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.
