Biological Systems Under Extreme Conditions

by Taniguchi, Yoshihiro; Stanley, H. Eugene; Ludwig, Horst

• ISBN13: 9783540659921
• ISBN10: 3540659927
• Format: Hardcover
• Copyright: 2002-01-01
• Publisher: Springer Verlag

Summary

Biological systems are regulated by the thermodynamic parameters of pressure and temperature. With the help of new spectroscopic methods it is now possible to study the structure and function of such systems under extreme pressures and temperatures. This book described the resulting theory and applications of these pressure and temperature effects. The subjects covered include the use of high pressure in food processing and even the theory of the origin and evolution of life. Readers exploring the world of biology in extreme environments will find this book particularly useful.

Table of Contents

Liquid Water at Low Temperature: Clues for Biology?	p. 1
Introduction	p. 1
What is the Puzzle of Liquid Water?	p. 2
Volume Fluctuations	p. 2
Entropy Fluctuations	p. 3
Volume-Entropy Cross-Correlations	p. 3
Why Do We Care About Liquid Water?	p. 4
Clues for Understanding Water	p. 5
Qualitative Picture: Locally Structured Transient Gel	p. 5
`Locally Structured'	p. 5
`Transient Gel'	p. 6
Microscopic Structure: Local Heterogeneities	p. 6
Liquid-Liquid Phase Transition Hypothesis	p. 8
Plausibility Arguments	p. 9
Tests of the Hypothesis: Computer Water	p. 11
Does <$>1/K_T^{\rm max}<$> Extrapolate to Zero at (<$>T_{c^{\prime}}, P_{c^{\prime}}<$>)?	p. 11
Is There a `Kink' in the P¿ Isotherms?	p. 11
Is There a Unique Structure of the Liquid near the Kink?	p. 12
Does the Coordination Number Approach Four as C' is Approached?	p. 12
Is It Possible that Two Apparent `Kink' Coexist Below C'?	p. 12
Do Fluctuations Appear at All Time Scales?	p. 13
Is There `Critical Slowing Down' of a Characteristic Time Scale?	p. 13
Is the Characteristic Dynamics of Each `Phase' Different?	p. 14
Is There Evidence for a HDL-LDL Critical Point from Independent Simulations?	p. 14
Tests of the Hypothesis: Real Water	p. 15
A Cautionary Remark	p. 15
Previous Work	p. 15
Recent Work	p. 16
Discussion	p. 18
Outlook	p. 19
References	p. 20
Ab Initio Theoretical Study of Water: Extension to Extreme Conditions	p. 25
Introduction	p. 25
Liquid Structure, Electronic and Thermodynamic Properties of Water	p. 26
Ab Initio Polarizable Model of Water	p. 28
Electronic Polarization and Energetics	p. 28
Solvation Structure of Liquid Water	p. 31
Hydrogen Bonding in Liquid Water	p. 34
Theoretical Prediction of pKw	p. 37
Description of the Auto-ionization Process in Water	p. 38
Solvation Structure of H2O, H3O+, and OH-	p. 39
Free Energy, Its Components and pKw	p. 43
Conclusions	p. 50
Electronic and Liquid Structure of Water	p. 50
The State Dependence of pKw	p. 51
References	p. 52
The Behavior of Proteins Under Extreme Conditions: Physical Concepts and Experimental Approaches	p. 53
Introduction	p. 53
Physical Concepts	p. 54
Volume and Hydration	p. 54
Compressibility and Volume Fluctuations	p. 55
Thermal Expansion and Volume-Entropy Fluctuations	p. 56
Heat Capacity and Entropy Fluctuations	p. 56
Gruneisen Parameter	p. 57
Protein Stability and Unfolding	p. 57
Glass Transitions	p. 60
Experimental Approaches	p. 60
Thermodynamic Properties	p. 61
Absorption Spectroscopy	p. 62
Emission Spectroscopy	p. 66
NMR Spectroscopy	p. 68
Diffraction and Scattering Techniques	p. 69
High-Pressure Computer Simulations	p. 69
Conclusions: Facts and Hypotheses	p. 70
References	p. 71
High-Pressure NMR Spectroscopy of Proteins	p. 75
Introduction	p. 75
Experimental Methods	p. 77
Survey of High-Pressure NMR Techniques	p. 77
Instrumention for the Autoclave Approach	p. 79
Model Proteins	p. 86
Ribonuclease A	p. 87
Hen Lysozyme	p. 88
Apomyoglobin	p. 88
Arc Repressor	p. 89
Results and Discussion	p. 89
Determination of the Activation Volume of the Uncatalyzed Hydrogen Exchange Reaction Between N-Methylacetamide and Water	p. 89
Cold, Heat, and Pressure Unfolding of Ribonuclease A	p. 91
Pressure-Assisted, Cold-Denatured Lysozyme Structure and Comparison with Lysozyme Folding Intermediates	p. 92
Denaturation of Apomyoglobin Mutants by High Pressure	p. 95
High-Pressure NMR Study of the Dissociation of the Arc Repressor	p. 96
Conclusions	p. 97
References	p. 97
Pressure-Induced Secondary Structure Changes of Proteins Studied by FTIR Spectroscopy	p. 101
Introduction	p. 101
Experimental Methods	p. 103
Sample amd Solutions	p. 103
Deuterated Solutions	p. 103
High-Pressure FTIR Measurements	p. 103
Results and Discussion	p. 104
Ribonuclease A	p. 104
Ribonuclease S	p. 109
Bovine Pancreatic Trypsin Inhibitor	p. 113
Conclusions	p. 117
References	p. 118
The Small Angle X-Ray Scattering from Proteins Under Pressure	p. 121
Introduction	p. 121
Protein Folding Under Pressure Related to SAXS	p. 122
Information Available from SAXS	p. 122
Experimental Methods	p. 124
High-Pressure Cell for SAXS	p. 124
Absorption of X-Rays	p. 125
Contrast Effect by Pressure	p. 126
High-Pressure SAXS Experiments at a Synchrotron Facility	p. 126
Data Analysis of SAXS Profiles	p. 127
Results and Discussion	p. 128
Pressure Denaturation of Metmyoglobin	p. 128
Pressure Dissociation of LDH	p. 130
Conclusion and Future Prospects	p. 136
References	p. 137
Accurate Calculations of Relative Melting Temperatures of Mutant Proteins by Molecular Dynamics/Free Energy Perturbation Methods	p. 139
Introduction	p. 139
Molecular Dynamics Simulation of Proteins	p. 142
Equilibrium Structure and Thermal Fluctuation	p. 146
Computational Mutagenesis	p. 149
Free Energy Perturbation Method	p. 150
Free Energy Component Analysis	p. 152
Calculation Results of ¿Tm and ¿¿G	p. 152
Stability Mechanism of Val74Ile RNaseHI Mutant	p. 154
Stability Mechanism of Ile→Val Lysozyme Mutants	p. 158
Approximation Level Dependence	p. 159
Conclusion	p. 161
Appendix: Relationship Between ¿Tm and ¿¿G	p. 162
References	p. 165
Enzyme Kinetics: Stopped-Flow Under Extreme Conditions	p. 167
Introduction	p. 167
Basic Principles	p. 168
Cryo-Baro-Enzymology	p. 168
Exploitation of Data	p. 169
The High-Pressure, Variable-Temperature, Stopped-Flow Technique(HP-VT-SF)	p. 170
General Design	p. 170
Source of Artifacts in Stopped-Flow Operating Under Extreme Conditions	p. 172
Recent Progress	p. 172
Examples of Application	p. 173
Steady-State Kinetics of Enzymes of Monomeric or Polymeric Quaternary Structure	p. 174
Structure-Function Relations: Case of Muscle Contraction	p. 176
Micellar Enzymology	p. 176
Transient Enzyme Kinetics	p. 179
Carbon Monoxide (CO) Binding	p. 180
Electron-Transfer Reactions	p. 180
Conclusions	p. 183
References	p. 184
Pressure Effects on the Intramolecular Electron Transfer Reactions in Hemoproteins	p. 187
Introduction	p. 187
Materials and Methods	p. 189
Preparation of the Ruthenium-modified Proteins	p. 189
Measurements of Flash Photolysis Under High Pressure	p. 191
Results	p. 191
Electron Transfer in Ruthenium-Modified Cytochrome b5	p. 191
Electron Transfer in Ruthenium-Modified, Zinc-Substituted Myoglobins	p. 194
Discussion	p. 197
Factors Regulating the Electron Transfer Reaction and Their Pressure Dependence	p. 197
The Pathway for Electron Transfer in Ruthenium-Modified Cytochrome b5	p. 198
The Pathway for Electron Transfer in Ruthenium-Modified, Zinc-Substituted Myoglobin	p. 199
References	p. 201
Marine Microbiology: Deep-Sea Adaptations	p. 205
Introduction	p. 205
Isolation and Taxonomy of Deep-Sea Barophilic (Piezophilic) Microorganisms	p. 206
Isolation and Growth Properties	p. 206
Taxonomy	p. 208
High-Pressure Sensing and Adaptation in Deep-Sea Microorganisms	p. 212
Introduction	p. 212
Pressure Regulation in Microorganisms Outside of the Genus Shewanella	p. 213
Pressure-Regulated Operons in Shewanella Species	p. 214
Pressure-Sensing Mechanisms	p. 216
Concluding Remarks	p. 217
References	p. 219
Submarine Hydrothermal Vents as Possible Sites of the Origin of Life	p. 221
Introduction	p. 221
Abiotic Formation of Bioorganic Compounds in Planetary Atmospheres	p. 222
Abiotic Formation of Bioorganic Compounds in Space	p. 224
The Primeval Ocean as a Cradle of Life on Earth	p. 225
Implication of the Present Hydrothermal Systems for the Condition of the Primeval Ocean	p. 226
Heat Energy and Quenching	p. 227
Reducing Environments	p. 228
High Concentration of Trace Metal Ions	p. 228
Experiments in Simulated Hydrothermal Vent Environments	p. 229
Synthesis of Amino Acids	p. 229
Stability of Amino Acids in Vent Environments	p. 231
Formation of Microspheres and Oligomers	p. 233
Conclusion	p. 235
References	p. 236
The Effect of Hydrostatic Pressure on the Survival of Microorganisms	p. 239
Introduction	p. 239
Experimental Methods	p. 240
Microorganisms	p. 240
High-Pressure Experiments	p. 240
Staining of E. coli Cells with Fluorescent Dyes	p. 240
Transmission Electron Microscopy of E. coli Cells	p. 241
Results and Discussion	p. 241
Barotolerance of Bacteria	p. 241
Kinetics of Pressure Inactivation	p. 244
Stainability of E. coli Cells and Electron Microscopy	p. 250
Conclusions	p. 254
References	p. 254
Dynamics of Cell Structure by Pressure Stressin the Fission Yeast Schizosaccharomyces pombe	p. 257
Introduction	p. 258
Experimental Methods	p. 258
Yeast Strain and Cultivation	p. 258
High-Pressure Treatments	p. 259
Colony-Forming Ability	p. 259
Dye Plate-Colony Color Assay	p. 259
Fluorescence Microscopy	p. 259
Conventional Electron Microscopy by Freeze-Substitution Fixation	p. 259
Immunoelectron Microscopy by Frozen Thin-Sectioning	p. 260
Results and Discussion	p. 260
Response of S. pombe Cells to Pressure Stress	p. 260
Induction of Diploidization in S. pombe	p. 261
Influence of Pressure Stress on the Cold-Sensitive nda3 Mutant	p. 261
Properties of the Cold-Sensitive nda3 Mutant Cytoskeleton	p. 263
Dynamics of the Cold-Sensitive nda3 Mutant Cytoskeleton	p. 264
Transmission Electron Microscopic Images of the Ultrastructure of Pressure Stress Cells	p. 267
Changes in Actin Cytoskeleton Induced by Pressure Stress	p. 272
Conclusions	p. 277
References	p. 277
Subject Index	p. 279
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