Single Molecule Biology (eBook)

Front Cover 1
Single Molecule Biology 4
Copyright Page 5
Contents 8
Preface 12
Acknowledgments 14
List of Contributors 16
Introduction: The "Single Molecule" Paradigm 18
The “Single Molecule” Paradigm 18
Life as a Molecule 24
Single Molecule Techniques 26
Overview of Single Molecule Biology 30
Conclusions 33
Acknowledgments 33
References 34
Chapter 1 Single Molecule Studies of Myosins 38
Introduction 39
Motility Assays 42
Molecular Mechanics 45
Technologies 47
The Myosin Working Stroke 51
Force and Stiffness 55
Kinetics 55
Conclusions 65
Acknowledgments 65
References 66
Chapter 2 Single Molecule Experiments and the Kinesin Motor Protein Superfamily: Walking Hand in Hand 72
Introduction 73
Overall Mechanical Parameters of Kinesins 74
Advanced Mechanochemistry of Kinesin-1 80
Lattice Diffusion as an Additional Motility Mode 83
Regulation of Kinesin Motors 87
Final Thoughts 91
Acknowledgments 91
References 92
Chapter 3 Force-Generating Mechanisms of Dynein Revealed through Single molecule Studies 98
Introduction 99
Molecular Organization of Dynein 102
Mechanism of Force Generation by Dyneins 112
Mechanical Properties of Dyneins Studied by Single molecule Methods 114
Dyneins in Axonemes 121
Perspectives: From Single Molecules to Ensembles 128
Acknowledgments 130
References 130
Chapter 4 The Bacterial Flagellar Motor 142
Introduction 142
Structure 145
Function 151
Outlook 167
References 168
Chapter 5 Single Molecule Studies of Chromatin Structure and Dynamics 180
Introduction 181
Sperm Chromatin 181
Spermiogenesis 183
Previous Studies of Toroid Structure 183
Single molecule Experiments 183
The Protamines P1 and P2 185
The Transition Proteins TP1 and TP2 187
Shaping of the Sperm Head and the Role of the Manchette 187
Posttranscriptional Modifications of Sperm Nuclear Proteins 188
Conclusions: Sperm Chromatin 189
Somatic Chromatin 189
Conclusion 199
Acknowledgments 200
References 200
Chapter 6 Single Molecule Studies of Nucleic Acid Enzymes 210
Introduction 210
Methods 211
Single molecule Studies of Nucleic Acid Enzymes 213
Conclusion 225
References 225
Chapter 7 Single Molecule Studies of Prokaryotic Translation 232
Introduction 233
Directly Observing Translation 234
Translation at Atomic Resolution 237
Single molecule Translation 238
Conclusions 250
References 251
Chapter 8 Single Ion Channels 260
Comparison of Fluorescence Methods with Single-Channel Recording 261
How to Get Information about Mechanisms from Single molecule Measurements 269
Some Recent Results from Single-Channel Recording 277
Conclusions 282
References 283
Chapter 9 Single Molecule Fluorescence in Membrane Biology 290
The Structure and Function of Cellular Membranes 290
Why Apply Single molecule Fluorescence to Membranes? 291
Fluorescent Labels and Artificial Cell Membranes 292
Single molecule Fluorescence Techniques 293
The Role of SMF in Studying Membranes and Membrane Proteins 297
Probing the Structure and Behavior of Cell Membranes 297
Membrane–Cytoskeleton Interactions 299
Lipid Rafts 301
Understanding the Dynamics and Interactions of Membrane Proteins 303
Signalling 303
Membrane Transport 307
Vesicle Tracking, Docking, and Fusion 310
Conclusions 312
References 313
Chapter 10 Single Molecule Microarray Analysis 326
Introduction 327
Speed and Sensitivity: Mutually Exclusive Demands? 328
Microarrays: Attempting a Definition 331
Microarray Surfaces: There is Plenty to Groom at the Bottom 332
Applications: Learning from Singles 336
DNA Methylation Analysis 341
DNA Fragment Sizing 341
DNA (Combing and) Mapping 342
Single Molecule Sequencing 343
Conclusions 344
Acknowledgments 344
References 345
Appendix 354
Index 362
A 362
B 362
C 362
D 363
E 363
F 363
G 364
H 364
I 365
J 365
K 365
L 365
M 365
N 366
O 366
P 367
Q 367
R 367
S 367
T 368
U 369
V 369
W 369
X 369
Y 369
Z 369