Empty Sites en route to Binding

A binding site in a receptor or enzyme protein is seen as a constellation of amino acid side chains and peptide bonds in the backbone. The spatial 

A constellation of recognition groups is said to be meaningful when it allows long-distance recognition of the ligand or substrate (see Section 2.3.3). 

The role of water with protein molecules, stated in (ii) above, can be illustrated by some dehydration-rehydration studies of lysozyme reviewed by Finney (1986). The interpretation of the experimental data leads to several conclusions. A certain amount of water is essential at key sites in the enzyme the water facilitates a flexibility that is critical for the enzyme function and finally, the water permits a proton redistribution as the polar and charged groups revert to the aqueous solution order. 

Another example of (ii) above can be found in the conclusion of Kuhn et al. (1992), who proposed that the deep grooves in protein surfaces are formed by protein-water interactions. 

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