Protein Stability and Folding

Transcription

1 Protein Stability and Folding

2 Methods in Molecular Biology TM John M. Walker, SER ES EDITOR 40. Protein Stability and Folding, edited by Bret A. Shirley, Baculovirus Expression Protocols, edited by Christopher Do Richardson, Cryopreservation and Freeze-Drying Protocols, edited by John G. Day and Mark R. McLellan, In Vitro Transcription and Translation Protocols, edited by Martin J. Tymms, Peptide Analysis Protocols, edited by Michael W. Pennington and Ben M. Dunn, Peptide Synthesis Protocols, edited by Ben M. Dunn and Michael W. Pennington, Immunocytochemical Methods and Protocols, edited by Lorette C. Javois, In Situ Hybridization Protocols, edited by K. H. Andy Choo, Basic Protein and Peptide Protocols, edited by John M. Walker, ~ Protocols for Gone Analysis, edited by Adrian J. Harwaad, DNA-Protein Interactions, edited by G. GeaffKneale, Chromosome Analysis Protocols, edited by John R. Gosden, Protocols for Nucleic Acid Analysis by Nonradioactive Probes, edited by Peter G. Isaac, Biomembrane Protocols: II. Architecture and Function, edited by John M. Graham and Joan A~ Higgins, Protocols for Oligonucleotide Conjugates, edited by Sudhir Agrawal, Computer Analysis of Sequence Data: Part II, edited by Annette M. Griffin and Hugh G. Griffin, Computer Analysis of Sequence Data: Part I, edited by Annette M. Griffin and Hugh G. Griffin, DNA Sequencing Protocols, edited by Hugh G. Griffin and Annette M. Griffin, Optical Spectroscopy, Microscopy, and Macroscopic Techniques, edited by Christopher Jones, Barbara Mulloy, and Adrian H. Thomas, Protocols in Molecular Parasitology, edited by John E. Hyde, Protocols for Oligonucleotides and Analogs, edited by Sudhir Agrawal, Biomembrane Protocols: I. Isolation and Analysis, edited by John M. Graham and Joan A. Higgins, Transgenesis Techniques, edited by David Murphy and David A~ Carter, Spectroscopic Methods and Analyses, edited by Christopher Jones, Barbara Mulloy, and Adrian H. Thomas, Enzymes of Molecular Biology, edited by Michael M. Burrell, 1993 Earlier volumes are still available. Contact Humana for details.

3 Methods in Molecular Bio1ogyTM 40 i.~.,t Protein Stability and Folding Theory and Practice Edited by Bret A. Shirley Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT Humana Press -~ Totowa, New Jersey

4 1995 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 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. Methods in Molecular Biology TM is a trademark of The Humana Press Inc. All authored papers, comments, opinions, conclusions, or recommendations are those of the author(s) and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. (~) ANSI Z (American National Standards Institute) Permanence of Paper for Printed Library Materials. Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $4.00 per copy, plus US $00.20 per page, is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [ /95 $ $00.20]. Printed in the United States of America Library of Congress Cataloging in Publication Data Main entry under title: Methods in molecular biology TM. Protein stability and folding: theory and practice/edited by Bret A. Shirley. p. cm.--(methods in molecular bioiogytm; 40) Includes index. ISBN Protein folding. 2. Proteins-42onformation. I. Shirley, Bret A. molecular biology TM (Totowa, N.J.); 40. QP551.P '245---dc20 II. Series: Methods in CIP

5 Preface The intent of this work is to bring together in a single volume the techniques that are most widely used in the study of protein stability and protein folding. Over the last decade our understanding of how proteins fold and what makes the folded conformation stable has advanced rapidly. The development of recombinant DNA techniques has made possible the production of large quantities of virtually any protein, as well as the production of proteins with altered amino acid sequence. Improvements in instrumentation, and the development and refinement of new techniques for studying these recombinant proteins, has been central to the progress made in this field. To give the reader adequate background information about the subject, the first two chapters of this book review two different, yet related, aspects of protein stability. The first chapter presents a review of our current understanding of the forces involved in determining the conformational stability of proteins as well as their three-dimensional folds. The second chapter deals with the chemical stability of proteins and the pathways by which their covalent structure can degrade. The remainder of the book is devoted to techniques used in the study of these two major areas of protein stability, as well as several areas of active research. Although some techniques, such as X-ray crystallography and mass spectroscopy, are used in the study of protein stability, they are beyond the scope of this book and will not be covered extensively. I would like to thank everyone whose time and effort made this work possible. I would especially like to thank all of the authors for their forbearance and understanding about the exceedingly painstaking process of getting a book into its final form. Finally, I would like to thank my wife, Francine, for the time that she gave up to allow me to complete this task. Bret A. Shirley

6 Contents Preface... Contributors... CH. 1. Noncovalent Forces Important to the Conformational Stability of Protein Structures, Kenneth P. Murphy... 1 CH. 2. Degradative Covalent Reactions Important to Protein Stability, David B. Volkin, Henryk Mach, and C. Russell Middaugh CH. 3. Fluorescence Spectroscopy, Catherine A. Royer CH. 4. Ultraviolet Absorption Spectroscopy, Henryk Mach, David B. Volkin, Carl J. Burke, and C. Russell Middaugh CH. 5. Circular Dichroism, Kunihiro Kuwafima CH. 6. Infrared Spectroscopy, C. Russell Middaugh, Henryk Mach, James A. Ryan, Gautam Sanyal, and David B. Volkin CH. 7. Identifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping, Kenneth R. Williams and Kathryn L. Stone CH. 8. Urea and Guanidine Hydrochloride Denaturation Curves, Bret A. Shirley CH. 9. Differential Scanning Calorimetry, Ernesto Freire CH. 10. Disulfide Bonds in Protein Folding and Stability, Nigel Darby and Thomas E. Creighton CH. ll. Solvent Stabilization of Protein Structure, Serge N. Timasheff CH. 12. Site-Directed Mutagenesis to Study Protein Folding and Stability, Philip N. Bryan Cn. 13. Hydrogen Exchange Techniques, J. Martin Scholtz and Andrew D. Robertson CH. 14. Protein Folding Kinetics, Thomas Kiefhaber vii v xi

7 viii Contents Cm 15. Ca. 16. Molten Globules, Anthony L. Fink Chaperonin-Assisted Protein Folding of the Enzyme Rhodanese by GroEL/GroES, Paul M. Horowitz Index

8 Contributors PHILIP N. BRYAN " Center for Advanced Research in Biotechnology, Biotechnology Institute, University of Maryland, Rockville, MD CARL J. BURKE Department of Pharmaceutical Research, Merck THOMAS E. CREIGHTON European Molecular Biology Laboratory, Heidelberg, Germany NIGEL DARBY European Molecular Biology Laboratory, Heidelberg, Germany ANTHONY L. FINK Department of Chemistry and Biochemistry, The University of California, Santa Cruz, CA ERNESTO FREIRE Departments of Biology and Biophysics and the Biocalorimetry Center, The Johns Hopkins University, Baltimore, MD PAUL M. HOROWITZ Department of Biochemistry, Health Science Center, University of Texas, San Antonio, TX THOMAS KIEFHABER Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA KUNIHIRO KUWAJIMA Department of Physics, School of Science, University of Tokyo, Tokyo, Japan HENRYK MACH Department of Pharmaceutical Research, Merck C. RUSSELL MIDDAUGH Department of Pharmaceutical Research, Merck KENNETH P. MURPHY Department of Biochemistry, University of Iowa, Iowa City, IA ANDREW D. ROBERTSON Department of Biochemistry, University of Iowa, Iowa City, IA CATHERINE A. ROYER School of Pharmacy, University of Wisconsin, Madison, WI ix

9 x Contributors JAMES A. RYAN" Department of Pharmaceutical Research, Merck GAUTAM SANYAL Department of Pharmaceutical Research, Merck J. MARTIN SCHOLTZ Department of Medical Biochemistry and Genetics, Texas A & M University, College Station, TX BRET A. SHIRLEY Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT KATHRYN L. STONE W. M. Keck Foundation Biotechnology Resource Laboratory and Howard Hughes Medical Institute Biopolymer Facility, Yale University, New Haven, CT SERGE N. TIMASHEFF Graduate Department of Biochemistry, Brandeis University, Waltham, MA DAVID B. VOLKIN Department of Pharmaceutical Research, Merck KENNETH R. WILLIAMS * W. M. Keck Foundation Biotechnology Resource Laboratory and Howard Hughes Medical Institute Biopolymer Facility, Yale University, New Haven, CT