Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems PDF
Preview Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems
MODERN ANALYTICAL ULTRACENTRIFUGATION EMERGING BIOCHEMICAL AND BIOPHYSICAL TECHNIQUES Series Editor: Todd M. Schuster MODERN ANALYTICAL ULTRACENTRIFUGATION Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems TODD M. SCHUSTER THOMAS M. LAUE -Editors- 118 Illustrations Birkhiiuser Boston • Basel • Berlin Todd M. Schuster Thomas M. Laue Department of Molecular & Cell Biology Department of Biochemistry and Analytical Ultracentrifugation Facility University of New Hampshire University of Connecticut Durham, NH 03824 75 North Eagleville Road USA Storrs, CT 06269-3125 USA Library of Congress Cataloging-in-Publication Data Modern analytical ultracentrifugation: acquisition and interpretation of data for biological and synthetic polymer systems / Todd M. Schuster, Thomas M. Laue, editors. p. cm. Includes bibliographical references and index. ISBN-13: 978-1-4684-6830-4 1. Ultracentrifugation. 2. Biomolecules-Analysis. 3. Polymers- Analysis. I. Schuster, Todd M., 1933- II. Laue, Thomas M., 1950- QP519.9.U47M63 1994 574.19'285~c20 94-20182 CIP m® Printed on acid-free paper. Birkhiiuser l!(J2> © 1994 Birkhauser Boston Softcover reprint of the hardcover 1st edition 1994 Copyright is not claimed for works of U.S. Government employees. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without prior permission of the copyright owner. The use of general descriptive names, trademarks, etc. in this publication even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act, may accordingly be used freely by anyone. Permission to photocopy for internal or personal use, or the internal or personal use of specific clients, is granted by Birkhauser Boston for libraries and other users registered with the Copyright Clearance Center (CCC), provided that the base fee of $6.00 per copy, plus $0.20 per page is paid directly to CCC, 222 Rosewood Drive, Danvers, MA 01923, U.S.A. Special requests should be addressed directly to Birkhauser Boston, 675 Massachusetts Avenue, Cambridge, MA 02139, U.S.A. ISBN-13: 978-1-4684-6830-4 e-ISBN-13: 978-1-4684-6828-1 DOl: 10.1007/978-1-4684-6828-1 Camera-ready text prepared by authors. Cover art by Maxine Marcy. 987654321 CONTENTS Preface ............................................................................................................... ix List of Contributors ........................................................................................... xi PART I: SEDIMENTATION EQUIliBRIUM Notes on the Derivation of Sedimentation Equilibrium Equations Hiroshi Fujita ................................................................................. 3 Association of REI Immunoglobulin Light Chain V L Domains: The Functional Linearity of Parameters in Equilibrium Analytical Ultracentrifuge Models for Self-Associating Systems Ian Brooks, Ronald Wetzel, Winnie Chan, Grace Lee, Donald G. Watts, K. Karl Soneson, and Preston Hensley ................. 15 Comments on the Analysis of Sedimentation Equilibrium Experiments Michael L Johnson and Martin Straume ........................................... 37 The Omega Analysis and the Characterization of Solute Self Association by Sedimentation Equilibrium Donald J. Winzor and Peter R. Wills ........ ............ ............ ................. 66 Conservation of Signal: A New Algorithm for the Elimination of the Reference Concentration as an Independently Variable Parameter in the Analysis of Sedimentation Equilibrium Allen P. Minton ................................................................................... 81 Analysis of Protein-Nucleic Acid and Protein-Protein Interactions Using Multi-Wavelength Scans from the XL-A Analytical Ultracentrifuge Marc S. Lewis, Richard I. Shrager, and Soon-Jong Kim .................... 94 vi Contents PART II: SEDIMENTATION VELOCITY Sedimentation Boundary Analysis of Interacting Systems: Use of the Apparent Sedimentation Coefficient Distribution Function Walter F. Stafford, Ill........................................................................ 119 Studies of Macromolecular Interaction by Sedimentation Velocity James C. Lee and Surendran Rajendran.......................................... 138 Measuring Sedimentation, Diffusion, and Molecular Weights of Small Molecules by Direct Fitting of Sedimentation Velocity Concentration Profiles John S. Philo .................................................................................... 156 Computer Simulation of the Sedimentation of Ligand-Mediated and Kinetically Controlled Macromolecular Interactions John R. Cann .................................................................................... 171 Refining Hydrodynamic Shapes of Proteins: The Combination of Data from Analytical Ultracentrifugation and Time-Resolved Fluorescence Anisotropy Decay Evan Waxman, William R. Laws, Thomas M. Laue, and J. B. Alexander Ross .................................................................. 189 PART III: ACQUISITION AND DATA REDUCTION On Line Data Acquisition for the Rayleigh Interference Optical System of the Analytical Ultracentrifuge David A. Yphantis, Jeffrey W Lary, Walter F. Stafford, Sen Liu, Philip H. Olsen, David B. Hayes, Thomas P. Moody, Theresa M. Ridgeway, Daryl A. Lyons, and Thomas M. Laue ......... 209 Extensions to Commercial Graphics Packages for Customization of Analysis of Analytical Ultracentrifuge Data Joe Hedges, Shokoh Sarra/zadeh, James D. Lear, and Donald K. McRorie ................................................................... 227 A Graphical Method for Determining the Ideality of a Sedimenting Boundary David B. Hayes and Thomas M. Laue. ............. ..... ....... ..... ....... ....... 245 Contents vii PART IV: SOME SPECIFIC EXAMPLES Analytical Ultracentrifugation and Its Use in Biotechnology Steven J. Shire.................................................................................. 261 Applications of Analytical Ultracentrifugation in Structure-Based Drug Design Thomas F. Holzman and Seth W. Snyder .......................... ................ 298 The Sedimentation Equilibrium Analysis of Polysaccharides and Mucins: A Guided Tour of Problem Solving for Difficult Heterogeneous Systems Stephen E. Harding .......................................................................... 315 Index ............................................................................................................... 343 PREFACE There are numerous examples in the history of science when the parallel develop ments of two or more disciplines, methodologies, technologies or theoretical in sights have converged to produce significant scientific advances. The decades following the 1950s have produced several such significant advances, as a result of a convergence of developments in molecular biology and in solid state-based electronics instrumentation. Since one of these areas of significant advancement, analytical ultracentrifu gation, has been undergoing a renaissance, we thought it would be a useful activity to call upon a group of researchers who have been developing either the experi mental or theoretical aspects of the methodology and gather in one place a group of articles summarizing the current status of the field. The success of recombinant DNA methodologies at producing biologically active macromolecules of commer cial interest has evoked interests in mechanisms of function. Pursuit of the related questions has emphasized the importance of studies of macromolecular binding and interaction. Several contributions to this volume remind us that analytical ultra centrifugation is rigorously based on solid thermodynamic theory and, as such, is fully capable of providing comprehensive quantitative descriptions of molecular interactions in solution. Furthermore, a number of the chapters provide examples, along with innovative methods for carrying out these characterizations. The past decade has seen several developments that reflect the rebirth of interest in analytical ultracentrifugation. One of these is the commercial development and availability of a new generation of instrumentation for analytical ultracentrifu gation. Other important developments have been the establishment of National Analytical Ultracentrifugation Facilities Laboratories in the u.S. (Storrs, CT) and u.K. (Leicester). A review of the chapter titles in this volume reveals that considerable effort has been devoted to developing computer assisted protocols for data analysis and interpretation. These approaches are both timely and necessary as researchers turn their attention to increasingly complex interacting and self associating systems. Examples are provided in the articles by Harding; Hensley, et al.; Cann; Shire; Philo; and by Holzman and Snyder. x Preface One can expect the future to bring more examples from biotechnology and pharmaceutical laboratories as the chapters by Philo, Shire, Hensley and Holzman clearly presage. An overview of this volume also reveals that the rebirth of interest in Analyti cal Ultracentrifugation will certainly call for a new generation of trained practi tioners. With this potential teaching requirement in mind we have attempted to include chapters that will have didactic as well as expository value to students and trainees as well as to advanced researchers. It should be noted that fully half of the number of authors of this volume had not completed their graduate training at the time of publication of Professor Fujita's classic monograph, "Foundations of Ultracentrifugation Analysis." These statistics reflect a continuation of a scientific tradition extending back more than 50 years to the pioneering developments of The Svedberg. The new computer controlled commercial analytical ultracentri fuge greatly simplifies the execution of experiments and the acquisition of data. Several of the chapters in this volume summarize novel approaches to the subse quent steps in ultracentrifuge investigation, data reduction, analysis and interpreta tion. The developments in Sedimentation Velocity analysis reported by Philo and by Stafford are particularly surprising since this oldest of Sedimentation method ologies was long thought to be of limited value for analysis of complex systems. But the ready availability of high speed and high capacity desk-top computers has made it possible to bring a new level of sophistication and rigor to the analysis of sedimenting boundaries. We look forward to these methods making Sedimenta tion Velocity a workhorse methodology of Modem Analytical Ultracentrifuga tion. We wish to acknowledge the long term support for biological instrumentation and methodology development provided by the Biophysics and the Instrumenta tion Programs of the U.S. National Science Foundation. Our thanks and acknowledgement to Ms. Alyson M. Blow for expert assis tance with manuscript preparation for this volume. T. M. Schuster Storrs, Connecticut T. M. Laue Durham, New Hampshire CONTRIBUTORS Ian Brooks Department of Macromolecular Sciences, Smithkline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406-0939, USA John R. Cann Department of Biochemistry/Biophysics/Genetics, University of Colorado, Health Sciences Center, B-121, 4200 East 9th Avenue, Denver, Colorado 80262, USA Winnie Chan Department of Macromolecular Sciences, Smithkline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406-0939, USA Hiroshi Fujita 35 Shimotakedono-Cho, Shichiku, Kita-Ku, Kyoto, Japan Stephen E. Harding University of Nottingham, School of Agriculture, Sutton Bonington LE12 5RD, United Kingdom David B. Hayes Department of Biochemistry, University of New Hampshire, Spaulding Life Science Building, Durham, New Hampshire 03824-3544, USA Joe Hedges Beckman Instruments, Inc., 1050 Page Mill Road, Palo Alto, California 94304, USA Preston Hensley Department of Macromolecular Sciences, Smithkline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406-0939, USA Thomas F. Holzman Abbott Laboratories, Protein Biochemistry, D-46Y Discovery Research, Pharmaceutical Products, Abbott Park, illinois 60048, USA Michael L. Johnson Departments of Pharmacology and Internal Medicine, Box 448, University of Virginia Health Sciences Center, Charlottesville, Verginia 22908, USA xii Contributors Soon-Jong Kim Laboratory of Biochemistry (LB), NCI, Building 37, Room 4C- 09, National Institute of Health, Bethesda, Maryland 20892, USA Jeffrey W. Lary Department of Molecular & Cell Biology and Analytical Ultracentrifugation Facility, University of Connecticut, 75 North Eagleville Road, Storrs, Connecticut 06269-3125, USA Thomas M. Lane Department of Biochemistry, University of New Hampshire, Durham, New Hampshire 03824, USA William R. Laws Mount Sinai School of Medicine of the City University of New York, New York, New York 10029, USA James D. Lear DuPont Merck Pharmaceutical Company, P.O. Box 80328, Wilmington, Delaware 19880-0328, USA Grace Lee PerSeptive Biosystems, Department ofImmunochemistry, Cambridge, Massachusetts 02139, USA James C. Lee Department of Human Biochemistry/Genetics, University of Texas Medical Branch, 617C Basic Science Building, F-47, Galveston, Texas 77555- 0647, USA Marc S. Lewis Biomedical Engineering and Instrumentation Branch (BEIP), NCRR, Building 35, Room BIOIC, National Institute of Health, Bethesda, Maryland 20892, USA Sen Lin Department of Muscle Research, Boston Biomedical Research Institute, 20 Saniford Street, Boston, Massachusetts 02114-2500, USA Daryl A. Lyons Department of Biochemistry, University of New Hampshire, Durham, New Hampshire 03824, USA Donald K. McRorie Beckman Instruments, Inc., 1050 Page Mill Road, Palo Alto, California 94304, USA Allen P. Minton Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA Thomas P. Moody Department of Biochemistry, University of New Hampshire, Durham, New Hampshire 03824, USA
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