Possible Allosteric Significance of Water Structures in Proteins

Abstract

In recent theoretical molecular dynamics studies of ion solvation and transport through the model peptide ionophore, gramicidin A, it has been observed that the waters forming a linear single file within the channel have solvation and dynamic properties quite different from those found in bulk water. Strongly correlated motions among the interior single file column of waters persist over 20 Å. A speculation is entertained that related water structures could provide a mechanism for long range enzymatic allosteric effects as an alternative to chemical action at a distance propagated through the protein itself. Two possible specific mechanisms are discussed, hydraulic and “proton wire”. As a further control mechanism, the possibility is considered of modulating the allosteric effect though protein motion to open or close the channel thus producing a “valve” in the hydraulic line or a “switch” in the proton wire.