ISBN: 3540659927
TITLE: Biological Systems Under Extreme Conditions
AUTHOR: Taniguchi, Stanley, Ludwig (Eds.)
TOC:

1 Liquid Water at Low Temperature: Clues for Biology?
H. Eugene Stanley 1
1.1 Introduction 1
1.2 What is the Puzzle of Liquid Water? 2
1.2.1 Volume Fluctuations 2
1.2.2 Entropy Fluctuations 3
1.2.3 Volume-Entropy Cross-Correlations 3
1.3 Why Do We Care About Liquid Water? 4
1.4 Clues for Understanding Water 5
1.5 Qualitative Picture: Locally Structured Transient Gel 5
1.5.1 'Locally Structured' 5
1.5.2 'Transient Gel' 6
1.6 Microscopic Structure: Local Heterogeneities 6
1.7 Liquid-Liquid Phase Transition Hypothesis 8
1.8 Plausibility Arguments 9
1.9 Tests of the Hypothesis: Computer Water. 11
1.9.1 Does l/K_T^max Extrapolate to Zero at (T_c', P_C')? 11
1.9.2 Is There a 'Kink' in the P_p Isotherms? 11
1.9.3 Is There a Unique Structure of the Liquid near the Kink? 12
1.9.4 Does the Coordination Number Approach Four as C is Approached? 12
1.9.5 Is It Possible that Two Apparent 'Kink' Coexist Below C? 12
1.9.6 Do Fluctuations Appear at All Time Scales? 13
1.9.7 Is There 'Critical Slowing Down' of a Characteristic Tie Scale? 13
1.9.8 Is the Characteristic Dynamics of Each 'Phase' Different? 14
1.9.9 Is There Evidence for a HDL-LDL Critical Point from Independent Simulations? 14
1.10 Tests of the Hypothesis: Real Water 15
1.10.1 A Cautionary Remark 15
1.10.2 Previous Work 15
1.10.3 Recent Work 16
1.11 Discussion 18
1.12 Outlook 19
References 20
2 Ab Initio Theoretical Study of Water: Extension to Extreme Conditions
Fumio Hirata and Hirofumi Sato 25
2.1 Introduction 25
2.2 Liquid Structure, Electronic and Thermodynamic Properties of Water 26
2.2.1 Ab Initio Polarizable Model of Water 28
2.2.2 Electronic Polarization and Energetics 28
2.2.3 Solvation Structure of Liquid Water 31
2.2.4 Hydrogen Bonding in Liquid Water 34
2.3 Theoretical Prediction of pK_W 37
2.3.1 Description of the Auto-ionization Process in Water 38
2.3.2 Solvation Structure of H_20, H_30^+, and OH^- 39
2.3.3 Free Energy, Its Components and pK_W 43
2.4 Conclusions 50
2.4.1 Electronic and Liquid Structure of Water 50
2.4.2 The State Dependence of pK_W 51
References 52

3 The Behavior of Proteins Under Extreme Conditions: Physical Concepts and Experimental Approaches
Karel Heremans and Lzl Smeller 53
3.1 Introduction 53
3.2 Physical Concepts 54
3.2.1 Volume and Hydration 54
3.2.2 Compressibility and Volume Fluctuations 55
3.2.3 Thermal Expansion and Volume-Entropy Fluctuations 56
3.2.4 Heat Capacity and Entropy Fluctuations 56
3.2.5 Grneisen Parameter 57
3.2.6 Protein Stability and Unfolding 57
3.2.7 Glass Transitions 60
3.3 Experimental Approaches 60
3.3.1 Thermodynamic Properties 61
3.3.2 Absorption Spectroscopy 62
3.3.3 Emission Spectroscopy 66
3.3.4 NMR Spectroscopy 68
3.3.5 Diffraction and Scattering Techniques 69
3.3.6 High-Pressure Computer Simulations 69
3.4 Conclusions: Facts and Hypotheses 70
References 71
4 High-Pressure NMR Spectroscopy of Proteins 
Lance Ballard and Jiri Jonas 75
4.1 Introduction 75
4.2 Experimental Methods 77
4.2.1 Survey of High-Pressure NMR Techniques 77
4.2.2 Instrumention for the Autoclave Approach 79
4.3 Model Proteins 86
4.3.1 Ribonuclease A 87
4.3.2 Hen Lysozyme 88
4.3.3 Apomyoglobin 88
4.3.4 Arc Repressor 89
4.4 Results and Discussion 89
4.4.1 Determination of the Activation Volume of the Uncatalyzed Hydrogen Exchange Reaction Between N-Methylacetamide and Water 89
4.4.2 Cold, Heat, and Pressure Unfolding of Ribonuclease A 91
4.4.3 Pressure-Assisted, Cold-Denatured Lysozyme Structure and Comparison with Lysozyme Folding Intermediates 92
4.4.4 Denaturation of Apomyoglobin Mutants by High Pressure 95
4.4.5 High-Pressure NMR Study of the Dissociation of the Arc Repressor 96
4.5 Conclusions 97
References 97
5 Pressure-Induced Secondary Structure Changes of Proteins Studied by FTIR Spectroscopy
Yoshihiro Taniguchi and Naohiro Takeda 101
5.1 Introduction 101
5.2 Experimental Methods 103
5.2.1 Sample and Solutions 103
5.2.2 Deuterated Solutions 103
5.2.3 High-Pressure FTIR Measurements 103
5.3 Results and Discussion 104
5.3.1 Ribonuclease A 104
5.3.2 Ribonuclease S 109
5.3.3 Bovine Pancreatic Trypsin Inhibitor 113
5.4 Conclusions 117
References 118
6 The Small Angle X-Ray Scattering from Proteins Under Pressure
Tetsuro Fujisawa and Minoru Kato 121
6.1 Introduction 121

6.1.1 Protein Folding Under Pressure Related to SAXS 122
6.1.2 Information Available from SAXS 122
6.2 Experimental Methods 124
6.2.1 High-Pressure Cell for SAXS 124
6.2.2 Absorption of X-Rays 125
6.2.3 Contrast Effect by Pressure 126
6.2.4 High-Pressure SAXS Experiments at a Synchrotron Facility 126
6.2.5 Data Analysis of SAXS Profiles 127
6.3 Results and Discussion 128
6.3.1 Pressure Denaturation of Metmyoglobin 128
6.3.2 Pressure Dissociation of LDH 130
6.4 Conclusion and Future Prospects 136
References 137
7 Accurate Calculations of Relative Melting Temperatures of Mutant Proteins by Molecular Dynamics/Free Energy Perturbation Methods 
Minoru Saito 139
7.1 Introduction 139
7.2 Molecular Dynamics Simulation of Proteins 142
7.3 Equilibrium Structure and Thermal Fluctuation 146
7.4 Computational Mutagenesis 149
7.5 Free Energy Perturbation Method 150
7.6 Free Energy Component Analysis 152
7.7 Calculation Results of delta T_m, and delta delta G 152
7.8 Stability Mechanism of Val74lle RNaseHI Mutant 154
7.9 Stability Mechanism of IIe(Val Lysozyme Mutants 158
7.10 Approximation Level Dependence 159
7.11 Conclusion 161
7.12 Appendix: Relationship Between deltaT_m, and delta delta G 162
References 165
8 Enzyme Kinetics: Stopped-Flow Under Extreme Conditions Claude Balny 167
8.1 Introduction 167
8.2 Basic Principles 168
8.2.1 Cryo-Baro-Enzymology 168
8.2.2 Exploitation of Data 169
8.3 The High-Pressure, Variable-Temperature, Stopped-Flow Technique (HP-VT-SF) 170
8.3.1 General Design 170
8.3.2 Source of Artifacts in Stopped-Flow Operating Under Extreme Conditions 172
8.3.3 Recent Progress 172
8.4 Examples of Application 173
8.4.1 Steady-State Kinetics of Enzymes of Monomeric or Polymeric Quatemary Structure 174
8.4.2 Structure-Function Relations: Case of Muscle Contraction 176
8.4.3 Micellar Enzymology 176
8.4.4 Transient Enzyme Kinetics 179
8.4.5 Carbon Monoxide (CO) Binding 180
8.4.6 Electron-Transfer Reactions 180
8.5 Conclusions 183
References 184
9 Pressure Effects on the Intramolecular Electron Transfer Reactions in Hemoproteins
Yoshiaki Furukawa, Yoichi Sugiyama, Satoshi Takahashi, Koichiro Ishimori,
and Isao Morishima 187
9.1 Introduction 187
9.2 Materials and Methods 189
9.2.1 Preparation of the Ruthenium-modified Proteins 189
9.2.2 Measurements of Flash Photolysis Under High Pressure 191
9.3 Results 191
9.3.1 Electron Transfer in Ruthenium-Modified Cytochrome b_5 191
9.3.2 Electron Transfer in Ruthenium-Modified, Zinc-Substituted Myoglobins 194
9.4 Discussion 197
9.4.1 Factors Regulating the Electron Transfer Reaction and Their Pressure Dependence 197
9.4.2 The Pathway for Electron Transfer in Ruthenium-Modified Cytochrome b_5 198
9.4.3 The Pathway for Electron Transfer in Ruthenium-Modified, Zinc-Substituted Myoglobin 199
References 201
10 Marine Microbiology: Deep Sea Adaptations
Chiaki Kato, Lina Li, Yuichi Nogi, Kaoru Nakasone, and Douglas H. Bartlett 205
10.1 Introduction 205
10.2 Isolation and Taxonomy of Deep-Sea Barophilic (Piezophilic) Microorganisms 206
10.2.1 Isolation and Growth Properties 206
10.2.2 Taxonomy 208
10.3 High-Pressure Sensing and Adaptation in Deep-Sea Microorganisms 212
10.3.1 Introduction 212
10.3.2 Pressure Regulation in Microorganisms Outside of the Genus Shewanella 213
10.3.3 Pressure-Regulated Operons in Shewanella Species 214
10.3.4 Pressure-Sensing Mechanisms 216
10.4 Concluding Remarks 217
References 219
11 Submarine Hydrothermal Vents as Possible Sites of the Origin of Life
Kensei Kobayashi and Hiroshi Yanagawa 221
11.1 Introduction 221
11.2 Abiotic Formation of Bioorganic Compounds in Planetary Atmospheres 222
11.3 Abiotic Formation of Bioorganic Compounds in Space 224
11.4 The Primeval Ocean as a Cradle of Life on Earth 225
11.5 Implication of the Present Hydrothermal Systems for the Condition of the Primeval Ocean 226
11.5.1 Heat Energy and Quenching 227
11.5.2 Reducing Environments 228
11.5.3 High Concentration of Trace Metal Ions 228
11.6 Experiments in Simulated Hydrothermal Vent Environments 229
11.6.1 Synthesis of Amino Acids 229
11.6.2 Stability of Amino Acids in Vent Environments 231
11.6.3 Formation of Microspheres and Oligomers 233
11.7 Conclusion 235
References 236
12 The Effect of Hydrostatic Pressure on the Survival of Microorganisms
Horst Ludwig, Gnter van Almsick, and Christian Schreck 239
12.1 Introduction 239
12.2 Experimental Methods 240
12.2.1 Microorganisms 240
12.2.2 High-Pressure Experiments 240
12.2.3 Staining of E. coli Cells with Fluorescent Dyes 240
12.2.4 Transmission Electron Microscopy of E. coli Cells 241
12.3 Results and Discussion 241
12.3.1 Barotolerance of Bacteria 241
12.3.2 Kinetics of Pressure Inactivation 244
12.3.3 Stainability of E. coli Cells and Electron Microscopy 250
12.4 Conclusions 254
References 254
13 Dynamics of Cell Structure by Pressure Stress in the Fission Yeast Schizosaccharomyces pombe
Masako Osumi, Mamiko Sato, and Shoji Shimada 257
13.1 Introduction 258
13.2 Experimental Methods 258
13.2.1 Yeast Strain and Cultivation 258
13.2.2 High-Pressure Treatments 259
13.2.3 Colony-Forming Ability 259
13.2.4 Dye Plate-Colony Color Assay 259
13.2.5 Fluorescence Microscopy 259
13.2.6 Conventional Electron Microscopy by Freeze-Substitution Fixation 259
13.2.7 Immunoelectron Microscopy by Frozen Thin-Sectioning 260
13.3 Results and Discussion 260
13.3.1 Response of S. pombe Cells to Pressure Stress 260
13.3.2 Induction of Diploidization in pombe 261
13.3.3 Influence of Pressure Stress on the Cold-Sensitive nda3 Mutant 261
13.3.4 Properties of the Cold-Sensitive nda3 Mutant Cytoskeleton 263
13.3.5 Dynamics of the Cold-Sensitive nda3 Mutant Cytoskeleton 264
13.3.6 Transmission Electron Microscopic Images of the Ultrastructure of Pressure Stress Cells 267
13.3.7 Changes in Actin Cytoskeleton Induced by Pressure Stress 272
13.4 Conclusions 277
References 277
Subject Index 279
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