It is a common understanding that the molecular recognition (MR) is an essential elementary process for protein to function. The molecular recognition is a thermodynamic process which is characterized by the free energy difference between two states of a host-guest system, bound and unbound. On the other hand, the time to reach the thermodynamic equilibrium depends on the free energy barrier mainly associated with the conformational fluctuation of protein. Therefore, the molecular recognition is a thermodynamic process conjugated with the conformational fluctuation of protein.It is widely accepted that water plays an essential role for MR processes, i.e., �hydration� and �dehydration.� However, water is not only the one which plays essential role in MR, but existence of �eletcrolytes� at active sites, in many cases, is crucial for determining the binding mode of a ligand. So, a theoretical treatment of a MR process should be able to account for both water and electrolytes in consistent manner.We have been developing a new theory for the molecular recognition by protein based on the statistical mechanics of liquids, or the 3D-RISM/RISM theory. The theory has demonstrated its amazing capability of predicting MR processes taking both water and electrolytes into account. In the talk, I will review some of our recent works concerning MR processes in which both water and electrolytes play crucial roles.

Ligand binding by protein probed with 3D-RISM microscope

244th National Meeting (2012)

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