Molecular dynamics simulation study on winter flounder antifreeze protein and its binding mechanism

Abstract

Antifreeze proteins(AFP) are known to depress freezing point of water via noncolligative manner. HPLC6, the major component of the winter flounder, $\it Pseudopleuronectus americanus}$, is an alanine-rich antifreeze proteins comprising 37 amino acids and its X-ray crystal structure has recently been solved at 2.5 Å. The reported structure is that of a partially amphiphilic α-helix with most of the hydrophilic residues falling on one side of the helix. In order to study the antifreezing mechanism of the AFP and its structural effects on the antifreezing activity, molecular dynamics simulation for this protein in aqueous solution was carried out at two different temperatures(300K,253K). The results of these simulations showed that the binding mechanism of the antifreeze protein is mainly due to the adsorption of the molecule to the ice crystal surface and thereby inhibiting the ice growth. The hydrogen bonds between the threonine residues and the oxygen atoms in the ice play an important role in this mechanism. Mutation study of these threonine residues was also carried out to support this mechanism.