Main description:

This second edition provides new and updated tools for studying protein-carbohydrate interactions ranging from traditional biochemical methods to state-of-the-art techniques. This book focuses on four different research themes detailing methods for screening and quantifying CAZyme activity, investigating the interactions between proteins, carbohydrate ligands, methods for the visualization of carbohydrates, protein-carbohydrate complexes, structural and "omic" approaches for studying systems of CAZymes. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Carbohydrate- Protein Interactions: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.

Contents:

Part I: Measurement of Carbohydrate Modification

1. A low-volume, parallel copper-bicinchoninic acid (BCA) assay for glycoside hydrolases Gregory Arnal, Mohamed A. Attia, Jathavan Asohan, Zhenhuan Lei, Benedikt Golisch, and Harry Brumer

2. Measuring enzyme kinetics of glycoside hydrolases using the 3,5-dinitrosalicylic acid assay He Li and Lauren S. McKee

3. Analyzing activities of lytic polysaccharide monooxygenases by liquid chromatography and mass spectrometry

Bjorge Westereng, Magnus O. Arntzen, Heidi Ostby, Jane Wittrup Agger, Gustav Vaaje-Kolstad, and Vincent G.H. Eijsink

4. Carbohydrate depolymerization by intricate cellulosomal systems

Sarah Morais, Johanna Stern, Lior Artzi, Carlos M.G.A. Fontes, Edward A Bayer, and Itzhak Mizrahi

5. Biomechanical weakening of paper and plant cell walls by bacterial expansins

Daniel J. Cosgrove, Nathan K. Hepler, Edward R. Wagner, and Daniel M. Durachko

Part II: Quantitation of Carbohydrate Binding

6. Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions

Darrell W Cockburn, Casper Wilkens, and Birte Svensson

7. Quantifying CBM carbohydrate interactions using microscale thermophoresis Haiyang Wu, Cedric Y. Montanier, and Claire Dumon

8. Qualitative and quantitative characterization of protein-carbohydrate interactions by NMR spectroscopy

Julie M. Grondin, David N. Langelaan, and Steven P. Smith

9. Isothermal Titration Calorimetry for quantification of protein-carbohydrate interactions

Haley A. Brown and Nicole M. Koropatkin

10. Surface plasmon resonance analysis for quantifying protein-carbohydrate interactions

Marie Sofie Moller, Darrell Cockburn, and Casper Wilkens

11. Bioinspired polymer assemblies of plant cell walls for measuring protein-carbohydrate interactions by FRAP

Berangere Lebas and Gabriel Paes

12. CBMs as probes to explore plant cell wall heterogeneity using immunocytochemistry

Louise Badruna, Vincent Burlat, and Cedric Y. Montanier

13. Flow Cytometry-based Detection of Siglec Ligands

Edward N. Schmidt, Jaesoo Jung, and Matthew S. Macauley

Part III: Purification and visualization of carbohydrates

14. Extraction and Verification of Mouse and Human Mucins from Tissue and Fecal Material

Mackenzie Melvin, Noah Fancy, Darrek Kniffen, and Kirk Bergstrom

15. Analysis of complex carbohydrate composition in plant cell wall using Fourier transformed mid-infrared spectroscopy

Ajay Badhan, Yuxi Wang, and Tim A. McAllister

16. Separation and Visualisation of Glycans by Fluorophore-Assisted Carbohydrate Electrophoresis

Melissa Robb, Joanne K. Hobbs, and Alisdair B. Boraston

17. A rapid protocol for preparing 8-aminopyrene-1,3,6-trisulfonate-labelled glycans for capillary electrophoresis-based enzyme assays

Jolene M. Garber, Osei B. Fordwour, and Wesley F. Zandberg

18. Visualization of Carbohydrate Uptake using Fluorescent Polysaccharides

Greta Reintjes, Leeann Klassen, and D. Wade Abbott

Part IV: Computational methods for studying protein-carbohydrate interactions

19. Long-read Metagenomics and CAZyme discovery

A. Ferrillo, C.M. Kobel, A.Vera-Ponce de Leon, S.Leanti La Rosa, B.J. Kunath, P.B. Pope, and L.H. Hagen

20. Identification of genes involved in the degradation of lignocellulose using comparative transcriptomics

Gruninger R.J., Tsang A., and McAllister T.A.

21. Isolation and preparation of extracellular proteins from lignocellulose degrading fungi for comparative proteomic studies using mass spectrometry

Gruninger R.J., Tsang A., and McAllister T.A.