Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface

Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca(2+)-dependent species of AFP, however, it has not been clarified how 1 mol of Ca(2+)-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca(2+)-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca(2+)-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca(2+)-binding site. Firstly, the side-chains of four of the five Ca(2+)-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca(2+)-bound state. Second, a Ca(2+)-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca(2+)-binding. Third, the Ca(2+)-binding induces a generation of ice-like clathrate waters around the Ca(2+)-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca(2+)-binding enables the ice-binding of this protein.