemoenzymatic technique, which uses 13 C labelling and lanthanide tagging to detect conformation-dependent paramagnetic effects by NMR spectroscopy. The NMR-validated molecular dynamics simulation produced the dynamic conformational ensemble of the dodecasaccharide. This determined its spatial distribution as well as the glycosidic linkage conformation of the terminal glucose determinant. Moreover, comparison of our results with previously reported crystallographic data indicates that the chaperone binding to its target oligosaccharides involves an induced-fit mechanism.

O-Acetyl Side-Chains in Monosaccharides: Redundant NMR Spin-Couplings and Statistical Models for Acetate Ester Conformational Analysis.

α- and β-d-glucopyranose monoacetates 1-3 were prepared with selective 13C enrichment in the O-acetyl side-chain, and ensembles of 13C-1H and 13C-13C NMR spin-couplings (J-couplings) were measured involving the labeled carbons. Density functional theory (DFT) was applied to a set of model structures to determine which J-couplings are sensitive to rotation of the ester bond θ. Eight J-couplings (1JCC, 2JCH, 2JCC, 3JCH, and 3JCC) were found to be sensitive to θ, and four equations were parametrized to allow quantitative interpretations of experimental J-values. Inspection of J-coupling ensembles in 1-3 showed that O-acetyl side-chain conformation depends on molecular context, with flanking groups playing a dominant role in determining the properties of θ in solution. To quantify these effects, ensembles of J-couplings containing four values were used to determine the precision and accuracy of several 2-parameter statistical models of rotamer distributions across θ in 1-3. The statistical method used to generate these models has been encoded in a newly developed program, MA'AT, which is available for public use. These models were compared to O-acetyl side-chain behavior observed in a representative sample of crystal structures, and in molecular dynamics (MD) simulations of O-acetylated model structures. While the functional form of the model had little effect on the precision of the calculated mean of θ in 1-3, platykurtic models were found to give more precise estimates of the width of the distribution about the mean (expressed as circular standard deviations). Validation of these 2-parameter models to interpret ensembles of redundant J-couplings using the O-acetyl system as a test case enables future extension of the approach to other flexible elements in saccharides, such as glycosidic linkage conformation.

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility.

The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ - ψ space and hydrogen-bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.

Ring inversion properties of 1→2, 1→3 and 1→6-linked hexopyranoses and their correlation with the conformation of glycosidic linkages

Enhanced-sampling molecular dynamics simulations performed within the GROMOS 56a6CARBO_R force field were applied in order to elucidate ring-inversion properties of hexopyranose residues in a chain for the case of α(1→n) and β(1→n) glycosidic linkages (n = 2, 3 or 6). The results indicate that ring-inversion free energies calculated for residues in a chain are weakly correlated with those of corresponding monomers, except of the case of 1→6 linkages. This, in combination with the results for O1-methyl-hexopyranosides (Plazinski et al, 2016), suggests that both the type of functionalization (glycolysation vs. methylation) and the topology of glycosidic linkage play an important role in possible alterations of the hexopyranose ring flexibility. Additionally, the correlation of the ring shape with the preferred geometry of glycosidic linkages was investigated. The linkages of the 1→2, 1→3 and 1→6 types do not follow the trend found in the case of the 1→4 linkages, i.e. there is no correlation between the range of changes in the glycosidic linkage conformation and the topological orientation of the glycosidic oxygen atoms. Overall, the ring shape affects the glycosidic linkages of the 1→6 type to the least extent in comparison to the remaining ones.

The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations

The conformation of the carbohydrate molecules is a subject of many theoretical and experimental studies. The different timescales associated with the particular degrees of freedom hinder the progress in both those fields. The present paper reports the results of computational studies aimed at elucidating and characterizing the potential correlations between the two main structural determinants of the carbohydrate structure, i.e. the ring conformation and the orientation of the glycosidic bonds (expressed in terms of the ϕ and ψ glycosidic dihedral angles). The free energy landscapes computed for 16 different oligomers composed of unsubstituted, 1,4-linked hexopyranose residues allowed for a detailed insight into how the ring geometry affects the glycosidic linkage conformation. The factor of main importance appeared to be the local changes of the chain length induced by the ring conformational rearrangements. This effect is important mainly for the carbohydrate chains exploiting the glycosidic bonds of uniform orientation with respect to the ring (i.e. either exclusively axially or exclusively equatorially oriented). The shape of the ring may affect the (ϕ,ψ) free energy maps but only if the population of the alternative ring conformers is relatively high and (at the same time) the presence of such conformers is associated with the significant shifts of the favorable ϕ and ψ values.

Energy maps for glycosidic linkage conformations.

Glycosidic linkage conformations are the main factors in determining the shapes of disaccharide, oligosaccharide, and polysaccharide molecules. The conformations are expressed in terms of the torsion angles about the bonds from each ring of the disaccharide moiety to its glycosidic oxygen atom, and the probability of a given conformation is often expressed in terms of its free or potential energy. The energy surface or map for a disaccharide is a display of the energy plotted against the two torsion angles. Successful mapping allows a particular kind of energy calculation to provide the energy values for each conformation and avoids possible pitfalls. Although different methods are discussed, the main emphasis of this chapter is on the technical production of the maps and their exploitation in further understanding the shape of the molecule in question.

Methyl 4-O-β-D-mannopyranosyl β-D-xylopyranoside

Methyl β-D-mannopyranosyl-(1→4)-β-D-xylopyranoside, C(12)H(22)O(10), (I), crystallizes as colorless needles from water, with two crystallographically independent molecules, (IA) and (IB), comprising the asymmetric unit. The internal glycosidic linkage conformation in molecule (IA) is characterized by a ϕ' torsion angle (O5'(Man)-C1'(Man)-O1'(Man)-C4(Xyl); Man is mannose and Xyl is xylose) of -88.38 (17)° and a ψ' torsion angle (C1'(Man)-O1'(Man)-C4(Xyl)-C5(Xyl)) of -149.22 (15)°, whereas the corresponding torsion angles in molecule (IB) are -89.82 (17) and -159.98 (14)°, respectively. Ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (-CH(2)OH) C atom in the β-Xylp and β-Manp residues, respectively. By comparison, the internal glycosidic linkage in the major disorder component of the structurally related disaccharide, methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside), (II) [Zhang, Oliver & Serriani (2012). Acta Cryst. C68, o7-o11], is characterized by ϕ' = -85.7 (6)° and ψ' = -141.6 (8)°. Inter-residue hydrogen bonding is observed between atoms O3(Xyl) and O5'(Man) in both (IA) and (IB) [O3(Xyl)...O5'(Man) internuclear distances = 2.7268 (16) and 2.6920 (17) Å, respectively], analogous to the inter-residue hydrogen bond detected between atoms O3(Xyl) and O5'(Gal) in (II). Exocyclic hydroxymethyl group conformation in the β-Manp residue of (IA) is gauche-gauche, whereas that in the β-Manp residue of (IB) is gauche-trans.

Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis.

Although the crystal structure of the disaccharide sucrose was solved more than 30 years ago, its conformational distribution in aqueous solution is still a matter of debate. We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron-mediated spin-spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably overstabilized in the calculations.

Disorder and conformational analysis of methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside

Methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside, C(12)H(22)O(10), (II), crystallizes as colorless needles from water with positional disorder in the xylopyranosyl (Xyl) ring and no water molecules in the unit cell. The internal glycosidic linkage conformation in (II) is characterized by a φ' torsion angle (C2'(Gal)-C1'(Gal)-O1'(Gal)-C4(Xyl)) of 156.4 (5)° and a ψ' torsion angle (C1'(Gal)-O1'(Gal)-C4(Xyl)-C3(Xyl)) of 94.0 (11)°, where the ring atom numbering conforms to the convention in which C1 denotes the anomeric C atom, and C5 and C6 denote the hydroxymethyl (-CH(2)OH) C atoms in the β-Xyl and β-Gal residues, respectively. By comparison, the internal linkage conformation in the crystal structure of the structurally related disaccharide, methyl β-lactoside [methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside], (III) [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719-1721], is characterized by φ' = 153.8 (2)° and ψ' = 78.4 (2)°. A comparison of β-(1→4)-linked disaccharides shows considerable variability in both φ' and ψ', with the range in the latter (~38°) greater than that in the former (~28°). Inter-residue hydrogen bonding is observed between atoms O3(Xyl) and O5'(Gal) in the crystal structure of (II), analogous to the inter-residue hydrogen bond detected between atoms O3(Glc) and O5'(Gal) in (III). The exocyclic hydroxymethyl conformations in the Gal residues of (II) and (III) are identical (gauche-trans conformer).

Effect of Solvent and Counterions upon Structure and NMR Spin−Spin Coupling Constants in Heparin Disaccharide

Density functional theory (DFT) has been used to analyze structure and NMR spin-spin coupling constants in heparin disaccharide. Both B3LYP/6-311++G** and M05-2X/6-311++G** methods have been used for optimization of disaccharide geometry. Solvent effect was treated by use of explicit water molecules. Solvent-caused variations of DFT-computed indirect one-bond proton-carbon coupling constants up to 17 Hz between isolated and solvated states, however, had a limited influence upon magnitudes of proton-proton spin-spin coupling constants. Interatomic distances and bond and torsion angles indicated that the structure of the 2-O-sulfated iduronic acid residue affected the geometry of the N,6-sulfated glucosamine residue. Optimized disaccharide geometry showed that the change of counterion (Ca(2+) instead of Na(+)) influenced geometry of pyranose rings and the glycosidic linkage conformation. DFT-computed three-bond proton-proton spin-spin coupling constants agreed well with published experimental data and indicated that the population of the (1)C(4) chair form of the 2-O-sulfated iduronic acid residue increased in the presence of Ca(2+) ions compared to the presence of Na(+) ions. Analysis also showed that the Fermi contact term was not always dominant and that paramagnetic and diamagnetic contributions considerably influenced magnitudes of proton-proton spin-spin coupling constants.

Methyl β-D-galactopyranosyl-(1→4)-β-D-allopyranoside tetrahydrate

The title compound, C13H24O11·4H2O, (I), crystallized from water, has an inter­nal glycosidic linkage conformation having φ′ (O5Gal—C1Gal—O1Gal—C4All) = −96.40 (12)° and ψ′ (C1Gal—O1Gal—C4All—C5All) = −160.93 (10)°, where ring-atom numbering conforms to the convention in which C1 denotes the anomeric C atom, C5 the ring atom bearing the exocyclic hydroxymethyl group, and C6 the exocyclic hy­droxy­methyl (CH2OH) C atom in the βGalp and βAllp residues. Inter­nal linkage conformations in the crystal structures of the structurally related disaccharides methyl β-lactoside [methyl β-d-galactopyranosyl-(1→4)-β-d-gluco­pyran­oside] methanol solvate [Stenutz, Shang & Serianni (1999). Acta Cryst. C55, 1719–1721], (II), and methyl β-cello­bioside [methyl β-d-gluco­pyran­osyl-(1→4)-β-d-gluco­pyran­oside] methanol solvate [Ham & Williams (1970). Acta Cryst. B26, 1373–1383], (III), are characterized by φ′ = −88.4 (2)° and ψ′ = −161.3 (2)°, and φ′ = −91.1° and ψ′ = −160.7°, respectively. Inter-residue hydrogen bonding is observed between O3Glc and O5Gal/Glc in the crystal structures of (II) and (III), suggesting a role in determining their preferred linkage conformations. An analogous inter-residue hydrogen bond does not exist in (I) due to the axial orientation of O3All, yet its inter­nal linkage conformation is very similar to those of (II) and (III).

Understanding the Interactions of Cellulose with Ionic Liquids: A Molecular Dynamics Study

Ionic liquids (ILs) have recently been demonstrated to be highly effective solvents for the dissolution of cellulose and lignocellulosic biomass. To date, there is no definitive rationale for selecting ionic liquids that are capable of dissolving these biopolymers. In this work, an all-atom force field for the IL 1-ethyl-3-methylimidazolium acetate [C2mim][OAc] was developed and the behavior of cellulose in this IL was examined using molecular dynamics simulations of a series of (1-4) linked beta-d-glucose oligomers with a degree of polymerization n = 5, 6, 10, and 20. Molecular dynamics simulations were also carried out on cellulose oligomers in two common solvents, water and methanol, which are known to precipitate cellulose from IL solutions, to determine the extent and energetics of the interactions between these solvents and the cellulosic oligomers. Thermodynamic properties, such as density and solubility, as well as the two-body solute-solvent interaction energy terms, were calculated. The structural and dynamic behavior of solutions was analyzed and the conformations of cellulose oligomers were compared in ionic liquid and water mixtures. It was found that the interaction energy between the polysaccharide chain and the IL was stronger than that for either water or methanol. In addition to the anion acetate forming strong hydrogen bonds with hydroxyl groups of the cellulose, some of the cations were found to be in close contact with the polysaccharides through hydrophobic interactions. These results support the concept that the cation may play a significant role in the dissolution of cellulose by [C2mim][OAc]. It is also observed that the preferred beta-(1,4)-glycosidic linkage conformation of the cellulose was altered when dissolved in [C2mim][OAc] as compared to that found in crystalline cellulose dispersed in water. To our knowledge, this report is the first theoretical study that addresses the key factors in cellulose dissolution using an ionic liquid.

Investigating the Molecular Basis for the Virulence of Escherichia coli K5 by Nuclear Magnetic Resonance Analysis of the Capsule Polysaccharide

The capsular polysaccharide of Escherichia coli K5 has been hypothesised to promote virulence through its molecular mimicry of host heparan sulphate. To test this hypothesis, we have produced pure oligosaccharides from K5 capsular polysaccharide and investigated their conformational properties with ultra-high-field nuclear magnetic resonance (NMR) (900 MHz). Ultra-high-field affords a significant resolution enhancement over previous studies and allowed a full-atomic assignment of the K5 hexasaccharide for the first time. All carbohydrate rings adopt a ⁴C₁ conformation, the amide sidechains have a trans orientation and the hydroxymethyl group is freely exposed to bulk solvent. Initial models of the glycosidic linkage conformation based upon simple interpretation of NOE cross-peaks suggests that the β1→4 linkage adopts a 3D geometry of φ ≈ 60°, ψ ≈ 0° and the α1→4 linkage prefers φ ≈ –30°, ψ ≈ –30° (φ and ψ being defined by dihedral angles involving linkage protons). In this conformation the overall molecular geometries of K5 polysaccharide, heparan sulphate and even fully-sulphated heparin are remarkably similar. These results substantiate the hypothesis that the K5 capsular polysaccharide confers virulence to E. coli K5 by being a 3D molecular mimetic of host heparan sulphate, helping it to evade detection by the mammalian immune system.

Glycosidic linkage conformation of methyl-α-mannopyranoside

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.