Glycosidic Oxygen Atom Research Articles

Thiooligosaccharides as tools for structural biology.

Oligosaccharides in which at least one glycosidic oxygen atom is replaced with a sulfur atom can be routinely synthesized and act as competitive inhibitors of various glycoside hydrolases. Recent studies using both X-ray crystallography and other biophysical techniques provide structural insight into binding, recognition, and the catalytic mechanism of action of these enzymes.

Synthesis of heteroanalogues of disaccharides as potential inhibitors of the processing mannosidase Class I enzymes

Three disaccharide analogues of α- d-Man-(1→2)- α- d-Man-OMe in which the ring and/or glycosidic oxygen atoms have been replaced by sulfur have been synthesized as potential inhibitors of Class I mannosidase enzymes. Glycosylation of appropriately protected methyl α- d-mannopyranosides, having free alcohol or thiol functional groups at the 2-position, with 2,3,4,6-tetra- O-acetyl-5-thio- α- d-mannopyranosyl trichloroacetimidate was selective for the synthesis of α-linked disaccharides in the case of the 2-alcohols, but yielded an α/ β mixture in the case of the 2-thiol glycosyl acceptors. A disaccharide containing a single sulfur in the linkage was synthesized by nucleophilic substitution of the 2-triflate of a methyl α- d-glucopyranoside derivative by the thiolate anion of 2,3,4,6-tetra- O-acetyl-1-thio- α- d-mannopyranose. Protecting groups were removed by standard methods to give the free heterosubstituted disaccharides.

The crystal and molecular structures of 4-cyanophenyl 1,5-dithio- β- d-xylopyranoside S-5 oxide and 4-ethyl-2-oxo-2 H- 1-benzopyran-7-yl 5-thio- β- d-xylopyranoside S-5 oxide

Crystals of 4-cyanophenyl 1,5-dithio- β- d-xylopyranoside S-5 oxide (1) and 4-ethyl-2-oxo-2 H-1-benzopyran-7-yl 5-thio- β- d-xylopyranoside S-5 oxide (2) are monoclinic, space group P2 1, with two independent thioxylosides molecules in the asymmetric unit. The unit cell dimensions are α = 26.385, b = 5.934, c = 8.902 Å, and β = 109.90 ° for 1 and α = 16.033, b = 16.676, c = 6.459 Å, and β = 91.26 ° for 2. The present work provides structural information on the influence of substitution of intracyclic and glycosidic oxygen atoms by sulfur atoms, as well as on the influence of aromatic rings and of sulfoxide groups on the carbohydrate moiety. In both molecules, the xylopyranosides rings have the classical 4C 1 conformation. For 1, the orientation of the phenyl substituent with respect to the xylopyranose is very similar in the two independent molecules: the φ and ψ torsion angles are respectively: (−99.5°, 153.8°) and (−102.1°, 154.2°). This is not the case for 2, for which these values are strikingly different: (− 79.4°, 172.1°) and (− 130.2°, −178.4°). In each structure, the molecules are hydrogen bonded within a network of infinite chains.

Molecular structure of [4-(4-cyanobenzoyl) phenyl] 1,5-dithio-β- d-xylopyranoside (naroparcil) in the solid state and in solution: An investigation by X-ray crystallography, molecular mechanics calculations, and NMR spectroscopy

The conformational behavior of a representative of a new class of oral venous antithrombotic agents, [4-(4-cyanobenzoyl) phenyl] 1,5-dithio-β- d-xylopyranoside (naroparcil) (1) has been characterized by X-ray crystallography, molecular modeling and NMR studies. The crystal structure of 1 belongs to the monoclinic space group P2 1, with two independent molecules in the asymmetric unit. The unit cell has dimensions of a = 11.641, b = 8.040, c = 20.020 A ̊ , and β = 102.29°. The present work provides structural information on the influence of substitution of intracyclic and glycosidic oxygen atoms by sulfur atoms, as well as on the influence of aromatic rings on the carbohydrate moiety. The xylopyranoside ring has the classical 4 C 1 conformation. As for the orientations of the phenyl substituent with respect to the xylopyranose the values observed in the two independent molecules are strikingly different (-85°, -177°) and (-102°, 144°). The 1H- 1H NOE across the glycosidic bond has been measured by NOESY experiments. In parallel, a conformational analysis using the crystal coordinates as the starting point has been made using the Tripos force field. The resulting potential energy surface indicates a high flexibility about the glycosidic linkage. The theoretical NMR data were calculated taking into account all the accessible conformations and using the averaging methods appropriate for slow internal motions. The agreement between experimental and theoretical data is excellent and constitutes a satisfactory test of the validity of the conformational energy surface.

A spectroscopic study of the interaction of the VO2+ cation with the two components of chondroitin sulfate.

The interaction of the vanadyl (IV) cation with N-acetyl-D-galactosamine, D-galactosamine, and D-glucuronic acid has been investigated by electron absorption spectroscopy at different metal to ligand ratios and pH values. In the case of D-glucuronic acid, a more detailed study was undertaken, using differential IR spectroscopy in solution. The results show that the cation interacts with the two nitrogenated molecules only at higher pH values, generating 2:1 ligand to metal complexes in which coordination occurs through two pairs of deprotonated OH groups of the rings. In the case of D-glucuronic acid, the IR-measurements allowed a wider insight into the structural characteristics of the complexes generated in acidic media. The involvement of the glycosidic oxygen atom in coordination, is suggested at pH = 3.

The conformational behaviour of complexes of alpha-cyclodextrin with p-chlorophenol and p-hydroxybenzoic acid in water as studied by molecular dynamics simulations.

Molecular dynamics simulations were performed to obtain information about the conformational behaviour and stabilization of alpha-cyclodextrin (alpha CD) complexes in water. Simulations of p-chlorophenol and p-hydroxybenzoic acid in alpha CD showed that the complex is a very flexible system. The guest compound rotates inside the cavity and partly moves in and out. alpha CD continuously adapts its conformation to the orientation of the guest compound (or vice versa): the hexagon of the glycosidic oxygen atoms is stretched parallel to the plane of the aromatic ring of the guest compound during 80% of the simulation. This suggests that Van der Waals interactions play an important role in the stabilization of the complex. Each intramolecular hydrogen bond between neighbouring glucose units is formed during 30-80% of the simulation. Hydrogen bonds between alpha CD and the guest compound, on the other hand, are rarely formed. Thus, intermolecular hydrogen bonding seems to play a minor role in the stabilization of alpha CD complexes.

Crystal structure of heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin complexes with m-iodophenol and 4-biphenylacetic acid. Guest-induced conformational change of a pyranose ring

Crystal structures of heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TM-β-CDx) complexes with m-iodophenol (MIP) and 4-biphenylacetic acid (BPA) have been determined by X-ray analysis. The macrocylic ring of TM-β-CDx is elliptically distorted in both complexes. The 2,3,6-tri-O-methylglucose residues incline against the plane through seven glycosidic oxygen atoms to relieve the steric hindrance involving methyl groups at the O(2), O(3) side. In the MIP complex, one glucose residue exhibits the skew (twist boat) conformation. The MIP molecule is fully included within the TM-β-CDx cavity, both ends of which are blocked by adjacent molecules, and the hydroxy group is hydrogen-bonded to O(2) of the host TM-β-CDx. In the BPA complex, the phenyl group is located at the centre of the cavity while half a molecule protrudes from the O(2), O(3) side. The carboxy group of BPA is located in intermolecular space to form a hydrogen bond with an adjacent TM-β-CDx molecule. The complex formation induces the chiral conformation in BPA. The biphenyl group is in the R-configuration with an angle of 42.4° between the two benzene rings.

Hydrogen bonding in the crystal structure of α,β-panose

The crystal structure of panose, O-α-d-glucopyranosyl-(1→6)-O-α-d-glucopyranosyl-(1→4)-d-glucose, C18H32O16, has been refined using low-temperature, 123 K, CuKα X-ray data. Difference syntheses and least-squares refinement showed a 16% substitution of α-panose by the β anomer. All the hydrogen atoms were located on difference synthesis with the exception of one attached to the low occupancy (β) O-1″. The final R-factor was 0.036 for 2135 observed structure amplitudes. The molecular conformation is stabilized by two interresidue intramolecular hydrogen bonds. All the hydroxyls and glycosidic oxygen atoms are involved in the hydrogen bonding, which is a two-dimensional network formed from finite and infinite chains.

A molecular modelling study of the distortion of α-cyclo-dextrin (cyclomaltohexaose) in complexes with guest molecules

Analysis of the crystal structures of complexes of cyclomaltohexaose (α-cyclodextrin, αCD) by molecular modelling techniques showed the αCD molecules to be distorted by the guest compounds. The ratio of the largest to the smallest diameter of the hexagon formed by the glycosidic oxygen atoms varied from 1.00 for a symmetrical to 1.12 for a distorted αCD molecule. The distortion was correlated with the van der Waals volume of the guest compounds. A procedure, based on crystallographic data, has been developed for constructing an αCD molecule with a specific distortion and a reasonable geometry for use in modelling experiments. Energy calculations on the complex of αCD with p-hydroxybenzoic acid showed that the lowest energy of interaction involved a distorted αCD molecule. MM2 calculations showed that the internal energies of the conformations of αCD studied were euqal to within 10 kJ/mol. The distortion of the αCD molecule is therefore an important factor in the formation of complexes.

The hydrogen bonding in the crystal structure of raffinose pentahydrate

The crystal structure of raffinose pentahydrate, O-α- d-galactopyranosyl-(1→6)- O-α- d-glucopyranosyl-(1↔2)-β- d-fructofuranose pentahydrate, C 18H 32O 16·5H 2O, has been redetermined using low-temperature, 119 K, CuKα X-ray data. All hydrogen atoms were unambiguously located on difference syntheses. The final R-factor is 0.036 for 2423 observed structure amplitudes. The hydrogen bonding is composed of infinite chains, which are linked through the water molecules to form a three-dimensional network containing a chain of five linked water molecules. Three of the infinite chains extend in the directions of the crystallographic axis of the space group P2 12 12 1. Four of the water molecules accept two hydrogen bonds and one accepts one. All the hydroxyls and the ring and glycosidic oxygen atoms are involved in the hydrogen bonding. With one exception, the ring and glycosidic oxygens are hydrogen-bonded by means of the minor components of unsymmetrical three-center bonds.

Monomer sequence determination of carbohydrates using fast-atom bombardment mass spectrometry of periodate-oxidized acetate ester derivatives

A derivatization method, adapted from that of Angel et al. (ref. 10), for sequencing sugar residues in partially degraded poly- and oligo-saccharides using positive-ion f.a.b.-m.s. is described. Derivative selection provides sequence information by directing fragmentation exclusively to both sides of glycosidic oxygen atoms and, in the case of opened rings, between glycosidic carbon and ring oxygen atoms. Polysaccharides or oligosaccharides are subjected to sequential periodate oxidation, borodeuteride reduction, and acetylation. The derivatized polysaccharides are then subjected to partial degradation, acetylation, and high-performance liquid chromatography (h.p.l.c.) purification. F.a.b.-m.s. data obtained on model compounds, using 3-nitrobenzyl alcohol as matrix for f.a.b.-m.s., demonstrated direction of fragmentation to both sides of the glycosidic oxygen atom in unoxidized residues, and to both sides of the acetal oxygen atoms in oxidized residues. Oligosaccharide linkage and sequence may thus be determined by observing fragmentation from both the reducing and non-reducing ends of the molecule. Two Salmonella lipopolysaccharides, derivatized by this procedure, were partially hydrolyzed and then acetylated. Analysis of the h.p.l.c.-purified oligosaccharide derivatives by f.a.b.-m.s. demonstrated the applicability of the technique for sequencing nmol quantities of branched structures.

A molecular mechanics analysis of molecular recognition by cyclodextrin mimics of α‐chymotrypsin

AbstractThe method of molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by β‐cyclodextrin and capped β‐cyclodextrin models of α‐chymotrypsin. Since capped β‐cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N‐methylformamide “cap” substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X‐ray structure of the β‐cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. The results indicate that the addition of the caps to the β‐cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by β‐cyclodextrin and capped β‐cyclodextrin are similar.

The crystal structures of octyl α-D-glucopyranoside monohydrate and hemihydrate: Mesogenic structures with interdigitizing alkyl chains

The crystal structure of octyl α-D-glucopyranoside monohydrate, C14H28O6·H2O, is monoclinic, C2, with Z = 4, a = 17.896(2), b = 5.154(1), c = 18.303(2) Å, β = 90.30(1)°. The hemihydrate, C14H28O6·0.5 H2O, is also monoclinic, C2, with Z = 4, a = 15.190(5), b = 5.136(3), c = 19.944(7), β = 92.74(3)°. The crystal structures were solved using SHELXTL and refined to R values of 0.037 and 0.052 for 1224 and 1231 observed structure amplitudes, respectively. The crystal structures have bilayer head-to-head molecular packing with interdigitizing alkyl chains similar to those observed in other long-chain alkyl pyranosides. The carbohydrate moieties are hydrogen-bonded in infinite chains which exclude the ring and glycosidic oxygen atoms. Both crystal structures transform to a smectic A liquid crystal at 72.3°, which has a clearing point at 116.5°.

Catalytic flexibility of glycosylases. The hydration of maltal by beta-amylase to form 2-deoxymaltose.

Crystalline, alpha-glucosidase-free sweet potato beta-amylase was found to catalyze hydration of the enolic bond of maltal (alpha-D-glucopyranosyl-(1----4)-2-deoxy-D-glucal) to form 2-deoxymaltose (alpha-D-glucopyranosyl-(1----4)-2-deoxy-D-glucose). The reaction at pH 5.0 showed Vmax 0.082 mumol/min/mg and km 94.5 mM. An exceptionally large solvent deuterium isotope effect, VH/VD = 8, was observed from pH(pD) 4.2 to 5.4; and at pH(pD) 5.0 the effect was found to be directly related to the mole fraction of 2H. The hydration product, isolated from a beta-amylase/maltal digest in acetate-d4/D2O buffer (pD 5.4) was identified through its 1H NMR spectrum as alpha-D-glucopyranosyl-(1----4)-2-deoxy-D-[2(a)-2H]glucose. beta-Amylase in 2H2O thus catalyzes deuteration of the double bond of maltal from a direction opposite that assumed for protonation of the glycosidic oxygen atoms of starch chains and maltosaccharides. This finding confirms the functional flexibility of the enzyme's catalytic groups first demonstrated in studies of the reactions catalyzed with alpha- and beta-maltosyl fluoride (Hehre, E. J., Brewer, C. F., and Genghof, D. S. (1979) J. Biol. Chem. 254, 5942-5950). A possible mechanism of the maltal hydration by beta-amylase involves protonation of substrate from above as the first and rate-limiting step, followed by formation of a transient carbonium ion-enzyme intermediate. Although other possible mechanisms cannot be ruled out, it is clear that this hydration reaction differs from reactions catalyzed with amylaceous substrates and with alpha- and beta-maltosyl fluoride. The ability of beta-amylase to catalyze different types of reactions with different substrates is discussed with respect to observations with other enzymes that, likewise, strongly support the view (Hehre et al.) that the catalytic groups of glycosylases in general may be functionally flexible beyond requirements of the principle of microscopic reversibility.

Structural, dynamic, and metal-ion binding studies of the core glycopeptides β- d-Gal-(1→3)-α- d-GalNAc→Ser, Thr by 13C-n.m.r. spectroscopy

13C-N.m.r. spectral data as well as spin-lattice relaxation times ( T 1 values) are presented for the core glycopeptides β- d-Gal-(1→3)-α- d-GalNAc→Ser, Thr. The binding of Gd 3+ to these model compounds containing N-terminal blocking groups and esterified carboxyl groups indicates that the disaccharide contains a rather weak, but unique, binding-site in the vicinity of C-2 of α- d-GalNAc (possibly involving N-2′, the acetamido carbonyl group, O-3′ and/or possibly the glycosidic oxygen atom (O-3)).

Structural investigation of the antibiotic sporaviridin: 11—Molecular secondary ion mass spectral studies on the constituent pentasaccharides viridopentaoses

AbstractMolecular secondary ion mass spectra of three pentasaccharides, viridopentaoses A, B and C, using various matrices, are discussed. The appearance of the molecular ion species is dependent upon the relative proton affinities between the sample and the organic matrix material. However, the presence of sodium ion, rather than proton, also greatly influences the appearance of the molecular ion species. The glycosidic linkages are mainly cleaved between the glycosidic oxygen atom and the anomeric carbon atom to give informative sugar sequence ions. These fragmentations have been confirmed by the linked scanning technique (B/E).

The Structure of the Cyclodextrin Complex. XVII. Crystal Structure of β-Cyclodextrin–Hexamethylenetetramine (1:1) Complex Hexahydrate

Abstract The crystal structure of β-cyclodextrin–hexamethylenetetramine (1:1) complex hexahydrate was determined by the X-ray diffraction method. The crystal ismonoclinic with the space group P21, Z=2, a=15.285(3), b=10.345(2), c=20.118(2) Å, and β=102.14(1)°. The structure was solved by inspection of a Patterson map and the trial-and-error method combined with the rigid-body least-squares technique and refined by the block-diagonal least-squares method to the R-value of 0.056 for 4369 reflections (sinθ⁄λ<0.55). The β-cyclodextrin molecule is slightly distorted from the regular heptagonal structure. The orientation of two primary hydroxyl groups is statistically disordered. The secondary hydroxyl groups form intramolecular hydrogen bonds between adjacent glucose residues. The guest hexamethylenetetramine molecule, being located roughly at the center of the β-cyclodextrin ring, is in van der Waals contact with the interior surface of the host molecule. Two out of four nitrogen atoms of hexamethylenetetramine form N···H–O hydrogen bonds with water and adjacent β-cyclodextrin molecules. β-Cyclodextrin molecules are stacked along the crystallographic b axis, with which the plane through seven glycosidic oxygen atoms makes an angle of 46.7°, forming a “cage-type” packing. Water molecules occupy the intermolecular spaces between β-cyclodextrin molecules.

13C-n.m.r.-spectral study of the mode of binding of Gd 3+ to various glycopeptides

Natural-abundance, 13C-n.m.r. spectroscopy was used to study the mode of binding of Gd 3+ to mono- O-glycosylated l-serine and tripeptides variously composed of Gly and l-Thr. When the amino and carboxyl groups of the amino acid are not blocked, strong interaction of Gd 3+ with them is observed; this is also readily apparent with some related, nonglycosylated peptides. When the amino and carboxyl groups of the amino acid are blocked, noticeable interaction of Gd 3+ with the glycosidic oxygen atom (O-3) and O-2′ for the glycopeptide containing α- d-Gal p, and with O-3 and N-2′ for the glycopeptide containing α- d-Gal pNAc, is observed. Weak interactions are also possible with O-4′ and O-6′ of the glycosyl groups. Although the amino acids were protected, these metal ion-carbohydrate interactions may still be mediated, to some extent, by the acetyl protecting the amino group and by the ester group on the amino acid.

The Acid-Catalyzed Hydrolysis of Anomeric Alkyl Fructofuranosides

Abstract The rate constants for the hydrolysis of some al-kyl α- and β-d-fructofuranosides in aqueous perchloric acid have been determined at various temperatures. The effects of varying the aglycon structure on the hydrolysis rate suggest, together with the markedly positive entropies of activation, that the substrate, protonated on the glycosidic oxygen atom, undergoes a rate-limiting unimolecular heterolysis to form a glycosyl oxocar-benium ion. The rate variations in mixtures of aqueous perchloric acid and dimethyl sulfoxide are interpreted as lending further support for the proposed mechanism.

Infrared spectroscopic study on metal pectates

According to EPR and Mössbauer spectroscopical measurements, some 3d-transition metal pectates in fully hydrated colour gel states form outer-sphere coordination complexes [1]. These outer-sphere complexes were transformed to inner-sphere coordination complexes with water elimination and change of colour after dehydration at 105 °C. The comparison of the IR-spectra of these dehydrated metal complexes with those of pectic acid may provide some information on the inner-sphere coordination structure. The dehydrated samples were pulverized and compressed into disks, after being stirred for 3 min in a vibrator with KI. IR-spectra were recorded on a Perkin Elmer Model 225 spectrophotometer. ▪ The observed characteristic frequencies of IR-spectra of dehydrated metal pectates and pectic acid can be seen in Table I. Within the range of 4000–2800 cm −1 and 1400–1000 cm −1 no significant difference can be detected in the IR absorption spectra of dehydrated metal pectates and pectic acid. Thus we came to the conclusion that probably no direct chemical bond exists between metal ions and carbohydrate OH groups of the pectic chain. Contrary to this, the intensity of the v CO stretching frequency of the carboxylic group of pectic acid at 1745 cm −1 decreases with the increase in the amount of metal ions substituting carboxylic hydrogen ions. According to the degree of substitution, two intensive bands can be simultaneously observed within the range of 1660–1580 cm −1 and 1430–1400 cm −1. The former band may be assigned to antisymmetric v as(COO −) stretching vibration of carboxylate groups and the latter band to symmetric v s(COO −) stretching. As the difference (Δ) between the frequencies of v as(COO −) and v s(COO −) is greater in the case of the covalently complexed carboxylate ion than in the uncomplexed anion (see Table II), an unidentate metalcarboxylate bond [2a, b] could be proposed in the case of dehydrated t001 Carboxylate Stretching Frequencies (cm −1) of Dehydrated Metal Pectates and the Difference between v as(COO −) and v as(COO −). Metal ion v as(COO −) v s(COO −) Δ = v as − v s Al 3+ 1656vs 1420vs 236 VO 2+ 1635vs 1400vs 235 Cr 3+ 1630vs 1408vs 222 Fe 2+ 1623vs 1412vs 211 Co 2+ 1626vs 1415vs 211 Zn 2+ 1625vs 1415vs 210 Ni 2+ 1622vs 1412vs 210 Cu 2+ 1620vs 1410vs 210 Mg 2+ 1632vs 1426vs 206 Mn 2+ 1619vs 1415vs 204 Ca 2+ 1613vs 1420vs 193 Na + 1613vs 1413vs 200 3d-transition metal and aluminium pectates in contrast to the bidentate bond [3]. Three interesting changes can be seen in the ‘finger print’ range of 1000–600 cm −1. The band at 946–950 cm −1, which can be assigned to pyranose ring skeletal mode displacement involving α-(1–4) linkage [4], shifts to higher frequencies within the range of 956–960 cm −1. This change may be brought about by the bond between metal ion and glycosidic oxygen atom, which results in the stretching of the C(1)O glycos.C(4′) angle in higher frequencies. The weak band at 790 cm −1 which could be assigned to the deformation of OCO − bending [5], shifts to range of 812–816 cm −1, depending on the polarizing properties of bonded metal ions. This shift is due to the covalent metalcarboxylate bond. Finally the weak band at 735 cm −1, which could be assigned to ring breathing vibration, shifts to the band at 762–766 cm −1 in the presence of metal bonds. This shift is probably caused by the metal bond to the ring oxygen atom. Similarly, the ring oxygen atom and Ca 2+ ion bond was assumed by Walkinshaw and Arnott [6] for the speculative model of calcium pectate on the basis of the X-ray fiber diffraction pattern. In the case of calcium alginate a glycosidic and a ring O and Ca 2+ bond was proposed by Angyal [7].