# Free Energy Perturbation Simulations Measure the Change in Binding Affinity of the Aβ25–35 Peptide to the Zwitterionic Bilayer Caused by Oxidation

## TL;DR

This study uses advanced simulations to show how oxidation of a specific amino acid in a peptide reduces its binding to a lipid bilayer, offering insights into its reduced toxicity.

## Contribution

A novel FEP/REST protocol was developed to measure binding affinity changes due to Met35 oxidation in Aβ25–35.

## Key findings

- Met35 oxidation reduces peptide binding free energy by 3.2 kcal/mol.
- Oxidation causes enthalpic loss but provides entropic gain in the bilayer.
- Structural changes from oxidation disrupt the peptide's helix and reduce lipid disorder.

## Abstract

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.