Glycosidic Bond Cleavage Research Articles

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond.

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

ChemInform Abstract: Synthesis and Biological Properties of Multivalent Iminosugars

AbstractReview: [89 refs.

Effect of γ-radiation on free radicals formation, structural changes and functional properties of wheat starch

Wheat starch was treated by different γ-radiation doses (3, 5, 10, 20, 35 and 50kGy). The effects of γ-radiation on structural, thermal, physicochemical, morphological and rheological properties of wheat starch were studied. The presence of free radicals after γ-radiation treatment, which number decreased with time was confirmed. Structural analysis revealed decreases in the intensities of the OH and CH stretches and glycosidic linkages indicating the depolymerization of amylose and probably amylopectin into shorter chain molecules, but showed that γ-radiation treatment did not affect the crystalline structure. Differential scanning calorimetric (DSC) thermograms showed the absence of significant differences in the gelatinization temperatures, as well as the corresponding transition enthalpies since the DSC parameters are related to the crystalline ordering within the granules. Apparent amylose content decreased linearly with increasing irradiation dose leading to an increase in water solubility index. An increase in the swelling power was observed after irradiation treatment until 20kGy, followed by a rapid decrease at higher doses. Microscopic observations showed that the effect of γ-radiation was more visible on starch pastes than on starch granules. Rheological properties of the starch pastes decreased with increasing irradiation dose as a result of glycosidic bond cleavage.

Optimization of synergism of a recombinant auxiliary activity 9 from Chaetomium globosum with cellulase in cellulose hydrolysis.

Auxiliary activity family 9 (AA9, formerly known as glycoside hydrolase family 61 or polysaccharide monooxygenase) is a group of fungal proteins that were recently found to have a significant synergism with cellulase in cellulose hydrolysis via the oxidative cleavage of glycosidic bonds of cellulose chains. In this study, we report the active expression of a recombinant fungal AA9 from Chaetomium globosum (CgAA9) in a bacterial host, Escherichia coli, and the optimization of its synergistic activity in cellulose hydrolysis by using cellulase. The recombinant CgAA9 (0.9 mg/g cellulose) exhibited 1.7-fold synergism in the hydrolysis of Avicel when incubated with 0.9 filter paper units of Celluclast 1.5 L/g cellulose. The first study of the active expression of AA9 using a bacterial host and its synergistic optimization could be useful for the industrial application of AA9 for the saccharification of lignocellulose.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-015-6592-3) contains supplementary material, which is available to authorized users.

1H NMR Spectroscopy-Based Configurational Analysis of Mono- and Disaccharides and Detection of β-Glucosidase Activity: An Undergraduate Biochemistry Laboratory

A 1H NMR spectroscopy-based laboratory experiment explores mono- and disaccharide structural chemistry, and the enzyme-substrate specificity of glycosidic bond cleavage by β-glucosidase towards cellobiose (β-linked gluco-disaccharide) and maltose (α-linked gluco-disaccharide). Structural differences between cellobiose, maltose, and the glycolytic product glucose are established in terms of chemical shift changes and J-coupling constants of the anomeric proton peaks. The distinct anomeric proton signals observed in the 4.0–5.5 ppm range of glucose, cellobiose, and maltose spectra serve as a signature NMR feature to monitor the substrate specificity of β-glucosidase towards cellobiose as a substrate. This experiment consolidates carbohydrate structural chemistry and NMR spectroscopy as applied to investigate enzyme specificity in the context of a biochemistry laboratory experiment with hands-on NMR experience for upper-division undergraduates.

Cellulose degradation by polysaccharide monooxygenases.

Polysaccharide monooxygenases (PMOs), also known as lytic PMOs (LPMOs), enhance the depolymerization of recalcitrant polysaccharides by hydrolytic enzymes and are found in the majority of cellulolytic fungi and actinomycete bacteria. For more than a decade, PMOs were incorrectly annotated as family 61 glycoside hydrolases (GH61s) or family 33 carbohydrate-binding modules (CBM33s). PMOs have an unusual surface-exposed active site with a tightly bound Cu(II) ion that catalyzes the regioselective hydroxylation of crystalline cellulose, leading to glycosidic bond cleavage. The genomes of some cellulolytic fungi contain more than 20 genes encoding cellulose-active PMOs, suggesting a diversity of biological activities. PMOs show great promise in reducing the cost of conversion of lignocellulosic biomass to fermentable sugars; however, many questions remain about their reaction mechanism and biological function. This review addresses, in depth, the structural and mechanistic aspects of oxidative depolymerization of cellulose by PMOs and considers their biological function and phylogenetic diversity.

Solvent influence on cellulose 1,4-β-glycosidic bond cleavage: a molecular dynamics and metadynamics study.

We explore the influence of two solvents, namely water and the ionic liquid 1-ethyl-3-methylimidazolium acetate (EmimAc), on the conformations of two cellulose models (cellobiose and a chain of 40 glucose units) and the solvent impact on glycosidic bond cleavage by acid hydrolysis by using molecular dynamics and metadynamics simulations. We investigate the rotation around the glycosidic bond and ring puckering, as well as the anomeric effect and hydrogen bonds, in order to gauge the effect on the hydrolysis mechanism. We find that EmimAc eases hydrolysis through stronger solvent-cellulose interactions, which break structural and electronic barriers to hydrolysis. Our results indicate that hydrolysis in cellulose chains should start from the ends and not in the centre of the chain, which is less accessible to solvent.

Evolving insights to understanding mycorrhizas

Evolving insights to understanding mycorrhizas

Structure elucidation of new acetylated saponins, Lessoniosides A, B, C, D, and E, and non-acetylated saponins, Lessoniosides F and G, from the viscera of the sea cucumber Holothuria lessoni.

Sea cucumbers produce numerous compounds with a wide range of chemical structural diversity. Among these, saponins are the most diverse and include sulfated, non-sulfated, acetylated and methylated congeners with different aglycone and sugar moieties. In this study, MALDI and ESI tandem mass spectrometry, in the positive ion mode, were used to elucidate the structure of new saponins extracted from the viscera of H. lessoni. Fragmentation of the aglycone provided structural information on the presence of the acetyl group. The presence of the O-acetyl group was confirmed by observing the mass transition of 60 u corresponding to the loss of a molecule of acetic acid. Ion fingerprints from the glycosidic cleavage provided information on the mass of the aglycone (core), and the sequence and type of monosaccharides that constitute the sugar moiety. The tandem mass spectra of the saponin precursor ions [M + Na]+ provided a wealth of detailed structural information on the glycosidic bond cleavages. As a result, and in conjunction with existing literature, we characterized the structure of five new acetylated saponins, Lessoniosides A–E, along with two non-acetylated saponins Lessoniosides F and G at m/z 1477.7, which are promising candidates for future drug development. The presented strategy allows a rapid, reliable and complete analysis of native saponins.

Evaluation of glycosidic bond cleavage and formation of oxo groups in oxidized barley mixed-linkage β-glucans using tritium labelling

This study investigated the formation of oxo groups in pure solutions of barley mixed-linkage (1→3),(1→4)-β-d-glucans (MLGs) incubated in the presence of hydrogen peroxide or Fenton reaction-generated hydroxyl radicals (OH), and it gives a fingerprint of products obtained after enzymic and acidic hydrolysis of OH-attacked MLG. Hydroxyl radical, but not hydrogen peroxide, introduced a range of NaB3H4-reducible functions into MLG chains. Driselase or lichenase digestion of NaB3H4-reduced MLGs released a complex mixture of 3H-labelled products due to the presence of unusual and incompletely digestible residues in OH-attacked polysaccharide chains. Complete acid hydrolysis of OH-treated MLGs yielded a mixture of 3H-aldoses (mainly glucose, mannose, galactose and allose) deriving from random OH attack at positions 2, 3 or 4 to form glycosulose residues which were NaB3H4-reducible to epimeric mixtures of 3H-aldose residues. Furthermore, the production of [3H]glucitol demonstrated the radical-mediated cleavage of mid-chain glucose residues to create new reducing termini. Oxidative scission of MLGs by hydroxyl radical caused a decrease in molecular weight of about 96%, which was partially inhibited by the addition of DMSO, an OH scavenger. The results can be a starting point for developing an assay to detect changes due to OH attack of MLGs in vivo, or during food processing and storage, based on the chemical or enzymic release of unusual sugar residues such as allose as diagnostic products after reduction/labelling treatment and partial purification (or selective digestion by lichenase) of polymeric material.

Low energy electron induced cytosine base release in 2'-deoxycytidine-3'-monophosphate via glycosidic bond cleavage: a time-dependent wavepacket study.

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2'-deoxycytidine-3'-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3' C-O bond cleavage from the lowest π* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π* orbital of the base to the σ* orbital of the glycosidic N-C bond. In addition, the metastable state formed after impinging LEE (0-1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N-C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ~35-55 fs. Comparison of salient features of the two dissociation events, i.e., 3' C-O single strand break and glycosidic N-C bond cleavage in 3'-dCMPH molecule are also provided.

Radical mediated dissection of oligosaccharides

Radical chemistry continues to play an increasingly important role in tandem mass spectrometry based experiments on biomolecules. Oligosaccharides represent a very important class of target molecules that require structural characterization in terms of both monosaccharide identity and overall connectivity. Herein, two methods that generate radical oligosaccharides for subsequent activation are described. In one approach, a radical precursor is covalently attached to the oligosaccharide by reductive amination. Radicals can then be generated by homolytic bond cleavage of specific carbon–iodine bonds in protonated systems by either collisional activation or photodissociation. Subsequent activation of the radical species generates information rich spectra including numerous cross-ring fragments. Alternatively, noncovalent complexation with iodophthalic acid can be used to generate radical disaccharides by photoactivation. Subsequent radical transfer, loss of the radical precursor adduct, and collisional activation of the radical disaccharide results in characteristic glycosidic bond cleavage and cross-ring cleavage products that can easily distinguish isomeric species. Radical chemistry is demonstrated to have several advantages for the characterization of oligosaccharides relative to other approaches, including the identification of isomeric molecules of various sizes or analysis of various charge states.

Synthesis and MALDI-TOF MS Analysis of Protected Oligosaccharide Components of N-Glycoproteins

Essential components of N-glycoproteins were synthesized in octyl glycoside form starting from 3-O-allyl-D-glucose derivative. The β-mannosidic linkage was formed by the oxidation reduction method. MALDI-TOF mass spectrometry and its post-source decay (PSD) mode were used for identification and structural elucidation of protected synthetic oligosaccharides related to N-glycoproteins. Most fragments, identified in the PSD spectra, were products of the cleavage of glycosidic bonds.

Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation.

The recently discovered lytic polysaccharide monooxygenases (LPMOs) are known to carry out oxidative cleavage of glycoside bonds in chitin and cellulose, thus boosting the activity of well-known hydrolytic depolymerizing enzymes. Because biomass-degrading microorganisms tend to produce a plethora of LPMOs, and considering the complexity and copolymeric nature of the plant cell wall, it has been speculated that some LPMOs may act on other substrates, in particular the hemicelluloses that tether to cellulose microfibrils. We demonstrate that an LPMO from Neurospora crassa, NcLPMO9C, indeed degrades various hemicelluloses, in particular xyloglucan. This activity was discovered using a glycan microarray-based screening method for detection of substrate specificities of carbohydrate-active enzymes, and further explored using defined oligomeric hemicelluloses, isolated polymeric hemicelluloses and cell walls. Products generated by NcLPMO9C were analyzed using high performance anion exchange chromatography and multidimensional mass spectrometry. We show that NcLPMO9C generates oxidized products from a variety of substrates and that its product profile differs from those of hydrolytic enzymes acting on the same substrates. The enzyme particularly acts on the glucose backbone of xyloglucan, accepting various substitutions (xylose, galactose) in almost all positions. Because the attachment of xyloglucan to cellulose hampers depolymerization of the latter, it is possible that the beneficial effect of the LPMOs that are present in current commercial cellulase mixtures in part is due to hitherto undetected LPMO activities on recalcitrant hemicellulose structures.

Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum

Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked β-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn2+ coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.

Triterpenoid saponins profiling by adducts-targeted neutral loss triggered enhanced resolution and product ion scanning using triple quadrupole linear ion trap mass spectrometry

Triterpenoid saponins (TSs) are a unique class of high molecular weight glycosides and have been frequently used in cosmetic and phytotherapy industry. There is a great need to comprehensively profile these plant metabolites for studying their functions. In the present study, a novel adducts targeted neutral loss (NL), triggered enhanced resolution (ER) and enhanced product ion (EPI) scanning approach were described for TSs profiling using a triple quadrupole linear ion trap mass spectrometry. This approach circumvented the disadvantages of poor glycosidic bond cleavage of TSs by monitoring the NH3 (NL17) and HCOOH (NL46) loss of their abundant ammonium and formate adducts, respectively. The sugar-loss independent NL scanning served as a sensitive survey scan and triggered information-dependent ER and EPI scans to increase peak assignment confidence. NL17 was superior to NL46 for TSs characterization due to the better fragmentation of ammonium adducts than formate adducts. For those TSs undetectable by NL17, precursor ion (PI) scan for sapogenin fragments could be used to screen out non-adducted TSs. The NL/PI-ER-EPI approach was applied for TSs profiling in Astragali Radix, a famous medicinal and nutritional plant widely used in Asian countries and United States. In total, 136 TSs were detected while previous research using high resolution mass spectrometry based full scan only detected 22 TSs in this herb.

Effect of Water on Hydrolytic Cleavage of Non-Terminal α-Glycosidic Bonds in Cyclodextrins To Generate Monosaccharides and Their Derivatives in a Dimethyl Sulfoxide–Water Mixture

Hydrolytic cleavage of the non-terminal α-1,4-glycosidic bonds in α-, β-, and γ-cyclodextrins and the anomeric-terminal one in d-maltose was investigated to examine how the cleavage rate for α-, β-, and γ-cyclodextrins is slower than that for d-maltose. Effects of water and temperature were studied by applying in situ (13)C NMR spectroscopy and using a dimethyl sulfoxide (DMSO)-water mixture over a wide range of water mole fraction, xw = 0.004-1, at temperatures of 120-180 °C. The cleavage rate constant for the non-anomeric glycosidic bond was smaller by a factor of 6-10 than that of the anomeric-terminal one. The glycosidic-bond cleavage is significantly accelerated through the keto-enol tautomerization of the anomeric-terminal d-glucose unit into the d-fructose one. The smaller the size of the cyclodextrin, the easier the bond cleavage due to the ring strain. The remarkable enhancement in the cleavage rate with decreasing water content was observed for the cyclodextrins and d-maltose as well as d-cellobiose. This shows the important effect of the solitary water whose hydrogen bonding to other water molecules is prohibited by the presence of the organic dipolar aprotic solvent, DMSO, and which has more naked partial charges and higher reactivity. A high 5-hydroxymethyl-2-furaldehyde (5-HMF) yield of 64% was attained in a non-catalytic conversion by tuning the water content to xw = 0.30, at which the undesired polymerization by-paths can be most effectively suppressed. This study provides a step toward designing a new optimal, earth-benign generation process of 5-HMF starting from biomass.

Characterization of Steroidal Saponins from Dioscorea villosa and D. cayenensis Using Ultrahigh Performance Liquid Chromatography/Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry

Yam (Dioscorea spp.) is an important edible tuber plant used for medicinal purposes to promote health and longevity in Chinese tradition. Steroidal saponins were reported to be the major physiologically active constituents in yams. In this current work, the structural characteristics of steroidal saponins in methanolic extracts from dried rhizomes of two Dioscorea species (D. villosa L. and D. cayenensis Lam.) and dietary supplements have been identified and analyzed using UHPLC/QTOF-MS in both negative and positive ion modes. The fragmentation patterns of reference standards were determined and the steroidal saponins in the extracts were identified or tentatively characterized from their retention times and mass spectra. The fragments produced by collision-induced dissociation (CID) revealed the characteristic cleavage of glycosidic bonds, and the fragmentation pattern provided structural information about the sugars. Twenty-one saponins, including four tentatively identified compounds, were detected in the crude extracts of two Dioscorea species. These saponins can be used to distinguish D. villosa from D. cayenensis. For example, asperin and gracillin are found only in D. cayenensis, and dioscoreavilloside A and B and parvifloside are only found in D. villosa. This can be used to determine the presence or absence of D. villosa in commercial products, which may help determine the spiking of plant material, and/or prevent the use of potentially mislabeled or misidentified "Dioscorea" material. The analytical method also provided an alternative, fast method for quality control of Dioscorea species in dietary supplements. Principal component analysis showed that Dioscorea species and commercial products were easily distinguished. From this a partial least squares model was constructed to determine what species are in different products.

Studies of the Hydrolysis of Hesperidin

A variety of hydrolytic mixtures for the cleavage of glycoside bonds in hesperidin was studied. The optimum system for complete hydrolysis of hesperidin to prepare the aglycone consisted of CH3COOH, H2SO4, and C2H5OH at a ratio of 1:1:9. Studies of the kinetics of the hesperidin hydrolysis reaction in this system showed that the process was a first-order reaction, as demonstrated by the constant k. The maximum aglycone yield over time, 98%, was obtained by boiling the reaction mix for 8.5 h. This confirmed the suitability of our model. Prepared of hesperidin-7-O-glucoside should be by fractional hydrolysis in a system consisting of CH3COOH, H2SO4, and C2H5OH at a ratio of 1:1:9.

How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis

Glycoside hydrolases (GHs) distort carbohydrate ring geometry along particular "catalytic itineraries" during the cleavage of glycosidic bonds, illustrating the relationship between substrate conformation and reactivity. Previous theoretical studies of thermodynamics of isolated monosaccharides offer insights into the catalytic itineraries of particular sugars. However, kinetic accessibility of carbohydrate puckering conformations and the role of exocyclic groups have not yet been thoroughly addressed. Here we present the first complete library of low-energy local minima and puckering interconversion transition states for five biologically relevant pyranose sugars: β-xylose, β-mannose, α-glucose, β-glucose, and β-N-acetylglucosamine. These were obtained by a thorough theoretical investigation each of the 38 IUPAC designated puckering geometries and all possible conformations of the exocyclic groups. These calculations demonstrate that exocyclic groups must be explicitly considered when examining these interconversion pathways. Furthermore, these data enable evaluation of previous hypotheses of why enzymes perturb ring geometries from the low-energy equatorial chair ((4)C1) conformation. They show that the relative thermodynamics alone do not universally correlate with GH catalytic itineraries. For some sugars, particular puckers offer both catalytically favorable electronic structure properties, such as anomeric carbon partial charge, and low kinetic barriers to achieve a given puckering conformation. However, different factors correlate with catalytic itineraries for other sugars; for β-N-acetylglucosamine, the key N-acetyl arm confounds the puckering landscape and appears to be the crucial factor. Overall, this study reveals a more comprehensive understanding of why particular puckering geometries are favored in carbohydrate catalysis concomitant with the complexity of glycobiology.