Table Of ContentMethods in
Molecular Biology 1588
D. Wade Abbott
Alicia Lammerts van Bueren Editors
Protein-
Carbohydrate
Interactions
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
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Protein-Carbohydrate
Interactions
Methods and Protocols
Edited by
D. Wade Abbott
Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
Alicia Lammerts van Bueren
Biotechnology Institute, University of Groningen, Groningen, The Netherlands
Editors
D. Wade Abbott Alicia Lammerts van Bueren
Agriculture and Agri-Food Canada Biotechnology Institute
Lethbridge, AB, Canada University of Groningen
Groningen, The Netherlands
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6898-5 ISBN 978-1-4939-6899-2 (eBook)
DOI 10.1007/978-1-4939-6899-2
Library of Congress Control Number: 2017933839
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Preface
Protein-carbohydrate interactions are involved in diverse processes required for life, includ-
ing the microbial degradation of plant biomass and marine polysaccharides and human
health and nutrition. Understanding and predicting how carbohydrates are recognized and
modified by carbohydrate-active enzymes (i.e., CAZymes) therefore is an important area of
basic research that spans multiple disciplines and holds vast promise for informing future
innovations in renewable resource utilization and medicine. Since the turn of the millennia,
the field of protein-carbohydrate interactions has been transformed by high-throughput
and ultrasensitive instrumentation, which has enabled us to study complex carbohydrate
utilization systems at the levels of metagenomes, metatranscriptomes, and metaproteomes.
This increase in technology has opened new doors for CAZyme discovery and application.
Here within we will provide a wide-ranging resource for studying protein-carbohydrate
interactions that extends from traditional biochemical methods to state-of-the-art tech-
niques, both of which will continue to propel the field forward in the coming years. In
particular, this volume will focus on four different research themes.
Part I describes methods for screening and quantifying CAZyme activity. These chap-
ters will survey each class of CAZyme, including glycoside hydrolases (Chap. 1, Copper-
Bicinchoninic Acid; Chap. 2, High-Performance Anion-Exchange Chromatography; and
Chap. 3, 3,5-Dinitrosalicylic Acid Assays), polysaccharide lyases (Chap. 4), carbohydrate
esterases (Chap. 5), glycosyltransferases (Chap. 6), and lytic polysaccharide monooxygen-
ases (Chap. 7). In addition, a method for investigating carbohydrate depolymerization by
cellulosomes, which can contain multiple enzyme classes and activities (Chap. 8), is
provided.
Part II contains methods for investigating the interactions between proteins and carbo-
hydrate ligands. These techniques include affinity gel electrophoresis of catalytic modules
(Chap. 9), microscale thermophoresis (Chap. 10), and NMR spectroscopy (Chap. 11).
The final chapter in this section describes current methods for detecting the biomechanical
activity of expansions (Chap. 12), a class of proteins involved in the loosening of plant cell
wall networks.
Part III discusses methods for the visualization of carbohydrates and protein-
carbohydrate complexes. These chapters include a novel bioinspired plant cell wall assembly
for measuring protein interactions by fluorescence (Chap. 13), using carbohydrate-binding
modules as probes within plant cell walls (Chap. 14), and investigating the subcellular local-
ization of CAZymes within Gram-negative bacteria (Chap. 15). These are followed by
three different methods for investigating carbohydrate structure. First is a method for using
Fourier transform mid-infrared spectroscopy to characterize the composition of plant cell
walls (Chap. 16); this is followed by methods for studying fluorescent glycans by electro-
phoresis (Chap. 17) and capillary electrophoresis (Chap. 18).
Finally, Part IV focuses on structural and “omics” approaches for studying systems of
CAZymes. First, a “dissect and build” approach for determining multimodular CAZyme
structure involving combinatorial small-angle X-ray scattering and X-ray crystallography is
described (Chap. 19) followed by methods describing the development of “omics” tech-
v
vi Preface
niques to identifying novel CAZyme systems using metagenomics (Chap. 20), transcriptomics
(Chap. 21), and proteomics (Chapter 22) approaches.
We anticipate that this collection of methods for studying carbohydrate modification
and protein-carbohydrate interactions will be a valuable resource to the glycomics research
community. As the field continues to advance, methods included within this volume will
have utility for illuminating the biology of glycomics, driving biotechnological innovation,
and developing solutions for human health and for sustainable resources within the emerg-
ing green economy.
Lethbridge, AB, Canada D. Wade Abbott
Groningen, The Netherlands Alicia Lammerts van Bueren
Contents
Preface.......................................................... v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Part I analysIs of Carbohydrate-aCtIve enzyme aCtIvIty
1 A Low-Volume, Parallel Copper-Bicinchoninic Acid (BCA) Assay
for Glycoside Hydrolases......................................... 3
Gregory Arnal, Mohamed A. Attia, Jathavan Asohan, and Harry Brumer
2 Quantitative Kinetic Characterization of Glycoside Hydrolases Using
High-Performance Anion-Exchange Chromatography (HPAEC) .......... 15
Nicholas McGregor, Gregory Arnal, and Harry Brumer
3 Measuring Enzyme Kinetics of Glycoside Hydrolases Using
the 3,5-Dinitrosalicylic Acid Assay.................................. 27
Lauren S. McKee
4 An Improved Kinetic Assay for the Characterization of Metal-Dependent
Pectate Lyases................................................. 37
Darryl R. Jones, Richard McLean, and D. Wade Abbott
5 Colorimetric Detection of Acetyl Xylan Esterase Activities................ 45
Galina Mai-Gisondi and Emma R. Master
6 Methods for Determining Glycosyltransferase Kinetics................... 59
Maria Ngo and Michael D.L. Suits
7 Analyzing Activities of Lytic Polysaccharide Monooxygenases by Liquid
Chromatography and Mass Spectrometry ............................ 71
Bjørge Westereng, Magnus Ø. Arntzen, Jane Wittrup Agger,
Gustav Vaaje-Kolstad, and Vincent G.H. Eijsink
8 Carbohydrate Depolymerization by Intricate Cellulosomal Systems......... 93
Johanna Stern, Lior Artzi, Sarah Moraïs, Carlos M.G.A. Fontes,
and Edward A. Bayer
Part II analysIs of ProteIn-Carbohydrate InteraCtIons
9 Affinity Electrophoresis for Analysis of Catalytic
Module- Carbohydrate Interactions................................. 119
Darrell Cockburn, Casper Wilkens, and Birte Svensson
10 Quantifying CBM Carbohydrate Interactions Using
Microscale Thermophoresis....................................... 129
Haiyang Wu, Cédric Y. Montanier, and Claire Dumon
11 Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy .. 143
Julie M. Grondin, David N. Langelaan, and Steven P. Smith
vii
viii Contents
12 Measuring the Biomechanical Loosening Action of Bacterial Expansins
on Paper and Plant Cell Walls ..................................... 157
Daniel J. Cosgrove, Nathan K. Hepler, Edward R. Wagner,
and Daniel M. Durachko
Part III vIsualIzatIon of Carbohydrates
and ProteIn-Carbohydrate ComPlexes
13 Bioinspired Assemblies of Plant Cell Walls for Measuring
Protein-Carbohydrate Interactions by FRAP.......................... 169
Gabriel Paës
14 CBMs as Probes to Explore Plant Cell Wall Heterogeneity Using
Immunocytochemistry .......................................... 181
Louise Badruna, Vincent Burlat, and Cédric Y. Montanier
15 Determining the Localization of Carbohydrate Active Enzymes
Within Gram- Negative Bacteria.................................... 199
Richard McLean, G. Douglas Inglis, Steven C. Mosimann,
Richard R.E. Uwiera, and D. Wade Abbott
16 Analysis of Complex Carbohydrate Composition in Plant Cell Wall
Using Fourier Transformed Mid-Infrared Spectroscopy (FT-IR) ........... 209
Ajay Badhan, Yuxi Wang, and Tim A. McAllister
17 Separation and Visualization of Glycans by Fluorophore- Assisted
Carbohydrate Electrophoresis..................................... 215
Mélissa Robb, Joanne K. Hobbs, and Alisdair B. Boraston
18 A Rapid Procedure for the Purification of 8-Aminopyrene
Trisulfonate (APTS)-Labeled Glycans for Capillary
Electrophoresis (CE)-Based Enzyme Assays........................... 223
Hayden J. Danyluk, Leona K. Shum, and Wesley F. Zandberg
Part Iv Cazyme struCture, dIsCovery, and PredICtIon methods
19 Probing the Complex Architecture of Multimodular Carbohydrate-Active
Enzymes Using a Combination of Small Angle X-Ray Scattering
and X-Ray Crystallography ....................................... 239
Mirjam Czjzek and Elizabeth Ficko-Blean
20 Metagenomics and CAZyme Discovery.............................. 255
Benoit J. Kunath, Andreas Bremges, Aaron Weimann, Alice C. McHardy,
and Phillip B. Pope
21 Identification of Genes Involved in the Degradation of Lignocellulose
Using Comparative Transcriptomics ................................ 279
Robert J. Gruninger, Ian Reid, Robert J. Forster, Adrian Tsang,
and Tim A. McAllister
Contents ix
22 Isolation and Preparation of Extracellular Proteins from Lignocellulose
Degrading Fungi for Comparative Proteomic Studies Using
Mass Spectrometry ............................................. 299
Robert J. Gruninger, Adrian Tsang, and Tim A. McAllister
Erratum to: ...................................................... E1
Index........................................................... 309
Contributors
d. Wade abbott • Functional Genomics of Complex Carbohydrate Utilization,
Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada,
Lethbridge, AB, Canada; Department of Chemistry and Biochemistry, University of
Lethbridge, Lethbridge, AB, Canada
Jane WIttruP agger • Center for BioProcess Engineering, Department of Chemical
and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
gregory arnal • Michael Smith Laboratories, University of British Columbia, Vancouver,
BC, Canada
magnus Ø. arntzen • Department of Chemistry, Biotechnology and Food Science,
Norwegian University of Life Sciences, Ås Akershus, Norway
lIor artzI • Faculty of Biochemistry, Department of Biomolecular Sciences, The Weizmann
Institute of Science, Rehovot, Israel
Jathavan asohan • Michael Smith Laboratories, University of British Columbia,
Vancouver, BC, Canada
mohamed a. attIa • Michael Smith Laboratories, University of British Columbia,
Vancouver, BC, Canada; Department of Chemistry, University of British Columbia,
Vancouver, BC, Canada
aJay badhan • Lethbridge Research and Development Centre, Agricultures and Agri-Food
Canada, Lethbridge, AB, Canada
louIse badruna • LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
edWard a. bayer • Faculty of Biochemistry, Department of Biomolecular Sciences, The
Weizmann Institute of Science, Rehovot, Israel
alIsdaIr b. boraston • Department of Biochemistry and Microbiology, University of
Victoria, Victoria, BC, USA
andreas bremges • Computational Biology of Infection Research, Helmholtz Centre for
Infection Research, Braunschweig, Germany; German Center for Infection Research
(DZIF), Braunschweig, Germany
harry brumer • Michael Smith Laboratories, University of British Columbia, Vancouver,
BC, Canada; Department of Chemistry, University of British Columbia, Vancouver,
BC, Canada; Department of Biochemistry and Molecular Biology, University of British
Columbia, Vancouver, BC, Canada
vInCent burlat • Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/
CNRS, Castanet-Tolosan, France
darrell CoCkburn • Department of Microbiology and Immunology, University of
Michigan, Ann Arbor, MI, USA
danIel J. Cosgrove • Department of Biology, Pennsylvania State University,
University Park, PA, USA
mIrJam CzJzek • UPMC Univ . Paris 06, CNRS, UMR 8227, Integrative Biology of
Marine Models, Sorbonne Universite, Roscoff, Bretagne, France
hayden J. danyluk • Simon Fraser University, Department of Molecular Biology and
Biochemistry, Burnaby, BC, Canada
xi
