Log In
Or create an account ->
Imperial Library
Home
About
News
Upload
Forum
Help
Login/SignUp
Index
Preface
Contents
Basis of ATP Hydrolysis Reaction
1 Free Energy Analyses for the ATP Hydrolysis in Aqueous Solution by Large-Scale QM/MM Simulations Combined with a Theory of Solutions
1.1 Introduction
1.2 Theoretical Method
1.2.1 Real-Space Grid Approach
1.2.2 QM/MM Approach
1.2.3 QM/MM-ER Method
1.2.4 Free Energy of Hydrolysis
1.3 Computational Details
1.4 Results and Discussion
1.5 Conclusion
References
2 Role of Metal Ion Binding and Protonation in ATP Hydrolysis Energetics
Abstract
2.1 Introduction
2.2 Theory
2.3 Results and Discussions
2.3.1 ATP Hydrolysis Energetics at pH 7.0
2.3.2 Apparent pKa’s for ATP, ADP, and Pi
2.3.3 Apparent pKMg’s for ATP, ADP, and Pi
2.3.4 Effect of Other Metal Ions on ATP Hydrolysis Energetics
2.4 Conclusions
References
3 Spatial Distribution of Ionic Hydration Energy and Hyper-Mobile Water
Abstract
3.1 Introduction
3.2 Hydration Measurement by Dielectric Relaxation Spectroscopy
3.2.1 Preparation of Aqueous Solutions of Salts
3.2.2 Dielectric Spectroscopy: Experimental Method
3.2.3 Dielectric Spectroscopy: Data Analysis
3.2.4 Hydration Properties of Salt Solutions
3.2.5 Correlation of HMW Against Water Structure
3.3 Hydration Energy Calculation Based on an MD Simulation
3.3.1 Theoretical Background
3.3.2 Computational Procedure
3.3.3 Radial Distribution Function
3.3.4 Solute–Solvent and Solvent–Solvent Interaction Energies
3.3.5 Extent of Spatial Localization of ΔE
3.3.6 Correlation Between Electric Field and Spatial Distribution
3.4 Conclusion
References
4 Theoretical Studies of Strong Attractive Interaction Between Macro-anions Mediated by Multivalent Metal Cations and Related Association Behavior: Effective Interaction Between ATP-Binding Proteins Can Be Regulated by Hydrolysis
Abstract
4.1 Introduction
4.2 Condensation of Acidic Proteins by Multivalent Metal Cations
4.3 Integral Equation Theory for Liquids
4.4 Potential of Mean Force (PMF) Between Macro-anions
4.5 Association and Dissociation Model Mechanism for the Engine of a Protein Linear Motor
4.6 Summary
References
5 Statistical Mechanical Integral Equation Approach to Reveal the Solvation Effect on Hydrolysis Free Energy of ATP and Its Analogue
Abstract
5.1 Introduction
5.2 The 3D-RISM Theory
5.3 Hybrid 3D-RISM and Electronic Structure Theories
5.4 Hydrolysis of Pyrophosphate
5.5 Hydrolysis of ATP
5.6 Summary
References
6 A Solvent Model of Nucleotide–Protein Interaction—Partition Coefficients of Phosphates Between Water and Organic Solvent
Abstract
6.1 Introduction
6.2 Measurement of Partition Coefficients of Phosphoric Compounds Between Water and Alkylamine/Octanol
6.3 Enhancement of Transfer of Phosphoric Compounds from Water to Organic Solvent by Alkylamine
6.3.1 Effect of Alkylamine on Partition of Phosphoric Compounds from Water to Organic Solvent
6.3.2 Homogenous Dispersion of Phosphoric Compounds in Alkylamine-Containing Organic Solvent
6.4 Acid/Base Properties of Alkylamine-Containing Octanol Solvent System
6.4.1 Acid/Base Properties and pH Control of Alkylamine-Containing Octanol
6.4.2 Thermodynamic Analysis of the Protonation/Deprotonation Accompanying Transfer of Phosphoric Compounds Form Water to Alkylamine/Octanol
6.5 Partition Coefficients of Phosphoric Compounds Between Aqueous Solution and Organic Solvent
6.6 Discussion and Conclusion
References
Basis of Protein-Ligand and Protein-Protein Interactions
7 Energetics of Myosin ATP Hydrolysis by Calorimetry
Abstract
7.1 Introduction
7.2 Instrumentation for Calorimetric Studies of Myosin ATP Hydrolysis
7.3 Energetics of Myosin ATP Hydrolysis
7.4 Sources of Large Entropy Changes and Their Implication During Myosin ATP Hydrolysis Cycle
Acknowledgement
References
8 Orchestrated Electrostatic Interactions Among Myosin, Actin, ATP, and Water
8.1 Electrostatic Interaction in Water
8.2 Electrostatic Interaction Between Myosin and Actin
8.3 ATP as an Energizing Electrostatic Modulator
8.4 Water as an Electrostatic Coordinator
References
9 Protonation/Deprotonation of Proteins by Neutron Diffraction Structure Analysis
Abstract
9.1 Introduction
9.2 Neutron Specific Features for Biomacromolecules
9.3 Neutron Sources and Diffractometers for NPC in the World
9.4 Neutron Diffractometer for Protein Crystallography in J-PARC-iBIX
9.5 Recent Results of iBIX—Protonation/Deprotonation
9.5.1 PcyA-BV Complex (Complex of Phycocyanobilin: Ferredoxin Oxidoreductase and Biliverdin IXα)
9.5.2 Cellullase and Substrate Complex
9.5.3 Farnesyl Pyrophosphate Synthase (FPPS)-Drug Complex
9.6 The Latest Progresses in Neutron Measurements for Protonation/Deprotonation
9.6.1 High-Pressure Freezing
9.6.2 Electron Spin Resonance Experiments for Dynamic Nuclear Polarization
9.6.3 Dynamic Nuclear Polarization
9.7 The Future Development in Neutron Sources—Expectation to the Second Target Station in J-PARC
9.8 Conclusion
Acknowledgements
References
10 All-Atom Analysis of Free Energy of Protein Solvation Through Molecular Simulation and Solution Theory
Abstract
10.1 Introduction
10.2 Energy-Representation Method as an Endpoint Calculation of the Solvation Free Energy
10.3 Equilibrium Fluctuation in Pure-Water Solvent: The Compensation Between the Intramolecular and Hydration Effects and the Governing Interaction Identified by Correlation Analysis
10.4 Energetic Mechanism of Unfolding by Urea
10.5 Conclusions
References
11 Uni-directional Propagation of Structural Changes in Actin Filaments
Abstract
11.1 Introduction
11.2 Polymorphism of Pure Actin Filaments
11.3 Actin Filaments Interacting with ABPs Are Cooperatively Polymorphic
11.3.1 Cofilin
11.3.2 Myosin
11.3.3 Other ABPs
11.4 Uni-directional Propagation of Structural Changes of Actin Filaments Induced by Actin-Binding Proteins
11.5 Possible Functional Implications of Uni-directional Propagation of Structural Changes of Actin Filaments
11.5.1 Role as Signaling Wires
11.5.2 Role in Force Generation by Myosin
References
12 Functional Mechanisms of ABC Transporters as Revealed by Molecular Simulations
Abstract
12.1 Introduction
12.2 Role of ATP and Water in the Mechanism of the NBD Engine
12.2.1 Thermodynamics of NBD Dimerization
12.2.2 Kinetics of NBD Dimerization
12.2.3 The Free Energy of ATP Hydrolysis and the Mechanism of Its Generation
12.2.3.1 ATP Hydrolysis in Solution
12.2.3.2 ATP Hydrolysis in the NBD
12.3 Role of Coupling Helices (CHs) as a Mechanical Transmission
12.4 Mechanisms of the IF↔OF Conformational Transition of TMDs
12.4.1 Concerted NBD–TMD Motion in Exporters
12.4.1.1 Alternating Access Mechanism
12.4.1.2 Outward-Only Mechanism
12.4.2 Concerted NBD–TMD Motions in Importers
12.5 Conclusion and Perspectives
Acknowledgements
References
13 Statistical Thermodynamics on the Binding of Biomolecules
Abstract
13.1 Introduction
13.2 Entropic Excluded-Volume Effect: The Physical Origin of Water-Entropy Gain upon Binding of Biomolecules
13.3 Calculation of the Thermodynamic Quantities
13.4 Mechanism of Binding Between Intrinsically Disordered Peptides and Their Target Molecules
13.4.1 Case 1: Binding of an IDP Region of Prion Protein to a Partner RNA Aptamer
13.4.2 Case 2: One-to-Many Molecular Recognition by p53CTD Accompanying Target-Dependent Structure Formation
13.5 Mechanism of Actin–Myosin Binding
13.6 A Unified Theoretical Framework
References
Functioning Mechanisms of Protein Machinery
14 Ratchet Model of Motor Proteins and Its Energetics
14.1 Introduction
14.2 Ratchet Model of Molecular Motors
14.3 Second Law of Thermodynamics and Heat
14.4 First Law of Thermodynamics and Work
14.5 Experimental Measurement of Work
14.6 In the Case of Perfect Coupling
14.7 Experimental Measurement of Heat
References
15 Single-Molecule Analysis of Actomyosin in the Presence of Osmolyte
Abstract
15.1 Introduction
15.2 The Effect of Sucrose on Ensemble Myosin-V Motility
15.3 The Effect of Sucrose on Single Myosin-V Motility
15.4 The Effect of Sucrose on Transient Kinetics of ATP Hydrolysis Cycle
15.5 Force Measurement in the Presence of Sucrose
15.6 Conclusion
References
16 Novel Intermolecular Surface Force Unveils the Driving Force of the Actomyosin System
Abstract
16.1 Introduction
16.2 Hydration State of Actomyosin
16.2.1 Preparation of Actomyosin for Hydration Measurements
16.2.2 Hydration Properties of Actomyosin S1 with ADP
16.3 Calculation of Solvation Free Energy of Glycine and Small Proteins Under an External Electric Field
16.3.1 Method of the Solvation Free Energy Calculation
16.3.2 Solvation Free Energy of a Polar Organic Molecule Under the Electric Field
16.3.3 Solvation Free Energy of Small Proteins Under the Electric Field
16.4 Conclusion
References
17 Extremophilic Enzymes Related to Energy Conversion
Abstract
17.1 Introduction
17.2 Extremophilic Environments and Microorganisms
17.2.1 Extreme Environments on the Earth
17.2.2 Extremophiles Living in Extreme Environments
17.2.3 The Concept of Habitability and Extremophiles Living on the Edge
17.3 Enzymatic Adaptations to Extreme Environments
17.3.1 Thermophilic Enzymes
17.3.2 Piezophilic Enzymes
17.3.3 Psychrophilic Enzymes
17.3.4 Halophilic Enzymes
17.3.5 Acidophilic and Alkaliphilic Enzymes
17.4 Energy Conversion of Thermophiles and Their Machineries
17.5 Energy Conversion of Halophiles and Their Machineries
17.5.1 ATP Hydrolysis by Halophiles
17.5.2 Hydrolysis of High-Energy Phosphate Compounds by Extreme Halophiles
17.5.2.1 Biochemical Features of Halophilic Enzymes Related to Energy Conversion
17.5.2.2 Thermodynamic Measurement of Enzymatic Reactions by Halophilic Enzymes
17.6 Summary and Perspective
17.7 Conclusions
References
18 Functioning Mechanism of ATP-Driven Proteins Inferred on the Basis of Water-Entropy Effect
Abstract
18.1 Introduction
18.2 Crucial Importance of Water-Entropy Effect in Biological Systems
18.3 Outline of Functioning Mechanism of ATP-Driven Proteins
18.3.1 Chemical Reaction: Hydrolysis or Synthesis of ATP
18.3.2 A Protein Coupled with Irreversible Chemical Reaction
18.4 Entropic Force and Entropic Potential
18.4.1 Entropic Force and Entropic Potential Induced Between a Planar Wall and a Large Sphere
18.4.2 Entropic Force and Entropic Potential Acting on a Large Sphere Along a Large Body
18.4.3 Control of a Movement of a Large Solute Along a Large Body
18.5 Mechanism of Unidirectional Movement of Myosin Head (S1) Along F-Actin
18.5.1 Physical Basis
18.5.2 Physical Picture of Unidirectional Movement Coupled with ATP Hydrolysis Cycle
18.5.2.1 Case (1)
18.5.2.2 Case (2)
18.5.3 Problems to Be Solved
18.5.4 Drawbacks of Conventional View
18.6 Roles of ATP Hydrolysis Cycle and Water
References
19 Controlling the Motility of ATP-Driven Molecular Motors Using High Hydrostatic Pressure
Abstract
19.1 Introduction
19.2 High-Pressure Microscope
19.3 Sliding Movements of Kinesin Motors Along a Microtubule
19.4 Single-Molecule Analysis of the Rotation of F1-ATPase
19.5 Future Direction
Acknowledgements
References
20 Modulation of the Sliding Movement of Myosin-Driven Actin Filaments Associated with Their Distortion: The Effect of ATP, ADP, and Inorganic Phosphate
Abstract
20.1 Introduction
20.2 Analyses of Fluctuations of Fluorescence and Motility
20.2.1 Fluorescence Labeling for Actin Filaments
20.2.2 Precise Determination of Displacements in the Motility Assay
20.2.3 Distribution Profile of Fluorescence Images
20.3 Correlation Between Fluctuation of the Fluorescent Image and Displacement
20.4 Effect of ADP and Pi on Motility with ATP Hydrolysis
20.4.1 Effect on Sliding Velocity and Its Variance
20.4.2 Effect on the Correlation Between Velocity and Distortion
20.5 The Concept of Coordination with Distortions
20.6 Conclusion and Perspective
References
← Prev
Back
Next →
← Prev
Back
Next →