Essentials of Glycobiology

Ajit Varki; Richard D. Cummings; Jeffrey D. Esko; Pamela Stanley; Gerald W. Hart; Markus Aebi; Debra Mohnen; Taroh Kinoshita; Nicolle H. Packer; James H. Prestegard; Ronald L. Schnaar; Peter H. Seeberger

doi:10.1101/9781621824213

Essentials of Glycobiology, 4th edition

Editors

Editors: Ajit Varki,¹ Richard D. Cummings,² Jeffrey D. Esko,³ Pamela Stanley,⁴ Gerald W. Hart,⁵ Markus Aebi,⁶ Debra Mohnen,⁷ Taroh Kinoshita,⁸ Nicolle H. Packer,⁹ James H. Prestegard,¹⁰ Ronald L. Schnaar,¹¹ and Peter H. Seeberger¹².

Affiliations

¹ Distinguished Professor of Medicine and of Cellular & Molecular Medicine, Co-Director, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California, USA

² Professor of Surgery, Beth Israel Deaconess Medical Center, Director, National Center for Functional Glycomics, Harvard Medical School, Boston, Massachusetts, USA

³ Distinguished Professor of Cellular & Molecular Medicine, Co-Director, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California, USA

⁴ Horace W. Goldsmith Foundation Chair, Professor of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA

⁵ Sr. Eminent Scholar in Drug Discovery, Georgia Research Alliance William Henry Terry Professor of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA

⁶ Professor of Mycology, ETH Zürich, Institute of Microbiology, Department of Biology, Zürich, Switzerland

⁷ Distinguished Research Professor, Georgia Athletics Association Professor in Complex Carbohydrate Research, Professor of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA

⁸ Endowed Chair and Professor, Yabumoto Department of Intractable Disease Research, Research Institute for Microbial Diseases, Immunology Frontier Research Center, Osaka University, Osaka, Japan

⁹ Distinguished Professor of Molecular Sciences, Macquarie University, Sydney, Australia and Principal Research Leader, Institute for Glycomics, Griffith University, Gold Coast, Australia

¹⁰ Professor and Eminent Scholar Emeritus, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA

¹¹ Professor, Departments of Pharmacology and Neuroscience, Johns Hopkins University, Baltimore, Maryland, USA

¹² Director of Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany, Professor, Freie Universität, Berlin, Germany

Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2022.

ISBN-13: 978-1-621824-21-3 (hardback)ISBN-13: 978-1-621824-22-0 (epub)

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Glycobiology is the study of the structure, biosynthesis, biology, and evolution of saccharides (sugar chains or glycans) that are widely distributed in nature, in all life-forms. Glycobiology is a rapidly growing field in the natural sciences, with broad relevance to many areas of basic research, biomedicine, and biotechnology. The field includes the chemistry of carbohydrates, the enzymology of glycan formation and degradation, the recognition of glycans by specific proteins, roles of glycans in complex biological systems, and glycan analysis or manipulation by various techniques. The fourth edition of this primary textbook in the field continues in the prior tradition to provide a basic overview of Glycobiology, directed toward the advanced undergraduate or the beginning graduate-level student of molecular and cellular biology and biomedicine. This edition includes a broader focus on all lineages of life-forms; a wider range of topics, from biology and medicine to chemistry, bioenergy, and materials science; a more diverse and international group of contributing authors with expertise in specific areas; further expansion of the monosaccharide symbol nomenclature for representation of glycans; and a greater attention to informatics, with relevance to exploring the glycome in relation to the genome, transcriptome, proteome, lipidome, and metabolome.

Printed in the United States of America

Library of Congress Control Number: 2021950841

Publisher and Acquisition Editor John Inglis

Senior Project Manager Inez Sialiano

Permissions Coordinator Carol Brown

Production Editor Kathleen Bubbeo

Production Manager Denise Weiss

Cover Designers Lorenzo Casalino and Rommie Amaro

Illustrator and Illustrations Coordinator Richard D. Cummings

Front cover artwork: Molecular representation of the full-length, fully glycosylated, all-atom model of the SARS-CoV-2 spike protein in the open state, embedded in the viral membrane. The model of the spike has been developed by Casalino et al. (ACS Cent Sci 6: 1722–1734 [2020]) based on the cryo-EM structure by Wrapp et al. (Science 367: 1260–1263 [2020]) (PDB ID: 6VSB). N-/O-glycans have been modeled according to Watanabe et al. (Science 369: 330–333 [2020]) and Shajahan et al. (Glycobiology 30: 981–988 [2020]).

On the left, the full-length SARS-CoV-2 spike in the open state—that is, with one receptor binding domain (RBD) in the “up” conformation—is shown with a cyan transparent surface overlaid on the cartoon representation of its secondary structure. The conformation of the spike was selected from molecular dynamics simulations performed by Casalino et al. (ACS Cent Sci 6: 1722–1734 [2020]). N-linked and O-linked glycans are depicted using the Symbol Nomenclature for Glycans (SNFG), in which blue filled squares are for N-acetyl-D-glucosamine (GlcNAc), green filled circles for D-mannose, yellow filled squares for N-acetyl-D-galactosamine (GalNAc), yellow filled circles for D-galactose (Gal), red filled triangles for L-fucose (Fuc), and purple filled diamonds for N-acetyl-D-neuraminic acid (Neu5Ac). The lipid bilayer of the viral membrane is depicted with a surface representation, in which the POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) are colored in pink, POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) in purple, POPI (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol) in orange, POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine) in red, and cholesterol in yellow.

On the right, the glycan shield (dark-blue bush-like structures) in the SARS-CoV-2 spike protein (cyan transparent surface) is shown by overlaying multiple conformations of the N-linked and O-linked glycans obtained at multiple, interspersed frames along 1 μsec of molecular dynamics simulations (Casalino et al., ACS Cent Sci 6: 1722–1734 [2020]). For each glycan, each conformation sampled along the dynamics is shown with dark-blue sticks. When multiple conformations of each glycan are overlaid, they form a protective bush-like structure providing a visual representation of the extent of protein surface covered over a specific time frame. When the receptor-binding domain (RBD), located in the apical portion of the spike, is in the “up” conformation, it emerges from the glycan shield (as shown in the image with transparent cyan surface) and becomes available for binding to the angiotensin-converting enzyme 2 (ACE2) receptors located on the host cell. The binding event between the RBD and ACE2 initiates infection.

The cover artwork was designed and created by Dr. Lorenzo Casalino in the Amaro Laboratory (University of California San Diego), based on the all-atom model published in ACS Cent Sci 6: 1722–1734 (2020).

Library of Congress Cataloging-in-Publication Data

Identifiers: LCCN 2021950841 | ISBN 978-1-621824-21-3 (hardcover) | ISBN 978-1-621824-22-0 (ePub3)

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Bookshelf ID: NBK579918PMID: 35536922DOI: 10.1101/9781621824213