NMR as a Structural Tool for Macromolecules: Current Status and Future Directions PDF
Preview NMR as a Structural Tool for Macromolecules: Current Status and Future Directions
NMR 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
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