Glycosaminoglycans: Methods and Protocols

ISBN-13: 9781071614006 / Angielski / Miękka / 2022 / 829 str.

Kuberan Balagurunathan; Hiroshi Nakato; Umesh Desai

Opis

This second edition volume expands on the previous edition with new information on the structural analysis of glycosaminoglycans (GAGs); chemical and enzymatic synthesis of GAGs; biophysical, biochemical, and computational analysis of GAG-protein interactions; molecular and genetic approaches to manipulating GAG cell biology; and molecular and genetic methods involving animal models and organoids. This volume also offers insight and guidance to non-glycoscience researchers who are performing advanced experiments on GAGs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. \

Cutting-edge and authoritative, Glycosaminoglycans: Methods and Protocols, Second Edition is a valuable experimental manual for practicing researchers including graduate and post-doctoral fellows, and provides them with the latest methodologies and practical tips to overcoming barriers in understanding the chemistry and biology of GAGs. 

Spis treści

Dedication…
Preface…
Table of Contents…
Contributing Authors…

Part I GAG Structures

1. One-Pot Enzymatic Synthesis of Heparin from N-Sulfoheparosan
Li Fu and Robert J. Linhardt

2. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions 
Prem Raj B. Joseph, Krishna Mohan Sepuru, Krishna Mohan Poluri, and Krishna Rajarathnam

3. Metabolic Labeling of Proteoglycans and Analysis of Their Synthesis and Sorting in Filter-Grown and Polarized Epithelial Cells
Kristian Prydz and Ravi Adusumalli

4. Fluorous-Tag Assisted Synthesis of GAG-Like Oligosaccharides
José L. de Paz and Pedro M. Nieto

5. Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins
Balaji Nagarajan and Umesh R. Desai 

6. A Non-Radioactive Method to Measure Hyaluronan Synthase Activity
Davide Vigetti, Evgenia Karousou, Manuela Viola, and Alberto Passi

7. A Glycoproteomic Approach to Identify Novel Proteoglycans
Fredrik Noborn, Mahnaz Nikpour, Andrea Persson, Carina Sihlbom, Jonas Nilsson,  and Göran Larson

8. Analysis of Protein-Glycosaminoglycan Interactions using Traveling Wave Ion Mobility Mass Spectrometry
Robert V. Williams and I. Jonathan Amster

9. Ascidian (Chordata-Tunicata) Glycosaminoglycans: Extraction, Purification, Biochemical, and Spectroscopic Analysis
Felipe C. O. B. Teixeira and Mauro S. G. Pavão

10. Quantitative Disaccharide Profiling of Glycosaminoglycans from Two Different Preparations by PMP and Deuterated PMP Labeling
Meng Zhang, Yi An, and Lijuan Zhang

11. Preparation and Characterization of Heparan Sulfate Derived Oligosaccharides to Investigate Protein-GAG Interaction and HS Biosynthesis Enzyme Activity
Cédric Laguri, Rabia Sadir, Evelyne Gout, Romain R. Vivès, and Hugues Lortat-Jacob

12. Heparan Sulfate Structure: Methods to Study N-sulfation and NDST Action
Anders Dagälv, Anders Lundequist, Beata Filipek-Górniok, Tabea Dierker, Inger Eriksson, and Lena Kjellén

13. Methods for the Production of Recombinant Heparosan: A Critical Heparin Precursor, from Non-Pathogenic E.coli Strains
Anindita Roy, Varun Garg, Sai K Mehta, Alessandro Rossi, and Balagurunathan Kuberan

14. De novo Sequencing of Heparin/Heparan Sulfate Oligosaccharides by Chemical Derivatization and LC-MS/MS
Quntao Liang and Joshua S. Sharp

15. Production and HPLC-Based Disaccharide Analysis of Xyloside-Primed Glycosaminoglycans
Andrea Persson, Emil Tykesson, Ulf Ellervik, and Katrin Mani

16. Nuclear Magnetic Resonance Methods in Structural Characterization of Glycosaminoglycans
Vitor H. Pomin and Barbara Mulloy

17. Aggrecan: Approaches to Study Biophysical and Biomechanical Properties
Hadi Tavakoli Nia, Christine Ortiz, and Alan Grodzinsky

18. Chromatographic Molecular Weight Measurements for Heparin: Its Fragments and Fractions, and Other Glycosaminoglycans
Barbara Mulloy and John Hogwood

19. Mass Spectrometric Methods for the Analysis of Heparin and Heparan Sulfate
Miroslaw Lech, Ishan Capila, and Ganesh V. Kaundinya

20. Affinity Purification of Glycosylphosphatidylinositol-Anchored Proteins by Alpha-Toxin
Kevin Huang and Sungjin Park

21. Thermodynamic Affinity and Nature of Forces Defining Glycosaminoglycan: Protein Systems Using Fluorescence Spectroscopy
Rio S. Boothello and Umesh R. Desai

22. Isolation and Characterization of Heparan Sulfate Containing Amyloid Precursor Protein Degradation Products
Katrin Mani

23. Chemical Approaches to Prepare Modified Heparin and Heparosan Polymers for Biological Studies
Karthik Raman and Sailaja Arungundram

24. Glycosaminoglycan Quality Control by Monosaccharide Analysis
Yiran Zhang, Xuexiao Ma, and Lijuan Zhang

25. Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions using Isothermal Titration Calorimetry
Amit K. Dutta, Krishna M. Sepuru, Jörg Rösgen, and Krishna Rajarathnam

26. Automated Synthesis of Chondroitin Sulfate Oligosaccharides
Chien-Fu Liang, Heung Sik Hahm, Narayana Murthy Sabbavarapu, and Peter H. Seeberger

27. Capillary Electrophoretic Analysis of Isolated Sulfated Polysaccharides to Characterize Pharmaceutical Products
Zachary Shriver and Ram Sasisekharan

28. Preparation of Isotope Enriched Heparan Sulfate Precursors for Structural Biology Studies
Victor V. Xylophone, My Vu Tran, Balagurunathan Kuberan, and Thao Kim Nu Nguyen

29. Methods for Measuring Exchangeable Protons in Glycosaminoglycans
Consuelo N. Beecher and Cynthia K. Larive

30. Advances in Studying Glycosaminoglycan–Protein Interactions Using Capillary Electrophoresis
Aiye Liang and Umesh R. Desai

31. anexVis: A Transcriptome Tool to Visualize Organ/Tissue-Specific Glycosaminoglycan Biosynthetic and Catabolic Pathways in Human Health and Diseases
Kishan Thambu and Balagurunathan Kuberan

Part II GAG Functions

32. Molecular Genetic Techniques for the Proteoglycan Functions in Drosophila
Nanako Bowden, Masahiko Takemura, and Hiroshi Nakato

33. Measuring Sulfatase Expression and Invasion in Glioblastoma 
Anna Wade, Jane R. Engler, Vy My Tran, and Joanna J. Phillips

34. Analyzing the Role of Heparan Sulfate Proteoglycans in Axon Guidance In Vivo in Zebrafish
Fabienne E. Poulain

35. Regulation of 3-O-Sulfation of Heparan Sulfate during Transition from the Naïve to the Primed State in Mouse Embryonic Stem Cells
Hayato Ota and Shoko Nishihara

36. Analysis of Human Hyaluronan Synthase Gene Transcriptional Regulation and Downstream Hyaluronan Cell Surface Receptor Mobility in Myofibroblast Differentiation
Adam C. Midgley and Timothy Bowen

37. Methods to Analyze the Effect of Diet-Derived Metabolites on Endothelial Inflammation and Cell Surface Glycosaminoglycans 
Brett Ronald Cutler, Jie Shi Chua, Balagurunathan Kuberan, and Pon Velayutham Anandh Babu 

38.     Assays for Evaluation of Substrates for and Inhibitors of β-1,4-Galactosyltransferase 7 
Emil Tykesson, Andrea Persson, Katrin Mani, and Ulf Ellervik

39. Enzymatic Alteration of ECM to Explore Muscle Function and Motor Control of a Learned Behavior
Caitlin Mencio, Balagurunathan Kuberan, and Franz Goller

40. Procedures to Evaluate the Role of Heparan Sulfate in the Reactivity of Resistance and Conductance Arteries Ex Vivo  
Jae Min Cho, Kellsey Ly, Steven Ly, Seul-Ki Park, Pon Velayutham Anandh Babu, Balagurunathan Kuberan, and J. David Symons

41. Computerized Molecular Modeling for Discovering Promising Glycosaminoglycan Oligosaccharides that Modulate Protein Function
Nehru Viji Sankaranarayanan and Umesh R. Desai

42. Imaging Glycosaminoglycan Modification Patterns In Vivo
Hannes E. Bülow

43. Isolation and Purification of Versican and Analysis of Versican Proteolysis
Simon J. Foulcer, Anthony J. Day, and Suneel S. Apte

44. Identification of Cell Autonomous and Non-Cell Autonomous Functions of Heparan Sulfate Glycosaminoglycan Chains by Creating Chimeric Mouse Embryos
Isao Matsuo and Chiharu Kimura-Yoshida

45. Methods for Assessing the Effects of Xylosides on Angiogenesis
Jie Shi Chua, Geethu Muruganandam, Yukio Saijoh, and Balagurunathan Kuberan

46. Role of HSPGs in Systemic Bacterial Infections
Rafael S. Aquino, Kazutaka Hayashida, Atsuko Hayashida, and Pyong Woo Park

47. Generation of Drosophila Heparan Sulfate Mutant Cell Lines from Existing Fly Strains
Eriko Nakato, Nanako Bowden, and Hiroshi Nakato

48. Application of a Mutant Cell Library to Determine the Structure-Function Relationship of Heparan Sulfate in Facilitating FGF-FGFR Signaling
John Faulkner, Xuehong Song, and Lianchun Wang

49. Manipulation of Glycosaminoglycans using Synthetic Xylosides to Study their Roles in Lung Branching Morphogenesis in Ex Vivo Lung Bud Culture System
Jie Shi Chua, Balagurunathan Kuberan, and Yukio Saijoh

50. Informatics Ecosystems to Advance the Biology of Glycans
Lewis J. Frey 

51. Analysis of 3'-phosphoadenosine 5'-phosphosulfate Transporters: Transporter Activity Assay, Real-Time Reverse Transcription Polymerase Chain Reaction, and Immunohistochemistry 
Hideo Egawa‍ and Shoko Nishihara

52. Preparation of Nanosensors for Detecting the Activity of Glycosaminoglycan Cleaving Enzymes
Mausam Kalita, April Joice, Khoi Dang Le, Yiling Bi, Gurusankar Ramamoorthy, Orlando Antelope, Anindita Roy, and Balagurunathan Kuberan

53. The Detection of Glycosaminoglycans in Pancreatic Islets and Lymphoid Tissues
Marika Bogdani,Charmaine Simeonovic, Nadine Nagy, Pamela Y. Johnson, Christina K. Chan, and Thomas N. Wight

54. Histochemical Analysis of Heparan Sulfate 3-O-sulfotransferase Expression in Mouse Brain
Tomio Yabe and Nobuaki Maeda

55. Mapping Proteoglycan Functions Using Novel Genetic Strategies
Mauricio Cortes, Leslie K. Cortes, and Nancy B. Schwartz

56. Xyloside Derivatives as Molecular Tools to Selectively Inhibit Heparan Sulfate and Chondroitin Sulfate Proteoglycan Biosynthesis
Caitlin Mencio, Balagurunathan Kuberan, and Mamoru Koketsu

57. A Strategic Approach to Identification of Selective Inhibitors of Cancer Stem Cells
Nirmita Patel, Somesh Baranwal, and Bhaumik B. Patel

58. Applications of Xylosides in the Manipulation of Stem Cell Niche to Regulate Human Neural Stem Cell Differentiation and Neurite Outgrowth
Jie Shi Chua, Geethu Muruganandam, Daeun Sung, Yukio Saijoh, and Balagurunathan Kuberan

59. Murine Models in the Evaluation of Heparan Sulfate-Based Anticoagulants
Bassem M. Mohammed, Qiufang Cheng, Ivan S. Ivanov, and David Gailani

60. Investigating the Roles of Heparan Sulfate Structures in Alpha-Synuclein Aggregation in Cell Culture Models
Anindita Roy, Akila V. Chalapathi, and Balagurunathan Kuberan

Subject Index List…