Biomolecular Electronics: An Introduction via Photosensitive Proteins

286 Pages·1996·9.578 MB·English

by  Nikolai Vsevolodov (auth.), David Amiel (eds.)

Bioengineering of Materials
Series Editor
David Kaplan
Biotechnology Center, Tufts University
Editorial Advisory Board
Hagan Bayley Buddy D. Ratner
Texas A&M University University of Washington, Seattle
Robert R. Birge Helmut Ringsdorf
Syracuse University Johannes Gutenberg-University, Mainz, Germany
Pierre-Gilles de Gennes Frederick J. Schoen
College de France, Paris Brigham and Women's Hospital, Boston
Larry L. Hench David A. Tirrell
Imperial College, United Kingdom University of Massachusetts, Amherst
Tadashi Kokubo Dan W. Urry
Kyoto University, Japan The University of Alabama, Birmingham
Stephen Mann Julian Vincent
University of Bath, United Kingdom University of Reading, United Kingdom
Antonios G. Mikos Christopher Viney
Rice University Oxford University, United Kingdom
Books in the Series
Protein-Based Materials
Kevin McGrath and David Kaplan, editors
Biomolecular Electronics: An Introduction via Photosensitive Proteins
Nikolai Vsevolodov
Forthcoming Books in the Series
What Sustains Life?
Dan W. Urry
Materials Inspired by Nature: The Architecture of Functional
Supramolecular Structures
Hagan Bayley
Collagen: A Universal Biomaterialfor Medical Devices
Richard Berg, editor
Introduction to Microencapsulation
Curt Thies
Nikolai V sevolodov
Biomolecular Electronics
An Introduction via
Photosensitive Proteins
Translated by Marina Georgadze
Edited by David Arniel
Birkhauser
Boston - Basel- Berlin
Nikolai Vsevolodov
Hyundai Network Systems
A Division of Hyundai Electronics America
Herndon, Virginia, USA
and
Institute of Theoretical and Experimental Biophysics
Russian Adacemy of Sciences
Pushchino, Russia
Marina Georgadze David Amiel
Jersey City, New Jersey Cambridge, Massachusetts
Library of Congress Cataloging-in-Publication Data
Vsevolodov, N. N.
Biomolecular electronics: an introduction via photosensitive
proteins I Nikolai Vsevolodov; translated by Marina Georgadze;
edited by David Amie!.
p. cm. -- (Bioengineering of materials)
Includes bibliographical references and index.
ISBN -13: 978-1-4612-7538-1 e-ISBN -13 :978-1-4612-2442-6
DOl: 10.1007/978-1-4612-2442-6
I. Bioelectronics. 2. Photosynthetic pigments. 3. Protein
engineering. 4. Proteins. 5. Rhodopsin. 6. Bacteriorhodopsin.
I. Title. II. Series.
QH509.5.V74 1998 98-12277
571.4' 5--DC21 CIP
Printed on acid-free paper r!JJ ®
© 1998 Birkhauser Boston Birkhiiuser lLIW
Softcover reprint of the hardcover 1st edition 1998
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.
Permission to photocopy for 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 A venue, Cambridge, MA 02139,
U.S.A.
ISBN -13:978-1-4612-7538-1
Typeset by Alden Bookset, Oxford, England
9 8 7 6 5 432 1
To my wife Olga
Contents
Series Preface by David Kaplan xi
Foreword by Robert R. Birge xiii
Note from the Translation Editor David Arniel xv
Preface xvii
Acknowledgements xix
Chapter 1. Introduction 1
A. Biophotonic Processes 3
B. Bioelectric Phenomena 8
C. Molecular Electronics 11
D. Biomolecular Electronics 13
E. Biomolecular Computing: An Overview of What Needs to
Be Done 15
Chapter 2. The Distinguished Family of Rhodopsins. 19
A. Visual Rhodopsin (VR) in Vertebrates 20
1. General Structure of Rhodopsins 21
2. The Photochemical Process in VR is Irreversible 26
3. Photoinduced VR Intermediates 28
4. Electrogenic VR Intermediates 30
5. Electrical Signals from the Retina 32
6. A Brief Look at Visual Pathways and Mechanisms 35
7. Measurement of Early and Late Receptor Potentials 37
8. VR Response to an Electric Field (Electrochromism) 39
9. The Boundary Between Photochromism and
Photoisomerism in Rhodopsins 42
10. The Influence of Ions on VR Spectra (Ionochromism) 43
11. Rhodopsin in Fish Eyes 43
B. Rhodopsins in Invertebrates and Microorganisms 44
1. Some Natural Examples of Rhodopsin-based
Photopigments 47
2. Retinochrome: A Photoisomerizing Enzyme 51
3. Retinal-binding Proteins 52
4. Rhodopsins for Use in Detecting UV Light 53
5. Chlamyrhodopsin: A Recently Discovered Photopigment 53
viii Contents
C. Bacterial Rhodopsin Isolated from Halobacteria 56
1. Discovery of a New Proton Pump 56
2. The Story of Discovery Unfolds 60
3. Biosynthesis of Purple Membranes 63
4. Purple Membranes: Two-dimensional Crystals 64
5. Halobacteria: A Riddle for Biological Evolution 65
D. Modification of Rhodopsins 68
Chapter 3. The Unique Properties of Bacteriorhodopdins (BR) as
Energy Converters 71
A. Wild-type Bacteriorhodopsin (BR) 71
1. Chemical and Physical Properties of BR 72
2. The Photochemical Process of BR is Reversible! 73
3. Photocycle Intermediates 77
4. The Effects of Various Parameters on the BR Photocycle 82
5. Photochromic Properties 89
6. Photoelectric Properties 90
7. Electrochromic Properties 92
8. BR Viewed as a "Black Box" Energy Converter 94
B. BR Variants 94
1. Random Mutagenesis 95
2. Site-specific Mutagenesis 96
3. How Many Strains of Halobacteria Have Been Found? 97
4. Photochromic Properties of BR Variants 97
C. BR Analogs 99
1. Apomembranes 100
2. Artificial Retinal-Proteins 102
3. Photochemistry ofBR Analogs 105
4. Analogs with Infrared Absorption 107
5. Analogs with Ultraviolet Absorption 109
D. BR Monolayers and BR Films 109
1. BR Solubilization 110
2. BR Films 111
3. BR Aggregates 112
4. The Possibility of a Three Dimensional BR Crystal 113
E. Halorhodopsin Acting as a Chloride Ion Pump 114
F. The Discovery of Sensory Rhodopsins (SR) 116
1. SR-I-An Attractant Receptor for Orange-red Light 117
2. SR-II-A Repellent Receptor for Blue-green Light 119
G. Phototaxis of Phoborhodopsins 120
1. Phoborhodopsins Isolated from Halobacteria 122
2. Pharaonis Phoborhodopsin 123
H. Yellow Protein Isolated from a Halophile 123
Contents ix
I. A Summary of Properties ofBR and BR Variants 125
J. From Electronics to Bioelectronics 126
Chapter 4. Photosensitive Materials for Use as Optical Memory 131
A. Photographic Films 132
1. 150 Years of Photography 133
2. The End of Halogen-Silver Films? 136
B. Photochromic Materials 137
1. 35 Years of Photochromic Materials Research 138
2. The Physics and Chemistry of Photoc hromic Processes 139
3. Organic and Inorganic Photochromic Materials 140
4. Is There a Future for Photochromic Materials? 142
C. Construction of Layered Purple Membranes 145
1. Air-dried Layers on Supports 145
2. Layers with Oriented Purple Membrane 146
3. Purple Membranes in a Polymeric Matrix 148
D. Biochrome: A BR-based Photochromic Film 149
1. The Discovery of Biochromic Films 153
2. Optical Characteristics 158
3. Holographic Properties 159
E. BR Analogs for New Photochromic Films 163
1. Properties of BR Analogs 165
2. 4-keto BR Films 167
3. 4-keto BR: A Potentially Useful Anomaly 168
F. More Photosensitive Materials 169
1. Chlorophyll Photographic Films 170
2. Visual Rhodopsin Photographic Films 172
3. Photographic Films with Enzymes 174
4. Other Types of Photochromic Materials in Nature 175
Chapter 5. BR as Optolectronic Materials 177
A. Molecular Computing Elements 179
B. Ultrafast Electro-optical Detectors 183
C. Biosensors 185
D. Photosensitive Hybrids of Purple Membrane with
Mitochondria and Nonphotosynthetic Bacteria 187
E. Position-sensitive Detectors 188
F. Photovoltaic Devices 190
G. 3-D memory in BR 193
Chapter 6. Applications of Biochrome and Similar Films 197
A. Optical Memory 198
B. Can Bacteriorhodopsin-based Compact Disks Exist? 199
C. The Generation of the Second Harmonic of Laser Radiation 201
x Contents
D. Increasing the Contrast of a Photostat copy 203
E. Polarization Holography 204
F. Real Time Holography 206
G. Holographic Connections for Optical Communication 207
H. Biomedical Applications 208
I. Military Use 209
J. Light Testers 210
K. From Toys to Computers 212
Chapter 7. Conclusion 215
A. Proteins in Bioelectronics 215
B. The Truth and Science Fiction of Biocomputers 217
Chapter 8. References 221
Chapter 9. Glossary and abbreviations 253
Chapter 10. Appendix 257
Index 267
Series Preface
The properties of materials depend on the nature of the macromolecules, small
molecules and inorganic components and the interfaces and interactions
between them. Polymer chemistry and physics, and inorganic phase structure
and density are major factors that influence the performance of materials. In
addition, molecular recognition, organic-inorganic interfaces and many other
types of interactions among components are key issues in determining the
properties of materials for a wide range of applications. Materials require
ments are becoming more and more specialized to meet increasingly demand
ing needs, from specific environmental stresses to high performance or
biomedical applications such as matrices for controlled release tissue scaf
folds. One approach to meet these performance criteria is to achieve better
control over the tailoring of the components and their interactions that govern
the material properties. This goal is driving a great deal of ongoing research in
material science laboratories. In addition, control at the molecular level of
interactions between these components is a key in many instances in order to
reach this goal since traditional approaches used to glue, stitch or fasten parts
together can no longer suffice at these new levels of manipulation to achieve
higher performance. In many cases, molecular recognition and self-assembly
must begin to drive these processes to achieve the levels of control desired.
This same need for improved performance has driven Nature over millenia
to attain higher and higher complexity. For example, the modification of
properties of the macromolecules comprising membrane structures was
critical to provide partitioning of cellular components and organelles.
Tough cellulosic fibers formed that extensively hydrogen bond to allow
plants to partially escape the demands of gravity at ground level and occupy
new niches. Efficient transduction mechanisms based on tailored material
structures are able to interconvert energy as a key to survival for biological
systems. Tailored organic-inorganic templates are employed by marine
molluscs to toughen ceramics made from available environmental feed
stocks. Development of life past the single and oligocellular levels would
have been difficult without controls over the synthesis of tailored materials and
their assemblies. At the same time, Nature effectively utilizes molecular
recognition and self-assembly to drive the formation of complex materials
necessary to achieve the performance required for survival. This is essential in
biology since all life exists within limited energy budgets. A full understanding
of these processes is still needed, since it remains difficult even to predict
protein folding, much less the driving forces required to created molecular
motors responsible for flagellar motion.
Assembly processes in biology take advantage of phase changes, ionic