A computational study on the hydration-shell properties of antifreeze and non-antifreeze proteins

Here we present a computational approach based on molecular dynamics (MD) simulation to study the hydration-shell density of several proteins which include a special group of proteins, namely antifreeze proteins, AFPs. AFPs have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. In particular, the hydration-shell density of eighteen dierent proteins comprising eight AFPs is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4{14%) for all studied proteins and that this increment strongly correlates with the protein size, while it does not depend on whether the protein is an AFP or not. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed according to which almost all of the hydration-density increase is located in pockets within, or at the surface of, the protein molecule. We then further investigated the local properties of the hydration shell around the ice-binding surface (IBS) of the AFPs. We found that the hydration shell density of the ice-binding surfaces is always higher than the bulk density and, thus, no ice-like (i.e. with a density lower than the bulk) layer is detected at the IBS. However, the local water-density around the IBS is found to be lower than that around the non-ice-binding surfaces and this dierence correlates to the higher hydrophobic character of the IBS with respect to the non-IBS. We hypothesize that the lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-icebinding surfaces might provide protection against ice growth. Finally, we tested our hypothesis by studying the dependence of the antifreeze activity of seven AFPs on various structural and chemical properties of the IBS and non-IBS and found that the activity strongly correlates with the dierence in the local hydration-shell properties of the non-ice-binding surfaces, rather than of the IBSs.