Conservation of water molecules in protein binding interfaces

The conservation of interfacial water molecules has only been studied in small data sets consisting of interfaces of a specific function. So far, no general conclusions have been drawn from large-scale analysis, due to the challenges of using structural alignment in large data sets. To avoid using structural alignment, we propose a solvated sequence method to analyse water conservation properties in protein interfaces. We first use water information to label the residues, and then align interfacial residues in a fashion similar to normal sequence alignment. Our results show that, for a water-contacting interfacial residue, substituting it into hydrophobic residues tends to desolvate the local area. Surprisingly, residues with short side chains also tend not to lose their contacting water, emphasising the role of water in shaping binding sites. Deeply buried water molecules are found more conserved in terms of their contacts with interfacial residues.