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 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2014949860 © Springer Science+Business Media New York 2 015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) 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