Section 23.4.4.3. Summary

Water molecules associated with proteins can be divided between those that are conserved as a result of their functional significance and those that are partially conserved or not conserved at all. The conserved water molecules are generally classified as buried or channel (by a variety of criteria). They tend to be present in the clefts between domains, are critical components of active sites, or bridge between secondary-structure elements. The water molecules that are not conserved occupy hydration sites with favourable hydrogen-bonding characteristics, where the presence of a water molecule is not essential for the structural or functional integrity of the protein.

The displacement of water molecules by organic solvent molecules in the elastase work described above showed that most displaced waters are those classified as surface or crystal-contact waters (Mattos et al., 2000). In the three cases where a buried water molecule was displaced, an alcohol hydroxyl oxygen was found to replace the protein–water hydrogen-bonding interactions. This is analogous to the active-site water molecule in the HIV aspartate protease that gets replaced by a carbonyl group of a potent cyclic urea inhibitor (Lam et al., 1994). In these situations, release of a tightly bound water molecule is entropically favourable, and its enthalpic interactions with the protein are compensated by similar protein–ligand interactions.

The effect of crystal contacts on the water structure was clearly illustrated in the T4 lysozyme work (Zhang & Matthews, 1994). The internal structurally conserved water molecules are unaffected by crystal contacts. Conversely, any of the surface water sites are potentially available either to be replaced by or to mediate crystal contacts, as 95% of the T4 lysozyme surface is involved in a crystal contact when all ten crystal forms are taken together.