Abstract
There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.
Highlights
There are two molecular processes that are essential for living bodies to maintain their life
It was demonstrated with a few examples that the theory is able to probe a ligand molecule, including water, recognized by protein at its active site or a cavity in atomistic detail
Water molecules recognized by protein at its active site or a cavity are of special importance, since those water molecules play multiple roles when protein expresses its function, i.e., as substrates and nucleophiles in enzymatic hydrolysis reactions, controlling the ion mobility in an ion channel, and so on
Summary
There are two molecular processes that are essential for living bodies to maintain their life. The solvation free energy, including the electrostatic as well as the hydrophobic interactions involving water molecules, plays crucial roles for protein to fold into its native state There is another physicochemical process that is concerned with both the molecular recognition and self-organization, which is the structural fluctuation [22,23,24,25]. If one views the solute molecule as a “source of external force” exerted on solvent molecules, ρg(r) = (ρg(r) + ρ) is identified as the density distribution of solvent molecules in the “external force.” This identification called “Percus trick” is the key concept that made the formulation of the molecular recognition process possible by means of statistical mechanics [36].
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