Mechanism of Functional Expression of F1-ATPase (SpringerBriefs in Molecular Science)

This book presents a new view of the mechanism of functional expression of ATP-driven motors (proteins or protein complexes). It is substantially different from the prevailing idea that the motor converts chemical energy to mechanical work. To facilitate understanding, the differences between the new and prevailing views are explained using many illustrations. The book is of interest to those who are not convinced of the notion of chemo–mechanical coupling. The claims presented are the following: The system, which comprises not only the motor but also water, does no mechanical work during the ATP hydrolysis cycle; a protein is moved or a protein in the complex is rotated by the entropic force generated by water. The highlight of the explanation in the book is that the mechanism of unidirectional rotation of the central shaft in F 1 -ATPase is discussed in detail on the basis of this new view. The hydration entropy of each β subunit to which a specific chemical compound (ATP, ADP and Pi, Pi, or nothing) is bound, the hydration entropy of the α 3 β 3 complex, and the dependence of the hydration entropy of F 1 -ATPase on the orientation of the γ subunit play essential roles. Preface Acknowledgments Contents 1 Introduction References 2 A New View on Mechanism of Functional Expression of an ATP-Driven Molecular Motor 2.1 Coupling of a Molecular Motor and ATP Hydrolysis Reaction 2.1.1 Thermodynamics of ATP Hydrolysis Reaction 2.1.2 ATP Hydrolysis Cycle Where a Molecular Motor Acts as a Catalyst for Hydrolysis Reaction 2.2 Involvement of a Protein or Protein Complex Catalyzing ATP Hydrolysis Reaction in ATP Hydrolysis Cycle 2.3 Crucial Importance of Hydration Entropy in Functional Expression of a Molecular Motor 2.4 Mechanism of Force Generation by Water for Moving or Rotating a Protein 2.5 Entropic Excluded-Volume Effect and Entropic Force and Potential Generated by Water 2.5.1 Entropy-Driven Formation of Ordered Structure 2.5.2 Simple Examples of Entropic Force and Potential 2.6 Roles of Electrostatic Interaction in Aqueous Solution Under Physiological Condition 2.7 Translational, Configurational Entropy of Water Leading Receptor-Ligand Binding and Protein Folding 2.8 Essential Roles of Water-Entropy Effect in Biological Processes 2.9 Recent Papers Pointing Out Crucial Importance of Hydration Effect on Unidirectional Movement of Myosin Along F-Actin 2.10 Problems in Prevailing View on Functional Expression of a Molecular Motor 2.11 Inconsistency of Prevailing View with Some of Recent Experimental Facts References 3 Mechanism of Unidirectional Rotation of γ Subunit in F1-ATPase 3.1 Definition of Packing Structure for a Protein or Protein Complex 3.2 Nonuniform Binding of Nucleotides to α3β3 or α3β3γ Complex 3.3 Theoretical Analyses on Packing Structure of α3β3γ Complex in Catalytic Dwell State 3.3.1 A State of α3β3γ Complex Stabilized: Catalytic Dwell State 3.3.2 Methods of Theoretical Analyses 3.3.3 Results of Theoretical Analyses 3.3.4 Packing Structure Stabilized by Water-Entropy Effect 3.3.5 Relation Between Chemical Compound Bound and Packing Efficiency in a β Subunit 3.4 Normal Rotation Under Solution Condition that ATP Hydrolysis Reaction Occurs: Rotation Mechanism 3.4.1 Basic Concept of Rotation Mechanism 3.4.2 Details of Rotation Mechanism 3.4.3 Crucial Importance of Water-Entropy Effect in Unidirectional Rotation 3.4.4 Change in System Free Energy During a Single Rotation 3.4.5 Effect of Electrostatic Attractive Interaction Between γ and β Subunits 3.5 Theoretical Analyses Based on Experimental Observations for Yeast F1-ATPase 3.6 Inverse Rotation Under Solution Condition that ATP Synthesis Reaction Occurs 3.6.1 State of α3β3γ Complex Stabilized 3.6.2 Details of Rotation Mechanism 3.7 Normal and Inverse Rotations with the Same Frequency (Rotations in Random Directions) Under Solution Condition that ATP Hydrolysis and Synthesis Reactions Are Equilibrated 3.8 Inverse Rotation Compelled by External Torque Imposed on Central Shaft and Occurrence of ATP Synthesis Under Solution Condition that ATP Hydrolysis Reaction Should Occur 3.8.1 What Will Happen When Inverse Rotation is Forcibly Executed? 3.8.2 Three Cases Where Normal Rotation Persists, Inverse Rotation Occurs, and Essentially no Rotations Occur When External Torque is Applied 3.8.3 Comparison with Experimental Results Observed When External Torque is Applied 3.8.4 Substantially Different Behavior Observed for a Mutant of F1-ATPase 3.8.5 FoF1-ATP Synthase References 4 Concluding Remarks 4.1 Functional Rotation of AcrB 4.2 Toward Investigation of Unidirectional Rotation of Central Shaft in V1-ATPase References 5 Appendix 1: Angle-Dependent Integral Equation Theory References 6 Appendix 2: Morphometric Approach References