Protein-nucleic acid interactions hydration

If intermolecular associations are formed, hydration water molecules are removed from the interacting parts of the surface of a protein or a nucleic acid. This occurs, if the macromolecules form complexes with other macromolecules or with small substrates as, for instance, in enzymatic reactions (see Fig. 23.11). Because the contact between these interacting molecules is direct, water of hydration molecules have to be displaced from both partners. The question arises whether the water molecules located at the surface jump into the bulk water or whether they glide along the surface of the macromolecule and give way to the incoming, interacting molecules. 

Cyclodextrins have had valuable industrial uses for a considerable time, particularly as agents to bind or release volatile molecules. Accurate predictions concerning the selectivity and stability of cyclodextrin-guest complexes are therefore of considerable interest both academically and practically." MD was used to simulate cyclodextrin hydrates" as a test of the applicability of the GROMOS program package to systems beyond proteins and nucleic acids. Other early MD simulations focused on interactions with guests such as enantiomers of methyl-2-chloropropionate. Comparisons between calculated thermodynamic properties for complexes formed by O -cyclodextrin with para-substituted phenols and the results of MM simulations led to improvements in force fields that described the interactions. MM2 simulations were used to support NMR data for the -cyclodextrin inclusion complex with benzoic acid. " The well-known catalytic effect of cyclodextrins has been modeled. For example, the relative rate increase of hydrolysis of S over R phenyl ester stereoisomers in the presence of -cyclodextrin... 

---