Aspects of Physical Biology: Biological Water, Protein Solutions, Transport and Replication (Lecture Notes in Physics, 752)

The application to Biology of the methodologies developed in Physics is attracting an increasing interest from the scientific community. It has led to the emergence of a new interdisciplinary field, called Physical Biology, with the aim of reaching a better understanding of the biological mechanisms at molecular and cellular levels. Statistical Mechanics in particular plays an important role in the development of this new field. For this reason, the XXth session of the famous Sitges Conference on Statistical Physics was dedicated to "Physical Biology: from Molecular Interactions to Cellular Behavior". As is by now tradition, a number of lectures were subsequently selected, expanded and updated for publication as lecture notes, so as to provide both a state-of-the-art introduction and overview to a number of subjects of broader interest and to favor the interchange and cross-fertilization of ideas between biologists and physicists. The present volume focuses on three main subtopics (biological water, protein solutions as well as transport and replication), presenting for each of the them the on-going debates on recent results. The role of water in biological processes, the mechanisms of protein folding, the phases and cooperative effects in biological solutions, the thermodynamic description of replication, transport and neural activity, all are subjects that are revised in this volume, based on new experiments and new theoretical interpretations. Cover 1 ISBN: 978-3-540-78764-8 5 Preface 6 Contents 8 Dynamics of Water at Low Temperatures and Implications for Biomolecules 11 Introduction 12 Bulk Water 17 Hydrated Biomolecules 19 Other Evidences of Changes at the Widom Line 21 Relation Between Thermodynamics and Dynamics 22 Conclusions 27 References 28 Anomalous Behaviour of Supercooled Water and Its Implication for Protein Dynamics 31 Introduction 31 Apparent Fragile to Strong Transitions of ConfinedSupercooled Water 36 Relation Between Solvent and Protein Dynamics 40 Conclusions 46 References 47 Interactions of Polarizable Media in Water and the Hydrophobic Interaction 51 Introduction 51 The Origin of Strong Attraction Between Hydrophobic Surfaces 54 Computer Simulation Treatment of PolarizableHydrophobic Solutes 59 The Influence of Solute Polarizabilityon the Hydrophobic Interaction 64 Outlook 67 References 69 Metastable Mesoscopic Phases in Concentrated Protein Solutions 71 Macroscopic and Mesoscopic Phases 72 Methods of Detection and Monitoring of Metastable Clusters 75 Intermolecular Interactions in Solutions of Lumazine Synthase and Hemoglobin 80 Lack of Liquid--Liquid Phase Separation in Solutions of Lumazine Synthase and Hemoglobin 81 Dense Liquid Clusters in Solutions of Lumazine Synthase and Hemoglobin 82 Monte Carlo Simulations of Formation and Decay of Clusters 93 Summary and Perspectives for Future Work 96 References 97 Application of Discrete Molecular Dynamics to Protein Folding and Aggregation 102 Introduction 102 Discrete Molecular Dynamics 103 Protein Folding 107 The One-Bead Go Model 107 Transition States of Realistic Proteins 112 The Two-Bead Go Model 115 The Two-Bead Model with Hydrogen Bonds: Studies of Protein Aggregation 117 The Four-Bead Model: Studies of the -Helix-to--Hairpin Transition 119 Simulations of Amino Acid--Specific Interactions 125 References 133 Cooperative Effects in Biological Suspensions: From Filaments to Propellers 137 Introduction 137 Semiflexible Filaments 139 Modeling Inextensible Semiflexible Filaments 139 Semiflexible Filaments Under External Forcing 142 Self-Propelling Particles 145 Short-Time Dynamics 147 Long-Time Dynamics 149 Conclusions 154 References 155 A Thermodynamic Description of Active Transport 157 Introduction 157 Energy Conversion in the Ca-ATPase 158 Towards a Thermodynamic Transport Theory 162 Mesoscopic Non-equilibrium Thermodynamics 165 Experimental Determination of Transport Coefficients 172 Conclusion 175 References 175 Energy Interconversion in Transport ATPases 177 Introduction 177 Concepts in Energy Transduction 179 Phosphate Compounds of High and Low Energy 179 Experimental Measurements 181 Energy Transduction by Enzymes: Conversion of Phosphate Bonds from High into Low Energy at the Catalytic Siteof Enzymes 183 Energy Transduction and Heat Production in Transport ATPases 186 References 187 A Novel Mechanism for Activator-Controlled Initiation of DNA Replication that Resolves the Auto-regulation Sequestration Paradox 190 Introduction 191 Analysis 199 Conclusions 211 References 213 Activity-Dependent Model for Neuronal Avalanches 215 Introduction 215 Neurons, Synapses, and Hebbian Plasticity 217 Neural Avalanches and Networks: Experimental Results 219 The Model 220 Pruning and Neuronal Avalanches 222 Power Spectra 225 Conclusions 228 References 229 Index 231 Front Matter....Pages I-IX Front Matter....Pages 1-1 Dynamics of Water at Low Temperatures and Implications for Biomolecules....Pages 3-22 Anomalous Behaviour of Supercooled Water and Its Implication for Protein Dynamics....Pages 23-42 Interactions of Polarizable Media inWater and the Hydrophobic Interaction....Pages 43-62 Front Matter....Pages 63-63 Metastable Mesoscopic Phases in Concentrated Protein Solutions....Pages 65-95 Application of Discrete Molecular Dynamics to Protein Folding and Aggregation....Pages 97-131 Cooperative Effects in Biological Suspensions: From Filaments to Propellers....Pages 133-152 Front Matter....Pages 153-153 A Thermodynamic Description of Active Transport....Pages 155-174 Energy Interconversion in Transport ATPases Role of Water in Ions Transport and in the Energy of Hydrolysis of Phosphate Compounds....Pages 175-187 A Novel Mechanism for Activator-Controlled Initiation of DNA Replication that Resolves the Auto-regulation Sequestration Paradox....Pages 189-213 Activity-Dependent Model for Neuronal Avalanches....Pages 215-230 Back Matter....Pages 231-233