A spoonful of sugar

MS-based glycomics and glycoproteomics methods enabling isomeric characterization

Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.

Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases

Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.

Computerized Molecular Modeling for Discovering Promising Glycosaminoglycan Oligosaccharides that Modulate Protein Function

Glycosaminoglycans (GAGs) are a class of highly negatively charged polysaccharides that plays a major role in various biological processes through their interaction with hundreds of proteins. A major challenge in understanding the specific protein-GAG interaction is their structural diversity and complexity. Recently, computational approaches have been used extensively in addressing this challenge. In this chapter, we present a generally-applicable methodology termed Combinatorial Virtual Library Screening (CVLS) that can identify potential high-affinity, high-specificity sequence(s) binding to a suitable GAG-binding protein from large GAG combinatorial libraries of various lengths and structural patterns.

The strategic use of para-quinone methides to access synthetically challenging and chemoselective α,α'-diarylmethyl N-glycosides from unprotected carbohydrate amines

Reported herein is a practical route to access synthetically challenging and chemoselective α,α'-diarylmethyl N-glycosides via Sc(OTf)3-catalyzed 1,6-conjugate addition of amino sugars with para-quinone methides (p-QMs). The reactions proceed smoothly without a base and under mild reaction conditions with a broad substrate scope and moderate to good yields.

Hydrogen/deuterium exchange in mass spectrometry

The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

A library of chemically defined human N-glycans synthesized from microbial oligosaccharide precursors

Synthesis of homogenous glycans in quantitative yields represents a major bottleneck to the production of molecular tools for glycoscience, such as glycan microarrays, affinity resins, and reference standards. Here, we describe a combined biological/enzymatic synthesis that is capable of efficiently converting microbially-derived precursor oligosaccharides into structurally uniform human-type N-glycans. Unlike starting material obtained by chemical synthesis or direct isolation from natural sources, which can be time consuming and costly to generate, our approach involves precursors derived from renewable sources including wild-type Saccharomyces cerevisiae glycoproteins and lipid-linked oligosaccharides from glycoengineered Escherichia coli. Following deglycosylation of these biosynthetic precursors, the resulting microbial oligosaccharides are subjected to a greatly simplified purification scheme followed by structural remodeling using commercially available and recombinantly produced glycosyltransferases including key N-acetylglucosaminyltransferases (e.g., GnTI, GnTII, and GnTIV) involved in early remodeling of glycans in the mammalian glycosylation pathway. Using this approach, preparative quantities of hybrid and complex-type N-glycans including asymmetric multi-antennary structures were generated and subsequently used to develop a glycan microarray for high-throughput, fluorescence-based screening of glycan-binding proteins. Taken together, these results confirm our combined synthesis strategy as a new, user-friendly route for supplying chemically defined human glycans simply by combining biosynthetically-derived precursors with enzymatic remodeling.

Supramolecular assembly of fluorogenic glyco-dots from perylenediimide-based glycoclusters for targeted imaging of cancer cells

Supramolecular self-assembly between perylenediimide-based glycoclusters and a red-emitting fluorophore produces structurally uniform and stable glyco-dots amenable to targeted fluorogenic imaging of liver and triple-negative breast cancer cells.

Conformations of cationized linear oligosaccharides revealed by FTMS combined with in-ESI H/D exchange

Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in-electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in-ESI source H/D exchange experiments with peptides and proteins.

Decoding glycome of Astragalus membranaceus based on pressurized liquid extraction, microwave-assisted hydrolysis and chromatographic analysis

Carbohydrates in herbs are a relatively untapped source of new drugs and health beneficial ingredients. Their analysis has been developed as a novel aspect in quality control and herbal glycomics. In this study, glycome of Astragalus membranaceus was decoded based on optimized pressurized liquid extraction (PLE), microwave-assisted acidic hydrolysis (MAAH) and comprehensive chromatographic approaches. Twelve saccharides including sucrose, galacturonic acid, mannitol, fructose, rhamnose, ribose, arabinose, fucose, xylose, mannose, glucose and galactose were quantitatively analyzed by GC-MS and HPLC-CAD (charged aerosol detectors). Different columns, including Prevail Carbohydrate ES, XBridge Amide and CARBOSep CHO-820 CA for HPLC-CAD analysis, were compared for evaluation of oligosaccharides. The polysaccharides in water extract of Astragalus membranaceus were characterized by high performance size exclusive chromatography (HPSEC) combined with multiple angle light scattering detection (MALSD) and refractive index detection (RID). The results showed that A. membranaceus contained more than 108.5mgg(-1) free sucrose and small amounts of glucose 9.6-26.0mgg(-1) and fructose 8.7-22.9mgg(-1). While its polymeric carbohydrates were composed of glucose 71.0-162.3mgg(-1), galacturonic acid 52.0-113.4mgg(-1), arabinose 22.8-54.4mgg(-1) and small amounts of galactose, rhamnose, xylose and mannose. CARBOSep CHO-820 CA showed its potential in simultaneously analyzing oligosaccharides and uronic acid, especially only the environment-friendly water mobile phase was used. HPSEC-MALSD-RID showed that there were three different molecular weight distributions of polysaccharides in A. membranaceus and the average molecular weight were 21901.1, 2038.5, and 353.4kDa. Hierarchical clustering analysis and principal component analysis demonstrated that A. membranaceus from different regions showed variations both in free and polymeric carbohydrates, which indicated that carbohydrates should be evaluated for the proper quality control of A. membranaceus. Rha, Ara, Xyl, Man and Gal were found to be the main elements for quality evaluation of polymeric carbohydrates in A. membranaceus by factor analysis. The strategy for decoding the glycome based on chromatographic approaches including GC-MS, HPLC-CAD and HPSEC-MALSD-RID after pressurized liquid extraction and microwave-assisted hydrolysis could be applied for carbohydrates profiling in herbs and beneficial for their quality control.

Synthesis of multifunctional cellulose nanocrystals for lectin recognition and bacterial imaging

Multifunctional cellulose nanocrystals have been synthesized and applied as a new type of glyconanomaterial in lectin binding and bacterial imaging. The cellulose nanocrystals were prepared by TEMPO-mediated oxidation and acidic hydrolysis, followed by functionalization with a quinolone fluorophore and carbohydrate ligands. The cellulose nanocrystals were subsequently applied in interaction studies with carbohydrate-binding proteins and in bacterial imaging. The results show that the functional cellulose nanocrystals could selectively recognize the corresponding cognate lectins. In addition, mannosylated nanocrystals were shown to selectively interact with FimH-presenting E. coli, as detected by TEM and confocal fluorescence microscopy. These glyconanomaterials provide a new application of cellulose nanocrystals in biorecognition and imaging.

Designing "high-affinity, high-specificity" glycosaminoglycan sequences through computerized modeling

The prediction of high-affinity and/or high-specificity protein-glycosaminoglycan (GAG) interactions is an inherently difficult task, due to several factors including the shallow nature of the typical GAG-binding site and the inherent size, flexibility, diversity, and polydisperse nature of the GAG molecules. Here, we present a generally applicable methodology termed Combinatorial Library Virtual Screening (CVLS) that can identify potential high-affinity, high-specificity protein-GAG interactions from very large GAG combinatorial libraries and a suitable GAG-binding protein. We describe the CVLS approach along with the rationale behind it and provide validation for the method using the well-known antithrombin-thrombin-heparin system.

Microwave assisted extraction-solid phase extraction for high-efficient and rapid analysis of monosaccharides in plants

Monosaccharides are the fundamental composition units of saccharides which are a common source of energy for metabolism. An effective and simple method consisting of microwave assisted extraction (MAE), solid phase extraction (SPE) and high performance liquid chromatography-refractive index detector (HPLC-RID) was developed for rapid detection of monosaccharides in plants. The MAE was applied to break down the structure of the plant cells and release the monosaccharides, while the SPE procedure was adopted to purify the extract before analysis. Finally, the HPLC-RID was employed to separate and analyze the monosaccharides with amino column. As a result, the extraction time was reduced to 17 min, which was nearly 85 times faster than soxhlet extraction. The recoveries of arabinose, xylose, fructose and glucose were 85.01%, 87.79%, 103.17%, and 101.24%, with excellent relative standard deviations (RSDs) of 1.94%, 1.13%, 0.60% and 1.67%, respectively. The proposed method was demonstrated to be efficient and time-saving, and had been applied to analyze monosaccharides in tobacco and tea successfully.

Linkage determination of linear oligosaccharides by MS(n) (n > 2) collision-induced dissociation of Z₁ ions in the negative ion mode

Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MS(n), n >2) and collision-induced dissociation (CID) of Z1 ions in the negative ion mode. Under low energy CID conditions, disaccharides (18)O-labeled on the reducing carbonyl group gave rise to Z1 product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS(3) CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z1 ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MS(n) CID (n = 3 - 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z1 ions. CID data of these Z1 ions were collected and compared with the standard database of Z1 ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

Software for automated interpretation of mass spectrometry data from glycans and glycopeptides

The purpose of this review is to provide those interested in glycosylation analysis with the most updated information on the availability of automated tools for MS characterization of N-linked and O-linked glycosylation types. Specifically, this review describes software tools that facilitate elucidation of glycosylation from MS data on the basis of mass alone, as well as software designed to speed the interpretation of glycan and glycopeptide fragmentation from MS/MS data. This review focuses equally on software designed to interpret the composition of released glycans and on tools to characterize N-linked and O-linked glycopeptides. Several websites have been compiled and described that will be helpful to the reader who is interested in further exploring the described tools.

Efficient Synthesis of Dispiropyrrolidines Linked to Sugars

An expedient method for the synthesis of glyco-dispiropyrrolidines is reported through 1,3-dipolar cycloaddition reaction (1,3 DC reaction). The novel glycosyl dipolarophiles derived from D-glucose underwent neat [3+2] cycloaddition reaction with the azomethine ylides generated from 1,2-diketones and sarcosine to give the corresponding glycosidic heterocycles in good yields.

Microfluidic digital isoelectric fractionation for rapid multidimensional glycoprotein analysis

Here we present an integrated microfluidic device for rapid and automated isolation and quantification of glycoprotein biomarkers directly from biological samples on a multidimensional analysis platform. In the first dimension, digital isoelectric fractionation (dIEF) uses discrete pH-specific membranes to separate proteins and their isoforms into precise bins in a highly flexible spatial arrangement on-chip. dIEF provides high sample preconcentration factors followed by immediate high-fidelity transfer of fractions for downstream analysis. We successfully fractionate isoforms of two potential glycoprotein cancer markers, fetuin and prostate-specific antigen (PSA), with 10 min run time, and results are compared qualitatively and quantitatively to conventional slab gel IEF. In the second dimension, functionalized monolithic columns are used to capture and detect targeted analytes from each fraction. We demonstrate rapid two-dimensional fractionation, immunocapture, and detection of C-reactive protein (CRP) spiked in human serum. This rapid, flexible, and automated approach is well-suited for glycoprotein biomarker research and verification studies and represents a practical avenue for glycoprotein isoform-based diagnostic testing.

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

Dye-doped silica nanoparticles as efficient labels for glycans

We report that dye-doped fluorescent silica nanoparticles (FSNPs) are highly efficient labels for glycans. Mono- and oligo-saccharides were conjugated to FSNPs using a general photocoupling chemistry. FSNP-labeled glycans were applied to image and detect bacteria, and to study carbohydrate-lectin interactions on a lectin microarray.

N-linked global glycan profiling by nanoLC mass spectrometry

A method is detailed for the global profiling of underivatized N-linked glycans that are derived from complex protein mixtures. The method consists of five main steps that include the following: (1) protein denaturation; (2) enzymatic digestion; (3) solid phase extraction; (4) nanoLC MS analysis; and (5) data interpretation. Materials, methods, and algorithms for the identification of both glycan composition and structure are summarized. In addition, potential problems and their resolutions are addressed.

Recent Advances in Electrochemical Glycobiosensing

Biosensors based on electrochemical transduction mechanisms have recently made advances into the field of glycan analysis. These glyco-biosensors offer simple, rapid, sensitive, and economical approaches to the measurement need for rapid glycan analysis for biomarker detection, cancer and disease diagnostics, and bioprocess monitoring of therapeutic glycoproteins. Although the prevalent methods of glycan analysis (high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy) provide detailed identification and structural analysis of glycan species, there are significantly few low-cost, rapid glycan assays available for diagnostic and screening applications. Here we review instances in which glyco-biosensors have been used for glycan analysis using a variety of electrochemical transduction mechanisms (e.g., amperometric, potentiometric, impedimetric, and voltammetric), selective binding agents (e.g., lectins and antibodies), and redox species (e.g., enzyme substrates, inorganic, and nanomaterial).

Glyconanomaterials: synthesis, characterization, and ligand presentation

Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins.

Functional glycomics and glycobiology: an overview

Glycomics is the study of the biological role of glycans and glycoconjugates, including glycoproteins, glycolipids, proteoglycans, and of protein-glycan interactions. This chapter outlines the scope of functional glycomics, from biological/biomedical significance to technology development.

Glycomic analysis: an array of technologies

Carbohydrates encode biological information necessary for cellular function. The structural diversity and complexity of these sugar residues have necessitated the creation of novel methodologies for their study. This review highlights recent technological advancements that are starting to unravel the intricate web of carbohydrate biology. New methods for the analysis of both glycoconjugates and glycan structures are discussed. With the use of these innovative tools, the field of glycobiology is poised to take center-stage in the postgenomic era of modern biology and medicine.

Systems biology coupled with label-free high-throughput detection as a novel approach for diagnosis of chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a treatable and preventable disease state, characterised by progressive airflow limitation that is not fully reversible. Although COPD is primarily a disease of the lungs there is now an appreciation that many of the manifestations of disease are outside the lung, leading to the notion that COPD is a systemic disease. Currently, diagnosis of COPD relies on largely descriptive measures to enable classification, such as symptoms and lung function. Here the limitations of existing diagnostic strategies of COPD are discussed and systems biology approaches to diagnosis that build upon current molecular knowledge of the disease are described. These approaches rely on new 'label-free' sensing technologies, such as high-throughput surface plasmon resonance (SPR), that we also describe.