Bionanotechnology Lessons from Nature - David S. Goodsell.pdf

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"Frontmatter". In: Bionanotechnology
BIONANOTECHNOLOGY
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BIONANOTECHNOLOGY
Lessons from Nature
David S. Goodsell, Ph.D.
Department of Molecular Biology
The Scripps Research Institute
La Jolla, California
A JOHN WILEY & SONS, INC., PUBLICATION
 
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Copyright © 2004 by Wiley-Liss, Inc., Hoboken, New Jersey. All rights reserved.
Published simultaneously in Canada.
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Library of Congress Cataloging-in-Publication Data:
Goodsell, David S.
Biotechnology : lessons from nature / David S. Goodsell.
p. ; cm.
Includes bibliographical references and index.
ISBN 0-471-41719-X (cloth : alk. paper)
1. Biomolecules. 2. Nanotechnology. 3. Biotechnology.
[DNLM: 1. Biotechnology. 2. Nanotechnology. QT 36 G655b 2004] I.
Title.
QP514.2.G658 2004
660.6—dc21
2003006943
Printed in the United States of America
10 987654321
 
CONTENTS
1 The Quest for Nanotechnology
1
Biotechnology and the Two-Week Revolution
3
From Biotechnology to Bionanotechnology
4
What is Bionanotechnology?
6
2 Bionanomachines in Action
9
The Unfamiliar World of Bionanomachines
10
Gravity and inertia are negligible at the nanoscale
10
Nanomachines show atomic granularity
11
Thermal motion is a significant force at the nanoscale
12
Bionanomachines require a water environment
13
Modern Biomaterials
14
Most natural bionanomachines are composed of protein
15
Nucleic acids carry information
21
Lipids are used for infrastructure
24
Polysaccharides are used in specialized structural roles
27
The Legacy of Evolution
28
Evolution has placed significant limitations on the properties
31
of natural biomolecules
Guided Tour of Natural Bionanomachinery
32
3 Biomolecular Design and Biotechnology 43
Recombinant DNA Technology 45
DNA may be engineered with commercially available enzymes 46
Site-directed mutagenesis makes specific changes in the genome 52
Fusion proteins combine two functions
52
v
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vi
Contents
Monoclonal Antibodies
54
Biomolecular Structure Determination
57
X-ray crystallography provides atomic structures
58
NMR spectroscopy may be used to derive atomic structures
61
Electron microscopy reveals molecular morphology
62
Atomic force microscopy probes the surface of biomolecules
64
Molecular Modeling
66
Bionanomachines are visualized with computer graphics
67
Computer modeling is used to predict biomolecular
68
structure and function
The protein folding problem
69
Docking simulations predict the modes of biomolecular
72
interaction
New functionalities are developed with computer-assisted
74
molecular design
4 Structural Principles of Bionanotechnology
75
Natural Bionanomachinery is Designed for a Specific
76
Environment
A Hierarchical Strategy Allows Construction of Nanomachines
77
The Raw Materials: Biomolecular Structure and Stability
80
Molecules are composed of atoms linked by covalent bonds
80
Dispersion and repulsion forces act at close range
84
Hydrogen bonds provide stability and specificity
86
Electrostatic interactions are formed between charged atoms
87
The hydrophobic effect stabilizes biomolecules in water
89
Protein Folding
91
Not all protein sequences adopt stable structures
93
Globular proteins have a hierarchical structure
93
Stable globular structure requires a combination of design
95
strategies
Chaperones provide the optimal environment for folding
98
Rigidity can make proteins more stable at high temperatures
100
Many proteins make use of disorder
101
 

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