Conformation of Carbohydrates [Kõva köide]

Preface		xiii
Configuration of Monosaccharides		1	(28)
Introduction		1	(1)
Classification		1	(1)
Simple Monosaccharides		1	(1)
Fischer Projection Formulae		2	(1)
Cahn-Ingold-Prelog System of Notation for Chiral Centers		3	(1)
Derivation of Monosaccharides from Trioses		3	(4)
Anomeric Forms of Sugars		7	(2)
Pyranose Form of Monosaccharides		9	(5)
Similarities Between Monosaccharides		14	(1)
Furanose Form of Monosaccharides		14	(1)
Derivatives of Monosaccharides		14	(10)
Deoxy sugars		14	(2)
Modifications of the hydroxyl groups		16	(1)
Amino derivatives		16	(2)
Acid and alcohol derivatives		18	(2)
Glycosans and anhydro sugars		20	(1)
Glycosides		21	(1)
Neuraminic acid		22	(1)
Muramic acid		23	(1)
Higher Monosaccharides		24	(5)
Methods of Conformational Analysis		29	(20)
Introduction		29	(2)
X-ray crystallography		29	(1)
Nuclear magnetic resonance spectroscopy		29	(2)
Resonance energy transfer method		31	(1)
Other spectroscopic methods		31	(1)
Computational Methods		31	(18)
Quantum chemical methods		32	(1)
Ab initio Hartree-Fock methods		32	(1)
Semi-empirical methods		32	(1)
Empirical methods		33	(1)
Contact criteria		33	(1)
Potential energy functions		34	(1)
Van der Waals's interactions		34	(1)
Electrostatic interactions		35	(1)
Hydrogen bond interactions		36	(1)
Torsional energy		36	(1)
Bond length deformation		37	(1)
Bond angle deformation		37	(1)
Exo-anomeric effect		37	(1)
Improper torsional term		38	(1)
Energy minimization		38	(1)
Simulation methods		39	(1)
Molecular dynamics simulations		39	(1)
Simulated annealing		39	(1)
Monte Carlo simulations		39	(1)
Free energy simulations		40	(1)
Effect of solvent		40	(1)
Force fields		40	(1)
PEFAC2		40	(1)
PEF91L		41	(1)
MM2CARB		41	(1)
Modification of CHARMM		41	(1)
CHEAT95		41	(1)
Modification of Tripos force field		41	(1)
Modifications of AMBER		41	(1)
GLYCAM_93		42	(7)
Conformation of Monosaccharides		49	(42)
Introduction		49	(1)
Theoretical Methods		50	(6)
Hassel-Ottar scheme		50	(1)
Reeves-Kelly scheme		50	(4)
Barker and Shaw scheme		54	(1)
Angyal scheme		55	(1)
Energy minimization studies		55	(1)
Experimental Methods		56	(4)
Complex formation		56	(1)
Nuclear magnetic resonance spectroscopy		57	(1)
X-ray crystallography		58	(2)
Theoretical and Solution Studies		60	(12)
Favored conformations of aldopyranoses		60	(3)
Flexibility of the pyranose ring		63	(1)
Conformation of hydroxyl and hydroxymethyl groups		64	(2)
Methyl glycopyranosides		66	(1)
Acetylated aldopyranoses		67	(2)
2-Acetamido-2-deoxy hexopyranoses		69	(1)
Muramic acids		70	(1)
Sialic acids		70	(1)
Aldohexopyranuronic acids		71	(1)
X-Ray Crystallographic Studies		72	(8)
Pyranose ring conformation		72	(4)
Deviations in the pyranose ring geometry		76	(4)
Conformation of the substituents at C1 atom and hydroxymethyl group		80	(1)
Hydrogen bonding		80	(1)
Ab Initio Molecular Orbital (MO) Studies		80	(11)
Anomeric and Δ2 effects		81	(1)
Anomeric effect of 1-OAc group		82	(1)
Reverse anomeric effect		83	(2)
The C--O bond length		85	(6)
Conformation of Disaccharides		91	(40)
Introduction		91	(2)
Conventions and Definitions		93	(1)
Exo-Anomeric Effect and Linkage Conformation		94	(4)
Conformation Around The α1→2-, &alpha1→3- and α1→4-Linkages		98	(13)
Kojibiose, nigerose and maltose		98	(1)
``Rigid pyranose ring'' studies		98	(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)-α-D-Glucan		205	(2)
Mannans		207	(1)
(1→4)-β-D-Mannan		207	(1)
(1→3)-α-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)-β-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)
ι-Carrageenan		255	(2)
κ-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)
Arabinose binding protein (ABP)		309	(2)
The galactose/glucose binding protein (GBP)		311	(1)
The maltose binding protein (MBP)		311	(1)
Plant lectins		311	(1)
Con A		312	(4)
Favin		316	(1)
Pea lectin		316	(1)
Lentil lectin		317	(1)
Lathyrus ochrus isolectin (LOL lectin)		318	(4)
Griffonia simplicifolia lectin (GS4)		322	(1)
Erythrina corallodendron lectin (EcorL)		323	(1)
Wheat germ agglutinin (WGA)		324	(2)
Snowdrop lectin (GNA)		326	(1)
Ricin		327	(2)
Animal lectins and their sugar complexes		329	(1)
C-type lectins		329	(1)
Mammalian mannose-binding proteins (MMBP)		329	(2)
S-type lectins (Gelectins)		331	(2)
E-type selectins --- cell adhesion molecules		333	(1)
Heparin and heparan sulfate complexes with fibroblast growth factor		333	(1)
Bacterial and Rickettsial lectins		334	(1)
LT-lactose complex		334	(1)
CT-B-pentamer-GM1 pentasaccharide complex		335	(2)
Viral lectins		337	(1)
Influenza virus hemagglutinin		337	(1)
Viral and cholera neuraminidases		337	(2)
Antibody-carbohydrate complexes		339	(1)
Enzyme-carbohydrate complexes		340	(1)
Glycogen phosphorylase a and b		340	(4)
α-Amylase		344	(3)
Cellobiohydrolase I and II		347	(8)
Index		355

Vallurupalli S. R. Rao is a Visiting Scientist in the Structural Glycobiology Section of the Laboratory of Experimental and Computational Biology at the National Cancer Institute, NIH, USA, and was formerly Professor and Chairman of the Molecular Biophysics Unit, Indian Institute of Science, Bangalore. Professor Rao is an elected fellow of the Indian Academy of Sciences and the Indian National Science Academy, a member of the editorial board of the International Journal of Carbohydrate Polymers, and has been an invited speaker at several international and national meetings., Pradman K. Qasba is head of the Structural Glycobiology Section of the Laboratory of Experimental and Computational Biology at the National Cancer Institute, NIH, USA. He received his Ph.D. degree in Pharmaceutical Synthetic Chemistry from Munich University, Germany, in 1965. He is currently investigating Golgi glycosyltransferases structure-function relationships, conformational preferences of their oligosaccharide substrates and sugar induced protein-protein interactions., Petety V. Balaji is currently Assistant Professor at the Biotechnology Center, Indian Institute of Technology, Bombay, India. After receiving his Ph.D. in 1991 he was a postdoctoral fellow in the Structural Glycobiology Section of the Laboratory of Experimental and Computational Biology at the National Cancer Institute, NIH, USA, where he carried out conformational analysis of N-linked oligosaccharides and structure and function studies of Golgi glycosyltransferases., Rengaswami Chandrasekaran is Professor of Structural Biochemistry in the Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, USA. Trained as an X-ray crystallographer, he earned his Ph.D. from the University of Madras, India. His research activities entail the study of the structure-function relationships in biopolymers elucidated by X-ray diffraction and computer modeling techniques. He has edited several books, authore