M E T H O D S I N M O L E C U L A R B I O L O G Y

Series EditorJohn M. Walker

School of Life SciencesUniversity of Hertfordshire

Hat fi eld, Hertfordshire, AL10 9AB, UK

For further volumes: http://www.springer.com/series/7651

Lectins

Methods and Protocols

Edited by

Jun Hirabayashi

National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan

ISSN 1064-3745 ISSN 1940-6029 (electronic)ISBN 978-1-4939-1291-9 ISBN 978-1-4939-1292-6 (eBook) DOI 10.1007/978-1-4939-1292-6 Springer New York Heidelberg Dordrecht London

Library of Congress Control Number: 2014945213

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Editor Jun Hirabayashi National Institute of Advanced Industrial

Science and Technology Tsukuba , Japan

v

Lectins, a wide range of carbohydrate-binding proteins, have an extraordinarily long his-tory of investigations, with its origin in the discovery of a plant toxin, “ricin,” in 1888 by Peter Hermann Stillmark in Russia. Since then, a number of plant lectins have been identi-fi ed with their detailed biochemical properties and biological implications in relevance to interaction with animal cell surface components (glycoconjugates). They have been used as useful tools in cell biology, basic biochemistry, glycan/glycoprotein separation as well as clinical applications as cell stimulants (e.g., mitogen). However, coming to the era of post- genome science with modern biotechnology, various new fi elds of lectin technology have emerged; these are represented by exploration of animal lectins including those of human membrane-integrated type. Their functional analyses necessitated development of new assay systems using live cells, while advanced microarray technology enabled a direct glycan profi ling without liberation of glycans from proteins. The latter approach established an old but new principle to analyze, or “decode,” extremely diverse and heterogeneous features of glycans under the concept “cellular glycome.”

The edition “Lectins” thereby summarizes not only classic lectin technologies, which are still important and more accessible ( Part I: Standard Techniques , comprising 19 chap-ters) but also a series of advanced techniques with high throughputs and sensitivities ( Part II: Emerging Techniques for Lectin-Based Glycomics , comprising 9 chapters). The former part includes conventional hemagglutination assay, serial lectin- affi nity chromatography procedure, lectin-probed western blot and histochemical analyses, quantitative interaction analyses based on equilibrium dialysis, isothermal calorimetry, surface plasmon resonance, etc. Line-up of these comparative methods will provide readers solid criteria for selection and optimization of their researches. The latter part is the latest collection of the most advanced techniques to analyze complex feature of glycans. Actually, lectin microarray rep-resents an advanced method for glycomics, which was investigated in the twenty-fi rst cen-tury, enabling an alternative, so-far inaccessible approach to glycoprotein without liberation of glycans from the core protein.

The edition also covers variable techniques for elucidating functions of endogenous animal lectins ( Part III: Techniques for Elucidating Functions of Endogenous Animal Lectins , comprising 8 chapters). Necessity of this approach is emphasized, because most of the ani-mal lectins, e.g., human lectins, are relatively unstable and show weaker binding activity compared with conventional plant lectins. Moreover, many animal lectins of interest are expressed in complex on the cell surface. For such “diffi cult” lectins, many effective meth-ods including various cell modifying technologies are described. These approaches have now been extensively utilized and seem essential to elucidate glycan/lectin functions in the context of animal cells. In Part IV (Structural Biology and Engineering of Lectins , compris-ing 8 chapters), more challenging methodologies are described, which include advanced ones to “engineer” novel lectins by evolutionary concepts. This approach is in particular important, because it is generally diffi cult to prepare anti-carbohydrate antibodies, where the epitope structures are common between the species. Of course, for this realization, detailed information of three-dimensional structures of extensive lectins is necessary, for which several useful approaches are also described in this Part.

Pref ace

vi

Although all of these features based on standard chapters of Methods and Protocols are suffi cient to learn both necessary and more advanced techniques for lectins, the present edition also provides as many as 9 Overviews, each of which reviews the relevant fi eld from a historical viewpoint referring to the “state-of-the arts” in front of each Part. Such intro-duction will guide readers more smoothly to the main part of Methods and Protocols, and make it more and more attractive. Another topic of this edition is two special equipments of “Comprehensive Lists” ( Part V ). However, these are not usual appendixes because they are edited based on the concept that this edition be not just for memory but for continu-ous use for not only lectin specialists but also non-experts including both young scientists and those who “happen” to meet necessity to use lectins. Lastly, as the editor of Lectins, I believe that researchers concerned with life sciences will meet every necessity to use lectins if they target glycans. Visiting old, learn new.

Tsukuba, Japan Jun Hirabayashi

Preface

vii

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

PART I STANDARD TECHNIQUES

1 History of Plant Lectin Research. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Els J. M. Van Damme

2 Fungal Lectins: A Growing Family . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Yuka Kobayashi and Hirokazu Kawagishi

3 The “White Kidney Bean Incident” in Japan . . . . . . . . . . . . . . . . . . . . . . . . . . 39 Haruko Ogawa and Kimie Date

4 Hemagglutination (Inhibition) Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Kotone Sano and Haruko Ogawa

5 Preparation of Affinity Adsorbents and Purification of Lectins from Natural Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Kimie Date and Haruko Ogawa

6 High-Performance Lectin Affinity Chromatography . . . . . . . . . . . . . . . . . . . . 69 Yuka Kobayashi

7 Determination of Glycan Motifs Using Serial Lectin Affinity Chromatography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Katsuko Yamashita and Takashi Ohkura

8 Lectin-Probed Western Blot Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 Takeshi Sato

9 Solid-Phase Assay of Lectin Activity Using HRP-Conjugated Glycoproteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Kyoko Kojima-Aikawa

10 A Simple Viral Neuraminidase-Based Detection for High- Throughput Screening of Viral Hemagglutinin–Host Receptor Specificity. . . . . . . . . . . . . . 107 Nongluk Sriwilaijaroen and Yasuo Suzuki

11 Lectin Affinity Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Yuka Kobayashi

12 Capillary-Based Lectin Affinity Electrophoresis for Interaction Analysis Between Lectins and Glycans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 Mitsuhiro Kinoshita and Kazuaki Kakehi

13 Basic Procedures for Lectin Flow Cytometry . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Kenta Moriwaki and Eiji Miyoshi

14 Histochemical Staining Using Lectin Probes . . . . . . . . . . . . . . . . . . . . . . . . . . 153 Yoshihiro Akimoto and Hayato Kawakami

Contents

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15 Equilibrium Dialysis Using Chromophoric Sugar Derivatives. . . . . . . . . . . . . . 165 Tomomitsu Hatakeyama

16 Centrifugal Ultrafiltration-HPLC Method for Interaction Analysis Between Lectins and Sugars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 Kanji Hori and Makoto Hirayama

17 Surface Plasmon Resonance as a Tool to Characterize Lectin–Carbohydrate Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Yasuro Shinohara and Jun-ichi Furukawa

18 Isothermal Calorimetric Analysis of Lectin–Sugar Interaction . . . . . . . . . . . . . 207 Yoichi Takeda and Ichiro Matsuo

19 Carbohydrate–Lectin Interaction Assay by Fluorescence Correlation Spectroscopy Using Fluorescence-Labeled Glycosylasparagines . . . . . . . . . . . . 215 Mamoru Mizuno

PART II EMERGING TECHNIQUES FOR LECTIN-BASED GLYCOMICS

20 Lectin-Based Glycomics: How and When Was the Technology Born? . . . . . . . 225 Jun Hirabayashi

21 Frontal Affinity Chromatography (FAC): Theory and Basic Aspects . . . . . . . . 243 Ken-ichi Kasai

22 Frontal Affinity Chromatography: Practice of Weak Interaction Analysis Between Lectins and Fluorescently Labeled Oligosaccharides . . . . . . . 257 Chihiro Sato

23 Differential Glycan Analysis of an Endogenous Glycoprotein: Toward Clinical Implementation—From Sample Pretreatment to Data Standardization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 Atsushi Kuno, Atsushi Matsuda, Sachiko Unno, Binbin Tan, Jun Hirabayashi, and Hisashi Narimatsu

24 Lectin-Microarray Technique for Glycomic Profiling of Fungal Cell Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287 Azusa Shibazaki and Tohru Gonoi

25 Application of Lectin Microarray to Bacteria Including Lactobacillus casei/paracasei Strains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295 Emi Yasuda, Tomoyuki Sako, Hiroaki Tateno, and Jun Hirabayashi

26 Live-Cell Imaging of Human Pluripotent Stem Cells by a Novel Lectin Probe rBC2LCN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313 Hiroaki Tateno, Yasuko Onuma, and Yuzuru Ito

27 Carbohydrate-Binding Specificity of Lectins Using Multiplexed Glyco-Bead Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319 Kazuo Yamamoto

28 Supported Molecular Matrix Electrophoresis: A New Membrane Electrophoresis for Characterizing Glycoproteins . . . . . . . . . . . . . . . . . . . . . . 327 Yu-ki Matsuno and Akihiko Kameyama

Contents

ix

PART III TECHNIQUES FOR ELUCIDATING FUNCTIONS OF ENDOGENOUS ANIMAL LECTINS

29 Overall Strategy for Functional Analysis of Animal Lectins. . . . . . . . . . . . . . . . 337 Norihito Kawasaki

30 Evaluation of Glycan-Binding Specificity by Glycoconjugate Microarray with an Evanescent-Field Fluorescence Detection System. . . . . . . . 353 Hiroaki Tateno

31 Potential Usage for In Vivo Lectin Screening in Live Animals Utilizing Cell Surface Mimetic Glyco- nanoparticles, Phosphorylcholine-Coated Quantum Dots (PC-QDs). . . . . . . . . . . . . . . . . . . 361 Maho Amano, Hiroshi Hinou, Risho Miyoshi, and Shin-Ichiro Nishimura

32 Remodeling Cell Surface Glycans Using Glycosylation Inhibitors . . . . . . . . . . 371 Norihito Kawasaki

33 Remodeling of Glycans Using Glycosyltransferase Genes . . . . . . . . . . . . . . . . . 379 Yuko Naito-Matsui and Hiromu Takematsu

34 Functional Assay Using Lectin Gene Targeting Technologies (Over-Expression) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389 Motohiro Nonaka and Toshisuke Kawasaki

35 Analysis of L-Selectin-Mediated Cellular Interactions Under Flow Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401 Hiroto Kawashima

36 Assessment of Weak Sugar-Binding Ability Using Lectin Tetramer and Membrane-Based Glycans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413 Kazuo Yamamoto

PART IV STRUCTURAL BIOLOGY AND ENGINEERING OF LECTINS

37 Perspectives in Glycomics and Lectin Engineering . . . . . . . . . . . . . . . . . . . . . . 421 Jan Tkac, Tomas Bertok, Jozef Nahalka, and Peter Gemeiner

38 Molecular Basis of a Pandemic of Avian-Type Influenza Virus . . . . . . . . . . . . . 447 Nongluk Sriwilaijaroen and Yasuo Suzuki

39 Basic Procedure of X-Ray Crystallography for Analysis of Lectin–Sugar Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481 Zui Fujimoto

40 A New Structure Determination Method of Lectins Using a Selenium-Containing Sugar Ligand . . . . . . . . . . . . . . . . . . . . . . . . . . 491 Hisayoshi Makyio and Ryuichi Kato

41 NMR Analysis of Carbohydrate-Binding Interactions in Solution: An Approach Using Analysis of Saturation Transfer Difference NMR Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501 Hikaru Hemmi

Contents

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42 Small-Angle X-Ray Scattering to Obtain Models of Multivalent Lectin–Glycan Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511 Stephen D. Weeks and Julie Bouckaert

43 Directed Evolution of Lectins by an Improved Error-Prone PCR and Ribosome Display Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527 Dan Hu, Hiroaki Tateno, and Jun Hirabayashi

44 Tracing Ancestral Specificity of Lectins: Ancestral Sequence Reconstruction Method as a New Approach in Protein Engineering . . . . . . . . 539 Tomohisa Ogawa and Tsuyoshi Shirai

PART V COMPREHENSIVE LISTS

45 Comprehensive List of Lectins: Origins, Natures, and Carbohydrate Specificities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555 Yuka Kobayashi, Hiroaki Tateno, Haruko Ogawa, Kazuo Yamamoto, and Jun Hirabayashi

46 Lectin Structures: Classification Based on the 3-D Structures . . . . . . . . . . . . . 579 Zui Fujimoto, Hiroaki Tateno, and Jun Hirabayashi

Erratum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . E1

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607

Contents

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YOSHIHIRO AKIMOTO • Department of Anatomy, Kyorin University School of Medicine , Mitaka , Japan

MAHO AMANO • Hokkaido University , Sapporo , Japan TOMAS BERTOK • Slovak Academy of Sciences , Bratislava , Slovakia JULIE BOUCKAERT • Université de Lille 1 , Villeneuve d’Ascq , France KIMIE DATE • Graduate School of Humanities and Sciences and Glycoscience Institute,

Ochanomizu University , Tokyo , Japan ZUI FUJIMOTO • Biomolecular Research Unit, National Institute of Agrobiological Sciences ,

Tsukuba , Japan JUN-ICHI FURUKAWA • Hokkaido University , Sapporo , Japan PETER GEMEINER • Slovak Academy of Sciences , Bratislava , Slovakia TOHRU GONOI • Medical Mycology Research Center, Chiba University , Chiba , Japan TOMOMITSU HATAKEYAMA • Nagasaki University , Nagasaki , Japan HIKARU HEMMI • National Food Research Institute, National Agriculture

and Food Research Organization (NARO) , Tsukuba , Japan HIROSHI HINOU • Hokkaido University , Sapporo , Japan JUN HIRABAYASHI • Research Center for Stem Cell Engineering, National Institute of

Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan MAKOTO HIRAYAMA • Graduate School of Biosphere Science, Hiroshima University ,

Higashi-Hiroshima , Japan KANJI HORI • Graduate School of Biosphere Science, Hiroshima University ,

Higashi-Hiroshima , Japan DAN HU • Institute of Traditional Chinese Medicine and Natural Products,

Jinan University , Guangzhou , People’s Republic of China YUZURU ITO • Research Center for Stem Cell Engineering, National Institute of Advanced

Industrial Science and Technology (AIST) , Tsukuba , Japan KAZUAKI KAKEHI • Department of Pharmaceutical Sciences, School of pharmacy,

Kinki University , Higashi-osaka , Japan AKIHIKO KAMEYAMA • Bioproduction Research Institute, National Institute of Advanced

Industrial Science and Technology (AIST) , Tsukuba , Japan KEN-ICHI KASAI • Department of Biological Chemistry, School of Pharmaceutical Sciences,

Teikyo University , Tokyo , Japan RYUICHI KATO • High Energy Accelerator Research Organization (KEK) , Tsukuba , Japan HIROKAZU KAWAGISHI • Shizuoka University , Shizuoka , Japan HAYATO KAWAKAMI • Department of Anatomy, Kyorin University School of Medicine ,

Mitaka , Japan TOSHISUKE KAWASAKI • Research Center for Glycobiotechnology, Ritsumeikan University ,

Shiga , Japan NORIHITO KAWASAKI • Food & Health Programme, Institute of Food Research ,

Norwich , UK HIROTO KAWASHIMA • Department of Biochemistry, School of Pharmacy and Pharmaceutical

Sciences, Hoshi University, Tokyo, Japan

Contributors

xii

MITSUHIRO KINOSHITA • Department of Pharmaceutical Sciences, School of pharmacy, Kinki University , Higashi-osaka , Japan

YUKA KOBAYASHI • J-Oil Mills, Inc. , Yokohama , Japan KYOKO KOJIMA-AIKAWA • Ochanomizu University , Tokyo , Japan ATSUSHI KUNO • Research Center for Medical Glycoscience, National Institute of Advanced

Industrial Science and Technology (AIST) , Tsukuba , Japan HISAYOSHI MAKYIO • High Energy Accelerator Research Organization (KEK) , Tsukuba , Japan ATSUSHI MATSUDA • Research Center for Medical Glycoscience, National Institute of

Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan YU-KI MATSUNO • Bioproduction Research Institute, National Institute of Advanced

Industrial Science and Technology (AIST) , Tsukuba , Japan ICHIRO MATSUO • Division of Molecular Science, Faculty of Science and Technology,

Gunma University , Kiryu , Japan RISHO MIYOSHI • Hokkaido University , Sapporo , Japan EIJI MIYOSHI • Department of Molecular Biochemistry and Clinical Investigation,

Osaka University Graduate School of Medicine , Suita , Japan MAMORU MIZUNO • Laboratory of Glyco-organic Chemistry, The Noguchi Institute ,

Tokyo , Japan KENTA MORIWAKI • Department of Molecular Biochemistry and Clinical Investigation,

Osaka University Graduate School of Medicine , Suita , Japan JOZEF NAHALKA • Slovak Academy of Sciences , Bratislava , Slovakia YUKO NAITO-MATSUI • Department of Cellular and Molecular Medicine, University of

California , San Diego , CA , USA HISASHI NARIMATSU • Research Center for Medical Glycoscience, National Institute of

Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan SHIN-ICHIRO NISHIMURA • Hokkaido University , Sapporo , Japan MOTOHIRO NONAKA • Sanford-Burnham Medical Research Institute , La Jolla , CA , USA HARUKO OGAWA • Graduate School of Humanities and Sciences and Glycoscience Institute,

Ochanomizu University , Tokyo , Japan TOMOHISA OGAWA • Tohoku University , Sendai , Japan TAKASHI OHKURA • Department of Reproductive Biology, National Center for Child Health

and Development , Tokyo , Japan YASUKO ONUMA • Research Center for Stem Cell Engineering, National Institute of

Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan TOMOYUKI SAKO • Yakult Europe B.V. , Almere , The Netherlands KOTONE SANO • Graduate School of Humanities and Sciences and Glycoscience Institute,

Ochanomizu University , Tokyo , Japan CHIHIRO SATO • Bioscience and Biotechnolgy Center, Nagoya University , Nagoya , Japan TAKESHI SATO • Laboratory of Glycobiology, Department of Bioengineering,

Nagaoka University of Technology , Nagaoka , Japan AZUSA SHIBAZAKI • Laboratory for Infl ammatory Regulation, RIKEN Research Center

for Integrative Medical Science (IMS- RCAI) , Yokohama , Japan YASURO SHINOHARA • Hokkaido University , Sapporo , Japan TSUYOSHI SHIRAI • Bioinfomatic Research Division, Nagahama Institute of Bio-Science

and Technology , Japan Science and Technology Agency , Nagahama , Japan NONGLUK SRIWILAIJAROEN • Department of Preclinical Sciences, Faculty of Medicine,

Thammasat University , Pathumthani , Thailand ; Health Science Hills, College of Life and Health Sciences, Chubu University , Kasugai , Japan

Contributors

xiii

YASUO SUZUKI • Health Science Hills, College of Life and Health Sciences, Chubu University , Kasugai , Japan

YOICHI TAKEDA • ERATO, Ito Glycotrilogy Project, Japan Science and Technology Agency (JST) , Wako , Japan

HIROMU TAKEMATSU • Graduate School of Medicine, Kyoto University , Kyoto , Japan BINBIN TAN • Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai

Center for Systems Biomedicine, Shanghai Jiao Tong University , Shanghai , China HIROAKI TATENO • Research Center for Stem Cell Engineering, National Institute of

Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan JAN TKAC • Slovak Academy of Sciences , Bratislava , Slovakia SACHIKO UNNO • Research Center for Medical Glycoscience, National Institute of Advanced

Industrial Science and Technology (AIST) , Tsukuba , Japan ELS J.M. VAN DAMME • Ghent University , Ghent , Belgium STEPHEN D. WEEKS • Pharmaceutical and Pharmacological Sciences , KU Leuven ,

Leuven , Belgium KAZUO YAMAMOTO • The University of Tokyo , Chiba , Japan KATSUKO YAMASHITA • Department of Histology and Cell Biology, School of Medicine,

Yokohama City University , Yokohama , Japan EMI YASUDA • Yakult Central Institute for Microbiological Research , Kunitachi , Japan

Contributors