Computational Studies of Beetle Anti-Freeze Protein Binding to Ice Ih

Many arctic fishes and polar terrestrial arthropods have evolved unique adaptive mechanisms as responses to frigid environments. Anti-freeze proteins (AFPs) can either prevent freezing by lowering the freezing point of internal fluids or (in combination with ice-nucleation proteins) reduce the damage by inhibiting recrystallization and stabilizing the cell membrane. In this thesis, I will present my research results on a computational study of beetle anti-freeze protein, specifically Dendroides Canadensis AFP (DAFP). Molecular dynamics (MD) simulation is a powerful technique for theoretical calculation which complements ongoing experimental efforts. OpenMD, a robust and efficient simulation package developed in my group, was utilized to investigate the mechanism of DAFP binding to the growth planes of ice-Ih. In order to sample the whole space, an orientational restraint was applied to drive the DAFP smoothly through the desired coordinates. Finally, weighted histogram analysis method (WHAM) was utilized to generate free energy profiles.