Tracking Water Molecules on Protein Surfaces

Abstract

Water is recognized to have many important roles in influencing protein structure, folding and function. Understanding protein hydration requires the elucidation of the effects of both the solvent and the protein. While a variety of physical techniques (e.g., X-ray crystallography, small-angle X-ray scattering (SAXS), electron microscopy, NMR spectroscopy, computer simulations) are available for the characterization of protein structures in the solid state and in solution, the description of the behavior of water molecules around proteins is much more problematic, owing to the peculiarities of preferentially bound waters (short residence times, higher average density than bulk water, etc.). Localizing water molecules on protein surfaces or in crevices requires the determination of anhydrous and hydrated protein volumes and surfaces, on the one hand, and elucidation of exact topographies of protein envelopes and possible (hydrophilic) water binding sites, on the other. The latter aspect requires knowledge of the 3D structure of proteins and of the amino acid (AA) building blocks.