Protein-Carbohydrate Interactions: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I Analysis of Carbohydrate-Active Enzyme Activity

1. A Low-Volume, Parallel Copper-Bicinchoninic Acid (BCA) Assay for Glycoside Hydrolases
Gregory Arnal, Mohamed A. Attia, Jathavan Asohan, and Harry Brumer

2. Quantitative Kinetic Characterization of Glycoside Hydrolases using High-Performance Anion-Exchange Chromatography (HPAEC)
Nicholas McGregor, Gregory Arnal, and Harry Brumer

4. An Improved Kinetic Assay for the Characterization of Metal-Dependant Pectate Lyases
Darryl R. Jones, Richard McLean, and D. Wade Abbott

5. Colorimetric Detection of Acetyl Xylan Esterase Activities
Galina Mai-Gisondi and Emma Master

6. Methods for Determining Glycosyltransferase Kinetics
Maria Ngo and Michael D.L. Suits

7. Analyzing Activities of Lytic Polysaccharide Monooxygenases by Liquid Chromatography and Mass Spectrometry
Bjørge Westereng, Magnus Ø. Arntzen, Jane Wittrup Agger, Gustav Vaaje-Kolstad, and Vincent G.H. Eijsink

8. Carbohydrate Depolymerization by Intricate Cellulosomal Systems
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
Darrell Cockburn, Casper Wilkens, and Birte Svensson

10. Quantifying CBM Carbohydrate Interactions using Microscale Thermophoresis
Haiyang Wu, Cédric Y. Montanier, and Claire Dumon

11. Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy
Julie M. Grondin, David N. Langelaan, and Steven P. Smith <

12. Measuring the Biomechanical Loosening Action of Bacterial Expansins on Paper and Plant Cell Walls
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
Gabriel Paës

14. CBMs as Probes to Explore Plant Cell Wall Heterogeneity using Immunocytochemistry
Louise Badruna, Vincent Burlat, and Cédric Y. Montanier

15. Determining the Localization of Carbohydrate Active Enzymes within Subcellular Compartments of Gram-Negative Bacteria
Richard McLean, G. Douglas Inglis, Steven C. Mosimann, Richard R. Uwiera, and D. Wade Abbott

16. Analysis of Complex Carbohydrate Composition in Plant Cell Wall using Fourier Transformed Mid-Infrared Spectroscopy (FT-IR)
Ajay Badhan, Yuxi Wang, and Tim A. McAllister

17. Separation and Visualization of Glycans by Fluorophore-Assisted Carbohydrate Electrophoresis
Mélissa Robb, Joanna K. Hobbs, and Alisdair B. Boraston

18. A Rapid Procedure for the Purification of 8-Aminopyrene Trisulfonate (APTS)-Labelled Glycans for Capillary Electrophoresis (CE)-Based Enzyme Assays
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   
Mirjam Czjzek and Elizabeth Ficko-Blean

20. Metagenomics and CAZyme Discovery
B.J. Kunath, A. Bremges, A. Weimann, A.C. McHardy, and P.B. Pope

21. Identification of Genes Involved in the Degradation of Lignocellulose using Comparative Transcriptomics
R.J. Gruninger, I. Reid, R.J. Forster, A. Tsang, and T.A. McAllister

22. Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies using Mass Spectrometry
R.J. Gruninger, A. Tsang, and T.A. McAllister