Browsing by Author "Lockhart, Christopher"
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Item All-Atom Explicit-Solvent Replica-Exchange Molecular Dynamics Simulations of the Alzheimer’s Disease Aβ Monomer(2015) Lockhart, Christopher; Lockhart, Christopher; Klimov, DmitriUsing all-atom explicit-solvent replica-exchange molecular dynamics simulations, we explored the changes in the conformational ensemble of the Aβ monomer in various environments. In the simplest case, the Aβ monomer in water forms mostly turn and random coil conformations. We show that the anti-aggregation agent ibuprofen, the zwitterionic DMPC lipid bilayer, and even the introduction of sequence truncation (to generate the Aβ29-40 monomer) are capable of dramatically altering Aβ conformations, resulting in a stable helical structure present in the peptide’s C-terminal. For comparison, the FDDNP biomarker and other sequence truncations (e.g., the Aβ23-40 and Aβ28-40 monomers) do not exhibit a strong influence on Aβ conformations. Thus, we conclude that there is an inherent helix propensity in the Aβ C-terminal that can only be revealed by certain environments.Item Methionine Oxidation Changes the Mechanism of Aβ Peptide Binding to the DMPC Bilayer(Scientific Reports, 2019) Lockhart, Christopher; Smith, Amy K.; Klimov, Dmitri K.Using all-atom explicit solvent replica exchange molecular dynamics simulations with solute tempering, we study the efect of methionine oxidation on Aβ10–40 peptide binding to the zwitterionic DMPC bilayer. By comparing oxidized and reduced peptides, we identifed changes in the binding mechanism caused by this modifcation. First, Met35 oxidation unravels C-terminal helix in the bound peptides. Second, oxidation destabilizes intrapeptide interactions and expands bound peptides. We explain these outcomes by the loss of amphiphilic character of the C-terminal helix due to oxidation. Third, oxidation “polarizes” Aβ binding to the DMPC bilayer by strengthening the interactions of the C-terminus with lipids while largely releasing the rest of the peptide from bilayer. Fourth, in contrast to the wild-type peptide, oxidized Aβ induces signifcantly smaller bilayer thinning and drop in lipid density within the binding footprint. These observations are the consequence of mixing oxidized peptide amino acids with lipids promoted by enhanced Aβ conformational fuctuations. Fifth, methionine oxidation reduces the afnity of Aβ binding to the DMPC bilayer by disrupting favorable intrapeptide interactions upon binding, which ofset the gains from better hydration. Reduced binding afnity of the oxidized Aβ may represent the molecular basis for its reduced cytotoxicity.