Cell Signaling Reactions (eBook)

Preface 6
Contents 8
Contributors 10
Chapter 1: Single-Molecule Kinetic Analysis of Receptor Protein Tyrosine Kinases 12
1.1 RTK Systems 13
1.2 Single-Molecule Imaging of RTK Systems in Living Cells 15
1.3 EGF and EGFR 17
1.4 Extracellular and Intermembrane Events in the EGFR System 19
1.4.1 Association Between EGF and EGFR Induces the Formation of Signaling Dimers 19
1.4.2 Amplification of the EGF Signal by Dynamic Clustering of EGFR Molecules 24
1.5 Cytoplasmic Events in the EGFR System 27
1.5.1 Interaction Between EGFR and Grb2 27
1.5.2 Calcium Signaling 30
1.6 NGF and NGF Receptors 32
1.6.1 Single-Molecule Behavior of NGF on the Growth Cone 33
1.6.2 Single-Molecule Behavior of NGF on PC12 Cells 34
1.7 Conclusions and Perspectives 36
References 38
Chapter 2: Single-Molecule Kinetic Analysis of Stochastic Signal Transduction Mediated by G-Protein Coupled Chemoattractant Receptors 44
2.1 Introduction 45
2.2 Gradient Sensing and Directional Cell Migration in Dictyostelium discoideum 46
2.3 Single-Molecule Imaging Analysis of Chemotactic Signaling System in Living Cells 48
2.4 Single-Molecule Kinetic Analysis of Stochastic Signal Inputs for Chemotaxis 53
2.5 Stochastic Signal Transduction and Processing by Chemoattractant Receptors 55
2.6 Kinetic Heterogeneity of Signaling Molecules and Cellular Polarity 60
2.7 Conclusion Remarks 65
References 65
Chapter 3: Single-Molecule Analysis of Molecular Recognition Between Signaling Proteins RAS and RAF 69
3.1 Intracellular Signaling from RAS to Its Effectors 70
3.2 Single-Molecule Kinetics of the Interactions Between RAS and RAF in Living Cells 72
3.3 Conformational Changes in RAF 75
3.4 Single-Molecule Imaging of the RAF Conformation in Living Cells 77
3.5 Molecular Recognition Between RAS and RAF Mutants 79
3.6 Mutual Molecular Recognition Between RAS and RAF 81
3.7 Spatial Heterogeneity of the Reaction Between RAS and RAF in Living Cells 81
3.8 Lateral Diffusion of RAS-RAF Complexes on the Plasma Membrane 84
3.9 Discussion and Perspectives 84
References 86
Chapter 4: Single-Channel Structure-Function Dynamics: The Gating of Potassium Channels 89
4.1 Introduction 90
4.2 The Gating Phenomenon 91
4.3 Gating Kinetics 92
4.3.1 Kinetics of the Macroscopic Current 92
4.3.2 From Hodgkin-Huxley Equation to Allostery 95
4.3.3 Single-Channel Current Recordings 95
4.3.3.1 Single-Molecule Kinetics of the KcsA Channel 98
4.4 Structural Dynamics 100
4.4.1 The Crystal Structures of Channel Proteins 101
4.4.1.1 The Circular Symmetry of the Channel Structure 101
4.4.1.2 Structure of the KcsA Channel 101
4.4.1.3 Open and Closed Conformations of Potassium Channels 103
4.5 Tracing Conformational Dynamics at the Single Molecule Level: The Diffracted X-ray Tracking (DXT) Method 104
4.5.1 The DXT Method 104
4.5.2 Random Brownian Motion of the KcsA Channel in the Closed State 106
4.5.3 Global Twisting Motion of the KcsA Channel upon Gating 106
4.5.4 Cytoplasmic Domain-Truncated Channel 109
4.5.5 Conformational Wave Propagation 110
4.6 Single Molecule Dynamics 110
4.6.1 Discrete vs. Brownian Motions 111
4.7 Conclusion 113
References 114
Chapter 5: Immobilizing Channel Molecules in Artificial Lipid Bilayers for Simultaneous Electrical and Optical Single Channel Recordings 116
5.1 Introduction 117
5.2 Annexin V Immobilizes Membrane Proteins [11] 118
5.3 PEG Supported Bilayers [24] 122
5.4 Gel/Gel Interface Bilayers [26] 123
5.5 Conclusion 127
References 128
Chapter 6: Single-Protein Dynamics and the Regulation of the Plasma-Membrane Ca2+ Pump 130
6.1 Introduction: The Plasma-Membrane Calcium Pump 131
6.2 Detection of Single PMCA Molecules 133
6.2.1 Fluorescence Probes for PMCA 134
6.2.2 Detecting Signals from Single Molecules 135
6.3 Calmodulin Binding Dynamics 138
6.4 Conformational States of PMCA-CaM Complexes: Single-Molecule Polarization Modulation Measurements 139
6.4.1 Orientational Mobility Measurements 140
6.4.2 Model for PMCA-CaM Orientational Mobility States 143
6.4.3 ATP-Dependent Changes of the PMCA-CaM Complex 145
6.4.4 Effect of Oxidative Modification 148
6.5 Single-Molecule FRET Measurements of PMCA 150
6.6 Dynamics of Autoinhibitory Domain Interchange 153
6.7 Conclusions 155
References 156
Chapter 7: Single-Molecule Analysis of Cell-Virus Binding Interactions 161
7.1 Introduction 162
7.2 Current Methods to Measure Cell-Virus Binding Interactions 164
7.3 Principles of Single-Molecule Force Spectroscopy 166
7.4 Single-Molecule Force Spectroscopy of Cell-Virion Binding Interactions 168
References 172
Chapter 8: Visualization of the COPII Vesicle Formation Process Reconstituted on a Microscope 175
8.1 Vesicular Transport 176
8.2 Microscopic Analysis of the Planar Lipid Bilayer 177
8.3 Visualization of the COPII Vesicle Formation Process 179
8.3.1 Microscopic Observation of Vesicle Budding from the Planar Lipid Bilayer Membrane 179
8.3.2 Single-Molecule Observation of the Cargo Protein (Bet1p-Cy3) Reconstituted in Planar Lipid Bilayer Membranes 180
8.3.3 Clusterization of the Prebudding Complex and Concentration of Bet1p-Cy3 by Sec13/31p 183
8.3.4 Why Does Hydrolysis of GTP by Sar1p Require Concentration of Cargo Proteins Inside the Clusters? 184
8.3.5 Exclusion of Non-cargo Proteins by the Minimum COPII Components 187
8.4 Conclusion 188
References 189
Chapter 9: In Vivo Single-Molecule Microscopy Using the Zebrafish Model System 191
9.1 Introduction 192
9.2 Total Internal Reflection Fluorescence Microscopy of Fluorescent Proteins in Zebrafish Embryos 195
9.3 Selective Plane Illumination Microscopy of Quantum Dots in Zebrafish Embryos 198
9.4 Fluorescence Correlation Spectroscopy of Fluorescent Proteins in Zebrafish Embryos 199
9.5 Conclusions 202
References 203
Chapter 10: Analysis of Large-Amplitude Conformational Transition Dynamics in Proteins at the Single-Molecule Level 206
10.1 Introduction 207
10.2 Bulk Versus Single-Molecule Measurements 208
10.3 Time Correlation Functions 210
10.4 Single-Molecule Förster-Type Resonance Energy Transfer 214
10.5 The Orientation Factor, k2 216
10.6 Information Bounds and Photon-by-Photon Analysis 218
10.7 Extracting Conformational Distributions 221
10.8 Example 222
10.9 Concluding Remarks 224
References 225
Chapter 11: Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series 227
11.1 Introduction 228
11.2 Complex Network 229
11.3 Time-Dependent Nature of Conformation Fluctuation, Energy Landscape and Reaction Network 232
11.3.1 Time-Dependence of Conformation Fluctuation 232
11.3.2 Revisiting the Concept of Free Energy Landscape - Its Time Dependency 233
11.4 Extraction of the Unique Reaction Scheme 236
11.4.1 The Construction of the State-Space Network 240
11.4.1.1 Evaluating the Transition Probabilities 240
11.4.1.2 Determining the States of the SSN 242
11.4.1.3 State Transitions in the SSN 242
11.4.2 Wavelet Multi-timescale Decomposition 243
11.4.3 Combining Different SSNs Constructed by Hierarchical Time Series Components in Wavelet Multiscale Decomposition 246
11.4.4 An Analytical Expression of Autocorrelation Derived from SSN 248
11.5 Outlook and Future Perspectives 251
11.6 Appendix 255
References 267
Chapter 12: Statistical Analysis of Lateral Diffusion and Reaction Kinetics of Single Molecules on the Membranes of Living Cells 270
12.1 Introduction 271
12.2 Models of Diffusion 273
12.2.1 Membrane-Integrated Molecules 273
12.2.1.1 Simple Diffusion (Model 1) 273
Diffusion Coefficient 273
Diffusion Equation 273
Displacement Distribution 274
Autocorrelation Function of the Squared Displacements 276
12.2.1.2 Multiple States with Different Diffusive Mobility (Model 2) 278
12.2.1.3 State Transitions (Model 3) 279
12.2.2 Membrane-Associating Molecules 280
12.2.2.1 Simple Diffusion with Membrane Dissociation (Model 4) 280
12.2.2.2 Multiple States with Different Diffusion Coefficients and Dissociation Rates (Model 5) 281
12.2.2.3 State Transitions and Membrane Dissociation (Model 6) 283
12.3 Method of Model Selection 285
12.3.1 Membrane Dissociation 285
12.3.2 Number of States 287
12.3.3 State Transitions 288
12.4 Analysis of Single-Molecule Trajectories 289
12.4.1 Model 1 290
12.4.2 Model 2 290
12.4.3 Model 3 291
12.4.4 Model 4 293
12.4.5 Model 5 295
12.4.6 Model 6 296
12.5 Concluding Remarks 296
Appendix 298
References 300
Chapter 13: Noisy Signal Transduction in Cellular Systems 302
13.1 Introduction 303
13.2 The Hierarchy of Molecular Noise 304
13.3 An Example: cAMP Receptor cAR1 in Dictyostelium Cells 309
13.4 The Gain-Fluctuation Relation 310
13.5 The Response-Fluctuation Relation 314
13.6 Propagation of Noise in Reaction Networks 317
13.7 Chemotaxis Is Limited by Noise: An Application to Chemotaxis in Eukaryotic Cells 319
13.8 Propagation of Noise in Linear Cascade Reaction 322
13.9 Concluding Remarks 328
References 328
Index 330