Carbohydrates and Nucleic Acids

299 Pages·1992·10.23 MB·English

by  Johannis P. Kamerling

Biological Magnetic Resonance
Volume 10
Carbohydrates and
Nucleic Acids
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Biological Magnetic Resonance
Volume 10
Carbohydrates and
Nucleic Acids
Edited by
Lawrence J. Berliner
Ohio State University
Columbus, Ohio
and
Jacques Reuben
Hercules Incorporated
Research Center
Wilmington, Delaware
Springer Science+Business Media, LLC
The Library of Congress has cataloged the first volume of this series as follows:
Library of Congress Cataloging in Publication Data
Main entry under title:
Biological magnetic resonance:
Includes bibliographies and indexes.
1. Magnetic resonance. 2. Biology-Technique. I. Berliner, Lawrence, J. II.
Reuben, Jacques.
QH324.9.M28B56 574.19'285 78-16035
AACRI
ISBN 978-1-4757-9476-2 ISBN 978-1-4757-9474-8 (eBook)
DOI 10.1007/978-1-4757-9474-8
ISBN 978-1-4757-9476-2
© Springer Science+Business Media New York 1992
Originally published by Plenum Press, New York in 1992
Softcover reprint of the hardcover 1st edition 1992
All rights reserved
No part of this book may be reproduced, stored in a retrieval system, or transmitted
in any form or by any means, electronic, mechanical, photocopying, microfilming,
recording, or otherwise, without written permission from the Publisher
Contributors
Johannis P. Kamerling • Bijvoet Center, Department of Bio-Organic
Chemistry, Utrecht University, Utrecht, The Netherlands
Johannes F. G. Vliegenthart • Bijvoet Center, Department of Bio-Organic
Chemistry, Utrecht University, Utrecht, The Netherlands
David E. Wemmer • Department of Chemistry, University of California,
and Chemical Biodynamics Division, Lawrence Berkeley Laboratory,
Berkeley, California 94720
v
Preface
In the past ten years or so, biological magnetic resonance (NMR and ESR)
has fully blossomed and become highly branched. In the 1970s and earlier,
a practitioner in biological magnetic resonance was using virtually all of
the available methods suitable for his research, with the latter covering a
diverse range of systems. Today, the focus of an individual laboratory is
actually much narrower, with respect to both the methods and the systems
investigated. Thus, those who investigate protein structure by multi
dimensional NMR spectroscopy do not usually engage in studies involving
in vivo spectroscopy. The conferences on biological magnetic resonance
now have parallel sessions rather than the single, common session of earlier
days. Moreover, topical meetings are becoming more frequent. Therefore,
this and future volumes of our series will also focus on specific topical areas.
We are proud to present Volume 10 of our series. It focuses on
Carbohydrates and Nucleic Acids. In an extensive chapter, Kamerling and
Vliegenthart use oligosaccharide-alditols released from mucin-type 0-
glycoproteins to illustrate the power of proton NMR spectroscopy in the
determination of carbohydrate structure. Wemmer gives a detailed coverage
of the arsenal of modern NMR methods now available for structural studies
of nucleic acids.
Forthcoming volumes will focus on In Vivo Spectroscopy and Protein
Structure.
As always, we are anxious to get feedback from the readers and hear
their comments and suggestions.
Lawrence J. Berliner
Jacques Reuben
vii
Contents
Chapter 1
High-Resolution IH-Nuclear Magnetic Resonance Spectroscopy of
Oligosaccharide-Alditols Released from Mucin-Type O-Glycoproteins
Johannis P. Kamerling and Johannes F. G. Vliegenthart
1. Introduction............................................ 1
1.1. General........................................... 1
1.2. Explanation of Code Systems Used in This Chapter .... 6
1.3. General NMR Features. ... ... . .. . . ... . .. . .. ... . . ... 7
2. Core Structures ......................................... 7
3. Backbone Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.1. Extensions of the Gal~l -+ 3Ga1NAc-ol Core Structure. . 23
3.2. Extensions of the GlcNAc~l -+ 3Ga1NAc-ol Core
Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.3. Extensions of the GlcNAc~ 1 -+ 6Ga1NAc-ol Core
Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.4. Extensions of the GlcNAc~l -+ 6(GlcNAc~1 -+ 3)
GalNAc-ol Core Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.5. Extensions of the GlcNAc~l -+ 6(Gal~1 -+ 3)GaINAc-ol
Core Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4. Peripheral Fucose in Neutral Oligosaccharide-Alditols ....... 45
4.1. Extensions of the Gal~l -+ 3Ga1NAc-ol Core Structure. . 45
4.2. Extensions of the GlcNAc~ 1 -+ 3Ga1NAc-ol Core
Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.3. Extensions of the GlcNAc~l-+ 6(Gal~1-+ 3)
GalNAc-ol Core Structure. . . .. . ... . ... . . .. .. . .. . . .. . 55
ix
x Contents
4.4. Extensions of the GlcNAc{31 ~ 6( GlcNAc{31 ~ 3)
GalNAc-ol Core Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5. Peripheral a 1 ~ 4-Linked N-Acetylglucosamine . . . . . . . . . . . . . 75
6. Peripheral a 1 ~ 3 -Linked N-Acetylgalactosamine ........... 80
7. Neutral N-Acetyl-(3-o-galactosamine-Containing
Oligosaccharide-Alditols ............................ 89
8. Sialylated Oligosaccharide-Alditols ........................ 90
8.1. Extensions of the Gal{31 ~ 3Ga1NAc-ol Core Structure 90
8.2. Extensions of the NeuAc/NeuGca2 ~ 6(Gal{31 ~ 3)
GalNAc-ol Core Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 98
8.3. Extension of the GlcNAc{31 ~ 3Ga1NAc-ol Core
Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 106
8.4. Extensions of the NeuAca2 ~ 6(GlcNAc{31 ~ 3)
GalNAc-ol Core Structure. .. . . . . . . . . . . . . . . . . . . . . . . .. 108
8.5. Extensions of the Gal{31 ~ 4GlcNAc{31 ~ 6( Gal{31 ~ 3)
GalNAc-ol Backbone Structure ...................... 115
8.6. Extensions of the Gal{31 ~ 4GlcNAc{31 ~ 6(NeuAca2
~ 3Gal{31 ~ 3)GaINAc-ol Structure. . . . . . . . . . . . . . . . .. 124
8.7. Extensions of the Gal{31 ~ 4GlcNAc{31 ~ 6(GlcNAc{31
~ 3)GaINAc-ol Backbone Structure. . . . . . . . . . . . . . . . .. 133
8.8. Extensions of the GalNAca 1 ~ 3Ga1NAc-ol Core
Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 141
8.9. Additional Sialylated Oligosaccharide-Alditols ......... 145
9. Peripheral Oeaminated Sialic Acid. . . . . . . . . . . . . . . . . . . . . . . .. 150
10. Sulfated Oligosaccharide-Alditols. . . . . . . . . . . . . . . . . . . . . . . . .. 150
11. Summary of General Features. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 154
11.1. Core Structures ................................... 155
11.2. Backbone Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 156
11.3. Peripheral Elements ............................... 157
12. Addendum............................................. 165
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 190
Chapter 2
NMR Studies of Nucleic Acids and Their Complexes
David E. Wemmer
1. Introduction............................................ 195
2. Basics of Nucleic Acid NMR . .. . . . . . . . . . . . . . . . . . . . . . . . . .. 196
3. NMR Techniques ....................................... 201
3.1. 20 NMR Experiments. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 202
3.2. Filtering Experiments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 207
Contents xi
4. Resonance Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 207
4.1. Exchangeable Protons .............................. 208
4.2. Nonexchangeable Protons. . . . . . . . . . . . . . . . . . . . . . . . . .. 211
4.3. Assignments Involving Heteroatoms .................. 214
5. Structure Analysis-Determination of Constraints ........... 219
5.1. NOE-Derived Distances. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 219
5.2. Coupling-Derived Angle Constraints. . . . . . . . . . . . . . . . .. 223
5.3. Identifying Structural Features. . . . . . . . . . . . . . . . . . . . . .. 224
6. Development of Structural Models ........................ 225
6.1. Distance Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 226
6.2. Molecular Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 227
6.3. Dynamics/Simulated Annealing. . . . . . . . . . . . . . . . . . . . .. 227
7. Analysis of Nucleic Acid Dynamics. . . . . . . . . . . . . . . . . . . . . . .. 229
7.1. Multiple Peaks, Line Shapes, Saturation Transfer. . . . . .. 229
7.2. Oriented Samples .................................. 230
7.3. Solution Relaxation. . .. ..... . . ... ... ... ... ... ... . ... 231
7.4. Imino Proton Exchange. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 231
8. Experimental Studies of Nucleic Acids. . . . . . . . . . . . . . . . . . . .. 233
8.1. Duplexes, Bends, and Hairpins ...................... 233
8.2. Mispairs, Extra Bases, and Modified DNAs. . . . . . . . . . .. 239
8.3. Noncovalent Interactions of Ions and Drugs with
Duplexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 244
8.4. Complex Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . .. 248
8.5. Protein-Nucleic Acid Complexes. . . . . . . . . . . . . . . . . . . .. 257
9. Summary............................................... 259
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 260
Contents of Previous Volumes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 265
Structure Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 273
Index. . . . .. . .. .. . . . . . .. . .. ... . .. .. ... .. . ... . ... .. ... . .. ... .. 289