Biological NMR Spectroscopy - J. Markley, S. Opella (Oxford, 1997) WW

375 Pages·1997·25.03 MB·English

BIOLOGICAL
NMR
SPECTROSCOPY

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BIOLOGICAL
NMR
SPECTROSCOPY

Edited by
John L. Markley

University of Wisconsin, Madison

Stanley J. Opella

University of Pennsylvania

New York
Oxford
Oxford University Press
1997

Oxford University Press

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Copyright © 1997 by Oxford University Press, Inc.

Published by Oxford University Press, Inc.
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All rights reserved. No part of this publication may be reproduced,
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Library of Congress Cataloging-in-Publication Data
Biological NMR spectroscopy / edited by John L. Markley, Stanley J. Opella.
p. cm.
Includes bibliographical references and index.
ISBN 0-19-509468-9
I. Nuclear magnetic resonance spectroscopy.
2. Biomolecules—Analysis.
I. Markley, John L. II. Opella, Stanley J.
QP519.9.N83B56
1997
574.19785—dc20
96-12586

9 8 7 6 5 4 3 2 1

Printed in the United States of America
on acid-free paper

Table of Contents

Introduction ix

Acknowledgments
.xi

Foreword: R.R. Ernst
.xiii

The Founders Medal
xv

Section 1:
History of Biological NMR Spectroscopy 1

Chapter 1:
Simple Insights from the Beginnings of Magnetic Resonance in
Molecular Biology
3
0. Jardetzky

Chapter 2:
Choice of Problems in the Early Days of Biological NMR
Spectroscopy
16
M. Cohn

Chapter 3:
Early Days of Biochemical NMR.
20
R.G. Shulman

Chapter 4:
William D. Phillips Memorial Lecture 23
J.J.H. Acker man

Section 2:
Protein Structural Studies.
.27

Chapter 5:
Flexibility and Function of the Excherichia coli trp Represser 29
M.R. Gryk and O, Jardetzky

Chapter 6:
Heteronuclear Strategies for the Assignment of Larger
protein/DNA complexes: Application to the 37 kDa trp
Represser-Operator Complex
50
M.J. Revington, W. Lee, and C.H. Arrowsmith

Chapter 7:
Design of Novel Hemoglobins
67
C, HoandH.-W. Kim

Chapter 8:
The Role of NMR Spcclroscopy in Understanding How
Proteins Fold...
.82
C.M. Dob son

vi
Biological NMR Spectroscopy

Chapter 9:
NMR Approaches To Understanding Protein Specificity
94
G.C.K. Roberts, L.-Y. Lian, I.L. Barsukov, S. Modi,
and W. U. Primrose

Chapter 10: NMR and Mutagenesis Investigations of a Model Cis:Trans
Peptide Isomerization Reaction: Xaa116-Pro117 of
Staphylococcal Nuclease and its Role in Protein Stability and
Folding
113
A.P. Hinck, W.F. Walkenhorsl, DM. Truckses,
and J.L. Markley

Chapter 11: A Solid-State NMR Approach to Structure Determination of
Membrane Associated Peptides and Proteins
.139
S.J. Opella, L.E. Chirlian, and R. Bechinger

Chapter 12: NMR Approaches to the Heat-, Cold-, and Pressure Induced
Unfolding of Proteins
157
K. Akasaka, T. Yamaguchi, H. Yamada, Y. Kamatari,
and T. Konno

Chapter 13: Multidimensional NMR Investigation of the Neurotoxic
Peptide Mastoparan in the Absence and Presence of
Calmodulin
169
F. Mari, X. Xie, J.H. Simpson, and D.J. Nelson

Chapter 14: NMR of Larger Proteins: An Approach to the Structural
Analyses of Antibody
183
Y. Arata

Chapter 15: Selective Chemical Deuteration of Aromatic Amino Acids:
A Retrospective
205
K.S. Matthews and R. Matthews

Chapter 16: The Interaction of Antigens and Superantigens with the
Human Class II Major Histocompatibility Complex Molecule
HLA-DR1 216
T. Jardetzky

Chapter 17: Chorismate Mutase, Essentially a Template Enzyme
235
W.N. Lipscomb, Y.M. Chook, and H. Ke

Contents
vii

Section 3:
Nucleic Acids 245

Chapter 18: Computing the Structure of Large Complexes; Modeling the
16S RibosomalRNA
247
R. Chen, D. Fink, and R.B. Altrnan

Chapter 19: Design and Characterization of New Sequence Specific DNA
Ligands
266
D. Wemmer

Chapter 20: Determination by 1H NMR of a Slow Conformational
Transition and Hydration Change in the Consensus TATAAT
PribnowBox
.277
C. Milhe, A. Lane, andJ.-F. Lefevre

Section 4:
In vivo Spectroscopy
301

Chapter 21: Clinicians Need Localized Proton MRS of the Brain in the
Management of HIV-Related Encephalopathies
303
P.J. Cozzone, J. Vion-Dury, S, Confort-Gouny,
F. Nicoli, A. -M. Salvan, and S. Lamoureux

Chapter 22: Nuclear Magnetic Resonance Spectroscopy Studies of Cancer
Cell Metabolism
317
O. Kaplan and J.S, Cohen

Chapter 23: Ex Vivo Multinuclear NMR Spectroscopy of Perfused,
Respiring Rat Brain Slices: Model Studies of Hypoxia,
Ischemia.and Excitotoxicity"
340
L. Litt, M.T. Espanol, Y. Xu, Y. Cohen, L.-H. Chang,
P.R. Weinstein, P.H. Chan, and T.L. James

Index
359

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Introduction

The founders of the field of biological nuclear magnetic resonance (NMR)
spectroscopy had a clear vision of its future potential. The 65th birthday of one
of these pioneers, Professor Oleg Jardetzky, provided an occasion for bringing
together the small group of scientists whose research defined the field at its
inception, Jardetzky and his mentors, Linus Pauling and William N. Lipscomb,
and Mildred Cohn and Robert G. Shulman. Another key figure in the early days
of the field, William D. Phillips who was expected to participate in the
Symposium and this book died shortly before the Symposium held at Stanford
University in March, 1994. The historical section of this volume (Section I)
conveys the excitement of the beginnings of biological NMR spectroscopy,
when every experiment was new and potentially important. Section II, which
constitutes the bulk of this Volume, provides a contemporary overview of the
legacy of these early experiments.
It is nothing short of astonishing to be able to say that biological NMR
spectroscopy has fulfilled the dreams of its founders. Its potential as a method
for determining structures and describing the dynamics of proteins and nucleic
acids in aqueous solution has been realized in recent years, and the approachhas
become an essential part of structural biology. These capabilities, which are
practically routine now, reflect the rapid pace of technological invention and the
scientific context of the period, 1957 to the present. Invention refers to the
continuous stream of advances in instrumentation and magnets, computers and
software, pulse sequences, and experimental design for NMR studies of proteins
and other biopolymers. Context refers to the advances in biology. Even the
most casual reader of newspaper headlines is aware that we live in the age of
molecular biology, since it is now recognized that all aspects of life reflect the
linear sequence of bases in DNA that store biological information and, in turn,
specify the amino acid sequences of the proteins that express biological
functions. However, we also realize that biology is fundamentally both three-
dimensional and dynamic. And here is where structural biology will come to
play the dominant role in describing the basic principles of biology and
furthering biomedical andbiotechnological applications. The limits of what can
be obtained from sequences alone are already at hand. The limits of what can be
obtained from structural biology, in general, and biological NMR spectroscopy,
in particular, have not even been approached. The frontiers of protein
complexes, membrane proteins, and carbohydrates, as well as more detailed
descriptions of the interplay between structure and dynamics in protein function
beckon.
Oleg Jardetzky is one of the pillars of biological NMR spectroscopy. He
identified at its earliest stages the importance of resolving and assigning
resonances from individual sites in a protein. This enabled the unique ability of