This brief discusses the mechanism of functional expression of a protein
or protein complex utilizing the ATP hydrolysis cycle or proton-motive
force from a unique point of view focused on the roles of water. A
variety of processes are considered such as the unidirectional movement
of a linear-motor protein along a filament, insertion of an unfolded
protein into a chaperonin and release of the folded protein from it,
transport of diverse substrates across the membrane by a transporter,
and directed rotation of the central subunit within a rotatory motor
protein complex. These topics are discussed in a unified manner within
the same theoretical framework. The author argues that water plays
imperative roles in the functional expression of these molecular
machines. A pivotal factor is the entropic force or potential
originating from the translational displacement of water molecules
coexisting with the molecular machines in the entire system.