Chapter 2
A New View on Mechanism of Functional
Expression of an ATP-Driven Molecular
Motor
Abstract The ATP hydrolysis reaction can hardly occur in bulk aqueous solution
without a catalyst. An ATP-driven molecular motor, which acts as the catalyst, is
coupled with the reaction. Consequently, the reaction proceeds as the ATP hydrolysis cycle comprising the following events: the ATP binding to the molecular motor,
hydrolysis of ATP into ADP and Pi, and dissociation of ADP and Pi from the molecular motor. Water in which ATP, ADP, and Pi are dissolved as well as the molecular
motor (a protein or protein complex) forms the system of interest. In this system, the
ATP hydrolysis reaction catalyzed by the molecular motor occurs as an irreversible
process (i.e., a spontaneously occurring process). Upon each event in the ATP hydrolysis cycle, the molecular motor exhibits sequential changes in its configuration for
minimizing the system free energy. We rationalize the argument that the translational,
configurational entropy of water is a principal component of the system free energy.
A protein (e.g., myosin) is moved or a protein in the complex (e.g., the γ subunit in
the α 3 β 3 γ complex of F 1 -ATPase) is rotated in the direction where the water entropy
already maximized can be retained.
Keywords Self-assembly · Protein folding · Molecular recognition · Hydrophobic
effect · ATP · ADP · Actomyosin
2.1 Coupling of a Molecular Motor and ATP Hydrolysis
Reaction
2.1.1 Thermodynamics of ATP Hydrolysis Reaction
In the prevailing view, the attention is paid to the chemical energy stored in an ATP
molecule or the free energy of ATP hydrolysis reaction. However, the important
quantity is the free energy of ATP hydrolysis reaction.
The change in standard free energy G° < 0 of the chemical reaction, ATP + H 2 O
→ ADP + Pi (this is written as “ATP
4− +H 2 O → ADP
3− +Pi
2− +H
+ ” when the charge
balance is emphasized), is ~−12k B T (T = 298 K) [1] where k B is the Boltzmann
© The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2021
M. Kinoshita, Mechanism of Functional Expression of F 1 -ATPase,
SpringerBriefs in Molecular Science,
https://doi.org/10.1007/978-981-33-6232-1_2
5
A New View on Mechanism of Functional
Expression of an ATP-Driven Molecular
Motor
Abstract The ATP hydrolysis reaction can hardly occur in bulk aqueous solution
without a catalyst. An ATP-driven molecular motor, which acts as the catalyst, is
coupled with the reaction. Consequently, the reaction proceeds as the ATP hydrolysis cycle comprising the following events: the ATP binding to the molecular motor,
hydrolysis of ATP into ADP and Pi, and dissociation of ADP and Pi from the molecular motor. Water in which ATP, ADP, and Pi are dissolved as well as the molecular
motor (a protein or protein complex) forms the system of interest. In this system, the
ATP hydrolysis reaction catalyzed by the molecular motor occurs as an irreversible
process (i.e., a spontaneously occurring process). Upon each event in the ATP hydrolysis cycle, the molecular motor exhibits sequential changes in its configuration for
minimizing the system free energy. We rationalize the argument that the translational,
configurational entropy of water is a principal component of the system free energy.
A protein (e.g., myosin) is moved or a protein in the complex (e.g., the γ subunit in
the α 3 β 3 γ complex of F 1 -ATPase) is rotated in the direction where the water entropy
already maximized can be retained.
Keywords Self-assembly · Protein folding · Molecular recognition · Hydrophobic
effect · ATP · ADP · Actomyosin
2.1 Coupling of a Molecular Motor and ATP Hydrolysis
Reaction
2.1.1 Thermodynamics of ATP Hydrolysis Reaction
In the prevailing view, the attention is paid to the chemical energy stored in an ATP
molecule or the free energy of ATP hydrolysis reaction. However, the important
quantity is the free energy of ATP hydrolysis reaction.
The change in standard free energy G° < 0 of the chemical reaction, ATP + H 2 O
→ ADP + Pi (this is written as “ATP
4− +H 2 O → ADP
3− +Pi
2− +H
+ ” when the charge
balance is emphasized), is ~−12k B T (T = 298 K) [1] where k B is the Boltzmann
© The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2021
M. Kinoshita, Mechanism of Functional Expression of F 1 -ATPase,
SpringerBriefs in Molecular Science,
https://doi.org/10.1007/978-981-33-6232-1_2
5