Handbook of Carbohydrate-Modifying Biocatalysts

1039 Pages·2016·36.24 MB·English

by  Peter Grunwald

Handbook of
Carbohydrate-Modifying
Biocatalysts
Pan Stanford Series on Biocatalysis
Series Editor
Peter Grunwald
Titles in the Series
Published
Vol. 1
Industrial Biocatalysis
Peter Grunwald, ed.
2015
978-981-4463-88-1 (Hardcover)
978-981-4463-89-8 (eBook)
Vol. 2
Handbook of Carbohydrate-Modifying Biocatalysts
Peter Grunwald, ed.
2016
978-981-4669-78-8 (Hardcover)
978-981-4669-79-5 (eBook)
Forthcoming
Vol. 3
Biocatalysis and Nanotechnology
Peter Grunwald, ed.
2017
978-981-4613-69-9 (Hardcover)
978-981-4613-70-5 (eBook)
Pan Stanford Series
Handbook of on Biocatalysis
Volume 2
Carbohydrate-Modifying
Biocatalysts
Peter Grunwald
edited by

PAN STANFORD PUBLISHING
Published by
Pan Stanford Publishing Pte. Ltd.
Penthouse Level, Suntec Tower 3
8 Temasek Boulevard
Singapore 038988
Email: [email protected]
Web: www.panstanford.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
Handbook of Carbohydrate-Modifying Biocatalysts
Copyright © 2016 Pan Stanford Publishing Pte. Ltd.
All rights reserved. This book, or parts thereof, may not be reproduced in any
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Cover image: Courtesy of Professor Jürgen Seibel, Institute of Organic
Chemistry, Julius-Maximilians-University Würzburg, Germany.
ISBN 978-981-4669-78-8 (Hardcover)
ISBN 978-981-4669-79-5 (eBook)
Printed in the USA
Contents
Preface
 1 Basics in Carbohydrate Chemistry xxii1i
Heinrich Hühnerfuss
1.1 Introduction 1
1.2 Classification of Carbohydrates 2
1.2.1 Monosaccharides 2
1.2.1.1 Configuration and nomenclature 4
1.2.1.2 Ring structures of carbohydrates 5
1.2.2 Disaccharides 10
1.2.3 Oligosaccharides 12
1.2.4 Polysaccharides 13
1.3 Reactions of carbohydrates 16
1.3.1 Oxidation of carbohydrates 16
1.3.2 Reduction of Carbohydrates 18
1.3.3 Nucleophilic Reactions 19
O N
1.3.4 Acylation and Alkylation of Monosaccharides 20
1.3.5 Formation of -Glycosides and -Glycosides 21

 2 G1.l4y coGclyocnojupgraotteesin: As Brief Overview 2269
Peter Grunwald
2.1 Introduction 29
2.2 Glycoconjugates: General Features and Glycosylation 31
2.3 Glycoproteins 35
N
2.3.1 Recombinant Glycoproteins 37
2.4  -Glycosylation of Proteins 44
2.4.1 Quality Control and ER-Associated Degradation 47
2.4.2 Cytosolic Degradation 55
vi Contents
2.5   Mucins 61
2.6   Glycosaminoglycans and Proteoglycans 67
 2.6.1 Heparin 69
 2.6.2 Heparan Sulfate 71
 2.6.3 Chondroitin and Dermatan Sulfate 73
 2.6.4 Keratan Sulfate 75
2.7   Peptidoglycans 76
2.8   Glycolipids, Lipopolysaccharides, and Toxins 79
 2.8.1 Lipopolysaccharides 83
 2.8.2 Toxins 88
2.9   Carbohydrates and Antibiotics 91
2.10 Antibiotics and Resistance 98
2.11 Glycan Analysis Methods 104
2.12 Glyconanotechnology 111
 3 2O.l1ig3o sCaocnchcalurdidiensg aRnedm Galrykcso conjugates in Recognition 115
Processes 147
Thisbe K. Lindhorst
3.1 Introduction 147
3.2 The Lectins and Their Ligands 148
3.2.1 Classification of Lectins 149
3.2.2 Characteristics of Important Lectin Classes 152
3.2.2.1 The R- and L-type lectins 152
3.2.2.2 The P-type lectins 153

3.2.2.3 The C-type lectins 154
3.2.2.4 The collectins: A subgroup of C-type
lectins 156
3.2.2.5 The selectins: A subgroup of C-type
lectins 156
3.2.2.6 The I-type lectins 159
3.2.2.7 The S-type lectins 161
3.3 Recognition of Carbohydrates 164
3.3.1 Formation of a Carbohydrate–Lectin Complex 164
3.3.2 Networks of Stabilizing Interactions 166
2+
3.3.3 Complexation via Ca 170
Contents vii
3.3.4 Weak Interactions and the Role of Water 173
3.3.5 Hydrophobic Interactions with
Carbohydrates 174
3.3.6 Binding to the Bacterial Lectin FimH 175
3.4 The Biological Role of Carbohydrate–Lectin
Interactions 176
3.4.1 Clearance of Glycoproteins by Interaction
with ASGPR 177
3.4.2 Leukocyte Trafficking 178
3.4.3 Galectins in Signaling 179
3.4.4 Type 1 Fimbriae-Mediated Bacterial Adhesion 184
3.5 Multivalency of Carbohydrate–Protein Interactions 185
3.6 Model Systems for the Investigation of Carbohydrate–
Protein Interactions 192
3.6.1 Multivalent Glycomimetics: Glycodendrimers
and Successors 193
3.6.2 Self-Assembled Monolayers: Glyco-SAMs 197
3.6.3 Testing Bacterial Adhesion 201
3.6.4 Tailoring Carbohydrate Surfaces to Mimic
Cellular Adhesion to the Glycocalyx 204
 4 3G.l7y coCsoindcel uHsyidornosl aasneds Outlook 220155
Motomitsu Kitaoka
4.1 Introduction 215
4.2 Classification 218
4.2.1 Anomeric Configuration of the Substrate 218
4.2.2 Location of the Hydrolyzed Linkage 218
4.2.3 Anomeric Retention and Inversion 219
4.3 Mechanisms of Action 220
4.3.1 Retaining GHs 220
4.3.1.1 Typical retaining GHs 220
4.3.1.2 Substrate-assisted catalysis of
retaining GHs 221
+
4.3.1.3 NAD -dependent catalysis of
retaining GHs 222
viii Contents
4.3.2 Inverting GHs 223
4.3.3 Hydrolysis and Transglycosylation 224
4.4 Chemoenzymatic Syntheses Using GHs with
Engineered Substrates 227
4.5 Chemoenzymatic Syntheses Using Mutant GHs 228
 5 4 D.i6sa cCcohnacrliudde iPnhgo Rsepmhoarryklsa ses: Mechanistic Diversity 232
and Application in the Glycosciences 237
Christiane Luley-Goedl and Bernd Nidetzky
5.1 Introduction 237
5.2 Disaccharide Phosphorylases: Classification,
Structure, and Function 240
5.3 Phosphorylase Mechanisms 244
5.3.1 Cellobiose and Chitobiose Phosphorylase 244
aa
5.3.2 Sucrose Phosphorylase 248
5.3.3 Retaining , -Trehalose Phosphorylase 252

5.4 Novel Application of Disaccharide Phosphorylases
in Synthesis 256
5.4.1 Multi-Step Enzymatic Synthesis of
Disaccharides and Other Glycosides 260
N
5.4.1.1 Coupling to sucrose conversion 260
5.4.1.2 Lacto- -biose 261
5.4.1.3 Glucosylglycerol 263
5.4.2 Engineering of Cellobiose Phosphorylase
for Altered Substrate Specificity 265
 6 5D.i5h yCdoronxcylaucseiotonns e Phosphate-Dependent Aldolases: 266
From Flask Reaction to Cell-Based Synthesis 275
Mohui Wei, Zijie Li, Baolin Wu, Yunpeng Liu, Tiehai Li,
Liuqing Wen, Jing Li, Jiansong Cheng, Junqiang Fang,
Xianwei Liu, and Peng George Wang
6.1 Introduction 275
6.2 Synthetic Applications 276
6.3 DHAP Generation 278
Contents ix
6.4 Overcoming DHAP Dependence 280
6.4.1 Substrate/Reaction Engineering 280
6.4.2 Discovery and Design of New Enzymes 281
6.4.3 Directed Evolution of Enzymes 282
6.5 Transforming DHAP-Dependent Aldolase-Mediated
Reactions from Flask into Cell-Based Synthesis 283
 7 6En.6z yCmoantciclu asniodn C hemoenzymatic Synthesis of Nucleotide 291
Sugars: Novel Enzymes, Novel Substrates, Novel Products,
and Novel Routes 297
Leonie Engels and Lothar Elling
7.1 Introduction 297
7.2 Novel Enzymes 301
7.2.1 UDP-Nucleotidylyltransferases 301
7.2.2 dTDP-Nucleotidylyltransferases 303
7.2.3 Salvage Pathway Enzymes 304
7.2.4 Glycosyltransferases 306
7.3 Novel Substrates and Novel Products 307
7.3.1 Screening of Novel Substrates 307
7.3.2 Novel Substrates for Nucleotidylyltransferases 309
7.3.3 Novel Substrates for Salvage Pathway
Enzymes 310
7.3.4 Nucleotide Furanose Sugars 312
7.3.5 Nucleotide Phosphono Sugars 313
7.3.6 Nucleotide Carba Sugars 314
7.4 Novel Routes 314
7.4.1 Combinatorial Biocatalysis for in situ
(Re)Generation of Nucleotide Sugars 314
 8 7It.e5r aCtiovneclylu Asciotinnsg Glycosyltransferases 331251
Songya Zhang and Andreas Bechthold
8.1 Introduction 321
8.2 Iterative Acting GTs Involved in Polysaccharide
Biosynthesis in Plants 323