201
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Ahmed J, Preissner S, Dunkel M, Worth CL, Eckert A, Preissner R. SuperSweet--a resource on natural and artificial sweetening agents. Nucleic Acids Res 2010; 39:D377-82. [PMID: 20952410 PMCID: PMC3013782 DOI: 10.1093/nar/gkq917] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A vast number of sweet tasting molecules are known, encompassing small compounds, carbohydrates, d-amino acids and large proteins. Carbohydrates play a particularly big role in human diet. The replacement of sugars in food with artificial sweeteners is common and is a general approach to prevent cavities, obesity and associated diseases such as diabetes and hyperlipidemia. Knowledge about the molecular basis of taste may reveal new strategies to overcome diet-induced diseases. In this context, the design of safe, low-calorie sweeteners is particularly important. Here, we provide a comprehensive collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Additionally, structural information and properties such as number of calories, therapeutic annotations and a sweetness-index are stored in SuperSweet. Currently, the database consists of more than 8000 sweet molecules. Moreover, the database provides a modeled 3D structure of the sweet taste receptor and binding poses of the small sweet molecules. These binding poses provide hints for the design of new sweeteners. A user-friendly graphical interface allows similarity searching, visualization of docked sweeteners into the receptor etc. A sweetener classification tree and browsing features allow quick requests to be made to the database. The database is freely available at: http://bioinformatics.charite.de/sweet/.
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Affiliation(s)
- Jessica Ahmed
- Charité - Universitätsmedizin Berlin, Institute of Physiology, Structural Bioinformatics Group, Lindenberger Weg 80, 13125 Berlin, Germany
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202
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Mariño K, Bones J, Kattla JJ, Rudd PM. A systematic approach to protein glycosylation analysis: a path through the maze. Nat Chem Biol 2010; 6:713-23. [PMID: 20852609 DOI: 10.1038/nchembio.437] [Citation(s) in RCA: 479] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein glycosylation is an important post-translational modification. It is a feature that enhances the functional diversity of proteins and influences their biological activity. A wide range of functions for glycans have been described, from structural roles to participation in molecular trafficking, self-recognition and clearance. Understanding the basis of these functions is challenging because the biosynthetic machinery that constructs glycans executes sequential and competitive steps that result in a mixture of glycosylated variants (glycoforms) for each glycoprotein. Additionally, naturally occurring glycoproteins are often present at low levels, putting pressure on the sensitivity of the analytical technologies. No universal method for the rapid and reliable identification of glycan structure is currently available; hence, research goals must dictate the best method or combination of methods. To this end, we introduce some of the major technologies routinely used for structural N- and O-glycan analysis, describing the complementary information that each provides.
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Affiliation(s)
- Karina Mariño
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing, Research and Training, University College Dublin Conway Institute, University College Dublin, Belfield, Ireland
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203
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Ruhaak LR, Zauner G, Huhn C, Bruggink C, Deelder AM, Wuhrer M. Glycan labeling strategies and their use in identification and quantification. Anal Bioanal Chem 2010; 397:3457-81. [PMID: 20225063 PMCID: PMC2911528 DOI: 10.1007/s00216-010-3532-z] [Citation(s) in RCA: 366] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/22/2010] [Accepted: 01/22/2010] [Indexed: 12/28/2022]
Abstract
Most methods for the analysis of oligosaccharides from biological sources require a glycan derivatization step: glycans may be derivatized to introduce a chromophore or fluorophore, facilitating detection after chromatographic or electrophoretic separation. Derivatization can also be applied to link charged or hydrophobic groups at the reducing end to enhance glycan separation and mass-spectrometric detection. Moreover, derivatization steps such as permethylation aim at stabilizing sialic acid residues, enhancing mass-spectrometric sensitivity, and supporting detailed structural characterization by (tandem) mass spectrometry. Finally, many glycan labels serve as a linker for oligosaccharide attachment to surfaces or carrier proteins, thereby allowing interaction studies with carbohydrate-binding proteins. In this review, various aspects of glycan labeling, separation, and detection strategies are discussed.
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Affiliation(s)
- L. R. Ruhaak
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - G. Zauner
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - C. Huhn
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - C. Bruggink
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - A. M. Deelder
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - M. Wuhrer
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
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204
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Frank M, Schloissnig S. Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci 2010; 67:2749-72. [PMID: 20364395 PMCID: PMC2912727 DOI: 10.1007/s00018-010-0352-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 03/08/2010] [Accepted: 03/11/2010] [Indexed: 12/11/2022]
Abstract
The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein-carbohydrate interaction are reviewed.
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Affiliation(s)
- Martin Frank
- Molecular Structure Analysis Core Facility-W160, Deutsches Krebsforschungszentrum (German Cancer Research Centre), 69120 Heidelberg, Germany.
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205
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Tharmalingam T, Mariño K, Rudd PM. Platform technology to identify potential disease markers and establish heritability and environmental determinants of the human serum N-glycome. Carbohydr Res 2010; 345:1280-2. [DOI: 10.1016/j.carres.2010.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/06/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
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206
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Hashimoto R, Hirose K, Sato T, Fukushima N, Miura N, Nishimura SI. Functional network of glycan-related molecules: glyco-net in glycoconjugate data bank. BMC SYSTEMS BIOLOGY 2010; 4:91. [PMID: 20584338 PMCID: PMC2907334 DOI: 10.1186/1752-0509-4-91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 06/29/2010] [Indexed: 11/28/2022]
Abstract
Background Glycans are involved in a wide range of biological process, and they play an essential role in functions such as cell differentiation, cell adhesion, pathogen-host recognition, toxin-receptor interactions, signal transduction, cancer metastasis, and immune responses. Elucidating pathways related to post-translational modifications (PTMs) such as glycosylation are of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids and various biological events are considered extremely valuable and convenient tools for the systematic investigation of PTMs. However, there is no database which dynamically draws functional networks related to glycans. Description We have created a database called Glyco-Net http://www.glycoconjugate.jp/functions/, with many binary relationships among glycan-related molecules. Using search results, we can dynamically draw figures of the functional relationships among these components with nodes and arrows. A certain molecule or event corresponds to a node in the network figures, and the relationship between the molecule and the event are indicated by arrows. Since all components are treated equally, an arrow is also a node. Conclusions In this paper, we describe our new database, Glyco-Net, which is the first database to dynamically show networks of the functional profiles of glycan related molecules. The graphical networks will assist in the understanding of the role of the PTMs. In addition, since various kinds of bio-objects such as genes, proteins, and inhibitors are equally treated in Glyco-Net, we can obtain a large amount of information on the PTMs.
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Affiliation(s)
- Ryo Hashimoto
- Division of Advanced Chemical Biology, Graduate School of Life Science, Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, Sapporo 001-0021, Japan
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207
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McDonald AG, Tipton KF, Stroop CJ, Davey GP. GlycoForm and Glycologue: two software applications for the rapid construction and display of N-glycans from mammalian sources. BMC Res Notes 2010; 3:173. [PMID: 20565879 PMCID: PMC2904795 DOI: 10.1186/1756-0500-3-173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 06/18/2010] [Indexed: 11/10/2022] Open
Abstract
Background The display of N-glycan carbohydrate structures is an essential part of glycoinformatics. Several tools exist for building such structures graphically, by selecting from a palette of symbols or sugar names, or else by specifying a structure in one of the chemical naming schemes currently available. Findings In the present work we present two tools for displaying N-glycans found in the mammalian CHO (Chinese hamster ovary) cell line, both of which take as input a 9-digit identifier that uniquely defines each structure. The first of these, GlycoForm, is designed to display a single structure automatically from an identifier entered by the user. The display is updated in real time, using symbols for the sugar residues, or in text-only form. Structures can be added to a library, which is recorded in a preference file and loaded automatically at start. Individual structures can be saved in a variety of bitmap image formats. The second program, Glycologue, reads a file containing columnar data of nine-digit codes, which can be displayed on-screen and printed at high resolution. Conclusion A key advantage of both programs is the speed and facility with which carbohydrate structures can be drawn. It is anticipated that these programs will be useful to glycobiologists, systems biologists and biotechnologists interested in N-glycosylation systems in mammalian cells.
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Affiliation(s)
- Andrew G McDonald
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.
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208
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Vanderschaeghe D, Festjens N, Delanghe J, Callewaert N. Glycome profiling using modern glycomics technology: technical aspects and applications. Biol Chem 2010; 391:149-161. [PMID: 20128687 DOI: 10.1515/bc.2010.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Glycomics research has become indispensable in many research fields such as immunity, signal transduction and development. Moreover, changes in the glycosylation of proteins and lipids have been reported in several diseases including cancer. The analysis of a complex post-translational modification such as glycosylation depends on the availability or development of appropriate analytical technologies. The research goal determines the sensitivity, resolution and throughput requirements and guides the choice of a particular technology. This review highlights the evolution of glycan profiling tools in the past 5 years. We focus on capillary electrophoresis, liquid chromatography, mass spectrometry and lectin microarrays.
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Affiliation(s)
- Dieter Vanderschaeghe
- Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Technologiepark 927, B-9052 Ghent, Belgium
| | - Nele Festjens
- Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Technologiepark 927, B-9052 Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Nico Callewaert
- Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Technologiepark 927, B-9052 Ghent, Belgium
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209
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Ritchie G, Harvey DJ, Stroeher U, Feldmann F, Feldmann H, Wahl-Jensen V, Royle L, Dwek RA, Rudd PM. Identification of N-glycans from Ebola virus glycoproteins by matrix-assisted laser desorption/ionisation time-of-flight and negative ion electrospray tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:571-85. [PMID: 20131323 PMCID: PMC3399782 DOI: 10.1002/rcm.4410] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The larger fragment of the transmembrane glycoprotein (GP1) and the soluble glycoprotein (sGP) of Ebola virus were expressed in human embryonic kidney cells and the secreted products were purified from the supernatant for carbohydrate analysis. The N-glycans were released with PNGase F from within sodium dodecyl sulphate/polyacrylamide gel electrophoresis (SDS-PAGE) gels. Identification of the glycans was made with normal-phase high-performance liquid chromatography (HPLC), matrix-assisted laser desorption/ionisation mass spectrometry, negative ion electrospray ionisation fragmentation mass spectrometry and exoglycosidase digestion. Most glycans were complex bi-, tri- and tetra-antennary compounds with reduced amounts of galactose. No bisected compounds were detected. Triantennary glycans were branched on the 6-antenna; fucose was attached to the core GlcNAc residue. Sialylated glycans were present on sGP but were largely absent from GP1, the larger fragment of the transmembrane glycoprotein. Consistent with this was the generally higher level of processing of carbohydrates found on sGP as evidenced by a higher percentage of galactose and lower levels of high-mannose glycans than were found on GP1. These results confirm and expand previous findings on partial characterisation of the Ebola virus transmembrane glycoprotein. They represent the first detailed data on carbohydrate structures of the Ebola virus sGP.
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Affiliation(s)
- Gayle Ritchie
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
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210
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Artemenko NV, Campbell MP, Rudd PM. GlycoExtractor: A Web-Based Interface for High Throughput Processing of HPLC-Glycan Data. J Proteome Res 2010; 9:2037-41. [DOI: 10.1021/pr901213u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natalia V. Artemenko
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew P. Campbell
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Pauline M. Rudd
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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211
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Unverzagt C, Gundel G, Eller S, Schuberth R, Seifert J, Weiss H, Niemietz M, Pischl M, Raps C. Synthesis of multiantennary complex type N-glycans by use of modular building blocks. Chemistry 2010; 15:12292-302. [PMID: 19806620 DOI: 10.1002/chem.200901908] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A modular set of oligosaccharide building blocks was developed for the synthesis of multiantennary N-glycans of the complex type, which are commonly found on glycoproteins. The donor building blocks were laid out for the elongation of a core trisaccharide acceptor (beta-mannosyl chitobiose) conveniently protected with a single benzylidene moiety at the beta-mannoside. Through two consecutive regio- and stereoselective couplings the donors gave N-glycans with three to five antennae in high yields. Due to the consistent protection group pattern of the donors the deprotection of the final products can be performed by using a general reaction sequence.
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Affiliation(s)
- Carlo Unverzagt
- Bioorganische Chemie, Universität Bayreuth, Gebäude NW1, 95440 Bayreuth, Germany.
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212
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Ahn J, Bones J, Yu YQ, Rudd PM, Gilar M. Separation of 2-aminobenzamide labeled glycans using hydrophilic interaction chromatography columns packed with 1.7 microm sorbent. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 878:403-8. [PMID: 20036624 DOI: 10.1016/j.jchromb.2009.12.013] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 12/08/2009] [Accepted: 12/08/2009] [Indexed: 11/28/2022]
Abstract
Separation by hydrophilic interaction chromatography (HILIC) with fluorescence detection utilizing a sub-2 microm glycan column for the separation of 2-aminobenzamide (2-AB) labeled N-linked glycans is described. The HILIC column packed with a 1.7 microm amide sorbent improves the peak capacity compared to a 3.0 microm HILIC column by a similar degree as observed in reversed-phase ultra-performance liquid chromatography (RP-UPLC). The results indicated that the optimal peak capacity was achieved at flow rate 0.2-0.5 mL/min. HILIC method transfer guidelines were shown to further enhance the resolution of glycans by changing initial gradient conditions, flow rate, column temperature, and different column lengths. Additionally, excellent resolution can be achieved in the separation of 2-AB labeled glycans released from fetuin, RNase B, and human IgG with a rapid analysis time.
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Affiliation(s)
- Joomi Ahn
- Biopharmaceutical Sciences, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
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213
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Abstract
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.
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Affiliation(s)
- Lakshmi Krishnamoorthy
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688
| | - Lara K. Mahal
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003-6688
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214
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Ranzinger R, Frank M, von der Lieth CW, Herget S. Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. Glycobiology 2009; 19:1563-7. [PMID: 19759275 DOI: 10.1093/glycob/cwp137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite ongoing harmonization efforts, the major carbohydrate sequence databases following the first initiative in this field, CarbBank, are still isolated islands, with mechanisms for automatic structure exchange and comparison largely missing. This unfavorable situation has been overcome with a systematic data integration effort, resulting in the GlycomeDB, a meta-database for public carbohydrate sequences. It contains at present 35,056 unique structures in GlycoCT encoding, referencing more than 100,000 external records from 1845 different taxonomic sources. We have created a user-friendly, web-based graphical interface which allows taxonomic and structural data to be entered and searched for. The structural search possibilities include substructure search, similarity search, and maximum common substructure. A novel search refinement mechanism allows the assembly of complex queries. With GlycomeDB (www.glycome-db.org), it is now possible to use a single portal to access all digitally encoded, public structural data in glycomics and to perform complex queries with the help of a web-based user interface.
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Affiliation(s)
- René Ranzinger
- German Cancer Research Center, Molecular Structure Analysis (W160), Molecular Modeling Group, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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215
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Liu Y, Palma AS, Feizi T. Carbohydrate microarrays: key developments in glycobiology. Biol Chem 2009; 390:647-56. [PMID: 19426131 DOI: 10.1515/bc.2009.071] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Carbohydrate chains of glycoproteins, glycolipids, proteoglycans, and polysaccharides mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is therefore a priority in biomedical sciences. Carbohydrate microarray technology is a new development at the frontier of glycomics that is revolutionizing the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, microbe-host interactions, and immune defense mechanisms. In this review, we briefly refer to the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept and have provided new biological information.
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Affiliation(s)
- Yan Liu
- Glycosciences Laboratory, Division of Medicine, Imperial College London, Northwick Park and St. Mark's Campus, Harrow HA1 3UJ, Middlesex, UK
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216
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Proposal for a standard system for drawing structural diagrams of N
- and O
-linked carbohydrates and related compounds. Proteomics 2009; 9:3796-801. [DOI: 10.1002/pmic.200900096] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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217
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Rudd PM, Rudan I, Wright AF. High-throughput glycome analysis is set to join high-throughput genomics. J Proteome Res 2009; 8:1105. [PMID: 19193056 DOI: 10.1021/pr900040s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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218
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Neville DCA, Dwek RA, Butters TD. Development of a single column method for the separation of lipid- and protein-derived oligosaccharides. J Proteome Res 2009; 8:681-7. [PMID: 19099509 DOI: 10.1021/pr800704t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent labeling of oligosaccharides with anthranilic acid (2-aminobenzoic acid; 2AA), or 2-aminobenzamide (2AB) permits the rapid, sensitive analysis of structures present in cells and tissues. Normal-phase (NP)/hydrophilic interaction chromatography (HILIC) is commonly used to separate fluorophore-derivatized oligosaccharides. Column elution is expressed as glucose units (GU) following calculation of relative retention when compared to an external glucose oligomer standard. However, there is significant overlap between sialylated and neutral oligosaccharides. Normal-phase anion-exchange (NP-AE) HPLC can separate differing classes of oligosaccharides according to the number of charged residues, but relative retention times in GU cannot be calculated across the entire gradient. We have overcome this difficulty by use of a Dionex AS11 column that combines both hydrophilic interaction and anion-exchange chromatographies, termed HIAX, which enables the calculation of GU values for oligosaccharides that carry sialylated or other negatively charged groups. The same method may also be employed for 2AB and other fluorophore-labeled oligosaccharides. Additionally, the same HPLC eluants are used for the differing HPLC columns. Therefore, analysis of HILIC- or HIAX-separated fluorophore-labeled oligosaccharides can be performed using a single HPLC system with a single set of eluents following a simple column change.
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Affiliation(s)
- David C A Neville
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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219
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Ruhaak LR, Deelder AM, Wuhrer M. Oligosaccharide analysis by graphitized carbon liquid chromatography-mass spectrometry. Anal Bioanal Chem 2009; 394:163-74. [PMID: 19247642 DOI: 10.1007/s00216-009-2664-5] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 01/21/2009] [Accepted: 01/28/2009] [Indexed: 11/30/2022]
Abstract
Structural analysis of complex mixtures of oligosaccharides using tandem mass spectrometry is regularly complicated by the presence of a multitude of structural isomers. Detailed structural analysis is, therefore, often achieved by combining oligosaccharide separation by HPLC with online electrospray ionization and mass spectrometric detection. A very popular and promising method for analysis of oligosaccharides, which is covered by this review, is graphitized carbon HPLC-ESI-MS. The oligosaccharides may be applied in native or reduced form, after labeling with a fluorescent tag, or in the permethylated form. Elution can be accomplished by aqueous organic solvent mixtures containing low concentrations of acids or volatile buffers; this enables online ESI-MS analysis in positive-ion or negative-ion mode. Importantly, graphitized carbon HPLC is often able to resolve many glycan isomers, which may then be analyzed individually by tandem mass spectrometry for structure elucidation. While graphitized carbon HPLC-MS for glycan analysis is still only applied by a limited number of groups, more users are expected to apply this method when databases which support structural assignment become available.
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Affiliation(s)
- L Renee Ruhaak
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300, RC, Leiden, The Netherlands
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220
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Luo Q, Rejtar T, Wu SL, Karger BL. Hydrophilic interaction 10 microm I.D. porous layer open tubular columns for ultratrace glycan analysis by liquid chromatography-mass spectrometry. J Chromatogr A 2009; 1216:1223-31. [PMID: 18945436 PMCID: PMC2658773 DOI: 10.1016/j.chroma.2008.09.105] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 09/17/2008] [Accepted: 09/19/2008] [Indexed: 11/24/2022]
Abstract
The sensitivity of glycan analysis using nano-liquid chromatography interfaced with electrospray ionization mass spectrometry (ESI-MS) increases with the decrease of the mobile phase flow rate, accompanied by reduced ion suppression. In this study, we describe the preparation and performance of high efficiency 10 microm I.D. amine-bonded poly(vinylbenzyl chloride-divinylbenzene) hydrophilic interaction (HILIC) porous layer open tubular (PLOT) columns operated at 20 nL/min for the separation and analysis of glycan mixtures. HILIC-PLOT columns with a uniform porous polymer layer were reproducibly prepared ( approximately 4% RSD in retention time from column-to-column) via in situ polymerization, followed by one step modification with ethylenediamine. When coupled on-line with negative ESI-MS, low detection limits (0.3fmol) for a 3-sialyl-tetrasaccharide were achieved using a 2.5mx10 microm I.D. HILIC-PLOT column. A dextran ladder standard was used to evaluate the performance of the column, and high efficiency separation was achieved with detection of the dextrans up to G22 from approximately 50 fmol amounts injected. As an example of the high sensitivity of the column, MS(6) characterization of glycan structures was possible from the injection of 10 fmol of a neutral and sialylated glycan. As another example of high sensitivity LC-MS analysis of 3 ng of a PNGase F digest of ovalbumin allowed 28 N-linked glycans to be confidently identified from a single analysis. High quality MS/MS spectra for each ovalbumin glycan were acquired and manually interpreted for structure analysis. The HILIC-PLOT column is a very promising approach for LC-MS analysis of glycans at the ultratrace level.
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Affiliation(s)
- Quanzhou Luo
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
| | - Tomas Rejtar
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
| | - Shiaw-Lin Wu
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
| | - Barry L. Karger
- Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
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Affiliation(s)
- Thomas Lütteke
- CMBI, NCMLS, Radboud University Nijmegen, P. O. Box 9010, 6500 GL Nijmegen (The Netherlands).
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223
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Knežević A, Polašek O, Gornik O, Rudan I, Campbell H, Hayward C, Wright A, Kolčić I, O’Donoghue N, Bones J, Rudd PM, Lauc G. Variability, Heritability and Environmental Determinants of Human Plasma N-Glycome. J Proteome Res 2008; 8:694-701. [DOI: 10.1021/pr800737u] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Knežević
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Ozren Polašek
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Olga Gornik
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Igor Rudan
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Harry Campbell
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Caroline Hayward
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Alan Wright
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Ivana Kolčić
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Niaobh O’Donoghue
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Jonathan Bones
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Pauline M. Rudd
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
| | - Gordan Lauc
- Department of Biochemistry and Molecular Biology, University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia, Andrija Štampar School of Public Health, University of Zagreb Medical School, Zagreb, Croatia, Croatian Centre for Global Health, University of Split Medical School, Split, and Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia, Public Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom, MRC Human Genetics
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