Covalent immobilization of carbohydrates on sol-gel-coated microplates

Carbohydrate microarrays have attracted increasing attention in recent years because of their ability to monitor biologically important protein-carbohydrate interactions in a high-throughput manner. Here we have developed an effective approach to immobilizing intact carbohydrates directly on polystyrene microtiter plates coated with amine-functionalized sol-gel monolayers. Lectin binding was monitored by fluorescence spectroscopy using these covalent arrays of carbohydrates that contained six mono- and di-saccharides on the microplates. In addition, binding affinities of lectin to carbohydrates were also quantitatively analyzed by determining IC(50) values of lectin-specific antibody with these arrays. Our results indicate that microplate-based carbohydrate arrays can be efficiently fabricated by covalent immobilization of intact carbohydrates on sol-gel-coated microplates. The microplate-based carbohydrate arrays can be applied for screening of protein-carbohydrate interactions in a high-throughput manner.     

Carbohydrate post-glycosylational modifications

Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented.     

Carbohydrate chips for studying high-throughput carbohydrate-protein interactions

Carbohydrate-protein interactions play important biological roles in living organisms. For the most part, biophysical and biochemical methods have been used for studying these biomolecular interactions. Less attention has been given to the development of high-throughput methods to elucidate recognition events between carbohydrates and proteins. In the current effort to develop a novel high-throughput tool for monitoring carbohydrate-protein interactions, we prepared carbohydrate microarrays by immobilizing maleimide-linked carbohydrates on thiol-derivatized glass slides and carried out lectin binding experiments by using these microarrays. The results showed that carbohydrates with different structural features selectively bound to the corresponding lectins with relative binding affinities that correlated with those obtained from solution-based assays. In addition, binding affinities of lectins to carbohydrates were also quantitatively analyzed by determining IC(50) values of soluble carbohydrates with the carbohydrate microarrays. To fabricate carbohydrate chips that contained more diverse carbohydrate probes, solution-phase parallel and enzymatic glycosylations were performed. Three model disaccharides were in parallel synthesized in solution-phase and used as carbohydrate probes for the fabrication of carbohydrate chips. Three enzymatic glycosylations on glass slides were consecutively performed to generate carbohydrate microarrays that contained the complex oligosaccharide, sialyl Le(x). Overall, these works demonstrated that carbohydrate chips could be efficiently prepared by covalent immobilization of maleimide-linked carbohydrates on the thiol-coated glass slides and applied for the high-throughput analyses of carbohydrate-protein interactions.     

Combinatorial chemistry toward understanding the function(s) of carbohydrates and carbohydrate conjugates

Combinatorial chemistry has contributed significantly to understanding the structure-function relationships of biologically important molecules such as proteins and nucleic acids. However, carbohydrates and carbohydrate conjugates, which have been identified as key modulators of several biological functions have not enjoyed the same measure of success. The complexity and synthetic challenges of carbohydrate conjugates have resulted in a number of conceptual approaches to rapidly access sufficient quantities of these biomolecules. This article summarizes these combinatorial approaches and also highlights fully automated library synthesis of artificial glycopeptides with the goals of understanding their biological roles.     

Carbohydrate microarrays: an advanced technology for functional studies of glycans

The biological significance of glycans in the post-genomic era requires the development of new technologies to enable functional studies of carbohydrates in a high-throughput manner. Recently, carbohydrate microarrays have been exploited as an advanced technology for this purpose. Efficient immobilization methods for carbohydrate probes on the proper surface are essential for the successful fabrication of carbohydrate microarrays. Up to date, several techniques have been developed to attach simple or complex carbohydrates to a solid surface. The developed glycan microarrays have been applied for functional glycomics, drug discovery, and diagnosis. In this concept article, we discuss the progress of immobilization methods of carbohydrates on solid surfaces, their potential uses for biological research and biomedical applications, and possible solutions for some remaining challenges to improve this new technology.     

Per-O-methylation reaction for structural analysis of carbohydrates by mass spectrometry

Per-O-methylation of carbohydrates is an important sample preparation step in structural analysis of complex carbohydrates, which has generated considerable interest as shown by thousands of citations in the last 10 years. This article provides a critical overview of the per-O-methylation methods applied for structural analysis of carbohydrates by mass spectrometry. The understanding of the O-methylation mechanism can help the researchers to apply the adequate O-methylation method and can generate new ideas in the effort of improving this reaction. The per-O-methylation of carbohydrates is relied upon stepwise reactions. The parameters that affect the reaction are discussed for the most important methods and are critically commented for each reaction step. The limits of each method are emphasized. The improvements of the per-O-methylation reaction are described in detail with their advantages and disadvantages and some illustrative examples are given. The methods that give complete O-methylation in non-hazardous conditions with high yields within minutes at room temperature with a very low amount of side-products are especially highlighted.     

RNA integrity as a quality indicator during the first steps of RNP purifications : A comparison of yeast lysis methods

Background  

The completion of several genome-sequencing projects has increased our need to assign functions to newly identified genes. The presence of a specific protein domain has been used as the determinant for suggesting a function for these new genes. In the case of proteins that are predicted to interact with mRNA, most RNAs bound by these proteins are still unknown. In yeast, several protocols for the identification of protein-protein interactions in high-throughput analyses have been developed during the last years leading to an increased understanding of cellular proteomics. If any of these protocols or similar approaches shall be used for the identification of mRNA-protein complexes, the integrity of mRNA is a critical factor.     

Analysis of glycosaminoglycan-derived disaccharides in biologic samples by capillary electrophoresis and protocol for sequencing glycosaminoglycans

Glycosaminoglycans are biologically significant carbohydrates which either as free chains (hyaluronan) or constituents of proteoglycans (chondroitin/dermatan sulfates, heparin, heparan sulfate and keratan sulfate) participate and regulate several cellular events and (patho)physiological processes. Capillary electrophoresis, due to its high resolving power and sensitivity, has been successfully used for the analysis of glycosaminoglycans. Determination of compositional characteristics, such as disaccharide sulfation pattern, is a useful prerequisite for elucidating the interactions of glycosaminoglycans with matrix effective molecules and, therefore, essential in understanding the biological functions of proteoglycans. The interest in the field of characterization of such biologically important carbohydrates is soaring and advances in this field will signal a new revolution in the area of glycomics equivalent to that of genomics and proteomics. This review focuses on the capillary electrophoresis methods used to determine the disaccharide pattern of glycosaminoglycans in various biologic samples as well as advances in the sequence analysis of glycosaminoglycans using both chromatographic and electrophoretic techniques.     

Carbohydrate monolayer strategy for electrochemical assay of cell surface carbohydrate

The study of glycobiology has been seriously hampered due to lack of an ideal assay tool. This work proposes a robust carbohydrate monolayer platform to solve the problems of active site inaccessibility and lectin denaturation associated with protein arrays reported for detection of cell surface carbohydrates and develops a convenient method for monitoring cell surface carbohydrate sites of interest, with high sensitivity, acceptable rapidity, low cost, and excellent extensibility. It utilizes the competitive binding of solid-surface-confined and cell-surface-residing carbohydrates to quantum dot labeled carbohydrate recognition protein and subsequent voltammetric quantification of the metal signature. The mannan monolayer strategy exhibited sensitive response to K562 cells and possessed potential specificity due to the specific interaction between lectin and corresponding carbohydrate. By comparing the competitive binding of K562 cells with mannan in solutions, the average Con A binding capacity of a single K562 cell could be estimated to correspond to 6.9 pg or 2.3 x 10(10) mannose moieties. This strategy integrates the advantages of surface assembly, nanotechnology, bioconjugate techniques, and electrochemical detection and can be expanded for profiling cell surface carbohydrates and high-throughput multiple detection by simultaneously using more pairs of lectin and carbohydrate owing to the multiple coding capability of QDs, which provides an important protocol for the quantitative evaluation of cell surface carbohydrate sites.     

A novel mass spectrometric method to distinguish isobaric monosaccharides that are phosphorylated or sulfated using ion-pairing reagents

Phosphorylation and sulfation are two important biological modifications present in carbohydrates, proteins, and glycoproteins. Typically, sulfation and phosphorylation cause different biological responses, so differentiating these two functional groups is important for understanding structure/function relationships in proteins, carbohydrates, and metabolites. Since phosphorylated and sulfated compounds are isobaric, their discrimination is not possible in routinely utilized mass spectrometers. Thus, a novel mass spectrometric method to distinguish them has been developed. Herein, we utilize basic peptides as ion-pairing reagents to complex to phosphorylated and sulfated carbohydrates via noncovalent interactions. By performing ESI-MS/MS on the ion-pair complexes, the isobaric compounds can be distinguished. This is the first study demonstrating that ion-pairing can be used for the detection of phosphorylated compounds and the first study to use ion-pairing in conjunction with MS/MS to obtain structural information about the analytes.     

Catalyst optimization strategy: selective oxidation of o-xylene to phthalic anhydride

The oxidation of o-xylene and/or naphthalene to phthalic anhydride is one of the important industrial processes based on catalytic selective oxidation reactions. Vanadia--titania catalysts have been used in the industrial phthalic anyhdride process for the last 50 years. The operation parameters like the temperature range of operation, reactor inlet pressures, contact times, o-xylene loadings, etc. were constantly improved during this period of continuous process optimization so as to optimize catalyst performance and increase its life time. However, a fundamental understanding of the mutual interaction of the rather complex reaction network and the catalyst formulation is still missing. Recently, a detailed study of by-product formation as function of process conditions allowed us to develop a novel, improved reaction scheme for the catalytic oxidation of o-xylene. Based on this understanding, a detailed investigation was conducted for the first time of the by-product formation under varying operation conditions and as a function of the active mass variation exploiting high-throughput, as well as bench scales reactors. This high-throughput testing allowed us to relate reaction kinetics to novel catalyst formulations.     

Probing cell proliferation in the human colon using vibrational spectroscopy: a novel use of FTIR-microspectroscopy

Recently, Fourier transform infrared (FTIR)-spectroscopy has been used to monitor cell growth by several works. Conventionally, the study of cell and tissue dynamics at molecular levels is carried out through various approaches like histochemical methods, application of molecular biology and immunology. Colonic crypts display a pattern in cell growth along their height. Histologically normal sections obtained from formalin fixed biopsies of colon cancer patients were studied in the present work through vibrational spectroscopy. The evolution and development of the normal human colonic crypts manifested in Fourier transform infrared-microspectroscopy (FTIR-MSP) as spectral changes in the levels of nucleic acids, proteins, carbohydrates and lipids. The results indicate that the level of carbohydrates, nucleic acids and lipids increases only till the middle of the crypt up to which the maturation zone is restricted and thereafter decreases till the top where the cells are exfoliated. These observations are in coherence with earlier reports on crypt proliferation. We identify the normal pattern of various biochemicals along the colonic crypt based on data analyzed from FTIR-MSP. This study affords an important example of the application of microscopic vibrational spectroscopy for understanding basic cell processes from formalin fixed tissues where in vivo studies and immunological methods are not feasible.     

Carbohydrate arrays for functional studies of carbohydrates

Carbohydrates, as components of glycoproteins, glycolipids and proteoglycans, play an important biological role as recognition markers through carbohydrate-protein interactions. For the most part, biophysical and biochemical methods have been used to analyze these biomolecular interactions. In contrast, less attention has been given to the development of high-throughput procedures to elucidate carbohydrate-protein recognition events. Recently, carbohydrate arrays were developed and employed as a novel high-throughput analytic tool for monitoring carbohydrate-protein interactions. This technique has been used to profile protein binding and enzymatic activity. The results have shown that carbohydrate binding to the corresponding lectins is highly selective and that the relative binding affinities are well correlated with those obtained from solution-based assays. In addition, this effort demonstrated that carbohydrate arrays could be also utilized to identify and characterize novel carbohydrate-binding proteins or carbohydrate-processing enzymes. Finally, the results of this investigation showed that lectin-carbohydrate binding affinities could be quantitatively assessed by determining IC50 values for soluble carbohydrates with the carbohydrate arrays. The results of these studies suggest that carbohydrate arrays have the potential of playing an important role in basic researches, the diagnoses of diseases and drug discovery.     

Inferring the chemical mechanism from structures of enzymes

Chemistry has once again embraced the study of enzyme mechanism as a core discipline. Chemists are uniquely able to contribute to the analysis of enzymes through their understanding of the reactivity of atoms. In this tutorial review for the Corday-Morgan medal, I will concentrate on the work from my lab over the past six years. I discuss enzymes which transform carbohydrates and incorporate halogens. The tutorial review will emphasise the strengths and limitations of structural biology as a means to deducing the chemical mechanism.     

Mapping protein: carbohydrate interactions

Many biologically important interactions occur between proteins and carbohydrates. The examination of these interactions at the atomic level is critical not only in understanding the nature of these interactions and their biological role, but also in the design of effective modulators of these interactions. While experimentally obtained structural information is preferred, quite often this information is unavailable. In order to address this, several methods have been developed to probe the interactions between protein and carbohydrate in the absence of structural data. These methods map the interactions between protein and carbohydrate, and identify the groups involved, both at the carbohydrate and protein level. Here, we review these developments, and examine the strengths, weaknesses, and pitfalls of these methods.     

High-throughput heterogeneous catalytic science

High-throughput experimentation in heterogeneous catalysis has recently experienced nearly exponential growth. Initial qualitative screening has evolved into quantitative high-throughput experimentation, characterization, and analysis. This allows high-throughput catalysis now to rise above simple screening to the level of fundamental understanding of reaction mechanisms, which will lead on a faster path to the Holy Grail of catalysis: rational catalyst design.     

作为信息分子的糖类

糖生物学是生物化学中最后一个重大的研究前沿。糖类研究的复杂性在于其结构的复杂多变, 但是近年来对糖类结构, 特别是糖复合物中的糖部分的测定取得了很大进展。糖结构的复杂性, 也使糖类成为携带着最大信息量的生物分子。作为信息分子的糖类在生物体内发挥多方面的生物作用: 决定了分子的抗原性和细胞的表型; 在很多生理和病理过程中起了关键的识别作用; 也可作为动态和时空调节的信号。     

Assigning kinetic 3D-signatures to glycocodes

Reconciling glycocodes and their associated bioactivities, via 3D-structure, will rationalise burgeoning high-throughput functional glycomics data and underpin a new era of opportunity in chemical biology. A major impasse to achieving this goal is a detailed understanding of pyranose sugar ring 3D-conformation (or pucker) and the affiliated microsecond-timescale exchange kinetics. Here, we perform hardware-accelerated kinetically-rigorous equilibrium simulations of fundamental monosaccharides to produce the hypothesis that pyranoses have microsecond-timescale kinetic puckering signatures in water, classified as unstable (rare in the glycome), metastable (infrequently observed) and stable (prevalent). The predicted μs-metastability of β-d-glucose explained hitherto irreconcilable experimental measurements. Twisted puckers seen in carbohydrate enzymes were present in the aqueous 3D-ensemble (suggesting preorganization) and pyranose-water interactions accounted for the relative stability of β-d-galactose. Characteristic 3D-shapes for biologically- and commercially-important carbohydrates and new rules linking chemical modifications with pyranose μs-puckering kinetics are proposed. The observations advance structural-glycomics towards dynamic 3D-templates suitable for structure-based design.     

Total syntheses of carbohydrates: organocatalyzed aldol additions of dihydroxyacetone

The selective total synthesis of carbohydrates with defined configuration has been of great interest for a long time. This field has been the domain of enzymatic methods so far. But now the recent development of several organocatalyzed aldol methodologies has made a selective synthetic approach to configuratively defined carbohydrates possible. This development and different strategies will be discussed in this concept article.     

Screening of carbohydrates in urine by capillary electrophoresis

Carbohydrate analysis of urine is clinically important in assisting diagnosis of disorders of carbohydrate metabolism and understanding its pathologic significance. Paper chromatography and thin-layer chromatography are the techniques that are often employed for the determination of urinary carbohydrates. An aim of our experiments was to investigate the utility of capillary electrophoresis to develop a fast screening procedure of urinary carbohydrates. Simultaneous resolution of eight carbohydrates involving maltose, lactose, D-mannose, D-glucose, D-ribose, D-xylose, L-arabinose and D-galactose as markers was obtained with 130 mM borate (pH 10.2). Ethanol/water (80/20 v/v) and acetonitrile proved to be efficient reagents for urine sample clean-up which produced symmetrical peaks. The urine sample from a normal subject was determined to contain lactose, glucose, xylose and arabinose that fall within normal ranges of these carbohydrates in urine. The investigations made in this study may be potentially useful in carbohydrate screening, especially in neonatal urine screening.