On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: a molecular dynamics simulation study.

The structure stability of three α-helix bundle (the B domain of protein A) in an imidazolium-based ionic liquid (1-butyl-3-methylimidazolium chloride (BMIM-Cl)) is studied by molecular dynamics simulations. Consistent with previous experiments, the present simulation results show that the native structure of the protein is consistently stabilized in BMIM-Cl solutions with different concentrations. It is observed that BMIM(+) cations have a strong tendency to accumulate on protein surface whereas Cl(-) anions are expelled from protein. BMIM(+) cations cannot only have electrostatic interactions with the carbonyl groups on backbone and the carboxylate groups on negatively charged side chains, but also have hydrophobic interactions with the side chains of non-polar residues. In the meanwhile, the accumulation of large-size BMIM(+) cations on protein surface could remove the surrounding water molecules, reduce the hydrogen bonding from water to protein, and thus stabilize the backbone hydrogen bonds. In summary, the present study could improve our understanding of the molecular mechanism of the impact of water-miscible ionic liquid on protein structure.