Showing papers on "Pyranose published in 2014"
TL;DR: It is found that a trans-fused 4O,5N-oxazolidinone group stabilizes the equatorial glycoside, i.e., reduces the anomeric effect, when compared to the4O, 5N-diacetyl protected systems.
Abstract: A method for the investigation of the influence of protecting groups on the anomeric equilibrium in the sialic acid glycosides has been developed on the basis of the equilibration of O-sialyl hydroxylamines by reversible homolytic scission of the glycosidic bond following the dictates of the Fischer–Ingold persistent radical effect. It is found that a trans-fused 4O,5N-oxazolidinone group stabilizes the equatorial glycoside, i.e., reduces the anomeric effect, when compared to the 4O,5N-diacetyl protected systems. This effect is discussed in terms of the powerful electron-withdrawing nature of the oxazolidinone system, which in turn is a function of its strong dipole moment in the mean plane of the pyranose ring system. The new equilibration method displays a small solvent effect and is most pronounced in less polar media consistent with the anomeric effect in general. The unusual (for anomeric radicals) poor kinetic selectivity of anomeric sialyl radicals is discussed in terms of the planar π-type structu...
31 citations
TL;DR: A novel electrochemical enzyme biosensor was developed for real-time detection of cellulase activity when acting on their natural insoluble substrate, cellulose, and it was found that the turnover for HjCel6A at saturating substrate concentration was similar and the substrate load at half-saturation was much lower for BMCC compared to Avicel.
22 citations
TL;DR: In this article, a full exploration of the conformational landscape of D-ribose and 2-deoxy-Dribose monosaccharides in the gas phase has been performed using DFT methods (B3LYP and M06-2X).
Abstract: A full exploration of the conformational landscape of D-ribose and 2-deoxy-D-ribose monosaccharides in the gas phase has been performed using DFT methods (B3LYP and M06-2X). Open-chain, furanose and pyranose configurations have been examined. Up to 954 and 668 stable structures have been obtained for D-ribose and 2-deoxy-D-ribose. Among these structures, up to 35 and 22 have relative energies smaller than 5 kJ mol−1 with respect to the absolute minimum of each molecule, respectively. For D-ribose, pyranose in α- and β-forms is the most populated according to both functionals, the β-diastereoisomer being the most populated. For 2-deoxy-D-ribose, the α-pyranose form is in majority. The β/α relationship of pyranose forms presents different results for both functionals: for M06-2X it increases in D-ribose and decreases in 2-deoxy-D-ribose at 0 K with respect to the room temperature results, the opposite case occurring in B3LYP. Intramolecular weak interactions have been characterized using the AIM and NBO methodologies.
22 citations
TL;DR: A new classification method is reported called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms, and is readily automated, easy to interpret, and maps trivially to IUPAC definitions.
Abstract: We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automated, easy to interpret, and maps trivially to IUPAC definitions. It also provides a qualitative measurement of the distortion of the ring. Example applications include the analysis of data from crystal structures and molecular dynamics simulations.
19 citations
TL;DR: High-throughput screening assays for oxygen reactivity and standard dehydrogenase activity were established using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach and confirmed the catalytic role of H512 and H556.
Abstract: Pyranose dehydrogenase (PDH), a member of the GMC family of flavoproteins, shows a very broad sugar substrate specificity but is limited to a narrow range of electron acceptors and reacts extremely slowly with dioxygen as acceptor. The use of substituted quinones or (organo)metals as electron acceptors is undesirable for many production processes, especially of food ingredients. To improve the oxygen reactivity, site-saturation mutagenesis libraries of twelve amino acids around the active site of Agaricus meleagris PDH were expressed in Saccharomyces cerevisiae. We established high-throughput screening assays for oxygen reactivity and standard dehydrogenase activity using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach. The low number of active clones confirmed the catalytic role of H512 and H556. Only one position was found to display increased oxygen reactivity. Histidine 103, carrying the covalently linked FAD cofactor in the wild-type, was substituted by tyrosine, phenylalanine, tryptophan and methionine. Variant H103Y was produced in Pichia pastoris and characterized and revealed a five-fold increase of the oxygen reactivity.
17 citations
TL;DR: Stereoelectronic hyperconjugative forces - essentially linked with the anomeric or gauche effect - and cooperative OH···O, OH·N and NH·O chains, extended along the entire molecule, are found to be the main factors driving the conformational behavior.
Abstract: The bioactive amino monosaccharide D-glucosamine has been generated in the gas phase via laser ablation of D-glucosamine hydrochloride. Three cyclic α-4C1 pyranose forms have been identified using Fourier transform microwave techniques. Stereoelectronic hyperconjugative forces – essentially linked with the anomeric or gauche effect – and cooperative OH⋯O, OH⋯N and NH⋯O chains, extended along the entire molecule, are found to be the main factors driving the conformational behavior. The orientation of the NH2 group within each conformer has been determined by the values of the nuclear quadrupole coupling constants. The results have been compared with those recently obtained for the archetypical D-glucose.
17 citations
TL;DR: Variants of POx with decreased oxidase activity and maintained dehydrogenase activity were identified and site-saturation mutagenesis on a set of eleven amino acids around the active site based on the crystal structure of the enzyme was rationalized based on structural properties.
Abstract: Pyranose 2-oxidase (POx), a member of the GMC family of flavoproteins, catalyzes the regioselective oxidation ofaldopyranoses at position C2 to the corresponding 2-ketoaldoses During the first half-reaction, FAD is reduced to FADH 2 and reoxidized in the second half-reaction by reducing molecular oxygen to H 2 O 2 Alternative electron acceptors includingquinones, radicals or chelated metal ions show significant and in some cases even higher activity While oxygen as cheapand abundantly available electron acceptor is favored for many processes, reduced oxygen reactivity is desirable for someapplications such as in biosensors/biofuel cells because of reduced oxidative damages to the biocatalyst from concomitantH 2 O 2 production as well as reduced electron ‘‘leakage’’ to oxygen The reactivity of flavoproteins with oxygen is ofconsiderable scientific interest, and the determinants of oxygen activation and reactivity are the subject of numerousstudies We applied site-saturation mutagenesis on a set of eleven amino acids around the active site based on the crystalstructure of the enzyme Using microtiter plate screening assays with peroxidase/2,29-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) and 2,6-dichlorophenolindophenol, variants of POx with decreased oxidase activity and maintaineddehydrogenase activity were identified Variants T166R, Q448H, L545C, L547R and N593C were characterized with respect totheir apparent steady-state constants with oxygen and the alternative electron acceptors DCPIP, 1,4-benzoquinone andferricenium ion, and the effect of the mutations was rationalized based on structural properties
16 citations
TL;DR: The successful synthesis of a new poly(vinyl alcohol) (PVA), containing L-arabinose, which branched in only two steps through enzymatic synthesis using alkaline protease from Bacillus subtilis as catalyst and two substrates.
13 citations
TL;DR: This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry and suggests that a similar approach could be applied to studypromiscuity of other enzymes.
Abstract: The flavoenzyme pyranose dehydrogenase (PDH) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications. A generalized approach to simulate all 32 possible aldohexopyranoses in the course of one or a few molecular dynamics (MD) simulations is reported. Free energy calculations according to the one-step perturbation (OSP) method revealed the solvation free energies (ΔGsolv) of all 32 aldohexopyranoses in water, which have not yet been reported in the literature. The free energy difference between β- and α-anomers (ΔGβ-α) of all d-stereoisomers in water were compared to experimental values with a good agreement. Moreover, the free-energy differences (ΔG) of the 32 stereoisomers bound to PDH in two different poses were calculated from MD simulations. The relative binding free energies (ΔΔGbind) were calculated and, where available, compared to experimental values, approximated from Km values. The agreement was very good for one of the poses, in which the sugars are positioned in the active site for oxidation at C1 or C2. Distance analysis between hydrogens of the monosaccharide and the reactive N5-atom of the flavin adenine dinucleotide (FAD) revealed that oxidation is possible at HC1 or HC2 for pose A, and at HC3 or HC4 for pose B. Experimentally detected oxidation products could be rationalized for the majority of monosaccharides by combining ΔΔGbind and a reweighted distance analysis. Furthermore, several oxidation products were predicted for sugars that have not yet been tested experimentally, directing further analyses. This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry. The results suggest that a similar approach could be applied to study promiscuity of other enzymes.
11 citations
TL;DR: A detailed description of binding modes that rationalize changes in the relative conversion rates of D-glucose and D-galactose are provided and can be used to refine future enzyme designs for more efficient use of lactose-hydrolysis byproducts.
Abstract: Each year, about six million tons of lactose are generated from liquid whey as industrial byproduct, and optimally this large carbohydrate waste should be used for the production of value-added products. Trametes multicolor pyranose 2-oxidase (TmP2O) catalyzes the oxidation of various monosaccharides to the corresponding 2-keto sugars. Thus, a potential use of TmP2O is to convert the products from lactose hydrolysis, D-glucose and D-galactose, to more valuable products such as tagatose. Oxidation of glucose is however strongly favored over galactose, and oxidation of both substrates at more equal rates is desirable. Characterization of TmP2O variants (H450G, V546C, H450G/V546C) with improved D-galactose conversion has been given earlier, of which H450G displayed the best relative conversion between the substrates. To rationalize the changes in conversion rates, we have analyzed high-resolution crystal structures of the aforementioned mutants with bound 2- and 3-fluorinated glucose and galactose. Binding of glucose and galactose in the productive 2-oxidation binding mode is nearly identical in all mutants, suggesting that this binding mode is essentially unaffected by the mutations. For the competing glucose binding mode, enzyme variants carrying the H450G replacement stabilize glucose as the α-anomer in position for 3-oxidation. The backbone relaxation at position 450 allows the substrate-binding loop to fold tightly around the ligand. V546C however stabilize glucose as the β-anomer using an open loop conformation. Improved binding of galactose is enabled by subtle relaxation effects at key active-site backbone positions. The competing binding mode for galactose 2-oxidation by V546C stabilizes the β-anomer for oxidation at C1, whereas H450G variants stabilize the 3-oxidation binding mode of the galactose α-anomer. The present study provides a detailed description of binding modes that rationalize changes in the relative conversion rates of D-glucose and D-galactose and can be used to refine future enzyme designs for more efficient use of lactose-hydrolysis byproducts.
10 citations
TL;DR: Herbicidins A and B efficiently inhibit the growth of Xanthomonas oryzae, which causes rice leaf blight, and they are also selectively toxic toward dicotyledon.
Abstract: Herbicidins A and B efficiently inhibit thegrowth of Xanthomonas oryzae, which causes rice leaf blight,and they are also selectively toxic toward dicotyledon. Thesecompounds have some interesting structural features:adenine is glycosylated at the 1b-position of an unusualsugar, undecose, which has a tricyclic furano-pyrano-pyranstructure; there is an internal hemiketal linkage between theC-3'- and -7'-positions which forms a trans junction for apyrano-pyran ring; and all of the substituents at the C-7'-,-8'-, -9'-, and -10'-positions on the second pyranose are fixedin axial positions due to the tricyclic structure of theundecose.
TL;DR: In this paper, a combination of isothermal titration calorimetry and quartz crystal microbalance-dissipation was used to investigate the influence of temperature on the concanavalin-lectin interaction.
Abstract: Although the carbohydrate–lectin interactions have been intensively investigated, there is little report concerning the factors that affect the carbohydrate–lectin interaction. The interactions between concanavalin A (Con A) and glycopolymers, namely poly(2-(methacrylamido)-glucopyranose) and poly(2-methacrylamido-2-deoxy-glucitol) containing pyranose ring form and open form of glucosamine, respectively, have been investigated by a combination of isothermal titration calorimetry and quartz crystal microbalance-dissipation. Our results show that not only the pyranose ring form of glucosamine but also the open form can bind to Con A. Moreover, we investigate the influence of temperature on the carbohydrate–lectin interaction. As the temperature increases, the carbohydrate–lectin interaction is enhanced.
TL;DR: The mutation H103Y slowed down the reductive half-reaction by three orders of magnitude and EPR spectroscopy identified a semiquinone radical in the wild-type and variant H 103Y.
TL;DR: Both the ionized and the unionized structures of D-ribose preferred the pyranose conformation, which was supported by (13)C NMR experiments, and electronic redistribution via resonance and intramolecular hydrogen-bond formation were proposed to account for the stabilization of the ionization structure.
Abstract: Determination of the pKa of OH groups present in d-ribose is crucial in order to elucidate the origin and mechanism of many catalytic processes that involve the ribose unit. However, there is hardly any reports about the experimental pKa of the OH group due to the lack of an appropriate method. In this study we investigated the protonation state of OH groups in d-ribose by introducing C–D labeling and measuring the changes in the isolated C–D frequency in several isotopologues of the compound with pH. The large shift in the νC–D of d-ribose-C1-D in ionized condition compared to other deuterium-substituted d-riboses (e.g., d-ribose-C2-D, d-ribose-C3-D, etc.) confirmed that the C1–OH group preferred ionization, and the ionization pKa was 11.8. Both the ionized and the unionized structures of d-ribose preferred the pyranose conformation, which was supported by 13C NMR experiments. Electronic redistribution via resonance and intramolecular hydrogen-bond formation were proposed to account for the stabilization...
TL;DR: The deprotected nonnatural branched polysaccharides synthesized through a series of site-specific modification reactions were readily soluble in neutral water as well as common organic solvents and would be promising as a new type of water-soluble amino poly Saccharides.
Abstract: Cellulose–chitin
hybrid-type branched polysaccharides, β-1,4-d-glucans having amino sugar branches at the C-6 position, have been synthesized through a series of site-specific modification reactions. Cellulose was first transformed to two kinds of acceptors having a reactive group only at C-6. Glycosylation reactions of these acceptors with an oxazoline donor derived from d-glucosamine resulted in the introduction of amino sugar branches into cellulose. An acceptor carrying the O-trimethylsilyl group at C-6 was particularly suitable for glycosylation in solution to form branched celluloses with various degrees of substitution up to about 0.5 per pyranose unit in a controlled manner. Deprotection of the product afforded the cellulose having N-acetyl-d-glucosamine or d-glucosamine branches depending on the reaction conditions. The deprotected nonnatural branched polysaccharides were readily soluble in neutral water as well as common organic solvents and would be promising as a new type of water-soluble amino polysaccharides.
TL;DR: Employing size‐exclusion chromatography, an entropically‐controlled separation technique, it is investigated whether or not the C3 and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses.
Abstract: The solution flexibility of carbohydrates influences a variety of molecular recognition and regulatory processes. For aldoses and other monosaccharides, this flexibility is dictated by the orientations of the various hydroxyl (OH) groups present, which influences conformer and anomer ratios, interactions among these OH groups, and interactions between them and the surrounding solvent. Depending on the number and position of axial OH groups, a variety of structures can coexist in solutions at equilibrium. In 1950, as part of his pioneering studies on the shape of pyranoside rings, Reeves described the Δ2 effect, the greater destabilization of the pyranose ring conformation when the OH group on carbon 2 (C2) is in the axial position. It was later proposed by Angyal that the Δ2 effect could be cancelled by the presence of an axial OH on C3, termed here the “C3 effect.” Employing size-exclusion chromatography, an entropically-controlled separation technique, we have investigated whether or not the C3 and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses. As will be seen, while qualitatively and semiquantitatively this mutual cancellation of effects does occur in aldohexoses, it does not appear to do so in aldopentoses. An explanation for the latter appears to lie in the variety of anomers and conformers present in equilibrium solutions of those aldopentoses studied and in the relative entropic contribution of individual conformers or anomers to the total solution flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 703–711, 2014.
TL;DR: The anti-proliferative activities of the 6-O-acyl derivatives of d-allose against the human leukemia MOLT-4F cell line were examined and an evaluation of the derivatives of 3 that occurred in a furanose form revealed the pyranose forms of 3 to be important for the anti- Propellerative activity.
Abstract: The anti-proliferative activities of the 6-O-acyl derivatives of d-allose against the human leukemia MOLT-4F cell line were examined. The activity of the 6-O-dodecanoyl derivative (3) was approximately 30 times stronger than that of d-allose. An evaluation of the derivatives of 3 that occurred in a furanose form revealed the pyranose forms of 3 to be important for the anti-proliferative activity.
Patent•
14 May 2014
Patent•
16 Apr 2014TL;DR: In this article, a method for detecting the presence of an anti-M and/or anti-A and anti-C/Y antibody in a sample is presented. But the method is not suitable for the detection of non-saccharide molecules.
Abstract: There is provided a method of detecting in a sample the presence of an anti-M and/or anti-A and/or anti-C/Y antibody, the method comprising contacting the sample with a diagnostic conjugate provided according to the invention, comprising an oligosaccharide which comprises at least two units of 4,6-dideoxy-4-acylamido-α-pyranose and comprising at least one -(1-3)- link between adjacent 4,6-dideoxy-4-acylamido-α-pyranose units, in which the carbon at position 5 in the pyranose is linked to an R group, where R is independently selected from —CH 2 OH, —H or an alkyl group having at least one C atom, the oligosaccharide being covalently linked to a non-saccharide molecule or to a surface.
Patent•
04 Feb 2014
TL;DR: In this article, the 3,6-O-crosslinked pyranose compound according to the present invention is a compound represented by general formula (1) (therein, R1 represents a -SR6 group (R6 being an optionally-substituted lower alkyl group or the like) and R2 represents a hydrogen atom or a like.
Abstract: The present invention addresses the problem of providing a highly-versatile method for easily producing α-O-pyranosides with a high degree of selectivity without establishing severe reaction conditions, and a pyranose donor used in said method. The 3,6-O-crosslinked pyranose compound according to the present invention is a compound represented by general formula (1) (therein, R1 represents a -SR6 group (R6 being an optionally-substituted lower alkyl group or the like) or the like, R2 represents a hydrogen atom or the like, R3 represents a hydrogen atom or the like, R4 and R5 each represent an optionally-halogenated lower alkyl group or the like, n represents an integer of 1-4, and p and q each represent an integer of 0-4), or an enantiomer thereof.
Patent•
16 Apr 2014
TL;DR: In this paper, a method for detecting the presence of an anti-M and/or anti-A and anti-C/Y antibody in a sample is presented. But the method is not suitable for the detection of non-saccharide molecules.
Abstract: There is provided a method of detecting in a sample the presence of an anti-M and/or anti-A and/or anti-C/Y antibody, the method comprising contacting the sample with a diagnostic conjugate provided according to the invention, comprising an oligosaccharide which comprises at least two units of 4,6-dideoxy-4-acylamido-[alpha]- pyranose and comprising at least one -(1-3)-link between adjacent 4,6-dideoxy-4-acylamido-[alpha]-pyranose units, in which the carbon at position 5 in the pyranose is linked to an R group, where R is independently selected from -CH2OH, -H or an alkyl group having at least one C atom, the oligosaccharide being covalently linked to a non-saccharide molecule or to a surface.
Patent•
29 May 2014
TL;DR: In this paper, a cellulose ester with an average acetyl group substitution degree of 1.9 or more was used to produce an optical film having excellent properties in suppressing haze and forming a slit when the film is stretched at a high magnification for broadening its width.
Abstract: PROBLEM TO BE SOLVED: To provide an optical film having excellent properties in suppressing haze and forming a slit when the film is stretched at a high magnification for broadening its width, and to provide a polarizing plate exhibiting excellent frontal contrast while suppressing dimensional changes, warpage and development of uneven colors.SOLUTION: The optical film comprises: at least a cellulose ester; and a (meth)acrylic copolymer or a sugar ester compound prepared from a compound having at least one furanose or one pyranose structure, in which 1 to 12 of furanose structures or pyranose structures are bonded and all of or a part of OH groups in the compound are esterified. The cellulose ester as a whole has an average acetyl group substitution degree of 1.9 or more. The optical film shows an elongation at a breaking point of 10% or more in both the TD direction and the MD direction when the film is stretched in an environment of 23°C and 55% RH, and a tear strength of 40 mN or more in both the TD direction and the MD direction.SELECTED DRAWING: None