Molecular Basis of Synergistic Tau Amyloid Core Inhibition by K311/K353 Acetylation via Microsecond MD Simulations

Neurofibrillary tangles, composed of aggregated Tau proteins, are a pathological hallmark of Alzheimer’s disease (AD). Within these tangles, the amyloid core is primarily formed by the microtubule-binding (MTB) repeats. Although site-specific acetylation has been implicated in the regulation of Tau aggregation, the atomic-level mechanisms by which individual acetylation events modulate the structure and interactions of amyloid-forming motifs remain incompletely understood. In particular, whether dual acetylation events may act cooperatively during early Tau assembly is still unclear. In this study, we used microsecond-scale all-atom molecular dynamics simulations to systematically examine the dimerization dynamics of the four Tau MTB repeat homodimers (R1–R4). Our simulations suggest that the relatively higher aggregation propensity of R3 and R4 may be associated with amyloidogenic, β-sheet-prone core sequences, in which the key lysine residues K311 and K353 are located. Further analysis indicates that acetylation at these sites attenuates early Tau dimerization: K353 acetylation appears to moderately destabilize the R4 dimer through steric effects and the disruption of intrachain salt bridges, resulting in a more disordered conformational ensemble. K311 acetylation shows a more pronounced inhibitory effect on R3 dimerization by neutralizing the positive charge of K311 and weakening key interchain salt bridges and π–cation interactions associated with the PHF6 motif. Notably, dual acetylation of K311 and K353 in the R3–R4 dimer produces a stronger-than-additive reduction in β-sheet formation. This potential synergistic effect arises from the combined disruption of the hydrophobic core and distal electrostatic interaction networks. In summary, our results provide a molecular-level explanation for how acetylation at K311 and K353 cooperatively modulates Tau dimerization and early amyloid nucleation, offering mechanistic insight into the role of lysine acetylation in Tau aggregation.