Water and Biomolecules: Physical Chemistry of Life Phenomena

Contents......Page 10
1.1 NMR Techniques for Studying Protein Folding......Page 19
1.4 The Upper Reaches of the Folding Landscape......Page 20
1.6 Model for Transient Interactions......Page 22
1.8 Folding of an Intrinsically Disordered Protein Upon Binding to a Target......Page 26
References......Page 29
2.1 Introduction......Page 31
2.2 Goat α-Lactalbumin......Page 32
2.3.1 Experimental Studies......Page 33
2.3.2 Simulation Studies......Page 36
2.3.3 Conclusions......Page 40
2.4.1 Experimental Studies......Page 41
2.4.2 Simulation Studies......Page 44
2.5 Summary and Perspectives......Page 50
References......Page 51
3.1 Introduction......Page 55
3.2.1 Primary, Secondary, and Higher-order Structures......Page 56
3.2.3 Looking at Single DNA Molecules......Page 58
3.3.1 Some Basis......Page 60
3.3.2 Continuous Transition in Flexible Polymers: Coil-Globule Transition......Page 61
3.3.3 Discontinuous Transition in Semiflexible Polymers......Page 63
3.3.4 Instability Due to the Remanent Charge......Page 69
3.4 Summary and Perspectives......Page 73
3.4.2 Toward Chromatin Structure......Page 74
References......Page 76
4.1 Introduction......Page 79
4.2.1 Multicanonical Algorithm......Page 81
4.3 Multidimensional Extensions of Multicanonical Algorithm......Page 85
4.3.1 Replica-Exchange Method......Page 87
4.3.2 Multidimensional Extensions of Replica-Exchange Method......Page 91
4.4 Examples of Simulation Results......Page 93
References......Page 108
5.1 Introduction......Page 115
5.2.1 The OPLS-AA/AGBNP Effective Potential......Page 118
5.2.2 Replica Exchange Molecular Dynamics......Page 120
5.2.4 Loop Prediction with Torsion Angle Sampling......Page 121
5.3.1 G-Peptide Folding......Page 122
5.3.3 Loop Prediction......Page 123
5.4.2 The G-Peptide has an α-Helical Intermediate During Folding from Coil Conformation......Page 126
5.4.3 A Molecular View of Kinetic Pathways......Page 127
5.5 Ligand Conformational Equilibrium in a Cytochrome P450 Complex......Page 128
5.5.1 Methodology......Page 129
5.6 Simple Continuous and Discrete Models for Simulating Replica Exchange......Page 130
5.6.2 RE Simulations using MC on a Continuous Potential......Page 132
References......Page 134
6.1 What is a Functional Unfolded Protein?......Page 141
6.3 How Are Functional Unfolded Proteins Studied?......Page 142
6.4 NMR Spectra: Practical Considerations......Page 143
6.5 Dynamic Complexes in CBP......Page 144
6.6 Role of Flexibility in the Function of IκBα......Page 146
References......Page 152
7.1 Solution X-ray Scattering......Page 155
7.2 Photoactive Yellow Protein......Page 156
7.3.1 High-Angle X-ray Scattering of PYP in the Dark and in the Light......Page 157
7.3.2 Analysis of High Angle Scattering......Page 160
7.4 Propagation Mechanism of the Structural Change......Page 162
7.5 Summary......Page 163
References......Page 164
8.1 Introduction......Page 167
8.2 Principle......Page 169
8.4 Time-Resolved Detection of Interprotein Interactions......Page 172
8.4.1 Protein–Protein Interaction of the Photoexcited Photoactive Yellow Protein......Page 173
8.4.2 Photoinduced Dimerization of AppA......Page 175
8.4.3 Photoinduced Dimerization and Dissociation of Phototropins......Page 181
8.4.4 Diffusion Detection of Interprotein Interaction......Page 186
References......Page 188
9.1 Introduction......Page 191
9.2 Thermodynamics......Page 192
9.3 Thermal Expansivity and ΔV......Page 197
9.4 Conclusions......Page 202
References......Page 204
10.1 Introduction......Page 205
10.2 Outline of the RISM and 3D-RISM Theories......Page 208
10.3 Recognition of Water Molecules by Protein......Page 214
10.4 Noble Gas Binding to Protein......Page 217
10.5 Selective Ion-Binding by Protein......Page 219
10.6 Pressure-Induced Structural Transition of Protein and Molecular Recognition......Page 222
10.7 Perspective......Page 225
References......Page 226
11.2 Brief Survey of Protein Motions......Page 229
11.3 Binding and Selectivity......Page 231
11.5 Molecular Clocks......Page 234
References......Page 235
12.1 Introduction......Page 237
12.2.1 Property of the Aqueous Solution of Trehalose......Page 239
12.2.2 Atomic-Level Picture of Hydration of Trehalose......Page 241
12.3.1 Polymorphism......Page 243
12.3.2 Glassy State of Trehalose......Page 245
12.4.1 Possible Mechanisms of Anhydrobiosis......Page 247
12.4.2 Strategy for Desiccation Tolerance in the Sleeping Chironomid......Page 248
12.4.3 Other Biological Roles of Trehalose......Page 252
12.5 Conclusion......Page 254
References......Page 256
13.1 Introduction......Page 259
13.2 The Importance of Normal and Aberrant Protein Folding in Biology......Page 260
13.3 Protein Aggregation and Amyloid Formation......Page 265
13.4 Molecular Evolution and the Control of Protein Misfolding......Page 271
13.5 Impaired Misfolding Control and the Onset of Disease......Page 273
13.6 Probing Misfolding and Aggregation in Living Organisms......Page 275
13.7 The Recent Proliferation of Misfolding Diseases and Prospects for Effective Therapies......Page 278
13.8 Concluding Remarks......Page 280
References......Page 281
14.1 Introduction......Page 285
14.2.1 Structural Perturbation......Page 286
14.3 UV Light as a Potent Structural Perturbant......Page 290
14.3.1 UV-Induced Aggregation of Prion Protein......Page 291
14.3.3 UV Exposure Alters Conformation of Prion Protein......Page 292
14.3.4 UV-Exposed Proteins Failed to Form Amyloid De Novo......Page 295
14.3.5 Is Subcritical Concentration of UV-Exposed Protein Responsible for Failure to Form Amyloid Fibrils?......Page 297
14.3.6 UV-Exposed Amyloidogenic Proteins Form Amyloid Upon Seeding......Page 298
14.3.7 UV-Exposed Prion Protein Fibrils Show Altered Fibril Morphology......Page 300
14.4 Discussion......Page 301
References......Page 304
15.1 Introduction......Page 307
15.2 Total Internal Reflection Fluorescence Microscopy......Page 308
15.3 Real-Time Observation of #&946;2-m and Aβ Fibrils......Page 309
15.4 Effects of Various Surfaces on the Growth of Aβ Fibrils......Page 310
15.5 Spontaneous Formation of Aβ(1–40) Fibrils and Classification of Morphologies......Page 313
15.6 Conclusion......Page 315
References......Page 316
A......Page 319
D......Page 320
H......Page 321
N......Page 322
R......Page 323
T......Page 324
X......Page 325