Free Energy Perturbation Simulations Measure the Change in Binding Affinity of the Aβ25-35 Peptide to the...

We designed and employed a relative free energy perturbation (FEP) combined with replica exchange with solute tempering (REST) all-atom molecular dynamics to investigate how Met35 oxidation affects the free energy of binding of the Aβ25-35 peptide to the DMPC lipid bilayer. We first showed that our restraint-free FEP/REST protocol delivers a converged sampling of alchemical transformations in the DMPC bilayer and in lipid-free water. Then, we determined that Met35 oxidation moderately reduced the peptide binding free energy by ΔΔG_b = 3.2 kcal/mol. Its reduction is driven by a partial cancellation of two large opposing factors. Oxidation makes binding less enthalpically favorable, but it also mitigates entropic losses. Ultimately, the entropic gain is insufficient to compensate for the enthalpic binding loss. Our analysis identified two sources of these energetic changes: (i) Met35 oxidation introduces minimal energetic frustration in water compared to the bilayer, and (ii) it produces strong entropic gains within the bilayer system. The latter takes place because Met35 oxidation disrupts the helical structure in Aβ25-35, expels the peptide from the bilayer core, and alleviates lipid disorder. Energetic and structural effects collected by us illuminate the molecular mechanism by which oxidation modulates Aβ25-35 properties, potentially explaining its reduced cytotoxicity.