The conformation and structure of GAGs: recent progress and perspectives.

The glycosaminoglycan (GAG) family of linear sulphated polysaccharides are involved in most regulatory processes in the extracellular matrix of higher organisms. The relationship between GAG substitution pattern and activity, however, remains unclear and experimental evidence suggests that subtle conformational factors play an important role. The difficulty of modelling these complex charged molecules shifts the burden of investigation towards experimental techniques. Recent advances in complementary physical-chemical, particularly spectroscopy-based approaches are reviewed, together with methods for analysing the resulting complex data. The prospects for combining some of these approaches and fitting them into the wider context of interactions, are also discussed.

Spectroscopic and theoretical approaches for the determination of heparin saccharide structure and the study of protein-glycosaminoglycan complexes in solution.

Glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are a class of linear, anionic polysaccharides that constitute the carbohydrate component of proteoglycans. The structure of GAG complexes with proteins can reveal details of their mechanisms of action in living systems and help to design new pharmaceuticals. Molecular modelling together with nuclear magnetic resonance (NMR) and other spectroscopic techniques such as circular dichroism (CD) provide indispensable information on structure and dynamics of GAGs and their complexes. The present review focuses on applications of high-resolution NMR, CD and molecular modelling to the analysis of GAGs. The most advanced theoretical methods used at present in GAG research, density functional theory methods (DFT), are also discussed.

B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide.

Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.

Relationship between structure and three-bond proton-proton coupling constants in glycosaminoglycans.

Theoretical calculations using the DFT theory at the B3LYP/6-311++G(**) level were used to determine the molecular geometry of various glycosaminoglycan (GAG) molecules. Three-bond proton-proton spin-spin coupling constants ((3)J(H-C-C-H)) were then computed and compared with the published experimental data of selected mono- and disaccharides. The computed (3)J(H-C-C-H) values showed a strong dependence on the molecular geometry and varied up to 12 Hz. This dependence was expressed in a simple analytical form relating (3)J(H-C-C-H) and torsion angles. The population of conformers in heparin and other biologically active GAGs has also been estimated using the computed coupling constants.

Structure of 2-C-(hydroxymethyl)-D-ribose (hamamelose) in the solid-state analyzed by CP MAS NMR and X-ray crystallography.

D-Hamamelose, a branched-chain ribose (2-C-(hydroxymethyl)-D-ribose), has been synthesized and its solid-state structure analyzed by (13)C CP MAS NMR spectra and X-ray data. The presence of the complex pattern of resonances in the anomeric region, as well as in the ring carbon region, in (13)C CP MAS NMR spectrum indicated that the mixture of four cyclic forms, alpha- and beta-furanoses, as well as both alpha- and beta-pyranoses were present in the solid-state. X-ray analysis of crystals showed that D-hamamelose belongs to the monoclinic system with unit cell: a=4.790A, b=8.671A, c=8.880A and beta=98.89 degrees , space group P2(1). The furanose ring has the (2)E conformation.

Conformation of heparin pentasaccharide bound to antithrombin III.

The interaction, in aqueous solution, of the synthetic pentasaccharide AGA*IA(M) (GlcN,6-SO(3)alpha 1-4GlcA beta 1-4GlcN,3,6-SO(3)alpha 1-4IdoA,2-SO(3)alpha 1-4GlcN,6-SO(3)alpha OMe; where GlcN,6-SO(3) is 2-deoxy-2-sulphamino-alpha-D-glucopyranosyl 6-sulphate, IdoA is l-iduronic acid and IdoA2-SO(3) is L-iduronic acid 2-sulphate), which exactly reproduces the structure of the specific binding sequence of heparin and heparan sulphate for antithrombin III, has been studied by NMR. In the presence of antithrombin there were marked changes in the chemical shifts and nuclear Overhauser effects (NOEs), compared with the free state. On the basis of the optimized geometry of the pentasaccharide the transferred NOEs were interpreted with full relaxation and conformational exchange matrix analysis. An analysis of the three-dimensional structures of the pentasaccharide in the free state, and in the complex, revealed the binding to be accompanied by dihedral angle variation at the A-G and I-A(M) (where G, I, A and A(M) are beta-d-glucuronic acid, 2-O-sulphated alpha-L-iduronic acid, N,6-O-sulphated alpha-D-glucosamine and the alpha-methyl-glycoside of A respectively) glycosidic linkages. Evidence is also provided that the protein drives the conformation of the 2-O-sulphated iduronic acid residue towards the skewed (2)S(0) form.

Effect of substitution pattern on 1H, 13C NMR chemical shifts and 1J(CH) coupling constants in heparin derivatives.

1H, 13C NMR chemical shifts and 1J(CH) coupling constants were measured for derivatives of heparin containing various sulfation patterns. 1H and 13C chemical shifts varied considerably after introducing electronegative sulfate groups. Chemical shifts of protons linked to carbons changed by up to 1 ppm on substitution with O- and N-sulfate or acetyl groups. Differences up to 10 ppm were detected for 13C chemical shifts in substituted glucosamine, but a less clear dependence was found in iduronate. 1J(CH) values formed two groups, corresponding to either sulfation or non-sulfation at positions 2 and 3 of glucosamine. O-sulfation caused increases up to 6 Hz in 1J(CH) and N-sulfation decreases up to 4 Hz. N-acetylation gave similar 1J(CH) values to N-sulfation. At positions 2 and 3 of iduronate the trend was less marked; 1J(CH) for O-sulfated positions usually increasing. Introduction of sulfate groups influences chemical shift and 1J(CH) values at the position of substitution, but also at more remote positions. 1J(CH) at the glycosidic linkage positions varied between free-amino and N-sulfated compounds, by up to 9 Hz. These results and changes in chemical shift values suggest that iduronate residues and the glycosidic linkages are affected, indicating overall conformational change. This may have important implications for biological activities.

Structure of heparin-derived tetrasaccharide complexed to the plasma protein antithrombin derived from NOEs, J-couplings and chemical shifts.

A complex of the synthetic tetrasaccharide AGA*IM [GlcN, 6-SO3-alpha(1-4)-GlcA-beta(1-4)-GlcN,3, 6-SO3-alpha(1-4)-IdoA-alphaOMe] and the plasma protein antithrombin has been studied by NMR spectroscopy. 1H and 13C chemical shifts, three-bond proton-proton (3JH-H) and one-bond proton-carbon coupling constants (1JC-H) as well as transferred NOEs and rotating frame Overhauser effects (ROEs) were monitored as a function of the protein : ligand molar ratio and temperature. Considerable changes were observed at both 20 : 1 and 10 : 1 ratios (AGA*IM : antithrombin) in 1H as well as 13C chemical shifts. The largest changes in 1H chemical shifts, and the linewidths, were found for proton resonances (A1, A2, A6, A6', A1*, A2*, A3*, A4*) in GlcN, 6-SO3 and GlcN,3,6-SO3 units, indicating that both glucosamine residues are strongly involved in the binding process. The changes in the linewidths in the IdoA residue were considerably smaller than those in other residues, suggesting that the IdoA unit experienced different internal dynamics during the binding process. This observation was supported by measurements of 3JH-H and 1JC-H. The magnitude of the three-bond proton-proton couplings (3JH1-H2 = 2.51 Hz and 3JH4-H5 = 2.23 Hz) indicate that in the free state an equilibrium exists between 1C4 and 2S0 conformers in the ratio of approximately 75 : 25. The chair form appears the more favourable in the presence of antithrombin, as inferred from the magnitude of the coupling constants. In addition, two-dimensional NOESY and ROESY experiments in the free ligand, as well as transferred NOESY and ROESY spectra of the complex, were measured and interpreted using full relaxation and conformational exchange matrix analysis. The theoretical NOEs were computed using the geometry of the tetrasaccharide found in a Monte Carlo conformational search, and the three-dimensional structures of AGA*IM in both free and bound forms were derived. All monitored NMR variables, 1H and 13C chemical shifts, 1JC-H couplings and transferred NOEs, indicated that the changes in conformation at the glycosidic linkage GlcN, 6-SO3-alpha(1-4)-GlcA were induced by the presence of antithrombin and suggested that the receptor selected a conformer different from that in the free state. Such changes are compatible with the two-step model [Desai, U.R., Petitou, M., Bjork, I. & Olson, S. (1998) J. Biol. Chem. 273, 7478-7487] for the interaction of heparin-derived oligosaccharides with antithrombin, but with a minor extension: in the first step a low-affinity recognition complex between ligand and receptor is formed, accompanied by a conformational change in the tetrasaccharide, possibly creating a complementary three-dimensional structure to fit the protein-binding site. During the second step, as observed in a structurally similar pentasaccharide [Skinner, R., Abrahams, J.-P., Whisstock, J.C., Lesk, A.M., Carrell, R.W. & Wardell, M.R. (1997) J. Mol. Biol. 266, 601-609; Jin, L., Abrahams, J.-P., Skinner, R., Petitou, M., Pike, R. N. & Carrell, R.W. (1997) Proc. Natl Acad. Sci. USA 94, 14683-14688], conformational changes in the binding site of the protein result in a latent conformation.

NMR study of virenose and dihydrohydroxystreptose isolated from Coxiella burnetii phase I lipopolysaccharide.

A lipopolysaccharide (LPS) isolated from Coxiella burnettii in virulent phase I contains in its O-polysaccharide chain two unusual sugars, virenose (6-deoxy-3-C-methylgulose) and dihydrohydroxystreptose [3-C-(hydroxymethyl)lyxose]. The sugars were isolated from LPS I, after acid hydrolysis and removal of lipid A, by a combination of HPLC and preparative paper chromatography. Their enantiomeric forms and ring conformations were established from optical rotation and NMR data. Two-dimensional COSY, HSQC, and HMBC as well as one- and two-dimensional NOEs were used to assign all proton and carbon signals in both monosaccharides. Virenose was found to be the D-gulo enantiomer with the 4C1 ring conformation and dihydrohydroxystreptose was shown to be the L-lyxo enantiomer also with the 4C1 conformation. The latter sugar was reported [S. Schramek, J. Radziejewska-Lebrecht, and H. Mayer, Eur. J. Biochem., 148 (1985) 455-461] to be present in LPS I in a furanose form, and it appears that a furanose to pyranose tautomerization took place in the course of the isolation procedure.

Motional properties of E. coli polysaccharide K5 in aqueous solution analyzed by NMR relaxation measurements.

13C NMR relaxation measurements at three different magnetic field strengths have been used to analyse the motional properties of a low molecular weight K5 polysaccharide (delta UA-[-->4)-beta-D-GlcNAc(1-->4)-beta-D-GlcA(1-->]n-GlcNAcred) from E. coli. Two-dimensional double INEPT spectra with suppression of cross-correlation effects between dipolar and chemical shift anisotropy relaxation mechanisms were collected in order to determine carbon longitudinal and transverse relaxation times. The values of the overall correlation time and the rate of internal motions were obtained using the model free spectral densities. The data indicate that the overall motion of the molecule is non-isotropic and can be approximated with the symmetric top model with an axial ratio of approximately 22. The magnitude of the generalized order parameters (S2 approximately 0.8) and the internal motion correlation time (tau e approximately 30 ps) differ from those found for iduronic acid-containing glycosaminoglycans and suggest that the internal motions in K5 polysaccharide are more limited.

Conformational analysis of heparin epoxide in aqueous solution. An NMR relaxation study.

1H and 13C NMR relaxation measurements at various magnetic fields have been used to characterize the nature of overall and internal motions in heparin epoxide in aqueous solution. A two-dimensional homonuclear NOESY experiment showed a considerable number of cross-relaxing protons in the molecule. The inter-proton distances calculated from NOE data were compared with those obtained by molecular mechanics calculations. Several discrepancies between the experimental and the theoretical inter-proton distances as well as the variations in 13C spin-lattice relaxation times, measured at two magnetic fields, indicated that the polysaccharide tumbles anisotropically in solution. The rates of overall and internal motions as well as the order parameters have been calculated using a model-free spectral density function. The numerical values indicate that the correlation times which characterize overall molecular motion are outside the extreme narrowing limit (tau parallel = 8 x 10(-10) s and tau perpendicular = 4.2 x 10(-8) s) and that internal motion correlation time is on a picosecond timescale.

Dynamics in aqueous solutions of the pentasaccharide corresponding to the binding site of heparin for antithrombin III studied by NMR relaxation measurements.

1H NMR and 13C NMR relaxation measurements at different magnetic field strengths were used to study the nature of overall and internal motions, in aqueous solution, of the synthetic pentasaccharide (A-G-A*-I-AM) corresponding to the binding site of heparin for antithrombin III. Two-dimensional double INEPT spectra were recorded at 11.7 T with and without suppression of cross-correlation effects between dipolar and chemical shift anisotropy relaxation mechanisms in measurements of spin-lattice and spin-spin relaxation times. Moreover, longitudinal relaxation times were collected at 7 T with the inversion recovery method. One dimensional NOESY spectra were recorded at 11.7 T and 9.4 T with various mixing times when spins of the A1* and A4* protons were inverted in the central residue of the pentasaccharide. Differences in the T1 relaxation times, as well as in the cross-relaxation rates between protons relaxing through fixed distances in the A* residue, indicated that the molecule tumbles anisotropically in solution. However, in order to achieve agreement between the spectral and the model data, the presence of internal motions had to be also considered, in addition to the assumption of a symmetric top model for the description of overall tumbling. The changes in the longitudinal and transversal relaxation times, collected with and without suppression of interference effects, supported the assumption that the cross-correlation between dipolar and chemical shift anisotropy relaxation mechanisms cannot be neglected in this medium-sized molecule. In fact, the influence of these effects was 10-15% in T1 and 20-25% in T2 relaxation times. The experimental data were analyzed using model free formalism and the computed order parameters indicate a decrease in spatial restriction from the central residue (S2 approximately 0.9) towards both ends of the pentasaccharide (S2 approximately 0.7). The anisotropy ratio found was approximately 3.3 with correlation times tau parallel = 450 ps and tau perpendicular = 1480 ps. The values of effective correlation time were within the range of tens of picoseconds. Thus, for a more precise interpretation of the experimental data for the pentasaccharide, in addition to internal motions and anisotropic tumbling, the effect of cross-correlation must be taken into account as well.

Synthesis of di- and tri-saccharides with intramolecular NH-glycosidic linkages: molecules with flexible and rigid glycosidic bonds for conformational studies.

Attempted dephthalimidation of the trisaccharide 1-O-acetyl-3,4-di-O-benzyl- 2,6-di-O-(3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-beta-D-glucopyranosyl )-alpha-D-mannopyranose (1) and its derivatives 2 and 3, as well as the disaccharide 1-O-acetyl-3,4,6-tri-O-benzyl-2-O-(3,4,6-tri-O-acetyl- 2-deoxy-2-phthalimido-beta-D-glucopyranosyl)-alpha-D-mannopyranose (13), with hydrazine hydrate in ethanol at 80 degrees C, produced the trisaccharide-6-O-(2-acetamido-3,4,6-tri-O-acetyl-2-deoxy-beta-D- glucopyranosyl)-3,4-di-O-benzyl-beta-D-mannopyranose-3',4',6'-tri-O-a cet yl- beta-D-glucopyranose 1,2'-N:1',2-O-dianhydride (4) and 3,4,6-tri-O-benzyl-beta-D-mannopyranose 3',4',6'-tri-O-acetyl-beta-D-glucopyranose 1,2'-N:1',2-O-dianhydride (14), respectively, containing an intramolecular NH-glycosidic linkage. The conventional deblocking of compounds 4 and 14 gave the completely deblocked trisaccharide 6-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-beta-D-mannopyranose beta-D-glucopyranose 1,2'-N:1',2-O-dianhydride (6) and the disaccharide beta-D-mannopyranose beta-D-glucopyranose 1,2'-N:1',2-O-dianhydride (16), respectively, containing an intact intramolecular NH-glycosidic bond. The unusual intra NH-glycosyl character makes the linkage rigid, and therefore these compounds should not only be useful for NMR studies but also as substrates or inhibitors of GlcNAc-transferases.

The conformational analysis of methyl beta-xylobioside: effect of choice of potential functions.

In order to determine the effect of the choice of potential function used in the conformational analysis of a carbohydrate, the NMR spectrum of methyl beta-xylobioside [beta-D-Xyl-(1-->4)-beta-D-Xyl-(1-->O)-Me] was interpreted using calculated J13C-H coupling constants and nuclear Overhauser effects for protons across the anomeric linkage. Conformational flexibility was described by calculating average phi and psi angles, and estimating their standard deviations. ECEPP2, ECEPP83, and HSEA potentials were used in the first series of calculations. The calculated coupling constants and nuclear Overhauser effects were averaged over the Boltzmann distribution of conformations of the disaccharide in which the entire phi, psi space was scanned in ten-degree steps while retaining fixed bond distances and angles in the remainder of the molecule. In the second series of calculations, MM2, MM2CARB, and PCILO parameters were used to calculate conformational energies. Conformational optimization was done. The effect of temperature and solvent on the calculated coupling constants was negligible. Calculated properties from conformations whose energies were based on the ECEPP parameters gave the best agreement with experiment. Exploration of the conformational space in breadth rather than on a detailed level of full optimization appears to be a preferable course of action.

Flexibility in a tetrasaccharide fragment from the high mannose type of N-linked oligosaccharides.

An analysis has been carried out of the three-dimensional structure of a tetrasaccharide, Man(alpha 1-3)Man(alpha 1-6)Man(beta 1-4)GlcN Ac beta 1-OCD3, which is a fragment from the high mannose type of N-linked oligosaccharides. Although earlier work had suggested that this fragment might adopt a stable three-dimensional structure, both n.m.r. and conformational energy calculations support the existence of an ensemble of structures. The conformational entropy calculated from the ensemble and the distribution of distances between the terminal Man(alpha 1-3) and GlcN Ac residues, however, suggests that a significant fraction of the ensemble has the two terminal residues in close proximity.

Detection of internal motions in oligosaccharides by 1H relaxation measurements at different magnetic fields.

The effect of internal motions on proton relaxation data in oligosaccharides has been investigated experimentally. 1H steady-state and transient NOEs together with 13C T1's have been measured at two magnetic field strengths. The existence of internal motions leads to additional modulations of the dipolar interaction between proton pairs, thus producing a range of spectral density functions for these interactions. As a result, it is possible to show that protons relaxing through fixed distances have a different ratio of relaxation parameters, acquired at 500 and 300 MHz, compared to those relaxing through fluctuating distances. This approach has been used to unequivocally establish for two disaccharides the existence of internal motions on the time scale of the overall tumbling.

Conformations of (1----4)-linked alpha-D-galacturono-di- and -tri-saccharides in solution analysed by n.m.r. measurements and theoretical calculations.

The conformations of the (1----4)-linked alpha-D-galacturono-di- (1) and -tri-saccharide (2) in aqueous solutions have been analysed by n.m.r. spectroscopy and MM2CARB calculations. The 3JC.H. and n.O.e. values did not change with temperature and were comparable for 1 and 2. Four energy regions were found on the relaxed (phi, psi) map for 1 computed by the MM2CARB method. Theoretical n.O.e. values, based on the geometry and the abundance of the most populated conformer, accorded with experimental values. The magnitudes of phi H and psi H for the glycosidic bond suggest that a right-handed three-fold helical arrangement can be formed by pectic acid oligosaccharides in solution.

Nuclear Overhauser effects and the flexibility of saccharides: methyl beta-xylobioside.

The behavior of methyl beta-xylobioside has been analysed by 1H-n.m.r. spectroscopy for solutions in water and methanol in the range - 15 degrees to 85 degrees. Experimental n.O.e. values did not change with temperature and solvent in contrast to the inter-glycosidic 3JC,H values. Experimental n.O.e. data accorded with the values calculated from time-averaged cross-relaxation terms. The tumbling times were determined from relaxation data and were in the sub-ns range.

Solution behavior of methyl beta-xylobioside: conformational flexibility revealed by n.m.r. measurements and theoretical calculations.

The conformations of methyl beta-xylobioside in solution have been determined by n.m.r. spectroscopy. Interglycosidic 3JC,H values and the chemical shifts of the 13C resonances were measured at various temperatures in the range 238-378 K for solutions in 1,4-dioxane, methanol, methyl sulfoxide, and water. The temperature and solvent dependencies of the data obtained suggest conformational flexibility. Quantum-chemical PCILO calculations, with evaluation of the solvent effects, and molecular mechanics calculations revealed the existence of 7 low-energy regions for which the geometries and energies were determined. The computed abundances of conformers and averaged J values accord with the experimental data.

Structural features of a water-soluble L-arabino-D-xylan from rye bran.

A water-soluble L-arabino-D-xylan, obtained from the chlorite holocellulose of de-lipidated, de-starched, and de-pectinated rye bran by ammoniacal extraction, was composed of L-Ara and D-Xyl in the molar ratio 7.8:10 and had Mw 36,500 and Mn 26,950. The backbone of the polysaccharide was shown to comprise (1----4)-linked beta-D-Xylp residues, with approximately 41% unsubstituted, approximately 33% 2- or 3-substituted, and approximately 26% disubstituted. Single alpha-L-Araf groups were attached to the xylan core; only a small proportion was 2-, 3-, or 5-linked.