Table Of ContentNMR as a Structural Tool
for Macromolecules
Current Status and Future Directions
NMR as a Structural Tool
for Macromolecules
Current Status and Future Directions
Edited by
B. D. Nageswara Rao and
Marvin D. Kemple
Indiana University-Purdue University, Indianapolis (IUPUI)
Indianapolis, Indiana
Plenum Press. New York and London
Library of Congress Cataloging-in-Publication Data
-----------------------------------------------
NMR as a structural tool for macromolecules current status and
future directions / edited by B.D. Nageswara Rao and Marvin D.
Kemple.
p. em.
"Proceedings of an International Symposium on NMR as a Structural
Tool for Macromolecules, Current Status and Future Directions, held
October 3D-November 1, 1994, in Indianapolis; Indiana"--T.p. verso.
Includes bibliographical references and index.
1. Nuclear magnetic resonance spectroscopy--Congresses.
2. Macromolecules--Structure--Congresses. I. Nageswara Rao, B. D.
II. Kemple, Marvin D. III. International Symposium on NMR as a
Structural Tool for Macromolecules, Current Status and Future
Directions (1994 Indianapolis, Ind.)
OP519.9.N83N383 1996
574. 19'285--dc20 96-21442
CIP
Proceedings of an International Symposium on NMR as a Structural Tool for Macromolecules: Current
Status and Future Directions, held October 30 - November I, 1994, in Indianapolis, Indiana
ISBN-13: 978-1-4613-8029-0 e-ISBN-13: 978-1-4613-0387-9
001: 10.1007/978-1-4613-0387-9
© 1996 Plenum Press, New York
Softcover reprint of the hardcover 1s t edition 1996
A Division of Plenum Publishing Corporation
233 Spring Street, New York, N. Y. 10013
All rights reserved
10987654321
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
PREFACE
The contemplation oft ruth and beauty is the proper object for which we were
created, which calls forth the most intense desires oft he soul, and ofw hich it never tires
-Hazlitt
In his Nobel lecture Purcell commented that when he saw snow in New England
after the discovery of NMR, it appeared like "heaps of protons quietly precessing in
earth's magnetic field." If he were to make the comment in the context of how NMR is
being used today, he could have conjured up an image of hydrogen, carbon, and nitrogen
nuclei in proteins of an earthbound 8rganism subtly orchestrating a quiet symphony of
frequencies, from 150 Hz to 2 kHz, carrying clues to the three-dimensional structure of
the macromolecules. The manner in which the basic discoveries of Bloch and Purcell
have led to the emergence of NMR, several decades later, as a major technique of
biological and medical physics (and chemistry) is a striking example of the power of
basic research. It is also a fascinating saga whereby whenever it was felt that the field
had reached a plateau, new directions, new technologies, and sometimes serendipity
produced new developments that revolutionized the technique and enhanced its
capability. As Richard Ernst points out "NMR is intellectually attractive, ... the practical
importance of NMR is enormous, and can justify much of the playful activities of an
addicted spectroscopist" (Nobel lecture). Specifically, in the case of high resolution
(HR) NMR, the 2D-revolution of the mid-70s accompanied by the development of
NOESY, launched the technique as a macromolecular structural tool by the early 80s.
This led to a feverish activity in the next decade with a bewildering array of
methodological refinements which established HRNMR as a powerful method for
structural investigations. Once again questions are being raised concerning whether the
technique has reached another methodological plateau, and about what new directions it
might take.
Thus, when one of us (BDNR) received the Glenn Irwin, Jr. Award from our
university, the decision was made to organize a symposium with the title "NMR as a
Structural Tool for Macromolecules: Current Status and Future Directions." The
organization was off to a flying start when Richard Ernst accepted the invitation to be the
keynote speaker. Practically every one of the scientists we approached agreed to speak.
We were thus able to assemble an impressive array of accomplished practitioners of
HRNMR as plenary speakers. The meeting was 3 days long, with a panel discussion at
the end of the lectures on each day, and poster sessions on the first two evenings after
dinner. The goal was that the symposium not be a massive presentation of the latest
results in biomolecular structures, but rather be a comprehensive evaluation of the
technique along the lines of "where do we stand, and where do we go from here?" The
three panel discussions addressing topics of current interest were designed to make an
important contribution in this regard. The symposium ended with a panel discussion on
"NMR vis-a-vis Other Structural Methods" moderated by Mildred Cohn.
v
Since this was a one-time only symposium on a specific theme, we felt that it
would be useful to publish a compendium of the lectures and discussions from the
symposium. Thus, it was decided to make a verbatim record of all the discussions
following each talk and of the three panel discussions. All of the invited speakers agreed
to provide manuscripts that summarized or included the context of their lectures. It took
about nine months to collect all of the manuscripts and another three months to put
everything together. Abstracts of all of the posters presented at the symposium are also
included in the book. We sincerely hope that this book will be useful to people in the
field, especially to the young scientists who aspire to become established investigators in
the area of biological NMR.
There were over 200 participants at the meeting other than the invited speakers
and panel members. The conferees were enthusiastic, the discussions were lively, and the
atmosphere at the University Place Conference Center at IUPUI during those three days
was exhilarating. We received a number of letters from attendees generously
commending us for organizing the meeting. We are deeply grateful to all of the speakers
and participants for making the symposium such a success. Weare especi~lly indebted to
Richard Ernst for opening 'the symposium and to Mildred Cohn for closing it. The
presence of these two distinguished scientists, who touched the careers of all the
participants in one form or another, made the symposium most memorable.
We wish to thank David Gorenstein, Allen Kline, and Stephen Wassall for
working with us on the Organizing Committee of the symposium, the IUPUI NMR group
for diligently recording the discussions, and Padmini Nallana who worked tirelessly as
Coordinator of the symposium and in compiling the lectures and discussions that are
included in this book. Financial support for the entire endeavor, received from the Glenn
Irwin, Jr. Award to BDNR, the School of Science and the Office of Faculty Development
of IUPUI, the National Institutes of Health (GM R13 51260), Eli Lilly, Varian
Associates, Isotec, Biosym Technologies, Cambridge Isotope Laboratories, and Nalorac,
is gratefully acknowledged.
B.D. Nageswara Rao
Marvin D. Kemple
vi
*
CONTENTS
The Theme of the Symposium
B.D. Nageswara Rao
Keynote Lecture: Intramolecular Dynamics of Biomolecules. Possibilities and
Limitations ofNMR ............................................. 15
R.R. Ernst, M.J. Blackledge, T. Bremi, R. Bruschweiler, M. Ernst,
C. Griesinger, Z.L. Mlidi, J.w. Peng, J.M. Scmidt, and Ping Xu
Discussion ............................................................. 3 1
Structural, Dynamic, and Folding Studies of SH2 and SH3 Domains .............. 35
Julie D. Forman-Kay, Steven M. Pascal, Alex U. Singer, Toshio Yamazaki,
Ouwen Zhang, Neil A. Farrow, and Lewis E. Kay
Discussion ..................................." .......................... 49
NMR Studies of Proteins Involved in Cell Adhesion Processes ................... 51
Gerhard Wagner, Daniel F. Wyss, Johnathan S. Choi, Antonio
R.N. Arulanandam, Ellis L. Reinherz, Andrzej Krezel, and Robert
A. Lazarus
Discussion ............................................................. 63
Combining 2H and l3C Selective Enrichment to Probe Protein Dynamics ........... 65
David M. LeMaster
Incorporating Motional Properties into the Interpretation of Three-Dimensional
Solution Structures .............................................. 77
Walter J. Chazin
Discussion ............................................................. 87
Phosphotyrosyl Peptide-Enzyme Complexes: How Much Structure Can We Get from
Transferred NOE's? .............................................. 91
Carol Beth Post and Michael L. Schneider
Discussion ............................................................. 101
• Names of moderators of panel discussions and authors who delivered the lectures are shown in bold face.
vii
Panel Discussion on Structural Refinement and Dynamics ...................... 103
DavId Case. Marvin D. Kemple, N. Rama Krishna, Carol B. Post, and
Gerhard Wagner
Recent Developments in Protein NMR Spectroscopy ........................... 117
Stephan Grzesiek, Geerten W. Vuister, Andy C. Wang, Frank Delaglio, and
AdBax
Discussion ............................................................. 121
Field-Cycling NMR Applied to Macromolecular Structure and Dynamics .......... 123
Alfred G. Redfield
Discussion ............................................................. 133
Cross-Correlations: Obstacles or Tools for Structure Determination of Biomolecules . 135
Anil Kumar
Discussion ............................................................. 143
Towards the Accurate Measurement ofInternuciear Distances in Biological
Macromolecules by Suppression of Spin Diffusion ..................... 145
Sebastien J. F. Vincent, Catherine Zwahlen, and Geoffrey Bodenhausen
Discussion ............................................................. 165
NMR of Symmetrical Assemblies of Self-Recognizing Oligonucleotides ........... 167
Maurice Gueron, Kalle Gehring, and lean-Louis Leroy
Discussion ............................................................. 173
Protein-DNA Interaction from NMR and Monte Carlo Docking .................. 175
R. Kaptein, M. Slijper, v.P. Chuprina, I.A.C. Rullmann, R.M.A. Knegtel, and
R. Boelens
Discussion ............................................................. 189
Dynamic Structure of Nucleic Acid Duplexes ................................. 191
Thomas L. James, Carlos Gonzalez, He Liu, Vii Schmitz, and
Nikolai B. Ulyanov
Discussion ............................................................. 205
Panel Discussion on Extension of Techniques to Larger Molecules ............... 207
G. Marius Clore, Stephen W. Fesik, David G. Gorenstein, David M. LeMaster,
and John L. Markley
NMR Structures of Proteins Involved in Signal Transduction .................... 221
S.W. Fesik, R.P. Meadows, E.T. Olejniczak, A.P. Petros, P.I. Hajduk,
H.S. Yoon, I.E. Harlan, T.M. Logan, M.-M. Zhou, D.G. Nettesheim, H.
Liang, and L. Yu
Discussion ............................................................. 235
viii
Structures of Multimeric Proteins by NMR ................................... 237
G. Marius Clore and Angela M. Gronenborn
Discussion ............................................................. 243
NMR Structural Studies of Flexible Molecules ................................ 245
Peter E. Wright and H. Jane Dyson
Iron-Sulfur Proteins: Investigations of Hyperfine-Shifted Hydrogen, Carbon, and
Nitrogen Resonances ............................................. 251
Bin Xia, Hong Cheng, Young Kee Chae, Lars Skjedal, William M. Westler, and
John L. Markley
On the Use ofNMR in Complex Biological Systems: NMR Studies of Calcium
Sensitive Interactions amongst Muscle Proteins ....................... 275
Brian D. Sykes, Carolyn M. Slupsky, David S. Wishart, Frank D. S6nnichsen,
and Stephane M. Gagne
Discussion ............................................................. 285
The Structure of Lentiviral Tat Proteins in Solution ............................ 287
Paul Rosch, Peter Bayer, Andrzej Ejchart, Rainer Frank, Arnona Gazit,
Franz Herrmann, Margot Kraft, Rina Rosin-Arbesfeld, Heinrich Sticht,
Dieter Willbold, and Abraham Yaniv
Discussion ............................................................. 305
A Structural Biologist's View of Precision and Accuracy of Structural Models of
Proteins Based on NMR Data ...................................... 307
A. Joshua Wand
Discussion ............................................................. 325
Panel Discussion on NMR vis-a.-vis Other Structural Methods ................... 327
Bernard Brooks, Mildred Cohn, Thomas L. James, Franklyn G. Prendergast,
and Janet L. Smith
Poster Abstracts ......................................................... 339
Index ................................................................. 379
ix
B. D. Nageswara Rao and Richard R. Ernst
THE THEME OF THE SYMPOSIUM
B. D. Nageswara Rao
Department of Physics, IUPUI
402 North Blackford Street
Indianapolis, IN 46202
INTRODUCTION
I wish to describe how I arrived at the theme of this Symposium, viz., Current
Status and Future Directions of NMR as a Structural Tool. This was an outgrowth of my
own interpretation of various events that impacted on the evolution of high resolution NMR
spectroscopy during the last 35 years or so. Many a time I was quite intrigued, if not
fascinated, by how major advances in a scientific field occur when seemingly unrelated
ideas and experimental technologies converge at a propitious time. The timing seems to be
crucial. There are times when good ideas do not come to fruition. Sometimes a productive
confluence of ideas and experimental methods occurs in a somewhat predictable fashion.
Some other times serendipity brings about a totally unforeseen change, which then takes us
in a inevitable and seemingly irreversible new direction. NMR has gone through all these
types of phases during the last 35 years. In order to illustrate this point, I need to take you
through a little bit of history.
HIGH RESOLUTION NMR IN EARLY 60'S
State of the Art
Spectrometers. The commercial high-resolution (HR) NMR spectrometers of the
day operated in the CW (continuous wave) mode at proton resonance frequencies of 60
NMR As a Structural Tool/or Macromolecules: Current Status and FUlure Directions
Edited by B.D. Nageswara Rao and Marvin D. Kemple, Plenum Press, New York, 1996 1
