Conformation of Carbohydrates

, by Rao, V. S. P.; Qasba, Pradman K.; Balaji, Petety V.; Chandrasekaran, Rengaswami

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ISBN: 9789057023156 | 9057023156
Cover: Paperback
Copyright: 10/1/1998

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This text offers a solid background in the conformation of carbohydrates with a brief description of the methods used for their analysis. It provides information on the conformations of mono-, di-, oligo-& polysaccharides & a basis for understanding the interactions between themselves & with proteins, nucleic acids or any other macromolecule. The authors have gathered a wealth of information on carbohydrate structures, different methods of conformational analysis, the role of carbohydrates as recognition molecules in biological systems, & their industrial applications. This book is a "one-stop" source of current information on carbohydrate conformation & the potential use of conformational properties in industry & also of their crucial role in important biological events such as cell-cell interaction, cell-adhesion, & cellular signaling mechanisms.

Preface

xiii

Configuration of Monosaccharides

(28)

Introduction

(1)

Classification

(1)

Simple Monosaccharides

(1)

Fischer Projection Formulae

(1)

Cahn-Ingold-Prelog System of Notation for Chiral Centers

(1)

Derivation of Monosaccharides From Trioses

(4)

Anomeric Forms of Sugars

(2)

Pyranose Form of Monosaccharides

(5)

Similarities Between Monosaccharides

(1)

Furanose Form of Monosaccharides

(1)

Derivatives of Monosaccharides

(10)

Deoxy sugars

(2)

Modifications of the hydroxyl groups

(1)

Amino derivatives

(2)

Acid and alcohol derivatives

(2)

Glycosans and anhydro sugars

(1)

Glycosides

(1)

Neuraminic acid

(1)

Muramic acid

(1)

Higher Monosaccharides

(5)

Methods of Conformational Analysis

(20)

Introduction

(2)

X-ray crystallography

(1)

Nuclear magnetic resonance spectroscopy

(2)

Resonance energy transfer method

(1)

Other spectroscopic methods

(1)

Computational Methods

(18)

Quantum chemical methods

(1)

Ab initio Hartree-Fock methods

(1)

Semi-empirical methods

(1)

Empirical methods

(1)

Contact criteria

(1)

Potential energy functions

(1)

Van der Waals's interactions

(1)

Electrostatic interactions

(1)

Hydrogen bond interactions

(1)

Torsional energy

(1)

Bond length deformation

(1)

Bond angle deformation

(1)

Exo-anomeric effect

(1)

Improper torsional term

(1)

Energy minimization

(1)

Simulation methods

(1)

Molecular dynamics simulations

(1)

Simulated annealing

(1)

Monte Carlo simulations

(1)

Free energy simulations

(1)

Effect of solvent

(1)

Force fields

(1)

PEFAC2

(1)

PEF91L

(1)

MM2CARB

(1)

Modification of CHARMM

(1)

CHEAT95

(1)

Modification of Tripos force field

(1)

Modifications of AMBER

(1)

GLYCAM_93

(7)

Conformation of Monosaccharides

(42)

Introduction

(1)

Theoretical Methods

(6)

Hassel-Ottar scheme

(1)

Reeves-Kelly scheme

(4)

Barker and Shaw scheme

(1)

Angyal scheme

(1)

Energy minimization studies

(1)

Experimental Methods

(4)

Complex formation

(1)

Nuclear magnetic resonance spectroscopy

(1)

X-ray crystallography

(2)

Theoretical And Solution Studies

(12)

Favored conformations of aldopyranoses

(3)

Flexibility of the pyranose ring

(1)

Conformation of hydroxyl and hydroxymethyl groups

(2)

Methyl glycopyranosides

(1)

Acetylated aldopyranoses

(2)

2-Acetamido-2-deoxy hexopyranoses

(1)

Muramic acids

(1)

Sialic acids

(1)

Aldohexopyranuronic acids

(1)

X-Ray Crystallographic Studies

(8)

Pyranose ring conformation

(4)

Deviations in the pyranose ring geometry

(4)

Conformation of the substituents at C1 atom and hydroxymethyl group

(1)

Hydrogen bonding

(1)

Ab Initio Molecular Orbital (MO) Studies

(11)

Anomeric and δ2 effects

(1)

Anomeric effect of 1-OAc group

(1)

Reverse anomeric effect

(2)

The C---O bond length

(6)

Conformation of Disaccharides

(40)

Introduction

(2)

Conventions and Definitions

(1)

EXO-Anomeric Effect and Linkage Conformation

(4)

Conformation Around The α1→2-, α1→3-and α1→4-Linkages

(13)

Kojibiose, nigerose and maltose

(1)

``Rigid pyranose ring'' studies

(3)

``Flexible pyranose ring'' studies

101

(5)

Neu5Ac-α2→3-Gal

106

(2)

Neu5Ac-α2→8-Neu5Ac

108

(1)

Disaccharides containing fructopyranose

109

(1)

Thio derivatives of disaccharides

109

(2)

Conformation Around the β1→2-, β1→3-and β1→4-Linkages

111

(6)

Sophorose, laminarabiose and cellobiose

111

(1)

``Rigid pyranose ring'' studies

111

(3)

``Flexible pyranose ring'' studies

114

(1)

Disaccharide units of chondroitin sulfates

114

(2)

Disaccharide units of carrageenans

116

(1)

Conformation Around the 1→6-Linkages

117

(1)

Conformation of the Non-Reducing Disaccharides

118

(3)

Trehalose

118

(1)

Sucrose

118

(3)

Conformation of C-Glycosides

121

(1)

Conformation in the Solid State

122

(9)

Conformation of Oligosaccharides

131

(60)

Introduction

131

(1)

ASN-Linked Oligosaccharides

131

(5)

Factors influencing N-glycosidic-linkage

131

(2)

Stereochemistry of N-glycosylation sites

133

(1)

Structure and classification

134

(2)

Modifications of the core pentasaccharide

136

(1)

Nomenclature

136

(1)

Conformational Studies of Asn-Linked Oligosaccharides

136

(5)

Conformation of oligosaccharides in glycopeptides/glycoproteins

136

(2)

MD Simulations of oligo-mannoses, hybrid and complex type oligosaccharides

138

(1)

β1→4-linkages

138

(2)

α1→3-linkages

140

(1)

α1→6-linkages

141

(1)

Importance of the torsion angle ψ of α1→6-linkages

141

(1)

α1→2-linkages

141

(1)

β1→2-linkages

141

(1)

Correlation of the Conformational Preferences of Oligosaccharides with the Biological Functions

141

(6)

Pathways for the processing of Man9GlcNAc2 to Man5GlcNAc2

142

(4)

Addition of terminal sugars to Man5GlcNAc2 by Golgi Glycosyltransferases

146

(1)

GlcNAc addition by GlcNAc transferase I

146

(1)

Effect of Bisecting GlcNAc on the extension of oligosaccharide chain

147

(1)

Addition of galactose to biantennary oligosaccharide by β1→4-galactosyltransferase

147

(1)

O-Linked Oligosaccharides

147

(4)

Mucins

148

(1)

Stereochemistry of O-glycosylation sites

148

(1)

Conformational studies of O-linked oligosaccharides

148

(3)

Blood Group Determinants and Related Oligosaccharides

151

(7)

ABO(H) system

151

(1)

Lewis system

151

(1)

Ii-system

151

(1)

Conformational studies

151

(1)

Blood group determinants

151

(1)

Constituent disaccharides

152

(1)

ABO(H) determinants

153

(2)

Lewis determinants

155

(1)

Sialylated oligosaccharides

156

(2)

Milk oligosaccharides

158

(1)

Glycosaminoglycans

158

(8)

Conformational studies of the oligosaccharides of glycosaminoglycans

162

(4)

Glycolipids

166

(3)

Conformational studies of cerebrosides

166

(2)

Conformational studies of globosides

168

(1)

Gangliosides

169

(8)

Conformational studies of monosialogangliosides

170

(4)

Conformational studies of di-, tri-and tetra-sialogangliosides

174

(3)

Conformational studies of fucogangliosides

177

(1)

Lipopolysaccharides

177

(3)

Conformational studies

178

(2)

Cyclic Oligosaccharides

180

(11)

Cyclodextrins

180

(1)

Conformation of cyclodextrins

181

(1)

Conformation in the solid state

181

(1)

Hydrogen bonding pattern in the solid state

181

(1)

Computer modeling studies

181

(1)

Other cyclic oligosaccharides

182

(1)

Conformation of cyclosophorans

182

(9)

Folding Patterns of Homopolysaccharides

191

(32)

Introduction

191

(2)

Representation of Polysaccharide Chain Conformation

193

(1)

Helix Representation

193

(2)

Conformational Energy Calculation and Preferred Conformation

195

(17)

α-D-Glucans

195

(1)

Flexibility of amylose helix

196

(3)

Amylopectin

199

(1)

(1→3)-α-D-Glucan

199

(1)

β-Glucans

199

(5)

Cellulose

204

(1)

(1→3)-β-D-Glucan

205

(2)

Mannans

207

(1)

(1→4)-β-D-Mannan

207

(1)

(1→3)-&apha;-D-Mannan

208

(1)

Xylans

208

(1)

(1→4)-β-D-Xylan

208

(2)

(1→3)-α-D-Xylan

210

(1)

Galactans

210

(1)

(1→4)-β-D-Galactans

211

(1)

Alginic acid

212

(1)

Linkage and Probable Conformations

212

(1)

Randomly Coiled Polysaccharides

212

(5)

Dimensions of freely rotating polysaccharide chain

213

(1)

Unperturbed dimensions of polysaccharides

213

(1)

Amylose

213

(2)

Cellulose

215

(2)

Xylan and mannan

217

(1)

Shapes of Polysaccharides and Their Biological Significance

217

(6)

Fiber Diffraction Analysis of Polysaccharides

223

(32)

Introduction

223

(1)

X-Ray Diffraction Analysis

223

(2)

Computer Model Building

225

(1)

General Remarks

226

(1)

Structures of Polymonosaccharides

226

(26)

Cellulose

226

(1)

Cellulose I

227

(1)

Cellulose II

227

(3)

Cellulose III and IV

230

(1)

Cellulose derivatives

230

(1)

Chitin

230

(1)

α-Chitin

230

(1)

β-Chitin

231

(1)

Mannan

232

(1)

Mannan I

232

(1)

Mannan II

232

(1)

Amylose

232

(2)

A-and B-Amylose

234

(1)

Abortive models

234

(1)

Correct models

235

(3)

V-Amylose

238

(1)

KOH-amylose complex

239

(1)

Amylose derivatives

239

(1)

(1→3)-α-D-Glucan

239

(1)

Curdlan

239

(3)

Curdlan I

242

(1)

Curdlan III

242

(3)

Curdlan II

245

(1)

Xylan

245

(1)

(1→3)-&beta-D-Xylan

245

(1)

(1→4)-β-D-Xylan

245

(1)

Pectin

245

(1)

Sodium pectate

246

(2)

Pectic acid

248

(1)

Calcium pectate and pectinic acid

248

(1)

Alginic acid

248

(1)

Polymannuronic acid

248

(1)

Polyguluronic acid

248

(4)

Inferences

252

(3)

Structures of Polyoligosaccharides

255

(22)

Introduction

255

(1)

Carrageenan

255

(3)

l-Carrageenan

255

(2)

k-Carrageenan

257

(1)

Agarose

258

(1)

Hyaluronan

258

(5)

Four-fold helix

258

(1)

Sodium hyaluronate (dry)

258

(3)

Sodium hyaluronate (relaxed)

261

(1)

Potassium hyaluronate (extended)

261

(1)

Potassium hyaluronate (relaxed)

261

(1)

Three-fold helix

261

(1)

Sodium hyaluronate

261

(2)

Calcium hyaluronate

263

(1)

Double helix

263

(1)

Sulfated Glycosaminoglycans

263

(5)

Chondroitin sulfate

265

(1)

Chondroitin 4-sulfate

265

(1)

Dermatan 4-sulfate

265

(3)

Keratan 6-sulfate

268

(1)

Polysaccharides with Large Repeating Units

268

(9)

Gellan

268

(3)

Welan

271

(1)

Xanthan

271

(3)

Galactomannan

274

(1)

Miscellaneous

274

(3)

Peptidoglycans

277

(26)

Introduction

277

(1)

Primary Structure of Peptidoglycans

278

(1)

The glycan strand

278

(1)

The peptide moiety

278

(1)

The Three-Dimensional Structure of Peptidoglycans

278

(8)

Peptidoglycan Degradation Enzymes

286

(5)

Lysozymes

286

(1)

Interaction of saccharide ligands with lysozyme

287

(2)

Comparison of the lysozyme-trisaccharide complexes

289

(1)

Mechanism of action of lysozyme

290

(1)

β-Lactam Antibiotics

291

(12)

Conformation of β-lactam antibiotics

291

(5)

Mechanism of action of β-lactam antibiotics

296

(7)

Carbohydrate-Protein Interactions

303

(52)

Introduction

303

(1)

Characteristic Features of Saccharide-Protein Interactions

303

(6)

Sugar binding pocket

303

(2)

Hydrogen bonds in the protein-carbohydrate complexes

305

(1)

Hydrophobic pocket in the sugar-binding site

306

(1)

Metal ion binding

306

(1)

Conformation of the saccharide ligands

307

(1)

Saccharide-binding induced conformational alterations or cross-linking of proteins

308

(1)

X-Ray Structure Data of Carbohydrate-Protein Complexes

309

(46)

Periplasmic sugar binding proteins

309

(1)

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Conformation of Carbohydrates

Summary

Table of Contents

Supplemental Materials