Membrane Protein Structure: Experimental Approaches

403 Pages·1994·10.633 MB·English

by  D. C. Rees, A. J. Chirino, K.-H. Kim, H. Komiya (auth.), Stephen H. White Ph.D. (eds.)

MEMBRANE PROTEIN STRUCTURE
THE AMERICAN PHYSIOLOGICAL SOCIETY
METHODS IN PHYSIOLOGY SERIES
1. White, Membrane Protein Structure: Experimental Approaches, 1994
2. Bassingthwaighte, Liebovitch, West, Fractal Physiology, 1994
MEMBRANE PROTEIN
STRUCTURE
Experimental Approaches
Edited by
Stephen H. White, Ph.D.
Professor of Physiology and Biophysics
University of California, Irvine,
College of Medicine
SPRINGER NEW YORK
1994
Copyright© 1994 by the American Physiological Society
Originally published by American Physiological Society in 1994
Softcover reprint of the hardcover 1st edition 1994
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 the prior permission of Oxford University Press.
Library of Congress Cataloging-in-Publication Data
Membrane protein structure : experimental approaches
edited by Stephen H. White
p. em. (Methods in physiology series ; I)
Includes bibliographical references and in<\ex.
ISBN 978-1-4614-7515-6 (eBook)
DOI 10.1007/978-1-4614-7515-6
1. Membrane proteins. I. White, Stephen H, II. Series.
[DNLM: 1. Membrane Proteins-ultrastructure.
2. Protein Conformation. QU 55 M513 1994]
QP552.M44M435 1994
574.87'5-dc20 DNLM/DLC
for Library of Congress 93-26101
135798642
Preface
The structures of membrane proteins are of vital interest to researchers in physiology,
cell biology, and biochemistry. Their determination, however, constitutes one of the
most challenging problems of structural biology. During the 18 years that have
elapsed since Henderson and Unwin (1975) reported the first low-resolution three
dimensional structure of bacteriorhodopsin, the structures of only two types of trans
membrane proteins have been determined to high resolution with three-dimensional
crystals. During the same time, hundreds, if not thousands, of amino acid sequences
for membrane proteins have been reported because studies of receptors, channels, and
transporters have come to the fore as major activities of the biological research com
munity. The creation of hypothetical protein structural models to serve as guides for
these studies is crucially important but problematic, because our knowledge of pro
tein folding in membrane environments is limited. The development of suitable
model structures requires an understanding of protein structure and structure-pre
diction methods as well as membrane biophysics and lipid physical chemistry.
Because the literature for each of these fields is expanding rapidly and can be daunt
ing even for the experts, I have attempted to assemble into a single compact volume
the experiences of some of the experts in these areas that I hope will be helpful to
researchers who need to know about the critical issues of membrane protein struc
ture.
My goal was not to provide an exhaustive compendium of information relevant to
the membrane protein problem but rather to plant some signposts. However, there
are several important destinations that the serious student of membrane protein
structure should consider but which are not explicitly posted as chapters: stability
and folding of globular proteins, sequence analysis, protein structure prediction, and
lipid physical chemistry. These subjects have been covered nicely by others. A very
readable and informative account of protein stability is given in the recent review of
Ken Dill (1990). Thomas Creighton (1992) has assembled an excellent volume on
various aspects of the protein folding problem and Russell Doolittle (1990) one on
the analysis of protein and nucleic acid sequences. Authoritative discussions of the
principles of protein conformation and structure prediction are provided in the vol
ume edited by Gerald Fasman (1989). The unique feature of membrane proteins is
that they are embedded in a lipid bilayer, and one cannot therefore ignore the phys
ical chemistry of lipids. A comprehensive account of this area is provided by Donald
Small (1986).
This volume would not have come into existence without the interest and enthu
siasm of Oxford University Press and the Publications and Technical Book Com-
v1 Preface
mittees of the American Physiological Society. In addition to the authors who con
tributed to the volume despite many other pressing obligations, I thank Brenda
Rauner, Directer of Publications for the American Physiological Society, and Jeffrey
House, Vice President of Oxford University Press, for their patience and under
standing during the prolonged birth of this project.
References
Creighton, T. E. (1992) Protein Folding. New York: W. H. Freeman.
Dill, K. A. (1990) Dominant forces in protein folding. Biochemistry 29: 7133-7155.
Doolittle, R. F. (1990) Methods in Enzymology, Vol. 783, Molecular Evolution: Computer Analysis of
Protein and Nucleic Acid Sequences. San Diego: Academic Press.
Fasman, G. D. (1989) Prediction of Protein Structure and the Principles of Protein Conformation. New
York: Plenum Press.
Henderson, R., and Unwin, P.N.T. (1975) Three-dimensional model of purple membrane obtained by
electron microscopy. Nature 257: 28-32.
Small, D. M. (1986) The Physical Chemistry of Lipids. New York: Plenum Press.
Contents
Contributors, ix
I The Nature of the Membrane Protein Structure Problem 1
1. Membrane Protein Structure and Stability: Implications of the First
Crystallographic Analyses, 3
D. C. Rees, A. f. Chirino, K.-H. Kim, and H. Komiya
2. Decoding the Signals of Membrane Protein Sequences, 27
Gunnar von Heijne
3. Folding and Assembly of Integral Membrane Proteins: An Introduction, 41
jean-Luc Popot, Catherine de Vitry, and Ariane Atteia
4. Hydropathy Plots and the Prediction of Membrane Protein Topology, 97
Stephen H. White
ll Biochemical and Molecular Biological
Approaches: Protein Topology 125
5. Experimental Determination of the Topography of Membrane Proteins:
Lessons from the Nicotinic Acetylcholine Receptor, a Multisubunit
Polytopic Protein, 127
David S. Cafiso
6. Use of Gene Fusions to Determine Membrane Protein Topology, 144
Dana Boyd
7. Structure ofF F AT Pases Determined by Direct and Indirect Methods, 164
1 0
L. Mario Amzel, Mario A. Bianchet, and Peter L. Pedersen
lll Direct Structural Approaches 179
8. Experimental Determination of Membrane Protein Secondary Structure
Using Vibrational and CD Spectroscopies, 181
Robert W. Williams
9. High-Resolution Electron Crystallography of Membrane Proteins, 206
Werner Kiihlbrandt
viii Contents
10. Site-Directed Spin Labeling of Membrane Proteins, 224
Wayne L. Hubbell and Christian Altenbach
11. Nuclear Magnetic Resonance Approaches
to Membrane Protein Structure, 249
Stanley]. Opel/a
12. Structure of Integral Membrane Proteins within Membranes via
X-Ray and Neutron Diffraction: From Oriented Multilayers
to a Single Monolayer, 268
]. Kent Blasie
IV Model and Physicochemical Approaches 281
13. Physical Studies of Peptide-Bilayer Interactions, 283
Lukas K. Tamm
14. Membrane Protein Structure: Lessons from Gramicidin, 314
G. Andrew Woolley and B. A. Wallace
15. Use of Synthetic Peptides for the Study
of Membrane Protein Structure, 335
]. D. Lear, Z. R. Wasserman, and W. F. DeGrado
16. Diffraction Studies of Model and Natural Helical Peptides, 355
Isabella L. Karle
Index,381
Contributors
Christian Altenbach A. J. Chirino
Jules Stein Eye Institute Division of Chemistry and Chemical
and Department of Chemistry & Biochemistry Engineering
University of California California Institute of Technology
Los Angeles, California Pasadena, California
L. Mario Amzel W. F. DeGrado
Department of Biological Chemistry DuPont Merck Pharmaceutical Company
and Department of Biophysics and Biophysical Wilmington, Delaware
Chemistry
Gunnar von Heijne
Johns Hopkins University
Department of Molecular Biology
School of Medicine
Karolinska Institute Center for Structural
Baltimore, Maryland
Biochemistry
Ariane Atteia Huddinge, Sweden
Institut de Biologie Physico-Chimique
College de France Wayne L. Hubbell
Paris, France Jules Stein Eye Institute
and Department of Chemistry & Biochemistry
Mario A. Bianchet University of California
Department of Biological Chemistry Los Angeles, California
and Department of Biophysics and Biophysical
Chemistry Isabella L. Karle
Johns Hopkins University Laboratory for the Structure of Matter
School of Medicine Naval Research Laboratory
Baltimore, Maryland Washington, D.C.
J. Kent Blasie K.-H.Kim
Department of Chemistry Division of Chemistry and Chemical
University of Pennsylvania Engineering
Philadelphia, Pennsylvania California Institute of Technology
Pasadena, California
Dana Boyd
Department of Microbiology and Molecular H.Komiya
Genetics Division of Chemistry and Chemical
Harvard Medical School Engineering
Boston, Massachusetts California Institute of Technology
Pasadena, California
David S. Cafiso
Department of Chemistry and Biophysics Werner Kiihlbrandt
University of Virginia European Molecular Biology Laboratory
Charlottesville, Virginia Heidelberg, Germany