Glycosaminoglycans: Chemistry and Biology

616 Pages·2015·22.32 MB·English

by  Kuberan Balagurunathan, Hiroshi Nakato, Umesh R. Desai (eds.)

Methods in
Molecular Biology 1229
Kuberan Balagurunathan
Hiroshi Nakato
Umesh R. Desai Editors
Glycosamino-
glycans
Chemistry and Biology
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Glycosaminoglycans
Chemistry and Biology
Edited by
Kuberan Balagurunathan
Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA
Hiroshi Nakato
Department of Genetics, Cell Biology and Development, The University of Minnesota,
Minneapolis, MN, USA
Umesh R. Desai
Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond , VA, USA
Editors
Kuberan B alagurunathan Hiroshi Nakato
Department of Medicinal Chemistry Department of Genetics, Cell Biology
University of Utah and Development
Salt Lake City, UT, USA The University of Minnesota
Minneapolis, MN, USA
Umesh R. D esai
Department of Medicinal Chemistry
Virginia Commonwealth University
Richmond, VA, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-1713-6 ISBN 978-1-4939-1714-3 (eBook)
DOI 10.1007/978-1-4939-1714-3
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Prefa ce
Glycosaminoglycans are structurally the most complex biopolymers among the many nat-
urally occurring polysaccharides. Complexity arises from the variation in the sugar residue-
type, interglycosidic linkage, chain length, sulfation level, and sulfation position. There are
six types of glycosaminoglycans including heparan sulfate, heparin, chondroitin sulfate,
dermatan sulfate, keratan sulfate, and hyaluronic acid. With the exception of hyaluronic
acid, all glycosaminoglycans are covalently attached to proteins. Glycosaminoglycans have
been shown to play signifi cant roles in many model organisms starting from early growth
period, through development and beyond. These complex carbohydrate polymeric chains
regulate numerous biological and pathological processes such as angiogenesis, morpho-
genesis, organogenesis, neurogenesis, stem cell differentiation, cell proliferation, cell
migration, left-right axis induction, synaptic plasticity, synapse formation, neuronal guid-
ance and growth, hemostasis, infection, and many others. Naturally, there is a considerable
interest in understanding the structural basis for their numerous biological actions and in
identifying protein ligands that orchestrate these functions through direct interaction with
glycosaminoglycan chains. There has been a steady growth in the appreciation for the roles
of glycosaminoglycan in many scientifi c disciplines ranging from developmental biology,
chemical biology, organic synthesis, structural biology, biochemistry, cell signaling, drug
discovery, stem cell biology, tissue engineering, bioinformatics, and computational glyco-
biology as seen by the large number of glycosaminoglycan-related papers published in the
last 10 years.
In this volume of Methods in Molecular Biology , we provide robust methods for study-
ing chemistry and biology of glycosaminoglycans. The volume emphasizes several areas of
glycosaminoglycan research including structural analysis of GAGs using a variety of
approaches, chemical and enzymatic synthesis of GAGs for therapeutic purposes; biophysi-
cal and biochemical methods for studying GAG–protein interactions; molecular approaches
for modulating and defi ning GAG biosynthesis; informatics approaches for deciphering
GAG code; computational approaches for establishing specifi c and/or nonspecifi c interac-
tions; and genetic and biochemical tools for manipulating/visualizing glycosaminoglycan
expression and studying their functions in a variety of model organisms. This volume has a
primary goal of providing practical guidance for the chemist to carry out biological experi-
ments, for the biologist to perform chemical/biochemical studies, and for the applied sci-
entist to harness therapeutic application possibilities using chemical, biochemical, genetic,
and computational tools. Overall, it is our expectation that this volume will serve as a valu-
able manual for cutting-edge methodologies and practical (hard to fi nd from the primary
literature) tips to overcome any obstacles with experimentation pertaining to chemistry and
biology of glycosaminoglycans.
Salt Lake City, UT, USA K uberan Balagurunathan
Minneapolis, MN, USA H iroshi N akato
Richmond, VA, USA Umesh R. Desai
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x i
PART I STRUCTURE
1 Automated Synthesis of Chondroitin Sulfate Oligosaccharides. . . . . . . . . . . . . 3
Chien-Fu L iang, Heung S ik H ahm, and P eter H . S eeberger
2 E nzymatic Synthesis of Heparan Sulfate and Heparin . . . . . . . . . . . . . . . . . . . 1 1
April Joice, Karthik Raman, Caitlin Mencio, M aritza V. Quintero,
Spencer Brown, T hao Kim Nu Nguyen, and B alagurunathan Kuberan
3 P roduction of Size-Defined Heparosan, Heparan Sulfate, and Heparin
Oligosaccharides by Enzymatic Depolymerization. . . . . . . . . . . . . . . . . . . . . . 21
Spencer Brown and Balagurunathan K uberan
4 C hemical Modification of Heparin and Heparosan . . . . . . . . . . . . . . . . . . . . . 3 1
Karthik R aman, B alagurunathan K uberan, and Sailaja A rungundram
5 Synthesis of Sulfur Isotope-Labeled Sulfate Donor, 3′-Phosphoadenosine-5′-
Phosphosulfate, for Studying Glycosaminoglycan Functions . . . . . . . . . . . . . . 3 7
Caitlin M encio, Vimal P . Swarup, M arcus Soliai,
and Balagurunathan Kuberan
6 P reparation of Isotope-Enriched Heparan Sulfate Precursors
for Structural Biology Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3
Xylophone V. V ictor, V y M . Tran, B alagurunathan Kuberan,
and Thao K im N u Nguyen
7 S ynthesis of Glycosaminoglycan Mimetics Through Sulfation
of Polyphenols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 9
Rami A . A l-Horani, R ajesh K aruturi, S tephen Verespy III,
and Umesh R. D esai
8 S ynthesis of Selective Inhibitors of Heparan Sulfate
and Chondroitin Sulfate Proteoglycan Biosynthesis. . . . . . . . . . . . . . . . . . . . . 69
Caitlin M encio, Dinesh R. Garud, B alagurunathan Kuberan,
and Mamoru Koketsu
9 Ascidian (Chordata-Tunicata) Glycosaminoglycans: Extraction,
Purification, Biochemical, and Spectroscopic Analysis . . . . . . . . . . . . . . . . . . . 79
Mauro S. G . Pavão
10 Human Blood Glycosaminoglycans: Isolation and Analysis . . . . . . . . . . . . . . . 9 5
Md. F erdous Anower-E-Khuda and K oji Kimata
11 Chromatographic Molecular Weight Measurements for Heparin,
Its Fragments and Fractions, and Other Glycosaminoglycans. . . . . . . . . . . . . . 105
Barbara Mulloy and John H ogwood
vii
viii Contents
12 Mass Spectrometric Methods for the Analysis of Heparin
and Heparan Sulfate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 19
Miroslaw L ech, I shan C apila, and Ganesh V . Kaundinya
13 Validated Capillary Electrophoretic Assays for Disaccharide
Composition Analysis of Galactosaminoglycans in Biologic Samples
and Drugs/Nutraceuticals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Athanasia P. Asimakopoulou, C hristina M alavaki, N ikolaos A. Afratis,
Achilleas D . Theocharis, F otini N . L amari, and N ikos K. Karamanos
14 F ast Screening of Glycosaminoglycan Disaccharides by Fluorophore-Assisted
Carbohydrate Electrophoresis (FACE): Applications to Biologic Samples
and Pharmaceutical Formulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Evgenia Karousou, A thanasia P. Asimakopoulou, V assiliki Zafeiropoulou,
Manuela V iola, L uca M onti, A ntonio R ossi, Alberto Passi,
and Nikos K . Karamanos
15 Capillary Electrophoretic Analysis of Isolated Sulfated Polysaccharides
to Characterize Pharmaceutical Products. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Zachary S hriver and Ram S asisekharan
16 M ethods for Measuring Exchangeable Protons in Glycosaminoglycans . . . . . . 1 73
Consuelo N. B eecher and Cynthia K. L arive
17 Heparan Sulfate Structure: Methods to Study N-Sulfation
and NDST Action. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Anders Dagälv, A nders L undequist, B eata Filipek-Górniok,
Tabea Dierker, I nger E riksson, and Lena Kjellén
18 A nalysis of Hyaluronan Synthase Activity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Davide V igetti, E vgenia Karousou, M anuela Viola, and Alberto Passi
1 9 A Rapid, Nonradioactive Assay for Measuring Heparan
Sulfate C-5 Epimerase Activity Using Hydrogen/Deuterium
Exchange-Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 09
Ponnusamy B abu, X ylophone V . V ictor, Karthik Raman,
and Balagurunathan K uberan
20 A ggrecan: Approaches to Study Biophysical and Biomechanical Properties . . . 2 21
Hadi Tavakoli N ia, C hristine O rtiz, and Alan Grodzinsky
21 Use of Flow Cytometry for Characterization and Fractionation of Cell
Populations Based on Their Expression of Heparan Sulfate Epitopes. . . . . . . . 239
Rebecca J . H olley, Raymond A. S mith, E ls M. A . van de Westerlo,
Claire E. Pickford, C . L. R. Merry, and Toin H. van Kuppevelt
22 A Transgenic Approach to Live Imaging of Heparan Sulfate
Modification Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Matthew Attreed and Hannes E. Bülow
PART II FUNCTIONS
23 Informatics Tools to Advance the Biology of Glycosaminoglycans
and Proteoglycans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Lewis J. F rey
Contents ix
24 Designing “High-Affinity, High-Specificity” Glycosaminoglycan Sequences
Through Computerized Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 89
Nehru Viji Sankaranarayanan, A urijit S arkar,
Umesh R . D esai, and P hilip D . M osier
25 Using Isothermal Titration Calorimetry to Determine Thermodynamic
Parameters of Protein–Glycosaminoglycan Interactions. . . . . . . . . . . . . . . . . . 315
Amit K . D utta, J örg Rösgen, and K rishna R ajarathnam
26 Characterizing Protein–Glycosaminoglycan Interactions Using Solution
NMR Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325
Prem R aj B. J oseph, K rishna M ohan P oluri, Krishna Mohan Sepuru,
and Krishna Rajarathnam
27 G lycosaminoglycan–Protein Interaction Studies
Using Fluorescence Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Rio S. Boothello, R ami A . Al-Horani, and U mesh R . Desai
28 S tudying Glycosaminoglycan–Protein Interactions
Using Capillary Electrophoresis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
Aiye Liang and U mesh R . D esai
29 H istochemical Analysis of Heparan Sulfate 3-O-Sulfotransferase
Expression in Mouse Brain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 77
Tomio Yabe and N obuaki M aeda
30 K eratan Sulfate: Biosynthesis, Structures, and Biological Functions . . . . . . . . . 3 89
Kenji Uchimura
31 T he Sulfs: Expression, Purification, and Substrate Specificity. . . . . . . . . . . . . . 4 01
Kenji Uchimura
32 T he Detection of Glycosaminoglycans in Pancreatic Islets
and Lymphoid Tissues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 13
Marika Bogdani, C harmaine S imeonovic, Nadine N agy,
Pamela Y. J ohnson, C hristina K. C han, and Thomas N . W ight
33 N onradioactive Glycosyltransferase and Sulfotransferase Assay
to Study Glycosaminoglycan Biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 31
Cheryl M. E then, M iranda Machacek, B rittany Prather,
Timothy T atge, Haixiao Y u, and Zhengliang L . W u
34 M apping Proteoglycan Functions with Glycosidases . . . . . . . . . . . . . . . . . . . . 4 43
Mauricio Cortes, Leslie K. C ortes, and Nancy B. Schwartz
35 Cell Substrate Patterning with Glycosaminoglycans to Study
Their Biological Roles in the Central Nervous System. . . . . . . . . . . . . . . . . . . 457
Tony W. Hsiao, V imal P . Swarup, C olin D. E ichinger,
and Vladimir H lady
36 A nalyzing the Role of Heparan Sulfate Proteoglycans in Axon Guidance
In Vivo in Zebrafish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 69
Fabienne E . P oulain
37 Murine Models in the Evaluation of Heparan Sulfate-Based
Anticoagulants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 83
David Gailani, Q iufang C heng, and I van S. Ivanov