Structure and Function of Water Molecules Buried in the Protein Core

Although the formation of the apolar core is crucial for protein folding, protein interior is often packed sub-optimally and incorporates water molecules that leave the bulk solvent. On average, one buried water molecules is observed every 20-90 amino acids, depending on the protein dimension and structural class: more buried water molecules are observed in large proteins and less in alpha proteins. From a structural perspective, it was shown that buried water molecules tend to be as rigid as buried protein atoms, incline to form hydrogen bonds with backbone residues of loops, and often are in contact with other buried water molecules. From a functional perspective, buried water molecules have a stabilizing effect by filling internal cavities and by interacting with polar atoms buried in the protein core and may also act as lubricants to favor loop dynamics. Their exchange kinetics with the bulk solvent is quite variable, ranging from few tens of nanoseconds to few tens of milliseconds.