Concluding Remarks: Mechanism of Functional Expression Common in the Molecular Machines

Abstract

Let us take protein folding as an example. The initial and final states of the folding process are visually different: Protein is in unfolded and folded states, respectively. Therefore, it can readily be understood that protein folding spontaneously occurs as an irreversible process accompanying a decrease in the system free energy. On the other hand, the conformations of F1-ATPase before and after a 120° rotation of the central subunit, for example, are the same. Nevertheless, the directed rotation occurs. Hence, in the prevailing view, this rotation process is differently treated: It is made possible by converting the free energy of ATP hydrolysis to a work, and F1-ATPase is referred to as “molecular rotatory machine.” The work is necessary for the central subunit (i.e., γ subunit) to rotate against the viscous resistance force by water. Similarly, the unidirectional movement of S1 is realized by converting the free energy of ATP hydrolysis to a work that is necessary for S1 to move against the viscous resistance force by water. We disagree with this view (also see Sect. 3.2.5) In this chapter, we argue that protein folding and the directed rotation, for example, can be treated within the same theoretical framework.