Protein glycosylation analysis with capillary-based electromigrative separation techniques

An impressive complexity is associated with glycoproteins due to the microheterogeneity of glycosylation as posttranslational modification giving rise to a vast number of isoforms. The full characterization of glycoproteins is difficult to achieve, and a number of analytical methods have to be combined for a detailed understanding of glycosylation. In this review, we focus on capillary electromigrative separation techniques in the formats capillary electrophoresis, micellar electrokinetic chromatography, and capillary sieving electrophoresis. These separation techniques can be applied to all levels of glycosylation analysis including intact glycoproteins, glycopeptides, and released glycans. We here discuss the separation characteristics for each method and the information that they can provide for each level. Detection issues, especially laser-induced fluorescence detection and mass spectrometry are taken into account. In addition, tables provide an overview on the achievements made from the very beginning of glycosylation research by electromigrative separation techniques. From the literature presented here it is clear, that glycosylation analysis by electromigrative separation techniques is on the edge of transition of basic research and method development towards applications. First proof-of-principle studies for in-depth glycoprotein characterization and clinical diagnosis are described. However, this overview also shows that many basic aspects of separation have not yet been fully understood and more research is necessary to be able to fully use the capabilities of electromigrative separation techniques.     

A new method for quantitative analysis of cell surface glycoproteome

As the altered glycosylation expressions of cell surface proteins are associated with many diseases, glycoproteomics approach has been widely applied to characterization of surface glycosylation alteration. In general, the abundances of proteolytic glycopeptides derived from corresponding glycoproteins can be measured to determine the abundances of glycoproteins. However, this quantification strategy cannot distinguish whether the changes are results from changes of protein abundance or changes in glycosite occupancy. For the accurate and specific quantification of the cell surface glycosylation profile, we proposed a modified cell surface‐capturing strategy where the glycopeptides were submitted to LC‐MS/MS analysis directly for identification of glycoproteins and the non‐glycopeptides were isotopically labelled for quantification of glycoproteins. This strategy was applied to comparatively analyze cell surface glycoproteins of two human cell lines, i.e. Chang Liver and HepG2 cells. Totally 341 glycoproteins were identified with 82.4% specificity for cell membrane proteins and 33 glycoproteins were quantified with significant expression change between the two cell lines. The differential expressions of two selected proteins (EMMPRIN and BCAM) were validated by Western blotting. This method enables specific and accurate analysis of the cell surface glycoproteins and may have broad application in the field of biomarker and drug target discovery.     

A new strategy for identification of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation

Characterization of glycoproteins using mass spectrometry ranges from determination of carbohydrate-protein linkages to the full characterization of all glycan structures attached to each glycosylation site. In a novel approach to identify N-glycosylation sites in complex biological samples, we performed an enrichment of glycosylated peptides through hydrophilic interaction liquid chromatography (HILIC) followed by partial deglycosylation using a combination of endo-beta-N-acetylglucosaminidases (EC 3.2.1.96). After hydrolysis with these enzymes, a single N-acetylglucosamine (GlcNAc) residue remains linked to the asparagine residue. The removal of the major part of the glycan simplifies the MS/MS fragment ion spectra of glycopeptides, while the remaining GlcNAc residue enables unambiguous assignment of the glycosylation site together with the amino acid sequence. We first tested our approach on a mixture of known glycoproteins, and subsequently the method was applied to samples of human plasma obtained by lectin chromatography followed by 1D gel-electrophoresis for determination of 62 glycosylation sites in 37 glycoproteins.     

糖组学研究技术及其进展

多细胞生物机体内,蛋白质糖基化是一个重要后修饰事件 . 蛋白质的糖链不仅仅是区别细胞种类的标志,且与众多的生物现象有关,如细胞发育、分化、形态、肿瘤转移、微生物感染等 . 糖组学的内容主要涉及单个个体的全部糖蛋白结构分析,确定编码糖蛋白的基因和蛋白质糖基化的机制 . 综述了糖组学的分离和结构鉴定技术及其最新进展 .     

A general approach for characterizing glycosylation sites of glycoproteins.

Recent advances in glycobiology have greatly stimulated carbohydrate research; however, improving techniques for identification and isolation of specific glycosylation sites in protein structure analysis remains a challenge. We report here a practical approach utilizing a membrane staining technique on Problott, a PVDF-type membrane, to screen glycoproteins and glycopeptides derived from enzymatic digests of glycoproteins. To improve the detection sensitivity, an amplified staining technique using biotinylated lectins, avidin, and biotinylated peroxidase was employed. In addition, we describe a micro-batch affinity binding procedure to isolate glycopeptides from complex glycoprotein enzymatic digests. These protocols allow us to start with a subnanomole quantity of glycoprotein and locate the glycosylation sites; isolate glycopeptides in a homogeneous form; and perform amino acid composition, amino acid sequence, and mass analyses on the isolated glycopeptides. The characterization of glycosylation site of a model glycoprotein, carboxypeptidase P, of which the structure is still largely unknown, has been investigated.     

Separation technologies for glycomics

Progress in genome projects has provided us with fundamentals on genetic information; however, the functions of a large number of genes remain to be elucidated. To understand the in vivo functions of eukaryotic genes, it is essential to grasp the features of their post-translational modifications. Among them, protein glycosylation is a central issue to be discussed, considering the predominant roles of glycoproteins in cell-cell and cell-substratum recognition events in multicellular organisms. In this context, it is necessary to establish a core strategy for analyzing glycosylated proteins under the concept of the "glycome" [Trends Glycosci. Glycotechnol. 12 (2000) 1]. Though the term glycome should be defined, in analogy to the genome and proteome, as "a whole set of glycans produced in a single organism", here we propose a glycome project specifically focusing on glycoproteins. Principal objectives in the project are to identify: (1) which genes encode glycoproteins (i.e. genome information); (2) which sites among potential glycosylation sites are actually glycosylated (i.e. glycosylation site information); (3) what are the structures of glycans (i.e. structural information); and (4) what are the effects (functions) of glycosylation (functional information). For these purposes, two affinity technologies have been introduced. One is named the "glyco-catch method" to identify genes encoding glycoproteins [Proteomics 1 (2001) 295], and the other is the recently reinforced "frontal affinity chromatography" [J. Chromatogr. A 890 (2000) 261]. By the former method, genes that encode glycoproteins as well as glycosylation sites are systematically identified by the efficient combination of conventional lectin-affinity chromatography and contemporary in silico database searching. The following three actions have been devised for rapid and systematic characterization of glycans: (1) mass spectrometry to acquire exact mass information; (2) 2-D/3-D mapping to obtain refined chemical information; and (3) reinforced frontal affinity chromatography to determine affinity constants (K(a)-values) for a set of lectins. Pyridylaminated glycans are used throughout the characterization processes. In this review, the concept and strategy of glycomic approaches are described referring to the on-going glycome project focused on the nematode Caenorhabditis elegans.     

Biochemical and histochemical effects of perorally applied endotoxin on intestinal mucin glycoproteins of the common carp Cyprinus carpio

Mucins are high molecular weight glycoproteins produced by goblet cells and secreted on mucosal surfaces. We investigated biochemical and histochemical properties of intestinal mucins of virus- and parasite-free common carp Cyprinus carpio in response to a single peroral application of endotoxin (lipopolysaccharide = LPS). Intracellular mucins were quantified histochemically by their carbohydrate content and characterized by specific, lectin-based methods. In addition, secreted epithelial (intracellular) and luminal (extracellular) mucins were isolated and separated by downward gel filtration. Carbohydrate and protein content were determined photometrically. Subsequently, terminal glycosylation was characterized by a lectin-binding assay. A peroral endotoxin application altered intestinal secretion and composition of intestinal mucin glycoproteins in common carp. A statistically significant decrease in mature luminal mucins was demonstrated, linked to a new biosynthesis of intracellular mucin glycoproteins. Simultaneous changes in the glycosylation pattern of isolated mucins were found. The intestinal mucosal system is purported to provide a removal mechanism for bacterial noxes by increasing secretion of mucins inducing a flushing-out effect, in combination with altered glycosylation patterns that change adhesion properties. Consequently, pseudofaeces of fish, which are a common sign of intestinal parasitical infections, may also be interpreted as an elimination mechanism for strong bacterial noxes.     

蛋白质糖基化分析方法及其在蛋白质组学中的应用

作为一种普遍存在的翻译后修饰,糖基化对蛋白质的结构和功能有着重要影响。弄清糖基化发生发展的规律是理解蛋白质复杂多样的生物功能的一个重要前提。糖基化发生的特点决定了糖基化相关研究是对分析技术的一大挑战。作为蛋白质组学研究的重要组成部分,目前蛋白质糖基化研究的重点和难点主要集中于糖蛋白／糖肽的分离富集和糖蛋白的鉴定／糖基化位点的确定2个方面,相关技术已用于蛋白质组学水平的糖基化研究,但都还不够成熟。以生物质谱为核心、多学科交叉的蛋白质组学技术始终处于不断发展之中。基于糖基化发生规律的富集检测技术的发展、移动质子理论的提出及电子捕获裂解技术的应用必将极大地促进包括糖基化在内的翻译后修饰研究。蛋白质糖基化的研究有助于从基因组-蛋白组-糖组这样一个宏观的综合的水平观察分析生命现象,从而达到对生命现象更本质的认识。     

Solid-phase extraction of N-linked glycopeptides

Protein glycosylation is a common post-translational modification and has been increasingly recognized as one of the most prominent biochemical alterations associated with malignant transformation and tumorigenesis. N-linked glycosylation is prevalent in proteins on the extracellular membrane, and many clinical biomarkers and therapeutic targets are glycoproteins. Here, we describe a protocol for solid-phase extraction of N-linked glycopeptides and subsequent identification of N-linked glycosylation sites (N-glycosites) by tandem mass spectrometry. The method oxidizes the carbohydrates in glycopeptides into aldehydes, which can be immobilized on a solid support. The N-linked glycopeptides are then optionally labeled with a stable isotope using deuterium-labeled succinic anhydride and the peptide moieties are released by peptide-N-glycosidase. In a single analysis, the method identifies hundreds of N-linked glycoproteins, the site(s) of N-linked glycosylation and the relative quantity of the identified glycopeptides.     

Carbohydrate analysis throughout the development of a protein therapeutic

This review discusses the challenges involved in the characterization of the glycosylation of therapeutic glycoproteins. The focus is on methods that are most commonly used in regulatory filings and lot release testing of therapeutic glycoproteins. The different types of assays for carbohydrate analysis are reviewed, including the distinction between assays appropriate for lot release or better suited to testing during early drug development or in-depth characterization of the glycosylation. Characteristics of the glycoprotein and production process that should be considered when determining the amount of testing, the number of different methods to employ and when the testing should be performed during development of protein therapeutics is also discussed.     

Surface glycoproteomic analysis of hepatocellular carcinoma cells by affinity enrichment and mass spectrometric identification

Cell surface glycoproteins are one of the most frequently observed phenomena correlated with malignant growth. Hepatocellular carcinoma (HCC) is one of the most malignant tumors in the world. The majority of hepatocellular carcinoma cell surface proteins are modified by glycosylation in the process of tumor invasion and metastasis. Therefore, characterization of cell surface glycoproteins can provide important information for diagnosis and treatment of liver cancer, and also represent a promising source of potential diagnostic biomarkers and therapeutic targets for hepatocellular carcinoma. However, cell surface glycoproteins of HCC have been seldom identified by proteomics approaches because of their hydrophobic nature, poor solubility, and low abundance. The recently developed cell surface-capturing (CSC) technique was an approach specifically targeted at membrane glycoproteins involving the affinity capture of membrane glycoproteins using glycan biotinylation labeling on intact cell surfaces. To characterize the cell surface glycoproteome and probe the mechanism of tumor invasion and metastasis of HCC, we have modified and evaluated the cell surface-capturing strategy, and applied it for surface glycoproteomic analysis of hepatocellular carcinoma cells. In total, 119 glycosylation sites on 116 unique glycopeptides were identified, corresponding to 79 different protein species. Of these, 65 (54.6?%) new predicted glycosylation sites were identified that had not previously been determined experimentally. Among the identified glycoproteins, 82?% were classified as membrane proteins by a database search, 68?% had transmembrane domains (TMDs), and 24?% were predicted to contain 2-13 TMDs. Moreover, a total of 26 CD antigens with 50 glycopeptides were detected in the membrane glycoproteins of hepatocellular carcinoma cells, comprising 43?% of the total glycopeptides identified. Many of these identified glycoproteins are associated with cancer such as CD44, CD147 and EGFR. This is a systematic characterization of cell surface glycoproteins of HCC. The membrane glycoproteins identified in this study provide very useful information for probing the mechanism of liver cancer invasion and metastasis.     

Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging

Protein post-translational modifications (PTMs), such as glycosylation and phosphorylation, are crucial for various signaling and regulatory events, and are therefore an important objective of proteomics research. We describe here a protocol for isotope-coded glycosylation site-specific tagging (IGOT), a method for the large-scale identification of N-linked glycoproteins from complex biological samples. The steps of this approach are: (1) lectin column-mediated affinity capture of glycopeptides generated by protease digestion of protein mixtures; (2) purification of the enriched glycopeptides by hydrophilic interaction chromatography (HIC); (3) peptide-N-glycanase-mediated incorporation of a stable isotope tag, 18O18O, specifically at the N-glycosylation site; and (4) identification of 18O-tagged peptides by liquid chromatography-coupled mass spectrometry (LC/MS)-based proteomics technology. The application of this protocol to the characterization of N-linked glycoproteins from crude extracts of the nematode Caenorhabditis elegans or mouse liver provides a list of hundreds to a thousand glycoproteins and their sites of glycosylation within a week.     

Two-dimensional electrophoresis replica blotting: a valuable technique for the immunological and biochemical characterization of single components of complex extracts

The combination of the high resolution electrophoresis (2-DE) with subsequent transfer onto a protein-binding membrane (blotting), immunological detection, and/or N-terminal sequencing is a powerful tool to identify and characterize single components of complex protein mixtures. Direct comparison of protein staining, immunological detection, and biochemical characterization of single protein spots was achieved by the replica blotting technique. The proteins were transferred from one two-dimensional gel onto several blotting membranes one after another. A canon of methods has been employed to identify and characterize allergens from different allergen sources. We have studied single major allergens as well as related major allergens from different grass species ("allergen groups") using patients' sera and allergen-specific monoclonal antibodies. The biochemical structure of the allergenic components has been analyzed by N-terminal and internal protein sequencing, precise mass determinations by matrix-assisted laser desorption/ionization mass spectrometry and investigations on post-translational modifications such as glycosylation. Here, we give a general survey of methods, and we describe an array of techniques suitable for characterization and identification of components of complex extracts, even if there is little or no previous information available.     

Oligosaccharide transfer from lipid sugar intermediates to endogenous protein(s) of rat liver microsomal subfractions

Summary The subcellular localization and characterization of some of the components involved in the glycosylation of asparagine type glycoproteins was attempted using dolichyl diphosphate [¹⁴c]mannose oligosaccharide as precursor of the glycosylation reaction in vitro. Isolated rough and smooth microsomel fractions were able to carry out the transfer of the carbohydrate moiety from lipid oligosaccharide to endogenous protein acceptors. The protein glycosylating activity remained practically the same after stripping the vesicles from their ribosomes or partially releasing their vesicular content. Isolation of polysomes from rough microsomes after glycosylation has taken place, reveals that a large proportion of mannose labeled glycoproteins is in the membranous fraction. The remaining labeled glycoproteins co-sediment with the polysomal fraction. If the isolation is carried out before glycosylation only the membranous fraction shows enzyme activity, whereas the polysomes alone are not able to carry out glycosylation. All these results taken together indicate that the protein glycosylating enzyme is a structural component of the rough and smooth microsomes of rat liver.     

Structural analysis of <Emphasis Type="Italic">N</Emphasis>-/<Emphasis Type="Italic">O</Emphasis>-glycans assembled on proteins in yeasts

Protein glycosylation, the most universal and diverse post-translational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species-and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.     

Purification and characterization of PSP-I and PSP-II, two major proteins from porcine seminal plasma.

Two major glycoproteins, designated PSP-I and PSP-II, were purified from porcine seminal plasma by ammonium sulfate fractionation, CM-cellulose chromatography, gel filtration on Sephadex G-75 (superfine), and reverse phase high performance liquid chromatography. These two proteins exist in several forms differing mainly in the carbohydrate moiety. The complete amino acid sequence of PSP-I has been determined by automated Edman degradation of peptides generated by proteolytic digestion and cyanogen bromide cleavage. The protein is 109 residues long and has a single glycosylation site at the asparagine residue at position 47. In addition, the N-terminal sequence of PSP-II has also been determined. PSP-I is a unique protein; a sequence homology search using the protein data base did not reveal any significant homology with other proteins. PSP-II shares 50% sequence homology with a family of zona pellucida-binding glycoproteins at the N-terminus.     

Online nanoliquid chromatography-mass spectrometry and nanofluorescence detection for high-resolution quantitative N-glycan analysis

The characterization of the repertoire of glycans at the quantitative and qualitative levels on cells and glycoproteins is a necessary step to the understanding of glycan functions in biology. In addition, there is an increasing demand in the field of biotechnology for the monitoring of glycosylation of recombinant glycoproteins, an important issue with regard to their safety and biological activity. The enzymatic release followed by fluorescent derivatization of glycans and separation by normal phase high-performance liquid chromatography (HPLC) has proven for many years to be a powerful approach to the quantification of glycans. Characterization of glycans has classically been performed by mass spectrometry (MS) with external standardization. Here, we report a new method for the simultaneous quantification and characterization of the N-glycans on glycoproteins without the need for external standardization. This method, which we call glycan nanoprofiling, uses nanoLC-coupled electrospray ionization (ESI)-MS with an intercalated nanofluorescence reader and provides effective single glycan separation with subpicomolar sensitivity. The method relies on the isolation and coumaric derivatization of enzymatically released glycans collected by solid phase extraction with porous graphitized carbon and their separation over polyamide-based nanoHPLC prior to serial nanofluorescence and nanoelectrospray mass spectrometric analysis. Glycan nanoprofiling is a broadly applicable and powerful approach that is sufficient to identify and quantify many glycan oligomers in a single run. Glycan nanoprofiling was successfully applied to resolve the glycans of monoclonal antibodies, showing that this method is a fast and sensitive alternative to available methods.     

A rapid mass spectrometric strategy for the characterization of N- and O-glycan chains in the diagnosis of defects in glycan biosynthesis

Glycosylation of proteins is a very complex process which involves numerous factors such as enzymes or transporters. A defect in one of these factors in glycan biosynthetic pathways leads to dramatic disorders named congenital disorders of glycosylation (CDG). CDG can affect the biosynthesis of not only protein N-glycans but also O-glycans. The structural analysis of glycans on serum glycoproteins is essential to solving the defect. For this reason, we propose in this paper a strategy for the simultaneous characterization of both N- and O-glycan chains isolated from the serum glycoproteins. The serum (20 microL) is used for the characterization of N-glycans which are released by enzymatic digestion with PNGase F. O-glycans are chemically released by reductive elimination from whole serum glycoproteins using 10 microL of the serum. Using strategies based on mass spectrometric analysis, the structures of N- and O-glycan chains are defined. These strategies were applied on the sera from one patient with CDG type IIa, and one patient with a mild form of congenital disorder of glycosylation type II (CDG-II) that is caused by a deficiency in the Cog1 subunit of the complex.     

Multiplexed fluorescence detection of phosphorylation, glycosylation, and total protein in the proteomic analysis of breast cancer refractoriness

The Multiplexed Proteomics (MP) technology is a new approach that permits quantitative, multicolor fluorescence detection of proteins in one-dimensional or two-dimensional gels. This methodology allows for multiplexed identification and differential analysis of phosphoproteins, glycoproteins, and total proteins within a single gel electrophoresis experiment. Here the MP system was applied to the differential proteomic analysis of pregnancy-induced refractoriness to breast cancer using a rat model system. Differential analyses identified multiple proteins with altered phosphorylation, glycosylation, or protein expression patterns.     

Profiling impaired hepatic endoplasmic reticulum glycosylation as a consequence of ethanol ingestion

Alcoholic liver disease (ALD) is a prominent cause of morbidity and mortality in the United States. Alterations in protein folding occur in numerous disease states, including ALD. The endoplasmic reticulum (ER) is the primary site of post-translational modifications (PTM) within the cell. Glycosylation, the most abundant PTM, affects protein stability, structure, localization, and activity. Decreases in hepatic glycosylation machinery have been observed in rodent models of ALD, but specific protein targets have not been identified. Utilizing two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry, glycoproteins were identified in hepatic microsomal fractions from control and ethanol-fed mice. This study reports for the first time a global decrease in ER glycosylation. Additionally, the identification of 30 glycoproteins within this fraction elucidates pathway-specific alterations in ALD impaired glycosylation. Among the identified proteins, triacylglycerol hydrolase (TGH) is positively affected by glycosylation, showing increased activity following the addition of sugar moieties. Impaired TGH activity is associated with increased cellular storage of lipids and provides a potential mechanism for the observed pathologies associated with ALD.