Free Energy Molecular Dynamics Analysis of pH Sensitivity in Coiled-Coil Peptide Secondary Structure

Stimuli-responsive peptides are emerging as versatile tools for the design of biomaterials with tunable structural and functional properties. This study employs all-atom molecular dynamics simulations and umbrella sampling to investigate the impact of the E15K mutation on the pH-sensitive conformational stability of a coiled-coil peptide (PDB: 5EON). Unrestrained MD simulations indicate that both the wild-type peptide and its E15K mutant maintain stable alpha-helical structures across various protonation states, showing limited correlation with experimental observations of pH-dependent conformational transitions. Umbrella sampling along an end-to-end distance coordinate reveals subtle differences in the free energy landscapes, with E15K displaying a slightly flatter profile under acidic conditions, consistent with its experimentally observed pH-sensitive behavior. However, analyses of lysine sidechain interactions and salt bridge formation suggest minimal influence of electrostatic repulsion between lysine residues, suggesting that single-peptide simulations, and single end to end distance reaction coordinate can not fully capture intermolecular interactions or environmental effects critical to the experimentally observed responsiveness. These results highlight the complexity inherent in correlating molecular-level simulations to macroscopic peptide behavior.