Part I: Basis of ATP Hydrolysis Reaction1. 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
About the Author: 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.
