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

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. 

Part I: 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

Hideaki Takahashi

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

Shun-ichi Kidokoro

3.    Spatial Distribution of Ionic Hydration Energy and Hyper-mobile Water

George Mogami, Makoto Suzuki and Nobuyuki Matubayasi

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.

Ryo Akiyama

5.    Statistical mechanical integral equation approach to reveal the solvation effect on hydrolysis free energy of ATP and its analogue

Norio Yoshida and Fumio Hirata

6.    A Solvent Model of Nucleotide–protein interaction - Partition coefficients of phosphates in solvent-water mixtures-

Hideyuki Komatsu

 

Part II: Basis of Protein-Ligand and Protein-Protein Interactions

7.    Energetics of myosin-ATP hydrolysis by calorimetry

      Takao Kodama

8.    Orchestrated electrostatic interactions among myosin, actin, ATP, and water

      Mitsunori Takano

9.    Protonation/deprotonation of proteins by neutron diffraction structure analysis

      Ichiro Tanaka, Katsuhiro Kusaka, Nobuo Niimura

10.  All-atom analysis of free energy of protein solvation through molecular simulation and solution theory

      Nobuyuki Matubayasi

11.  Uni-directional propagation of structural changes in actin filaments

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

12.  Functional mechanisms of ABC transporters as revealed by molecular simulations

Tadaomi Furuta, Minoru Sakurai

13.  Statistical thermodynamics on the binding of biomolecules

Tomohiko Hayashi

 

Part III: Functioning Mechanisms of Protein Machinery

14.  Ratchet model of motor proteins and its energetics

Yohei Nakayama and Eiro Muneyuki

15.  Single Molecule Analysis of Actomyosin in the Presence of Osmolyte

Mitsuhiro Iwaki, Kohji Ito and Keisuke Fujita

16.  Novel intermolecular surface force unveils the driving force of actomyosin system

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

17.  Extremophilic enzymes related to energy conversion

Satoshi Wakai and Yoshihiro Sambongi

18.  Functioning mechanism of ATP-driven proteins inferred on the basis of water-entropy effect

Masahiro Kinoshita

19.  Controlling the motility of ATP-driven molecular motors using high hydrostatic pressure

Masayoshi Nishiyama

20.  Modulation of the sliding movement of myosin-driven actin filaments associated with their distortion: The effect of ATP, ADP, and inorganic phosphate

Kuniyuki Hatori and Satoru Kikuchi

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.