Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid -peptide

Alzheimer's disease (AD) is a neurodegenerative disorder that is characterized by the formation of extracellular amyloid-beta (A beta) plaques. The underlying cause of AD is unknown, however, post-translational modifications (PTMs) of A beta 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 beta, Glu3 and Glu11. This modification of A beta involves the truncation and charge-neutralization of N-terminal glutamate, causing A beta to become more hydrophobic and prone to aggregation. The molecular mechanism by which the introduction of pyroglutamate (pE) promotes aggregation has not been determined. To gain a greater understanding of the role that charge neutralization and truncation of the N-terminus plays on A beta conformational sampling, we used the Drude polarizable force field (FF) to perform molecular dynamics simulations on A beta(pE3-42) and A beta(pE11-42) and comparing their properties to previous simulations of A beta(1-42). The Drude polarizable FF allows for a more accurate representation of electrostatic interactions, therefore providing novel insights into the role that charge plays in protein dynamics. Here, we report the parametrization of pE in the Drude polarizable FF and the effect of pyroglutamylation on A beta. We found that A beta(pE3-42) and A beta(pE11-42) alter the permanent and induced dipoles of the peptide. Specifically, we found that A beta(pE3-42) and A beta(pE11-42) have modification-specific backbone and sidechain polarization response and perturbed solvation properties that shift the A beta conformational ensemble.