Alkyl-tuned hydrophobic assistance boosts hydrogen bond-directed solvation regulation of α-helix magainin in choline...

Understanding the interaction mechanisms between ionic liquids (ILs) and proteins is crucial for advancing IL-based biocatalysis and pharmaceutical applications. This study employed molecular dynamics (MD) simulations to systematically demonstrate the structural and solvation behaviors of the α-helical peptide Magainin 2 (Mag2) in choline carboxylate ILs (ChoCn ILs, n = 2, 6, 10) across varying concentrations. Analyses of structural parameters and conformational snapshots revealed that ChoCn ILs with longer anionic alkyl chains enhance Mag2's α-helical stability, with intensifying effects at higher IL concentrations. Specifically, 0.50 M choline hexanoate (ChoC6) and 0.20 M or 0.50 M choline decanoate (ChoC10) systems effectively preserve Mag2's helical structural integrity, while other systems fail to preserve native conformation. This protective effect extends to two additional antimicrobial peptides, hylaseptin-4 (HSP-4) and Palustrin-Ca. Solvent distribution analysis, hydrogen bonds (H-bonds) and binding free energy calculations indicated that ChoCn ILs stabilize Mag2 through a chain length-dependent dual mechanism: C6^- anions anchor to Mag2 via carboxyl groups whereas C10^- anions form micelle-like assemblies enveloping the peptide. Anion accumulation near Mag2 is primarily driven by electrostatic interactions with positively charged residues, while hydrophobic interactions further enhance binding affinity. This unique polar/hydrophobic synergy positions ChoCn ILs as tunable peptide stabilizers. Our findings elucidate how hydrophobicity-tuned ChoCn ILs stabilize helical structures, establishing a theoretical foundation for rationally designing IL-based protein formulations.