On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics

The stability of two small proteins, one composed of three α-helices (α-peptide) and another composed of a β-sheet (β-peptide) solvated in five different ionic liquids (ILs), is analyzed using replica exchange molecular dynamics (REMD) simulations. ILs are composed of 1-butyl-3-methylimidazolium (BMIM) cations, paired with five different anions of varying hydrophilicity and size, namely, Cl–, NO3–, BF4–, PF6–, and NTf2–. REMD simulations greatly improve structure sampling and mitigate bias toward the initial folded peptide structure, thereby providing more adequate simulations to study protein stability. Cluster analysis, DSSP analysis and derivation of radius of gyration, interaction energies, and hydrogen bonding are used to quantify structural peptide changes in a large temperature range from 250 to 650 K. α-Peptides are least stable in ILs that contain small anions with localized negative charge, such as in BMIM–Cl and BMIM–NO3. Destabilization is caused by direct electrostatic interactions of anions with α-helices that are exposed to the solvent. This destabilization is characterized not by unfolded but instead by compact misfolded structures. Also, β-peptides retain compact structures up to at least 400 K, below which unfolding hardly occurs. However, intrapeptide hydrogen bonds that constitute the β-sheet are not exposed to the solvent. Therefore, β-peptides are generally more stable than α-peptides in all considered ILs. Moreover, on contrary to α-peptides, β-peptides are least stable in less polar ILs, such as BMIM–PF6 and BMIM–NTf2, because dissolving β-sheets requires large structural changes of the peptide. Such transitions are energetically less opposed in ILs with weaker mutual ion coordination. A large interaction density within ILs, for example, in BMIM–Cl, is thus kinetically trapping β-peptides in the original folded state. Additionally, in BMIM–BF4, interactions with β-peptides are so weak, compared to an aqueous solvent, resulting in stronger interactions within the peptide, which extend β-sheets, hence causing misfolding of a different kind. The results reveal how direct ion–peptide interactions and solvent reorganization energy in ILs are both crucial in determining protein stability. These insights could translate into guidelines for the design of new IL solvents with improved protein stability