Fukuda Glycomics

1. Auflage 2010
ISBN: 978-0-12-381002-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, Band Volume 478, 664 Seiten

Reihe: Methods in Enzymology

In this 3 volume collection focusing on glycomics, readers will appreciate how such discoveries were made and how such methods can be applied for readers' own research efforts - Each chapter has been designed so that enough scientific background will be given in each chapter for further development of methods by readers themselves - Useful for all levels of scientists starting from the last years of colleges, graduate students, postdoctoral fellows to professors and to all levels of scientists in research institutes including industry

Autoren/Hrsg.

Fukuda, Minoru

Inhaltsverzeichnis

1;Front Cover;1
2;Methods in Enzymology: Glycomics;4
3;Copyright Page;5
4;Contents;6
5;Contributors;16
6;Preface;26
7;Methods in Enzymology;28
8;Section One: Glycomics Revealed by Mass Spectrometric Analysis;56
8.1;Chapter One: Mass Spectrometric Analysis of Sulfated N- and O-Glycans;58
8.1.1;1. Introduction and Overview;59
8.1.2;2. Sample Preparation;62
8.1.3;3. MS Analyses and Data Interpretation;68
8.1.4;4. Future Perspectives;78
8.1.5;Acknowledgments;79
8.1.6;References;79
8.2;Chapter Two: Mass Spectrometric Analysis of Mutant Mice;82
8.2.1;1. Overview;83
8.2.2;2. Methods;86
8.2.3;3. Interpretation of Glycomic Data;114
8.2.4;4. Example Project: Characterization of Pancreatic Tissue from Wild-Type and Mgat4a Knockout Mice;117
8.2.5;5. Summary of Glycan Structural Observations in Murine Tissues, Cells, and Knockouts;124
8.2.6;Acknowledgments;128
8.2.7;References;129
8.3;Chapter Three: Glycosaminoglycan Characterization by Electrospray Ionization Mass Spectrometry Including Fourier Transform Mass S;134
8.3.1;1. Overview;136
8.3.2;2. Preparation of Crude PG/GAG;138
8.3.3;3. Disaccharide Profiling Using Ion-Pairing Reverse-Phase (IP RP) HPLC with MS Detection;139
8.3.4;4. CS/DS Disaccharide Preparation;139
8.3.5;5. ESI IP RP LC MS Analysis of CS/DS Disaccharides;140
8.3.6;6. HS Disaccharide Preparation;143
8.3.7;7. ESI IP RP LC MS Analysis of HS Disaccharides;145
8.3.8;8. Direct Infusion ESI FTMS Analysis of Oligosaccharides and Polysaccharides Separated by Preparative Continuous-Elution PAGE.;147
8.3.9;9. Preparation of Bikunin GAG;148
8.3.10;10. An Approach to FTMS Data Interpretation;155
8.3.11;11. Direct Infusion ESI FT-ICR MS Analysis of Bikunin GAG Mixture;156
8.3.12;12. Structural Characterization of GAG Oligosaccharides by Tandem Mass Spectrometry;157
8.3.13;13. Summary;160
8.3.14;Acknowledgments;161
8.3.15;References;161
8.4;Chapter Four: Large-Scale Glycomics for Discovering Cancer-Associated N-Glycans by Integrating Glycoblotting and Mass Spectromet;164
8.4.1;1. Introduction;165
8.4.2;2. Overview of Glycoblotting Utilized by BlotGlyco Beads;166
8.4.3;References;179
8.5;Chapter Five: In Vitro and In Vivo Enzymatic Syntheses and Mass Spectrometric Database for N-Glycans and O-Glycans;182
8.5.1;1. Overview;183
8.5.2;2. In Vitro Syntheses of N- and O-Linked Glycan Libraries Using Recombinant Human Glycosyltransferases;184
8.5.3;3. In Vivo Production of Mammalian-Type O-Linked Glycopeptides in Yeast;191
8.5.4;4. An Application of the Library to Glycan Analysis;196
8.5.5;5. Glycan Analysis Using the Glycan Mass Spectral Database ``GMDB´´;198
8.5.6;6. Navigator System for Glycan Analysis Using the Glycan Mass Spectral Database;201
8.5.7;Acknowledgments;203
8.5.8;References;203
9;Section Two: Glycomics Revealed by Carbohydrate-Binding Proteins;206
9.1;Chapter Six: Identification of Fucosylated Haptoglobin as a Novel Tumor Marker for Pancreatic Cancer and Its Possible Applicati;208
9.1.1;1. Introduction;209
9.1.2;2. Discovery of Fucosylated Haptoglobin as a Marker for Pancreatic Cancer;210
9.1.3;3. Mass Spectrometry Analysis of the Oligosaccharide Structure on Haptoglobin;211
9.1.4;4. Identification of an Inducible Factor that Stimulates the Production of Haptoglobin;212
9.1.5;5. Clinical Application of Lectin-Antibody ELISA to Measure Fucosylated Haptoglobin;215
9.1.6;6. Closing Remarks;217
9.1.7;Acknowledgments;217
9.1.8;References;218
9.2;Chapter Seven: Differential Glycan Profiling by Lectin Microarray Targeting Tissue Specimens;220
9.2.1;1. Overview;221
9.2.2;2. Differential Analysis of Glycoproteins Derived from One-Dot Sections of Tissue Microarray;223
9.2.3;3. Differential Glycan Analysis Between Cancer Lesions and Normal Regions in the Same Tissue Section;229
9.2.4;4. (Optional)Glycan Profiling of a Target Glycoprotein Extracted from Tissue Specimens;231
9.2.5;Acknowledgments;232
9.2.6;References;232
9.3;Chapter Eight: A Versatile Technology for Cellular Glycomics Using Lectin Microarray;236
9.3.1;1. Introduction;237
9.3.2;2. Strategy for Systematic Development of Cell Discrimination Procedures Using Lectin Microarray;237
9.3.3;3. Production of the Lectin Microarray;238
9.3.4;4. Sample Preparation and Lectin Microarray Hybridization;240
9.3.5;5. Data Normalization;240
9.3.6;6. Glycan Profiles of CHO, Lec2, Lec8, and Lec1;241
9.3.7;7. Unsupervised Clustering and Principal Component Analysis;244
9.3.8;8. Significance Difference Test;245
9.3.9;9. Discriminant Analysis;246
9.3.10;10. Differential Analysis Between CHO and Lec1;247
9.3.11;11. Validation;248
9.3.12;12. Concluding Remarks;248
9.3.13;Acknowledgments;250
9.3.14;References;250
9.4;Chapter Nine: Applications of Heparin and Heparan Sulfate Microarrays;252
9.4.1;1. Introduction;253
9.4.2;2. Preparation of Amino-Functionalized HS/Heparin Oligosaccharides;256
9.4.3;3. Microarray Analysis of HS/Heparin-FGF Binding;257
9.4.4;4. A HS/Heparin Microarray to Determine the Binding Profiles of Heparin Dendrimers to FGF-2;262
9.4.5;5. HS/Heparin Interaction with Chemokines as Determined by Microarray Analysis;266
9.4.6;6. HS/Heparin Microarray for Determination of Their Interaction with NCRs;268
9.4.7;7. Conclusions;269
9.4.8;Acknowledgments;270
9.4.9;References;270
9.5;Chapter Ten: Measurement of Glycan-Based Interactions by Frontal Affinity Chromatography and Surface Plasmon Resonance;274
9.5.1;1. Introduction;275
9.5.2;2. Frontal Affinity Chromatography (FAC) as a Tool for the Measurement of Glycan-Based Interactions;276
9.5.3;3. Surface Plasmon Resonance (SPR)-Based Biosensors as a Tool for the Measurement of Glycan-Based Interactions...;282
9.5.4;4. Conclusions;285
9.5.5;Acknowledgments;286
9.5.6;References;286
9.6;Chapter Eleven: Detection of Weak-Binding Sugar Activity Using Membrane-Based Carbohydrates;288
9.6.1;1. Introduction;289
9.6.2;2. Construction of Plasmids for Biotinylated Soluble Lectins;289
9.6.3;3. Preparation of Biotinylated Soluble Lectins and PE-Labeled Lectin Tetramer;291
9.6.4;4. Construction of Plasmids for the Fc-Fusion Protein and Purification of the Lectin-Fc Fusion Protein;292
9.6.5;5. Binding Assay for PE-Labeled Lectin Tetramer Using Flow Cytometry;293
9.6.6;6. Cells with Altered Glycans or Modification of Cell-Surface Glycans;294
9.6.7;References;295
9.7;Chapter Twelve: Fluorescence-Based Solid-Phase Assays to Study Glycan-Binding Protein Interactions with Glycoconjugates;296
9.7.1;1. Overview;297
9.7.2;2. Biotinylation of Glycopeptides, Oligosaccharides, and Cells;299
9.7.3;3. Fluorescence Labeling of GBPs and Cells;302
9.7.4;4. P- and L-Selectin Binding to Immobilized Glycosulfopeptides and Determination of Apparent Binding Affinity;304
9.7.5;5. Galectin-1 Binding to Immobilized Glycopeptides and Glycans and Determination of Apparent Binding Affinity;309
9.7.6;6. Galectin-1 Binding to Immobilized HL-60 Cells and Determination of Apparent Binding Affinity;312
9.7.7;Acknowledgments;317
9.7.8;References;317
9.8;Chapter Thirteen: Multifaceted Approaches Including Neoglycolipid Oligosaccharide Microarrays to Ligand Discovery for Malectin;320
9.8.1;1. Overview;321
9.8.2;2. Preparation of Recombinant Soluble Human Malectin;323
9.8.3;3. Preparation of Glucan Oligosaccharides;326
9.8.4;4. Preparation of Glucosylated High-Mannose N-Glycans;329
9.8.5;5. Preparation of NGL Probes;333
9.8.6;6. Carbohydrate Microarray Analysis of Human Malectin;336
9.8.7;7. Conclusions;339
9.8.8;Acknowledgments;339
9.8.9;References;339
9.9;Chapter Fourteen: Imaging Mass Spectrometry of Glycolipids;342
9.9.1;1. Overview;343
9.9.2;2. Preparation of Tissue Sections;344
9.9.3;3. Matrix Selection and Applying Matrix;345
9.9.4;4. Measurements by Imaging Mass Spectrometry;347
9.9.5;5. Data Analyses;348
9.9.6;6. Identification of Molecules;349
9.9.7;7. Application of IMS;351
9.9.8;Acknowledgments;354
9.9.9;References;354
10;Section Three: Chemical Glycobiology;358
10.1;Chapter Fifteen: Dynamics and Interactions of Glycoconjugates Probed by Stable-Isotope-Assisted NMR Spectroscopy;360
10.1.1;1. Introduction;361
10.1.2;2. Assignments of NMR Signals Derived from Glycoprotein Glycan;361
10.1.3;3. Dynamics of Glycoprotein Glycans;364
10.1.4;4. Identification of Binding Surfaces in Glycoprotein/Ligand Complexes;368
10.1.5;5. NMR-Based Screening of Glycopeptides Reactive with Lectin;370
10.1.6;6. NOE Analyses of Lectin-Ligand Interactions;373
10.1.7;7. Perspective;373
10.1.8;Acknowledgments;374
10.1.9;References;374
10.2;Chapter Sixteen: Self and Nonself Recognition with Bacterial and Animal Glycans, Surveys by Synthetic Chemistry;378
10.2.1;1. Overview;379
10.2.2;2. Bacterial Glycoconjugates for Nonself Recognition-Lipopolysaccharide (LPS);380
10.2.3;3. Synthesis of H. pylori Kdo-Lipid A Backbone;382
10.2.4;4. Glycosylation with Kdo Donor 11;382
10.2.5;5. Cytokine (IL-6) Induction in Human Peripheral Whole-Blood Cell Cultures;383
10.2.6;6. Bacterial Glycoconjugates for Nonself Recognition-Peptidoglycan (PGN);384
10.2.7;7. Synthesis of Disaccharide Moiety 15 in Tracheal Cytotoxin with beta-Selective Glycosylation;386
10.2.8;8. Synthesis of Tracheal Cytotoxin 20 and Its Fragment 21;387
10.2.9;9. Immunostimulatory Activities of DAP Containing PGN Fragments;388
10.2.10;10. Visualizing the In Vivo Dynamics of Animal N-Glycans;388
10.2.11;11. PET Imaging of Glycoproteins;389
10.2.12;12. Method for 68Ga-DOTA Labeling and MicroPET Imaging in Rabbit;390
10.2.13;13. PET Imaging of Glycoclusters;392
10.2.14;14. Method for Preparation of N-Glycan Clusters and PET Imaging in Mouse;393
10.2.15;Acknowledgments;394
10.2.16;References;395
10.3;Chapter Seventeen: Multivalent Ligands for Siglecs;398
10.3.1;1. Introduction;399
10.3.2;2. Materials and Methods;405
10.3.3;3. Conclusions and Future Directions;414
10.3.4;Acknowledgments;415
10.3.5;References;416
10.4;Chapter Eighteen: Intramolecular Glycan-Protein Interactions in Glycoproteins;420
10.4.1;1. Introduction;420
10.4.2;2. O-Linked Glycoproteins;422
10.4.3;3. N-Linked Glycoproteins;429
10.4.4;Acknowledgments;437
10.4.5;References;437
10.5;Chapter Nineteen: Methods to Study the Biosynthesis of Bacterial Furanosides;444
10.5.1;1. Introduction;445
10.5.2;2. Chemoenzymatic Preparation of Furanose Nucleotides;448
10.5.3;3. Pyranose-Furanose Mutases Involved in Furanose Nucleotide Biosynthesis;453
10.5.4;4. Galactofuranosyltransferases Involved in Galactofuranoside Biosynthesis;457
10.5.5;Acknowledgments;462
10.5.6;References;462
10.6;Chapter Twenty: The Synthesis of 1,2-cis-Amino Containing Oligosaccharides Toward Biological Investigation;468
10.6.1;References;486
10.7;Chapter Twenty-One: Aminoglycosides;492
10.7.1;1. Introduction;493
10.7.2;2. Aminoglycoside Antibiotics: Their Mode of Action and Major Drawbacks;495
10.7.3;3. Strategies Toward Development of Improved Antibiotics;498
10.7.4;4. Aminoglycosides as Readthrough Inducers for the Treatment of Genetic Diseases;509
10.7.5;5. Concluding Remarks and Future Perspectives;513
10.7.6;Acknowledgments;513
10.7.7;References;514
10.8;Chapter Twenty-Two: Solid Phase Synthesis of Oligosaccharides;518
10.8.1;1. Introduction;519
10.8.2;2. Solid Phase Techniques and Strategies;520
10.8.3;3. Solid Phase Synthesis of Carbohydrates;523
10.8.4;4. Automated Solid Phase Synthesis of Carbohydrates;527
10.8.5;5. Conclusions and Outlook;531
10.8.6;6. Experimental Data for the Synthesis of Protected Globo-H 47;534
10.8.7;Acknowledgments;536
10.8.8;References;536
10.9;Chapter Twenty-Three: Novel Synthesis of Functional Mucin Glycopeptides Containing Both N- and O-Glycans;540
10.9.1;1. Overview;541
10.9.2;2. Design of MUC1-Related Neoglycoprotein;542
10.9.3;3. Solid-Phase Glycopeptide Synthesis Using Microwave-Assisted Protocol;543
10.9.4;4. Production and Purification of SrtA;545
10.9.5;5. SrtA-Mediated Ligation;546
10.9.6;6. Endo-M-Mediated Transglycosylation;549
10.9.7;7. One-Pot Enzymatic Sugar Elongation Catalyzed by Glycosyltransferases;551
10.9.8;8. Chemoselective Polymer Blotting;554
10.9.9;9. BLase-Catalyzed Cleavage from Supporting Polymer;554
10.9.10;10. Compound Characterization by Mass Spectrometry and Amino Acid Analysis;555
10.9.11;References;556
10.10;Chapter Twenty-Four: Synthesis of Glycopeptides;558
10.10.1;1. Introduction;559
10.10.2;2. Preparation of N-Linked Complex Type Oligosaccharides;559
10.10.3;3. Synthesis of Large Glycopeptides by Use of Efficient Peptide Coupling Method;566
10.10.4;4. Native Chemical Ligation of Glycopeptide;566
10.10.5;5. Expanding Scope of Native Chemical Ligation;568
10.10.6;6. Conclusion;572
10.10.7;References;572
10.11;Chapter Twenty-Five: Renewed Synthetic Approach to Gangliosides Exploiting Versatile and Powerful Synthetic Units;576
10.11.1;1. Background;577
10.11.2;2. Design of a Systematic Strategy Toward Gangliosides Found in Mammals;578
10.11.3;3. Renewal of the Synthesis of Sialyl Galactose Unit;580
10.11.4;4. Sialyl Galactose Unit for Ganglio-Series Ganglioside Synthesis;583
10.11.5;5. Cassette Approach to Glycolipid Synthesis;584
10.11.6;6. Synthesis of Echinoderm Ganglioside;586
10.11.7;7. Experimental Procedure;589
10.11.8;References;594
10.12;Chapter Twenty-Six: Metabolic Labeling of Glycoconjugates with Photocrosslinking Sugars;596
10.12.1;1. Introduction;597
10.12.2;2. Synthesis of Photocrosslinking Sugars;600
10.12.3;3. Metabolic Incorporation of Photocrosslinkers into Glycans in Cell Culture;603
10.12.4;4. Analysis of CMP-Sialic Acids in Cell Lysates by HPAEC;605
10.12.5;5. Cell Surface Display of SiaDAz in Sialic Acid-Deficient Cells;607
10.12.6;6. Characterization of SiaDAz-Containing Gangliosides;610
10.12.7;7. Covalent Capture of Glycan-Mediated Interactions Using Photocrosslinking Sialic Acid;612
10.12.8;8. Conclusion;614
10.12.9;Acknowledgments;614
10.12.10;References;615
10.13;Chapter Twenty-Seven: Identification of Carbohydrate-Binding Proteins by Carbohydrate Mimicry Peptides;618
10.13.1;1. Overview;619
10.13.2;2. Materials;619
10.13.3;3. Preparation of an Affinity Ligand Agarose Column;620
10.13.4;4. Visualization of Carbohydrate-Binding Proteins;620
10.13.5;5. Peptide Affinity Chromatography;622
10.13.6;6. Use of Carbohydrate Mimicry Peptides as a Research Reagent;625
10.13.7;Acknowledgments;625
10.13.8;References;626
11;Author Index;628
12;Subject Index;654
13;Color Plates;668