Synthesis of 1,2-phenylenediamine capturing molecule for the detection of diacetyl.

Here we describe the design of 1,2-phenylenediamine capturing molecule and the synthesis steps necessary for its preparation. The designed 1,2-phenylenediamine derivative is able to capture diacetyl in solution, as shown by ESIMS, forming a chemical adduct, 1-4-quinoxaline. The methyl esters of diacetyl-adduct (DAA) and pentanedione-adduct (PDA) are incorporated to the lysines in BSA and the conjugate used for antibody screening and selection. In the research article is described an enzyme-linked immunosorbent assay developed to detect and quantify diacetyl in complex media.

An enzyme-linked immunosorbent assay for the detection of diacetyl (2,3-butanedione).

Diacetyl (2,3-butanedione) is an important metabolic marker of several cancers, as well as an important off-flavour component produced during fermentation. As a small molecule in a complex mixture with many other analytes, existing methods for identification and quantitation of diacetyl invariably involves a chromatographic separation step followed by signal integration with an appropriate stoichiometric detector. Here we demonstrate that the chemical reaction of diacetyl with a 1,2-phenylenediamine derivative yields a chemical adduct, 1,4-quinoxaline which can be conjugated on BSA. The BSA-diacetyl adduct can be used to select an adduct-specific monoclonal antibody in a Fab-format from a 45-billion member phage-display library. The availability of this antibody allowed the development of an enzyme-linked immunosorbent assay for diacetyl, based on the 1,4-quinoxaline competition for the antibodies with the diacetyl adduct immobilized on the plate. The described ELISA assay can detect the captured diacetyl in micromolar concentrations, both in water samples and in cell culture medium.

An efficient arabinoxylan-debranching α-L-arabinofuranosidase of family GH62 from Aspergillus nidulans contains a secondary carbohydrate binding site.

An α-L-arabinofuranosidase of GH62 from Aspergillus nidulans FGSC A4 (AnAbf62A-m2,3) has an unusually high activity towards wheat arabinoxylan (WAX) (67 U/mg; k cat = 178/s, K m = 4.90 mg/ml) and arabinoxylooligosaccharides (AXOS) with degrees of polymerisation (DP) 3-5 (37-80 U/mg), but about 50 times lower activity for sugar beet arabinan and 4-nitrophenyl-α-L-arabinofuranoside. α-1,2- and α-1,3-linked arabinofuranoses are released from monosubstituted, but not from disubstituted, xylose in WAX and different AXOS as demonstrated by NMR and polysaccharide analysis by carbohydrate gel electrophoresis (PACE). Mutants of the predicted general acid (Glu(188)) and base (Asp(28)) catalysts, and the general acid pK a modulator (Asp(136)) lost 1700-, 165- and 130-fold activities for WAX. WAX, oat spelt xylan, birchwood xylan and barley ß-glucan retarded migration of AnAbf62A-m2,3 in affinity electrophoresis (AE) although the latter two are neither substrates nor inhibitors. Trp(23) and Tyr(44), situated about 30 Å from the catalytic site as seen in an AnAbf62A-m2,3 homology model generated using Streptomyces thermoviolaceus SthAbf62A as template, participate in carbohydrate binding. Compared to wild-type, W23A and W23A/Y44A mutants are less retarded in AE, maintain about 70 % activity towards WAX with K i of WAX substrate inhibition increasing 4-7-folds, but lost 77-96 % activity for the AXOS. The Y44A single mutant had less effect, suggesting Trp(23) is a key determinant. AnAbf62A-m2,3 seems to apply different polysaccharide-dependent binding modes, and Trp(23) and Tyr(44) belong to a putative surface binding site which is situated at a distance of the active site and has to be occupied to achieve full activity.

A Chromogenic Assay Suitable for High-Throughput Determination of Limit Dextrinase Activity in Barley Malt Extracts.

Twenty-four malt samples were assayed for limit dextrinase activity using a chromogenic assay developed recently in our group. The assay utilizes a small soluble chromogenic substrate which is hydrolyzed selectively by limit dextrinase in a coupled assay to release the chromophore 2-chloro-4-nitrophenol. The release of the chromophore, corresponding to the activity of limit dextrinase, can be followed by measuring the UV absorption at 405 nm. The 24 malt samples represented a wide variation of limit dextrinase activities, and these activities could be clearly differentiated by the assay. The results obtained were comparable with the results obtained from a commercially available assay, Limit-Dextrizyme from Megazyme International Ireland. Furthermore, the improved assay uses a soluble substrate. That makes it well suited for high-throughput screening as it can be handled in a 96-well plate format.

Synergistic amylomaltase and branching enzyme catalysis to suppress cassava starch digestibility.

Starch provides our main dietary caloric intake and over-consumption of starch-containing foods results in escalating life-style disease including diabetes. By increasing the content of α-1,6 branch points in starch, digestibility by human amylolytic enzymes is expected to be retarded. Aiming at generating a soluble and slowly digestible starch by increasing the content and changing the relative positioning of the branch points in the starch molecules, we treated cassava starch with amylomaltase (AM) and branching enzyme (BE). We performed a detailed molecular analysis of the products including amylopectin chain length distribution, content of α-1,6 glucosidic linkages, absolute molecular weight distribution and digestibility. Step-by-step enzyme catalysis was the most efficient treatment, and it generated branch structures even more extreme than those of glycogen. All AM- and BE-treated samples showed increased resistance to degradation by porcine pancreatic α-amylase and glucoamylase as compared to cassava starch. The amylolytic products showed chain lengths and branching patterns similar to the products obtained from glycogen. Our data demonstrate that combinatorial enzyme catalysis provides a strategy to generate potential novel soluble α-glucan ingredients with low dietary digestibility assets.

Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase.

Complete hydrolytic degradation of starch requires hydrolysis of both the α-1,4- and α-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the α-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact α-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual α-1,6- and α-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis.

Direct study of fluorescently-labelled barley ß-glucan fate in an in vitro human colon digestion model.

ß-Glucans from cereals are ß(1-3)(1-4)-mixed linkage linear homopolysaccharides of D-glucopyranosyl residues, recently recognised as functional components of foods with benefits in maintaining the health of the digestive tract not least through a prebiotic effect. Here we describe the development of methodology to facilitate the study of ß-glucans as prebiotics. Relatively short ß-glucan fragments (DP 6-50) were produced by partial hydrolysis of ß-glucan fibres with Lichenase then functionalised at their reducing end with a tetramethylrhodamine dye. Their enzymatic break down by human colon microbiota in an in vitro fermentation model was examined. Digestion products were isolated by virtue of their fluorescence labels, identified and characterised using capillary electrophoresis and mass spectrometry. Complete digestion of the labelled substrates was indicated, as fluorescently labelled glucose was obtained as the final product. Furthermore, a pathway of enzymatic breakdown was proposed on the basis of a time course experiment; initial fast hydrolysis with an endo-1,3(4)-ß-glucanase was followed by slow degradation with an exo-1,4-ß-glucanase and finally slow action of an exo-1,3-ß-glucanase.

NMR characterization of chemically synthesized branched α-dextrin model compounds.

1H and 13C NMR chemical shifts were accurately determined by consistent referencing for an extensive set of chemically synthesized branched α-glucan model compounds. The model compounds include anomerically fixed and reducing oligosaccharides ranging in size from isomaltose to a doubly branched decasaccharide. Both the 13C1 chemical shift and the 13C6 chemical shifts in α-(1→6) glycosidic bonds are strongly dependent on the chemical structure in the vicinity of the branch point, especially on the addition of glucopyranosyl units towards the non-reducing end of the backbone chain. The conformational sampling at the branch point of the branched α-glucan model compounds was experimentally probed with homo-nuclear scalar couplings. Substitution at O6 consistently increases the fraction of C6-O6 trans conformations, but to a lesser extent, if the attachment occurs at the reducing end residue. Increasingly complex structures in the vicinity of the branch point increase the population of the gauche-trans conformation of the C5-C6 bond. This population change is found to correlate with the 13C6 chemical shift.

Structures of a human blood group glycosyltransferase in complex with a photo-activatable UDP-Gal derivative reveal two different binding conformations.

Glycosyltransferases (GTs) catalyse the sequential addition of monosaccharides to specific acceptor molecules and play major roles in key biological processes. GTs are classified into two main families depending on the inverted or retained stereochemistry of the glycosidic bond formed during the reaction. While the mechanism of inverting enzymes is well characterized, the precise nature of retaining GTs is still a matter of much debate. In an attempt to clarify this issue, studies were initiated to identify reaction-intermediate states by using a crystallographic approach based on caged substrates. In this paper, two distinct structures of AA(Gly)B, a dual-specificity blood group synthase, are described in complex with a UDP-galactose derivative in which the O6'' atom is protected by a 2-nitrobenzyl group. The distinct conformations of the caged substrate in both structures of the enzyme illustrate the highly dynamic nature of its active site. An attempt was also made to photolyse the caged compound at low temperature, which unfortunately is not possible without damaging the uracil group as well. These results pave the way for kinetic crystallography experiments aiming at trapping and characterizing reaction-intermediate states in the mechanism of enzymatic glycosyl transfer.

Structural elucidation of the capsular polysaccharide from Streptococcus pneumoniae serotype 47A by NMR spectroscopy.

The structure of the serotype 47A (Danish nomenclature system) capsular polysaccharide from Streptococcus pneumoniae was elucidated by NMR spectroscopy. The following structure of the repeating heptasaccharide was deduced: [structure: see text]. The serotype 47A capsular polysaccharide is one of 91 structurally and serologically distinct capsular polysaccharides that have been recognized in S. pneumoniae, a significant human pathogenic bacterium and model system in medical microbiology. Structure and NMR spectra are compared to previously solved capsular polysaccharide structures of other serotypes.

A fluorescence assay that detects long branches in the starch polysaccharide amylopectin.

Long α(1-4)-linked glucopyranose branches in the starch polysaccharide amylopectin can be detected by the specific binding of an anionic amphiphilic fluorescent probe. The probe forms spermidine-stabilised micelles in water resulting in fluorescence quenching. By extracting the probe from the micelles polysaccharides are detected in a "turn-on" fluorescence assay.

Profiling of carbohydrate mixtures at unprecedented resolution using high-precision 1H-13C chemical shift measurements and a reference library.

Complex mixtures of carbohydrates pose distinct challenges in routine and high-throughput analysis, so that only a few carbohydrate components are routinely resolved and identified in biofluids, extracts, foods and other complex mixtures. Here, we conduct precise measurements of (1)H and (13)C anomeric chemical shifts to construct a reference library of specific carbohydrate signals with high-resolution two-dimensional (1)H-(13)C NMR spectra. High-resolution multidimensional NMR spectra largely abolish resolution problems in carbohydrate analysis with state-of-the-art instrumentation. Accurate measurements of anomeric (1)H-(13)C chemical shifts at parts per billion precisions permit robust carbohydrate identification using a very limited number of instrument-independent reference values.

(1)H NMR spectroscopy for profiling complex carbohydrate mixtures in non-fractionated beer.

A plethora of biological and biotechnological processes involve the enzymatic remodelling of carbohydrates in complex mixtures whose compositions affect both the processes and products. In the current study, we employed high-resolution (1)H NMR spectroscopy for the analysis of cereal-derived carbohydrate mixtures as exemplified on six beer samples of different styles. Structural assignments of more than 50 carbohydrate moieties were obtained using (1)H1-(1)H2 groups as structural reporters. Spectroscopically resolved carbohydrates include more than ''20 different'' small carbohydrates with more than 38 isomeric forms in addition to cereal polysaccharide fragments with suspected organoleptic and prebiotic function. Structural motifs at the cleavage sites of starch, ß-glucan and arabinoxylan fragments were identified, showing different extent and specificity of enzymatic polysaccharide cleavage during the production of different beer samples. Diffusion ordered spectroscopy supplied independent size information for the characterisation and identification of polysaccharide fragments, indicating the presence especially of high molecular weight arabinoxylan fragments in the final beer.

A chromogenic assay for limit dextrinase and pullulanase activity.

A new chromogenic substrate to assay the starch debranching enzymes limit dextrinase and pullulanase is described. The 2-chloro-4-nitrophenyl glycoside of a commercially available branched heptasaccharide (Glc-maltotriosyl-maltotriose) was found to be a suitable specific substrate for starch debranching enzymes and allows convenient assays of enzymatic activities in a format suited for high-throughput analysis. The kinetic parameters of these enzymes toward the synthesized substrate are determined, and the selectivity of the substrate in a complex cereal-based extract is established.

Probing helical hydrophobic binding sites in branched starch polysaccharides using NMR spectroscopy.

Branched starch polysaccharides are capable of binding multiple hydrophobic guests, but their exploitation as multivalent hosts and in functional materials is limited by their structural complexity and diversity. Linear α(1-4)-linked glucose oligosaccharides are known to bind hydrophobic guests inside left-handed single helices in solution and the solid state. Here, we describe the development of an amphiphilic probe that binds to linear α(1-4)-linked glucose oligosaccharides and undergoes a conformational switch upon complexation, which gives rise to dramatic changes in the (1)H NMR spectrum of the probe. We use this probe to explore hydrophobic binding sites in the branched starch polysaccharides amylopectin and ß-limit dextrin. Diffusion-ordered (DOSY), nuclear Overhauser effect (NOESY) and chemical shift perturbation (HSQC) NMR experiments are utilised to provide evidence that, in aqueous solution, branched polysaccharides bind hydrophobic guests in well-defined helical binding sites, similar to those reported for complexation by linear oligosaccharides. By examining the binding affinity of the probe to systematically enzymatically degraded polysaccharides, we deduce that the binding sites for hydrophobic guests can be located on internal as well as external branches and that proximal α(1-6)-linked branch points weaken but do not prevent complexation.

Time-resolved in-situ observation of starch polysaccharide degradation pathways.

Analytical challenges in the direct time-resolved observation of starch metabolism have been addressed by using optimized multidimensional NMR experiments. Starch provides the main source of human dietary energy intake and is a raw material for beverage and renewable fuel production. Use of direct in situ observations of starch remodeling pathways could facilitate our understanding and control of processes of biotechnological, medical, and environmental relevance. Processes involving starch synthesis or degradation are difficult to monitor directly in aqueous solution, however, because starch consists of glucopyranosyl homopolymers that are built up from and degraded into structurally similar fragments that yield only small signal dispersion in optical and NMR spectroscopy. By focusing on acetal groups only, (1) H,(13) C HSQC experiments sampling narrow spectral windows in the highly resolved (13) C dimension have been employed in order to observe the amylopectin cleavage pathway in real time with a temporal resolution of 150 s. Quantifiable signals for more than 15 molecular species emerging during starch fragmentation by human saliva have been resolved and tracked over time in this manner. Altered accumulation of intermediates in the digestion of amylopectin in the presence of black tea acting as an effector have been monitored.

Nature's dendrimer: characterizing amylopectin as a multivalent host.

Hang on to those branches! Amylopectin, the major polysaccharide of starch, is a predominantly α(1,4)-linked glucan whose properties are defined by its size and the number, distribution, and length of its α(1,6)-linked branches. The amphiphilic probe HPTS-C16 H33 binds to terminal helical branches longer than 12 glucose units (green), which allows for a detailed quantitative characterization of polysaccharide branching by (1) H NMR spectroscopy.

Fast and accurate quantitation of glucans in complex mixtures by optimized heteronuclear NMR spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy is a widely used technique for mixture analysis, but it has shortcomings in resolving carbohydrate mixtures due to the narrow chemical shift range of glycans in general and fragments of homopolymers in particular. Here, we suggest a protocol toward fast spectroscopic glycan mixture analysis. We show that a plethora of oligosaccharides comprising only α-glucopyranosyl residues can be resolved into distinct quantifiable signals with NMR experiments that are substantially faster than chromatographic runs. Conceptually, the approach fully exploits the narrow line widths of glycans (ν1/2 < 3 Hz) in the (13)C spectral dimension while disregarding superfluous spectral information in compound identification and quantitation. The acetal (H1C1) groups suffice to spectroscopically resolve ∼20 different starch fragments in optimized (1)H-(13)C NMR with a narrow (13)C spectral width (3 ppm) that allows sampling the indirect (13)C dimension at high resolution within 15 min. Rapid quantitations by high-resolution NMR data are achieved for glycans at concentrations as low as 10 µg/mL. For validation, comparisons were made with quantitations obtained by more time-consuming chromatographic methods and yielded coefficients of determination (R(2)) above 0.99.

A convenient synthesis of GDP-D-rhamnose: the donor substrate for D-rhamnosyltransferase WbpZ from Pseudomonas aeruginosa PAO1.

Gram negative bacteria have lipopolysaccharides (LPS) that are critical for their survival. LPS molecules are composed of antigenic exopolysaccharide chains (O antigens). We are interested in discovering the enzymes involved in the biosynthesis of O antigens in Pseudomonas aeruginosa. The common polysaccharide antigen contains α-linked D-rhamnose residues. We have now synthesized GDP-D-rhamnose by a convenient synthesis in aqueous solution, and have shown that it can be used without extensive purification as the donor substrate for D-rhamnosyltransferase (WbpZ) from the P. aeruginosa strain PAO1. The availability of this nucleotide sugar preparation allows for characterization of D-rhamnosyltransferases.