Functional and Structural Proteomics of Glycoproteins (eBook)

Preface 4
Contents 6
Contributors 7
1 Glycoproteomics in Health and Disease 9
1.1 Introduction 12
1.1.1 Basic Glycan Structure 12
1.1.2 Biosynthetic Pathway for N- and O-Linked Glycosylation 13
1.1.3 Glycan Diversity and Biological Function 16
1.2 Glycan and Glycoprotein Analytics 18
1.2.1 Mass Spectrometry 19
1.2.2 High Performance Liquid Chromatography 20
1.2.3 2D Gel Electrophoresis 21
1.3 Glycosylation and Disease 22
1.3.1 Glycosylation in Cancer Biology 22
1.3.1.1 Glycosyltransferases and Cancer Progression 22
1.3.1.2 Glycoproteins as Markers for Cancer Detection 26
1.3.2 Role of Glycosylation in Autoimmune Diseases 29
1.3.3 Congenital Disorders of Glycosylation (CDGs) 30
1.3.4 Lysosomal Storage Diseases (LSDs) 31
1.4 Glycobiology in the Treatment of Disease 31
1.4.1 Bioproduction of Glycoprotein Therapeutics 32
1.4.2 Manipulating Glycosylation for Enhanced Biotherapeutic Function 36
1.5 Systems Glycobiology, Glycoproteomics and Glycogenomics in Disease Diagnosis and Pathology 37
References 38
2 Glyco-engineering of Fc Glycans to Enhance the Biological Functions of Therapeutic IgGs 47
2.1 Introduction 48
2.2 Significance of Fc Glycosylation for IgG Effector Functions 50
2.3 Impact of Terminal Sugars on the Effector Functions of IgGs 52
2.3.1 N-acetylglucosamine 52
2.3.2 Galactose 53
2.3.3 Sialic Acid 54
2.4 Impact of Core Sugars on the Effector Functions of IgGs 58
2.4.1 Bisecting N-acetylglucosamine 58
2.4.2 Core Fucose 59
2.4.3 High Mannose Glycans 59
2.5 Impact of Non-human Glycan Epitopes 60
2.6 Conclusions 61
References 61
3 Bioinformatics Databases and Applications Available for Glycobiology and Glycomics 67
3.1 Introduction 68
3.2 Glycobioinformatics Web Portals 69
3.3 Databases 70
3.3.1 Carbohydrate Structure Databases 70
3.3.2 Glycoenzyme and Lectin Databases 76
3.3.3 Other Carbohydrate-Related Databases 77
3.4 GlycomeDB 77
3.4.1 Situation 77
3.4.2 GlycomeDB Project 79
3.4.3 Content and Quality Control 80
3.4.4 Web Portal Glycome-DB.org 80
3.4.5 Web Services 84
3.4.6 Future Perspectives 85
3.5 Tools 85
3.5.1 Structure Input and Display 85
3.5.2 Tools for Processing Analytical Data 86
3.5.2.1 MS 86
3.5.2.2 NMR 92
3.5.2.3 HPLC 92
3.5.3 Prediction and Analysis of Glycosylation Sites 92
3.5.4 Carbohydrate-/Glycoprotein-Related 3D Structure Applications 93
3.6 Conclusions 94
References 94
4 Lectin Microarrays: Simple Tools for the Analysis of Complex Glycans 99
4.1 Introduction 100
4.2 Lectins in Carbohydrate Analysis 100
4.3 Development of Lectin Microarray Technology 101
4.4 Analysis of Complex Mixtures with Lectin Microarrays 102
4.4.1 Analysis of Whole Cells 102
4.4.2 Analysis of Isolated Glycoprotein Fractions 103
4.5 Comparative Glycomics of Human Immunodeficiency Virus (HIV) and Microvesicles: An Illustration of the Power of Lectin Microarrays for Glycomic Analysis 106
4.6 Advantages and Limitations 107
4.7 Conclusions 107
References 108
5 The Application of High Throughput Mass Spectrometry to the Analysis of Glycoproteins 111
5.1 Introduction 112
5.1.1 Introduction to Glycoproteomics and MS 112
5.1.2 Challenges in Glycoproteomics 113
5.2 Glycopeptide Enrichment Techniques in Glycoproteomics 114
5.2.1 Glycan-Modifying Enrichment Techniques 115
5.2.1.1 Schiff-Base Reaction (O-GlcNAc Ketone Enrichment) 115
5.2.1.2 Staudinger Ligation 115
5.2.1.3 Periodate-Acid Schiff Coupled Affinity Chromatography (PAS) 118
5.2.2 Glycan-Non-modifying Enrichment Techniques 119
5.2.2.1 Lectin Affinity Purification 119
5.2.2.2 Hydrophilic Interaction Chromatography (HILIC) 120
5.2.2.3 Other, Non-modifying Enrichment Techniques 120
5.3 Structural Characterization of Protein Glycosylation Using MS 121
5.3.1 MS Instrumentation for Glycoproteomics 121
5.3.1.1 Ion Sources and Mass Analyzers 121
5.3.1.2 Tandem MS Fragmentation of Glycopeptides 122
5.3.2 Structural Characterization of Glycopeptides 124
5.3.2.1 Identification of Glycoproteins and Their Glycosylation Sites in Glycoproteomics 124
5.3.2.2 Characterization of Glycan Structures from Glycopeptides 125
5.4 Conclusions 127
References 128
6 Solutions to the Glycosylation Problem for Low- and High-Throughput Structural Glycoproteomics 134
6.1 Introduction 136
6.2 Glycosylation and Protein Folding 137
6.3 The Glycosylation Problem 139
6.3.1 O-Glycosylation 139
6.3.2 N-Glycosylation 140
6.3.2.1 Chemical Heterogeneity Of N-Linked Glycans 140
6.3.2.2 Conformational Heterogeneity of N-Linked Glycans 143
6.4 Solving the Glycosylation Problem 143
6.4.1 Shielding N-Linked Glycans from Lattice Contacts 143
6.4.2 Depletion of Glycosylation by Sequon Mutation 144
6.4.3 Deglycosylation with peptide-N-glycosidase 145
6.4.4 Exoglycosidase Treatment 145
6.4.5 N-Glycan Remodeling and Endoglycosidase Treatment 147
6.4.5.1 Insect Cell-Derived Glycoproteins 147
6.4.5.2 Fungally-Expressed Glycoproteins 148
6.4.5.3 Mammalian Expression Systems 148
6.5 Does Glycan Removal Affect Protein Function? 154
6.6 Putting the Sugar Back 155
6.7 Conclusions 157
References 158
7 Role of Glycoproteins in VirusHuman Cell Interactions 166
7.1 Introduction 168
7.2 Paramyxoviruses 171
7.2.1 Paramyxovirus Attachment -- Receptor Switching on a Common Scaffold 172
7.2.2 Paramyxovirus Fusion -- An Example of Type I Fusion Machines 173
7.3 New World Arenavirus Glycoprotein Structure A New Protein Fold 174
7.4 Flaviviruses Combine Attachment and Fusion Functions in the E Protein 176
7.5 Filoviruses A Deadly Receptor-Binding Chalice 177
7.6 Influenza Virus Glycosylation Modulates Pathogenicity 180
7.7 HIV A Glycan Shield 181
7.8 Conclusions 181
References 182
Subject Index 188