Proceedings of the

3rd Beilstein Glyco-Bioinformatics Symposium

Discovering the Subtleties of Sugars

 

10 – 14 June 2013, Potsdam, Germany

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Preface

The Beilstein Symposia address contemporary issues in the chemical and related sciences by employing and interdisciplinary approach. Scientists from a wide range of areas are invited to present aspects of their work for discussion, with the aim of not only advancing sciences, but also enhancing interdisciplinary communication. Traditionally, the Beilstein Symposia are kept small with up to 50 participants to provide a convivial atmosphere for the both lectures and lively discussions and the ready exchange of thoughts and ideas.

The appreciation and understanding of the role that carbohydrates play in nature has grown over the last few years driven by the advances in our ability to analyze and synthesize their structures. Their role not only as primary energy-storage molecules but also as structural modifiers of e.g. glycoproteins and glycolipids, as well as in physiological and pathological events such as adherence, cell-cell interaction, transport, signaling and protection is becoming clearer and more accessible to researchers. Over the last decade the fields of glycobiology and glycochemistry in combination with in-silico applications have been augmented by a further field - glycomics. A major aim of glycomics research is to achieve a comprehensive identification and characterization of the repertoire of glycan structures present in an organism, cell or tissue at a defined time. The continual improvement of analysis methods and computational techniques leads to glycan characterization and identification with increased depth, speed and efficiency but also generates ever increasing amounts of data of variable quality and completeness.

Thus the many web-accessible repositories result in a highly fragmented knowledgebase which in consequence complicates the development and application of bioinformatics tools for the analysis of this data.

This situation has led to  a general consensus that community wide efforts should be spent towards consolidating and systematizing the collective knowledgebase with integration of universal bioinformatics tools for both the representation, mining as well as annotation of experimental data sets to advance and interface glycomics with related genomics and proteomics projects. Additionally, both experimentalists and bioinformaticians also expressed their demands for data reporting practices that include the comprehensive description of conditions, techniques and experimental results to enable researchers to evaluate the degree of structural definitions, to interpret the results and to reproduce the experiments.

The previous symposia held in 2009 and 2011 brought the stakeholders in the area of glycomics together and provided a platform to discuss the role of bioinformatics in this emerging field. One important outcome was the founding of a new working group called MIRAGE (Minimum Information Required for a Glycomics Experiment) under the auspices of the Beilstein-Institut. This group has the function, with involvement of the scientific community, to draw up proposals for reporting standards for glycomics experiments and for setting up a framework to integrate glyco-bioinformatics in a comprehensive platform that will serve biologists, chemists and all interested in glycosciences.

This symposium continued successfully to bring together those scientists that “produce” data with those that “use” the data and make it available to the community. In particular, in their presentations speakers delivered insights into the diverse physiological and structural subtleties of sugars by covering aspects such as: structure-function relationships of carbohydrates, modeling carbohydrate structure and carbohydrate interactions with other biomacromolecules, deciphering carbohydrate signals, carbohydrate identification, annotation and analysis, metadata for the description of glycomics experiments, software tools for data mining and analysis.

We would like to thank particularly the authors who provided us with written versions of the papers that they presented. Special thanks go to all those involved with the preparation and organization of the symposium, to the chairmen who piloted us successfully through the sessions and to the speakers and participants for their contribution in making this symposium a success.

 

Frankfurt/Main, December 2014                                                       

Martin Hicks
Carsten Kettner
Peter Seeberger

Metabolic Engineering of Bacteria

Elisabeth Memmel and Jürgen Seibel

Institute of Organic Chemistry, University of Würzburg, Germany

Metabolic glycoengineering is a technique introduced in the early 90s of the last century by Reutter et al. It utilises the ability of cells to metabolically convert sugar derivatives with bioorthogonal side chains like azides or alkynes and by that incorporation into several glycostructures. Afterwards, the carbohydrates can be labelled to study their distribution, dynamics and roles in different biological processes. So far many studies were performed on mammal cell lines as well as in small animals. Very recently, bacterial glyco structures were targeted by glycoengineering, showing promising results in infection prevention by reducing pathogen adhesion towards human epithelial cells.

Prediction of Binding Poses and Binding Affinities for Glycans and their Binding Proteins using a Robust Scoring Function for General Protein-Ligand Interactions

Nan-Lan Huang1 and Jung-Hsin Lin1,2,3

1Research Center for Applied Sciences and 2Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
3School of Pharmacy, National Taiwan University, Taipei, Taiwan

The binding of glycans to proteins represents the major way in which the information contained in glycan structures is recognised, deciphered and put into biological action. The physiological and pathological significance of glycan–protein interactions are drawing increasing attention in the field of structure-based drug design. We have implemented a quantum chemical charge model, the Austin-model 1-bond charge correction (AM1-BCC) method, into a robust scoring function for general protein ligand interactions, called, AutoDockRAP. Here we report its capability to predict the binding poses and binding affinities of glycans to glycan-binding proteins. Our benchmark indicates that this generally applicable scoring function can be adopted in virtual screening of drug candidates and in prediction of ligand binding modes, given the structures of the well-defined recognition domains of glycan-binding proteins.

Glycomics and Glycoproteomics Databases in Japan and Asia

Hisashi Narimatsu

Research Center for Medical Glycoscience (RCMG) and
National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba, Ibaraki, Japan

The ‘‘Integrated Database Project’’ was initiated to establish a publically accessible database to integrate all useful life science databases in Japan. Our JCGGDB (Japan Consortium for Glycobiology and Glycotechnology Database) was selected as a promotion program in the project, focussing on the integration of all the glycan-related databases and establishment of user-friendly search systems. As part of the project, we intend the integration of databases not only within Asia but also with other countries. Working closely with various institutes in Japan and the world, we continuously develop base technologies for the database integration, facilitate interactions between databases in the field of glycoscience as well as other associated study areas, and build bioinformatics tools to support experimental study. Our goal is to create a truly useful database that could be easily and intuitively  understood by every user.

Semantic Web Technologies Applied to Glycoscience Data to Integrate with Life Science Databases

Kiyoko F. Aoki-Kinoshita

Department of Bioinformatics, Faculty of Engineering, Soka University, Tokyo, Japan

The World Wide Web (WWW) essentially consists of web pages containing data that are linked to other resources or pages on the internet. Therefore, to accumulate information regarding a particular carbohydrate, for example, a user would either make searches in individual databases and/or read the scientific literature and then follow various links on the Web to get relevant information. In order to overcome such tedious tasks, the Semantic Web was born from the concept of incorporating semantics, or meanings, into each data item, which is represented as a web page, or URI (Uniform Resource Identifier). Thus, a single carbohydrate structure, for example ‘‘Man_9’’, would be assigned a URI, and then semantics are assigned to it by preparing a dataset containing information, or annotations, about it. Each data item is annotated in the form of triples consisting of Subject, Predicate and Object. Thus, for example, ‘‘Man_9 part_of N-linked_glycan’’ would be a triple where Man_9 is the Subject, part_of is the Predicate  and N-linked_glycan is the Object. If there was another triple, ‘‘Mannose part_of Man_9,’’ then it can be computationally inferred that Mannose is a part of N-linked_glycan. Moreover, this triple data can be queried as a database...

Utilising the Carbohydrate Fragmentation Database UniCarb-DB for Glyco Research

Catherine A. Hayes, Sarah Flowers, Liaqat Ali, Samah M.A. Issa, Chunsheng Jin and Niclas G. Karlsson

Medical Biochemistry, Sahlgrenska Academy, University of Gothenburg, Sweden

UniCarb-DB is an experimental database consisting of structural information of O-linked and N-linked oligosaccharides and associated LC-MS/MS fragmentation data. This report illustrates how the database can be useful for future software development for the interpretation of glycomic mass spectrometric data. The information rich  fragmentation spectra generated for O-linked oligosaccharides in negative ion mode allows matching with candidate spectra in the database for accurate assignment of oligosaccharide sequence and in some cases, linkage information. Furthermore, peak matching can be used for selected m/z regions to identify sites of sulfation and identification of the sequence of the neutral oligosaccharide backbone of sialylated structures. The reproducibility of the fragmentation patterns of oligosaccharides present in the database suggests that targeted mass spectrometric approaches can be developed for glycomic discovery and validation, using such methods as multiple/selected reaction monitoring (MRM/SRM).

UniCarbKB: First Year Report Card

Matthew P. Campbell1, Robyn Peterson1, Elisabeth Gasteiger2, Jingyu Zhang1, Yukie Akune3, Jodie L. Abrahams1, Julien Mariethoz4, Catherine A. Hayes5, Daniel Kolarich6, Niclas G. Karlsson5, Kiyoko F. Aoki-Kinoshita3, Frederique Lisacek4, Nicolle H. Packer1

1Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, Sydney, NSW 2109, Australia
2Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
3Department of Bioinformatics, Faculty of Engineering, Soka University, Tokyo, Japan
4Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
5Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Sweden
6Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany

At the Beilstein Workshop on Glycoinformatics in 2011 we introduced UniCarbKB as an international initiative that aims to collect and distribute resources and practices from glycobiology practitioners to the whole biological research community. The mission was, and still is, to provide a comprehensive, high quality catalogue of information on carbohydrates, and to continue efforts to advance the interpretation of captured data through the development of novel data analysis methods and algorithms for the efficient representation and mining of large experimental data sets.
Here, we report the progress we have made on establishing the infrastructure and content of the fledgling UniCarbKB. This will include our current work on the integration, into the publically available Uni-CarbKB portal, of data from UniCarb-DB, GlycoSuiteDB, GlycoBase, EUROCarbDB, SugarBind and PubChem. In the future it is hoped that the UniCarbKB knowledgebase, based on a central database of curated glycan structures, will become the key resource of quality information for glycobiology research.

High-throughput Workflow for Glycan Profiling and Characterisation

Henning Stöckmann, Giorgio Carta, Ciara A. McManus, Mark Hilliard, and Pauline M. Rudd

NIBRT GlycoScience Group, NIBRT – The National Institute for Bioprocessing Research and Training, Dublin, Ireland

Over the last 40 years, the understanding of glycosylation changes in health and disease has evolved significantly and glycans are now regarded as excellent biomarker candidates because of their high sensitivity to pathological changes. However, the discovery of clinical glycobiomarkers has been slow, mainly as a consequence of the lack of high-throughput glycoanalytical workflows that allow rapid glycoprofiling of large clinical sample sets. To generate high-quality quantitative glycomics data in a high-throughput fashion, we have developed a robotised platform for rapid N-glycan sample preparation and glycan characterisation. The sample preparation workflow features a fully automated, rapid glycoprotein affinity purification followed by sequential protein denaturation and enzymatic glycan release on a multiwell ultrafiltration device, thus greatly streamlining all required biochemical manipulations. After glycan purification on solidsupported hydrazide, glycans are fluorescently labelled to allow accurate quantification by ultra-high pressure liquid chromatography (ultra HPLC or UPLC). Subsequent peak assignment can be carried out utilising GlycoBase, a bespoke chromatographic data system developed to aid the analysis of glycans performed using different chromatographic techniques (UPLC, HPLC, Reverse Phase-UPLC, Capillary Electrophoresis).

Automated Detection and Identification of N- and O-glycopeptides

Peter Hufnagel, Anja Resemann, Wolfgang Jabs, Kristina Marx, and Ulrike Schweiger-Hufnagel

Bruker Daltonik GmbH, Bremen, Germany

Because it can provide detailed information about aglycons, glycosylation sites, and the composition and structure of glycans, mass spectrometry is highly suited for the analysis of glycopeptides and released N- and O-glycans. Here we present the bioinformaticsplatform ProteinScape, which can process entire LC-MS/MS runs, localise spectra that contain glycan-related information, and perform searches against glycan structure databases. An intuitive user interface facilitates interactive validation of results. If glycans are not released and glycopeptides are analysed, the heterogeneity of glycosylation at the various protein glycosylation sites can be assessed. The integration of protein- and glycan-related functionality in a single software platform is particularly useful not only in glycoproteomics research, but also in biopharmaceutical development and QC. We provide several examples illustrating the efficiency of glycopeptide analysis using mass spectrometry. However, a comprehensive analysis requires information on the glycoprotein’s mass profile. Therefore, the interpretation of mass spectra from intact glyco-proteins is also discussed.

New Structure–function Relationships of Carbohydrates

Thisbe K. Lindhorst

Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Germany

The potential of glycoarrays for the investigation of carbohydrate interactions has not been fully exploited to date. In addition to the saccharide specificity of lectins, carbohydrate recognition and carbohydrate binding most likely also comprises aspects of pattern formation, density regulation, as well as the mode of sugar presentation on a surface. When glycoarrays – which allow for systematic alteration of such parameters – become available, new structure–function relationships are likely to be discovered in the carbohydrate regime. In this account some of our work on fabrication of special glycoarrays is summarised including the ‘dual click approach’ to glyco-SAMs, and fabrication of photo-sensitive glycoarrays which allow ‘switching’ of carbohydrate orientation between two distinct states.

Tools to MSn Sequence and Document the Structures of Glycan Epitopes

Hailong Zhang1, David J. Ashline2 and Vernon N. Reinhold1,2

1The Glycomics Center, University of New Hampshire, Durham, NH, USA
2Glycan Connections, LLC, Lee, NH, USA

Sequential disassembly (MSn) has been applied to fully characterise and document native samples containing glycan epitopes with their synthetic analogues. Both sample types were prepared by methylation, solvent phase extracted, directly infused and spatially resolved. Product ions of all samples were compiled and contrasted using management tools prepared for the fragment ion library. Each of the epitopes was further disassembled to confirm the multiple structural isomers probable within component substructures of linkage and branching. All native samples tested proved to be matched with their synthetic analogues and reasonably identical on either linear or cylindrical ion traps. Not surprisingly, spectra of mixed epitopes fragment independently, being uninfluenced by similarities. The approach has been coupled with computational tools for data handling and presentation.

Isolation and Purification of Glycans from Natural Sources for Positive Identification

Milos V. Novotny1 and William R. Alley, Jr.1,2

1Department of Chemistry, Indiana University, Bloomington, Indiana, USA
2Department of Chemistry, University of Texas at San Antonio, TX, USA

The great structural diversity of glycans demands powerful analytical methodologies, such as different combinations of capillary separations with mass spectrometry (MS), to identify the correct structures involved in key glycan interactions of biological importance. Precise structural assignments, in turn, necessitate the availability of pure authentic glycans as absolute analytical standards. It is particularly evident with the cases of glycan isomerism, which are seemingly involved in the search for glyco-biomarkers of human diseases. While novel synthetic approaches are being developed toward the acquisition of new glycan standards, it is still prudent, feasible, and profitable to consider the isolation of pure glycans from some hitherto unexplored natural sources. It is demonstrated here that recycling high-performance liquid chromatography (R-HPLC) can accomplish isolation of isomeric glycans to be used as analytical standards or valuable reagents in the fabrication of glycan arrays for biomarker discovery.

Towards Identifying Protective Carbohydrate Epitopes in the Development of a Glycoconjugate Vaccine Against Cryptococcus neoformans

Lorenzo Guazzelli and Stefan Oscarson

Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Ireland

Cryptococcus neoformans is an opportunistic encapsulated yeast that causes cryptococcal meningoencephalitis (cryptococcosis) in immunocompromised individuals, including AIDS patients, organ transplant recipients or other patients receiving immuno-suppressive drugs. Infection with C. neoformans is acquired by inhalation of desiccated yeast cells into the lungs, which causes a local pulmonary infection. The yeast cells can enter the blood-stream and disseminate to the skin, bone and the central nervous system, thereby causing a systemic infection. The pathogen is able to cross the blood-brain-barrier, the mechanism of which is not fully understood yet. Once inside the brain the pathogen destroys the surrounding tissue. Studies showed that most adults in New York City have antibodies against C. neoformans but cryptococcosis is a relatively rare disease in immunocompetent individuals despite the widespread occurrence of C. neoformans in the environment.[...]