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Glycosidic Linkages (glycosidic + linkage)
Selected AbstractsSynthesis of a New Type of Glycosidic Linkage: Acetal-Linked Disaccharides and Trisaccharides of Acyclic and Cyclic Sugars,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 15 2005Soni Kamlesh Madhusudan Abstract New types of di- and trisaccharides related to a unique trisaccharide present in the cell walls of Proteus have been synthesized by coupling of acyclic sugar dithioacetals and di- and monohydroxy cyclic sugars. In this class of compounds an acyclic sugar is linked to a cyclic sugar through an acetal linkage. The formation of these acetal-linked pseudodi- and-trisaccharides has been achieved by a generalized reaction procedure mediated by 1,3-dibromo-5,5-dimethylhydantoin under mild, metal-free and neutral conditions. Sixteen protected and twelve deprotected di- and trisaccharides related to the trisaccharide found in the Proteus cell wall have been synthesized. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Transgalactosylation by thermostable ,-glycosidases from Pyrococcus furiosus and Sulfolobus solfataricusFEBS JOURNAL, Issue 16 2000-glycosides during lactose conversion, Binding interactions of nucleophiles with the galactosylated enzyme intermediate make major contributions to the formation of new The hyperthermostable ,-glycosidases from the Archaea Sulfolobus solfataricus (Ss,Gly) and Pyrococcus furiosus (CelB) hydrolyse ,-glycosides of d -glucose or d -galactose with relaxed specificities pertaining to the nature of the leaving group and the glycosidic linkage. To determine how specificity is manifested under conditions of kinetically controlled transgalactosylation, the major transfer products formed during the hydrolysis of lactose by these enzymes have been identified, and their appearance and degradation have been determined in dependence of the degree of substrate conversion. CelB and Ss,Gly show a marked preference for making new ,(1,3) and ,(1,6) glycosidic bonds by intermolecular as well as intramolecular transfer reactions. The intramolecular galactosyl transfer of CelB, relative to glycosidic-bond cleavage and release of glucose, is about 2.2 times that of Ss,Gly and yields ,- d -Galp- (1,6)- d -Glc and ,- d -Galp- (1,3)- d -Glc in a molar ratio of ,,1 : 2. The partitioning of galactosylated Ss,Gly between reaction with sugars [kNu (m,1·s,1)] and reaction with water [kwater (s,1)] is about twice that of CelB. It gives a mixture of linear ,- d -glycosides, chiefly trisaccharides at early reaction times, in which the prevailing new glycosidic bonds are ,(1,6) and ,(1,3) for the reactions catalysed by Ss,Gly and CelB, respectively. The accumulation of ,- d -Galp- (1,6)- d -Glc at the end of lactose hydrolysis reflects a 3,10-fold specificity of both enzymes for the hydrolysis of ,(1,3) over ,(1,6) linked glucosides. Galactosyl transfer from Ss,Gly or CelB to d -glucose occurs with partitioning ratios, kNu/kwater, which are seven and >,170 times those for the reactions of the galactosylated enzymes with 1-propanol and 2-propanol, respectively. Therefore, the binding interactions with nucleophiles contribute chiefly to formation of new ,-glycosides during lactose conversion. Likewise, noncovalent interactions with the glucose leaving group govern the catalytic efficiencies for the hydrolysis of lactose by both enzymes. They are almost fully expressed in the rate-limiting first-order rate constant for the galactosyl transfer from the substrate to the enzyme and lead to a positive deviation by ,,2.5 log10 units from structure,reactivity correlations based on the pKa of the leaving group. [source] Structures and energies of D -galactose and galabiose conformers as calculated by ab initio and semiempirical methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Majda Rahal-Sekkal Abstract Optimized geometries and total energies of some conformers of ,- and ,- D -galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of ,- and ,- D -galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units , 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles , and , of the glycosidic linkage are considered. In each calculation, at each increment of , and ,, using a step of 30° from 0 to 330°, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 806,818, 2003 [source] Characterization of the glycosidic linkage of underivatized disaccharides by interaction with Pb2+ ionsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2007Ahlam El Firdoussi Abstract Electrospray ionization in combination with tandem mass spectrometry and lead cationization is used to characterize the linkage position of underivatized disaccharides. Lead(II) ions react mainly with disaccharides by proton abstraction to generate [Pb(disaccharide)m, H]+ ions (m = 1,2). At low cone voltages, an intense series of doubly charged ions of general formula [Pb(disaccharide)n]2+ are also observed. Our study shows that MS/MS experiments have to be performed to differentiate Pb2+ -coordinated disaccharides. Upon collision, [Pb(disaccharide) , H]+ species mainly dissociate according to glycosidic bond cleavage and cross-ring cleavages, leading to the elimination of CnH2nOn neutrals (n = 2,4). The various fragmentation processes allow the position of the glycosidic bond to be unambiguously located. Distinction between glc-glc and glc-fru disaccharides also appears straightforward. Furthermore, for homodimers of D -glucose our data demonstrate that the anomericity of the glycosidic bond can be characterized for the 1 , n linkages (n = 2, 4, 6). Consequently, Pb2+ cationization combined with tandem mass spectrometry appears particularly useful to identify underivatized disaccharides. Copyright © 2007 John Wiley & Sons, Ltd. [source] Unambiguous structural elucidation of base-modified purine nucleosides using NMRMAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2008Raman Narukulla Abstract A general and unambiguous approach has been developed for structural elucidation of modified purine nucleosides using NMR spectroscopy. Systematic assignment of proton and carbon signals of modified nucleosides was firmly established by COSY and the anomerism of the glycosidic linkage of synthetic nucleosides clearly elucidated by NOESY experiments. Characteristic properties of 15N-isotopic labelling at specific positions of nucleosides were also employed for structural studies. The reported approach is applicable to other modified nucleosides and nucleotides, as well as nucleobases. Copyright © 2007 John Wiley & Sons, Ltd. [source] 13C-detected IPAP-INADEQUATE for simultaneous measurement of one-bond and long-range scalar or residual dipolar coupling constantsMAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2007Lan Jin Abstract The sensitivity of cryoprobes, which are rapidly becoming available, means that the measurement of coupling constants involving 13C, 13C pairs at the natural abundance of 13C can now, in principle, be done by using tens rather then hundreds of milligrams of compounds. However, a robust method that would yield reliable values of small long-range carbon--carbon coupling constants is still missing. In this Communication, we describe a novel 13C,detected incredible natural-abundance double-quantum transfer experiment (INADEQUATE) experiment for simultaneous correlation of one-bond and long-range 13C13C pairs and the measurement of both types of coupling constants in 13C natural abundance samples. This method yields accurate values of one-bond and long-range coupling constants by manipulation of pure phase in-phase (IP) and antiphase (AP) doublets, and is referred to as 13C-detected IPAP-INADEQUATE. It is illustrated by the measurement of interglycosidic 3JCCOC coupling constants in a disaccharide molecule providing important information about the conformation of the glycosidic linkage. Owing to the simplicity of INADEQUATE spectra the carbon,carbon coupling constants are particularly suitable for studies of partially oriented molecules through the measurement of carbon,carbon residual dipolar couplings (RDCs). An example of this approach is presented. We expect the method to find a variety of applications in the conformational analysis of small molecules, determination of diastereoisomers and enantiomers, and studies of molecules in aligned media. Copyright © 2007 John Wiley & Sons, Ltd. [source] Starch phosphorylation,Maltosidic restrains upon 3,- and 6,-phosphorylation investigated by chemical synthesis, molecular dynamics and NMR spectroscopyBIOPOLYMERS, Issue 3 2009Peter I. Hansen Abstract Phosphorylation is the only known in vivo substitution of starch, yet no structural evidence has been provided to explain its implications of the amylosidic backbone and its stimulating effects on starch degradation in plants. In this study, we provide evidence for a major influence on the glucosidic bond in starch specifically induced by the 3-O-phosphate. Two phosphorylated maltose model compounds were synthesized and subjected to combined molecular dynamics (MD) studies and 950 MHz NMR studies. The two phosphorylated disaccharides represent the two possible phosphorylation sites observed in natural starches, namely maltose phosphorylated at the 3,- and 6,-position (maltose-3,-O-phosphate and maltose-6,-O-phosphate). When compared with maltose, both of the maltose-phosphates exhibit a restricted conformational space of the ,(1,4) glycosidic linkage. When maltose is phosphorylated in the 3,-position, MD and NMR show that the glucosidic space is seriously restricted to one narrow potential energy well which is strongly offset from the global potential energy well of maltose and almost 50°degrees from the , angle of the ,-maltose crystal structure. The driving force is primarily steric, but the configuration of the structural waters is also significantly altered. Both the favored conformation of the maltose-3,-phosphate and the maltose-6,-phosphate align well into the 6-fold double helical structure of amylopectin when the effects on the glucosidic bond are not taken into account. However, the restrained geometry of the glucosidic linkage of maltose-3,-phosphate cannot be accommodated in the helical structure, suggesting a major local disturbing effect, if present in the starch granule semi-crystalline lattice. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 179,193, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Consistent Bioactive Conformation of the Neu5Ac,(2,3)Gal Epitope Upon Lectin BindingCHEMBIOCHEM, Issue 18 2008Anirban Bhunia Dr. Get to NOE MAG: Partial structures of GQ1b,, the natural ligand of the myelin-associated glycoprotein (MAG), have been synthesized and subjected to NOE experiments to determine their bioactive conformations. The experiments show that the flexible ,(2,3)-glycosidic linkage between N -acetylneuraminic acid and galactose present in all ligands adopts a "sialyl Lewisx -type" binding mode. This information is valuable for the future design of conformationally preorganized MAG inhibitors. [source] Conformational studies on a unique bis-sulfated glycolipid using NMR spectroscopy and molecular dynamics simulationsFEBS JOURNAL, Issue 23 2000Naoko Iida-Tanaka The time-averaged solution conformation of a unique bis-sulfated glycolipid (HSO3)2 -2,6Man,-2Glc,-1- sn -2,3- O -alkylglycerol, was studied in terms of the torsional angles of two glycosidic linkages, , (H1-C1-O-Cx) and , (C1-O-Cx-Hx), derived from heteronuclear three-bond coupling constants (3JC,H), and inter-residual proton,proton distances from J-HMBC 2D and ROESY experiments, respectively. The dihedral angles of Glc,1Gro in glycolipids were determined for the first time. The C1-C4 diagonal line of the ,-glucose ring makes an angle of ,,120 ° with the glycerol backbone, suggesting that the ,-glucose ring is almost parallel to the membrane surface in contrast with the perpendicular orientation of the ,-isomer. Furthermore, minimum-energy states around the conformation were estimated by Monte Carlo/stochastic dynamics (MCSD) mixed-mode simulations and the energy minimization with assisted model building and energy refinement (AMBER) force field. The Glc,1Gro linkage has a single minimum-energy structure. On the other hand, three conformers were observed for the Man,2Glc linkage. The flexibility of Man,2Glc was further confirmed by the absence of inter-residual hydrogen bonds which were judged from the temperature coefficients of the chemical shifts, d,/dT (,10,3 p.p.m.·°C,1), of hydroxy protons. The conformational flexibility may facilitate interaction of extracellular substances with both sulfate groups. [source] Structural stability of Sclerotium rolfsii ATCC 201126 ,-glucan with fermentation time: a chemical, infrared spectroscopic and enzymatic approachJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009J.I. Fariña Abstract Aims:,Sclerotium rolfsii ATCC 201126 exopolysaccharides (EPSs) recovered at 48 h (EPS I) and 72 h (EPS II) of fermentation, with differences in rheological parameters, hydrogel topography, salt tolerance, antisyneresis, emulsifying and suspending properties, were subjected to a polyphasic characterization in order to detect structural divergences. Methods and Results:, Fermenter-scale production led to productivity (Pr) and yield (YP/C) values higher at 48 h (Pr = 0·542 g l,1 h,1; YP/C = 0·74) than at 72 h (Pr = 0·336 g l,1 h,1; YP/C = 0·50). Both EPSs were neutral glucose-homopolysaccharides with a ,-(1,3)-glycosidic backbone and single ,-(1,6)-glucopyranosyl sidechains regularly attached every three residues in the main chain, as revealed by chemical analyses. The infra-red diagnostic peak at 890 cm,1 confirmed ,-glycosidic linkages, while gentiobiose released by ,-(1,3)-glucanases confirmed single ,-1,6-glycosidic branching for both EPSs. Conclusions:, The true modular repeating unit of S. rolfsii ATCC 201126 scleroglucan could be resolved. Structural stability was corroborated and no structural differences could be detected as to account for the variations in EPSs behaviour. Significance and Impact of the Study:, Recovery of S. rolfsii ATCC 201126 scleroglucan at 48 h might be considered based on better fermentation kinetic parameters and no detrimental effects on EPS structural features. [source] Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2009Amanda M. Salisburg Abstract The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (,, ,, ,) and (,, ,, ,), whereas for three-bond linkages, there are 54 possible regions that can be defined by (,, ,, ,, ,) and (,, ,, ,, ,). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Anomeric information obtained from a series of synthetic trisaccharides using energy resolved mass spectraJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2007Shusaku Daikoku Abstract The majority of structural investigations of oligosaccharides based on mass spectrometry use naturally occurring oligosaccharides, which do not allow extracting any common feature associated with anomeric structures and linkage positions. In order to address the issue to find such characteristics possibly contained in oligosaccharide structure, a synthetic combinatorial trisaccharide library was analyzed. The trisaccharides used in the analysis consisted of L -fucose, D -galactose and D -glucose, in which individual glycosidic linkages existed in either ,- or ,-anomers. The analysis of energy-resolved mass spectra (ERMS) and the scattered plot analysis of some parameters obtained from ERMS for a series of trisaccharides revealed that lower activation energy was required for the dissociation of ,-glycosides of these sugars compared to those of the corresponding ,-anomers. It is suggested that this finding may be useful in structural analysis of natural oligosaccharides. Copyright © 2007 John Wiley & Sons, Ltd. [source] Effect of periodontal treatment on the activity of chitinase in whole saliva of periodontitis patientsJOURNAL OF PERIODONTAL RESEARCH, Issue 4 2002G. J. Van Steijn Human salivary chitinase could play a role in the defence against chitin-containing oral pathogens. The activity levels of chitinase in the whole saliva of periodontitis patients were significantly higher than those in saliva from controls. Periodontal treatment for a period of 5,6 months resulted in a three- to fourfold decrease in this enzyme activity. The activity of ,- N -acetylhexosaminidase, which is another enzyme that hydrolyses glycosidic linkages, also decreased as a result of treatment, although to a lesser extent. The decrease in chitinase activity upon treatment of the disease did not correlate with the decrease that was seen in clinical attachment loss and bleeding on probing, and only a weak correlation was observed with the changes in probing pocket depth and plaque index. No correlations were found between the above clinical parameters and the decrease in ,- N -acetylhexosaminidase activity. [source] Protein glycosylation analysis by HILIC-LC-MS of Proteinase K-generated N - and O -glycopeptidesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 6-7 2010Gerhild Zauner Abstract Analysis of protein glycosylation is essential in order to correlate certain disease types with oligosaccharide structures on proteins. Here, a method for the MS characterization of site-specific protein glycosylation is presented. Using asialofetuin and fetuin as model substances, a protocol for glycopeptide dissection was developed based on unspecific proteolysis by Proteinase K. The resulting glycopeptides were then resolved by nanoscale hydrophilic interaction liquid chromatography-electrospray multistage MS. The early elution range of O -glycopeptides was clearly separated from the late elution range of N -glycopeptides. Glycopeptides were analyzed by ion trap-MS/MS, which revealed fragmentations of glycosidic linkages and some peptide backbone cleavages; MS3 spectra predominantly exhibited cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N - and O -glycan attachment sites of fetuin could be confirmed; moreover using our method, the occupation of a new, additional O -glycosylation site serine 296 was found. In conclusion, this approach appears to be a valuable technique for in-depth analysis of the site-specific N -glycosylation and O -glycosylation of individual glycoproteins. [source] Interactions of Enzymes and a Lectin with a Chitin-Based Graft Copolymer Having Polysarcosine Side ChainsMACROMOLECULAR BIOSCIENCE, Issue 6 2004Rikiya Nakamura Abstract Summary: The molecular-recognition abilities of a water-soluble chitin derivative, chitin- graft -polysarcosine (2) were investigated using chitinase, lysozyme, and wheat germ agglutinin (WGA). The enzymatic degradabilities of 2 were evaluated using chitinase and lysozyme. The molecular weight of those compounds of 2 with a higher affinity toward water decreased rapidly, as compared with partially deacetylated chitin (1). The 1H NMR spectrum of the low-molecular-weight fraction, yielded after lysozymic hydrolysis, indicated that saccharide residues in the chitinous backbone were specifically recognized by the lysozyme, then , -glycosidic linkages in the backbone were selectively hydrolyzed. Furthermore, the molecular-recognition ability of the chitinous backbone of graft copolymer 2 toward the lectin WGA was elucidated by the enzyme-linked lectin-binding assay (ELLA). It was revealed that the graft copolymer with a lower degree of substitution (DS) value efficiently interacted with WGA. Interestingly, a graft copolymer having longer polysarcosine side chains showed higher recognition ability toward WGA than that having short side chains. The structure of the graft copolymer, chitin- graft -polysarcosine 2, used here. [source] Crystallization and preliminary X-ray crystallographic studies of the thermoactive pullulanase type I, hydrolyzing ,-1,6 glycosidic linkages, from Fervidobacterium pennivorans Ven5ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2000Joyce H. G. Lebbink Crystals of the thermoactive recombinant F. pennivorans type I pullulanase, purified from the supernatant of a Bacillus subtilis culture, have been obtained by the vapour-diffusion method in the presence of the inhibitor ,-cyclodextrin (2,mM) by mixing protein (15,mg,ml,1) with an equal volume of crystallization solution containing 0.1,M bis,tris propane pH 6.5, 50,mM MgCl2 and 15% polyethylene glycol 3350. Crystals diffracted to 3.0,Å using conventional Cu,K, radiation and belong to space group P212121, with unit-cell parameters a = 76.8, b = 96.2, c = 98.5,Å. The asymmetric unit contains one monomer. A preliminary 26% complete data set has been collected at 2.2,Å resolution using synchrotron radiation. [source] Galacto-Oligosaccharides: Production, Properties, Applications, and Significance as PrebioticsCOMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY, Issue 5 2010Duarte P.M. Torres Currently, GOS are produced by glycoside hydrolases (GH) using lactose as substrate. Converting lactose into GOS by GH results in mixtures containing GOS of different degrees of polymerization (DP), unreacted lactose, and monomeric sugars (glucose and galactose). Recent and future developments in the production of GOS aim at delivering purer and more efficient mixtures. To produce high-GOS-content mixtures, GH should not only have good ability to catalyze the transgalactosylation reaction relative to hydrolysis, but also have low affinity for the GOS formed relative to the affinity for lactose. In this article, several microbial GH, proposed for the synthesis of GOS, are hierarchized according to the referred performance indicators. In addition, strategies for process improvement are discussed. Besides the differences in purity of GOS mixtures, differences in the position of the glycosidic linkages occur, because different enzymes have different regiochemical selectivity. Depending on oligosaccharide composition, GOS products will vary in terms of prebiotic activity, as well as other physiological effects. This review focuses on GOS production from synthesis to purification processes. Physicochemical characteristics, physiological effects, and applications of these prebiotic ingredients are summarized. Regulatory aspects of GOS-containing food products are also highlighted with emphasis on the current process of health claims evaluation in Europe. [source] | |||||||||||||