An algorithm-based investigation reveals the differential dynamics of water inside protein cavity as a function of distance from its wall
Hydration forces exerted by water in the form of hydrogen bonding networks or electrostatic interactions play an essential role in protein structure and function. These interactions often govern chemical catalysis, ion transport, protein stability, and folding. While waters role as a biological solvent and on the protein surface is widely studied, its function inside protein cavities is often neglected due to the existing challenges in its detection using experimental and computational approaches. The importance of studying these special protein-water interactions is further underscored by the fact that water spatially confined within cavities exhibits deviations from bulk behavior, directly impacting processes occurring inside protein cavities. With these challenges in mind and building upon our method that accurately identifies the protein inner cavity surface (CICLOP), we have developed a tool that can accurately distinguish water occurring within cavities from the bulk solvent around the protein. Our tool can characterize the dynamic properties of water within protein cavities, such as diffusion, residence time, and rotational and orientational relaxation, using molecular dynamics (MD) simulation trajectories as input. We demonstrate the robustness of our tool on several cavity-containing proteins and describe its applicability in characterizing the biological function of water confined within the cavity of an archaeal group II chaperonin.