Justin Lemkul

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Alzheimer’s disease (AD) is a neurodegenerative disorder that is characterized by the formation of extracellular amyloid- β (A β) plaques. The underlying cause of AD is unknown, however, post-translational modifications (PTMs) of A β have been found in AD patients and are thought to play a role in protein aggregation. One such PTM is pyroglutamylation, which can occur at two sites in A β, Glu3 and Glu11. This modification of A β involves the truncation and charge-neutralization of N-terminal glutamate, causing A β to become more hy- drophobic and prone to aggregation. The molecular mech- anism by which the introduction of pyroglutamate (pE) pro- motes aggregation has not been determined. To gain a greater understanding of the role that charge neutralization and trun- cation of the N-terminus plays on A β conformational sam- pling, we used the Drude polarizable force field (FF) to per- form molecular dynamics simulations on A β pE3-42 and A β pE11-42 and comparing their properties to previous simulations of A β 1-42. The Drude polarizable FF allows for a more accurate representation of electrostatic interactions, therefore pro- viding novel insights into the role that charge plays in pro- tein dynamics. Here, we report the parametrization of pE in the Drude polarizable FF and the effect of pyroglutamyla- tion on A β. We found that A β pE3-42 and A β pE11-42 alter the permanent and induced dipoles of the peptide. Specifically, we found that A β pE3-42 and A β pE11-42 have modification- specific backbone and sidechain polarization response and perturbed solvation properties that shift the A β conforma- tional ensemble.