The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery

1. Front Matter

   Pages i-ix

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2. Basis of ATP Hydrolysis Reaction

   1. Front Matter

      Pages 1-1

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   2. Free Energy Analyses for the ATP Hydrolysis in Aqueous Solution by Large-Scale QM/MM Simulations Combined with a Theory of Solutions

      • Hideaki Takahashi

      Pages 3-23

   3. Role of Metal Ion Binding and Protonation in ATP Hydrolysis Energetics

      • Shun-ichi Kidokoro

      Pages 25-32

   4. Spatial Distribution of Ionic Hydration Energy and Hyper-Mobile Water

      • George Mogami, Makoto Suzuki, Nobuyuki Matubayasi

      Pages 33-52

   5. 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

      • Ryo Akiyama

      Pages 53-67

   6. Statistical Mechanical Integral Equation Approach to Reveal the Solvation Effect on Hydrolysis Free Energy of ATP and Its Analogue

      • Norio Yoshida, Fumio Hirata

      Pages 69-85

   7. A Solvent Model of Nucleotide–Protein Interaction—Partition Coefficients of Phosphates Between Water and Organic Solvent

      • Hideyuki Komatsu

      Pages 87-99

3. Basis of Protein-Ligand and Protein-Protein Interactions

   1. Front Matter

      Pages 101-101

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   2. Energetics of Myosin ATP Hydrolysis by Calorimetry

      • Takao Kodama

      Pages 103-111

   3. Orchestrated Electrostatic Interactions Among Myosin, Actin, ATP, and Water

      • Mitsunori Takano

      Pages 113-122

   4. Protonation/Deprotonation of Proteins by Neutron Diffraction Structure Analysis

      • Ichiro Tanaka, Katsuhiro Kusaka, Nobuo Niimura

      Pages 123-140

   5. All-Atom Analysis of Free Energy of Protein Solvation Through Molecular Simulation and Solution Theory

      • Nobuyuki Matubayasi

      Pages 141-155

   6. Uni-directional Propagation of Structural Changes in Actin Filaments

      • Taro Q. P. Uyeda, Kien Xuan Ngo, Noriyuki Kodera, Kiyotaka Tokuraku

      Pages 157-177

   7. Functional Mechanisms of ABC Transporters as Revealed by Molecular Simulations

      • Tadaomi Furuta, Minoru Sakurai

      Pages 179-201

   8. Statistical Thermodynamics on the Binding of Biomolecules

      • Tomohiko Hayashi

      Pages 203-227

4. Functioning Mechanisms of Protein Machinery

   1. Front Matter

      Pages 229-229

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   2. Ratchet Model of Motor Proteins and Its Energetics

      • Yohei Nakayama, Eiro Muneyuki

      Pages 231-243

   3. Single-Molecule Analysis of Actomyosin in the Presence of Osmolyte

      • Mitsuhiro Iwaki, Kohji Ito, Keisuke Fujita

      Pages 245-256

   4. Novel Intermolecular Surface Force Unveils the Driving Force of the Actomyosin System

      • Makoto Suzuki, George Mogami, Takahiro Watanabe, Nobuyuki Matubayasi

      Pages 257-274

This book introduces recent progress in biological energetics from ATP hydrolysis to molecular machineries. The role of water is now recognized to be essential in biological molecular energetics. Although energetics is a rather distant field to many biologists, any working models for protein machineries such as protein motors, transporters, and other enzymes must be consistent with their energetics. Therefore, the book is intended to help scientists build systematic models of biomolecular functions based on three categories: (1) ATP hydrolysis reactions including ionic hydration and protonation–deprotonation of biomolecules, (2) protein–ligand/protein–protein interactions including hydration–dehydration processes, and (3) functioning mechanisms of protein machineries based on water functions. 

• ATP hydrolysis
• protein machinery
• motor mechanism
• hydration free energy
• biological energetics
• Protein-Ligand Interactions

• Institute of Engineering Education, Tohoku University, Sendai, Japan

  Makoto Suzuki

Makoto Suzuki graduated from Yamagata University in 1974 and received his Doctor of Engineering degree from Tohoku University in 1981. Following his studies, he worked at the Mechanical Engineering Laboratory (MEL/AIST) for eleven years, and at the National Institute for Advanced Interdisciplinary Research (NAIR/AIST) for five years. He moved from NAIR to Tohoku University as a professor in 1996. Using his improved-high-precision system of dielectric spectroscopy, he discovered hyper-mobile water (HMW) in the hydration layer of actin filaments, one of the contractile muscle proteins, in 2003. He organized "Water Plays the Main Role in ATP Energy Transfer" (2008-2012) as an Innovative Scientific Research Area, an interdisciplinary project focused on the energetics of protein machineries.

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