Biothermodynamics, Part D (eBook)

Front Cover 1
Biothermodynamics,Part D 4
Copyright 5
Contents 6
Contributors 10
Preface 14
Methods in Enzymology 16
Chapter 1: A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands 46
1. Introduction 47
2. Materials and Methods 49
3. Results and Discussion 53
4. Conclusions 68
Acknowledgments 69
References 69
Chapter 2: Thermodynamics of Biological Processes 72
1. Introduction: Thermodynamics is Not Just for Dead Stuff 73
2. States and Weights from the Boltzmann Rule 74
3. Binding Reactions and Biological Thermodynamics 78
4. The Unreasonable Effectiveness of Random-Walk Models 97
5. Conclusions 100
Acknowledgments 101
References 101
Chapter 3: Protein Stability in the Presence of Cosolutes 106
1. Introduction 107
2. Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte 109
3. Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures 123
4. Osmolyte-Induced Unfolding at Variable Temperature 131
5. Thermal Unfolding in the Presence of Osmolytes 137
6. Where Do the Little Equations Come From? 146
Acknowledgments 166
References 166
Chapter 4: Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell a-Defensin Cryptdin 172
1. Introduction 173
2. X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions 177
3. Preparation of Peptide-Lipid Complexes for X-Ray Measurements 182
4. Summary 190
Acknowledgments 190
References 190
Chapter 5: Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery 196
1. Allostery 197
2. Arginine Repressor 199
3. Preparation for Simulations 202
4. Sampling of States 204
5. Equilibration 205
6. Observing System Motions 208
7. Correlated Motions 208
8. Structural Features of Correlated Motions 209
9. Arg Residues Promote Rotation and Oscillation 212
10. Structural Correlates of Rotational Oscillation 214
11. Single-Arginine Simulations 214
12. Rotational Ensembles 215
13. Energetic Contributions 218
14. Reconciliation with Crystallographic Data 222
15. Complementarity and Synergy of MD and ITC 224
16. Prospects 229
Acknowledgments 231
References 231
Chapter 6: Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes 234
1. Introduction 235
2. Issues with Managing Light Scattering from Liposomes 236
3. Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes 245
4. Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins.. 250
5. Conclusions 252
6. Materials and Methods 254
Acknowledgments 255
References 255
Chapter 7: Non-B Conformations of CAG Repeats Using 2-Aminopurine 258
1. Introduction 259
2. Materials and Methods 261
3. Structure and Thermodynamics of Isolated and Integrated (CAG)8 268
4. Conclusions 274
Acknowledgments 274
References 274
Chapter 8: Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretio 278
1. Protein Secretion: An Essential Component of Bacterial Virulence 279
2. The Autotransporter Secretion Pathway 279
3. Overview of Cys-Loop Stalling 281
4. Architecture and Processing of AT Passenger Domains 281
5. Heterologous Passenger Domain Secretion 284
6. Selecting a Model Autotransporter for Cys-Loop Stalling 285
7. Disulfide Mediated Passenger Domain Stalling 286
8. Methods to Measure OM Secretion and Folding of the Stalled AT Passenger 289
9. Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion 293
References 294
Chapter 9: Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native Stat 298
1. Introduction 299
2. A Mutation Strategy to Amplify Locally Unfolded States 301
3. Thermodynamic Properties of Linked Folding and Binding Reactions 305
4. Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System 310
5. Interplay of Local Mutational Effects, Global Stability, and Binding Affinity 313
6. Success of the Strategy in Preserving Structure 318
7. Comparison of Interaction Versus Entropy Based Mutation Strategy 319
8. How Similar Are Local and Global Unfolding? 321
9. Summary 324
References 325
Chapter 10: Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions 328
1. Overview of AUC 329
2. Fluorescence Optics for the Ultracentrifuge 330
3. Advantages of AU-FDS 332
4. Sample Requirements for Fluorescence Detection 333
5. Applications of AU-FDS 338
6. Current Challenges for AU-FDS 343
7. Conclusion 346
References 347
Author Index 350
Subject Index 362
Color plate 370