Stability and Dynamics of the N-Terminal Domain of TDP-43 and the Effect of Point Mutations

TAR DNA-binding protein (TDP-43) has been identified as a major pathological protein in several neurodegenerative diseases. The stable, folded structure of its N-terminal domain (NTD) is thought to be requisite for its physiological function, with any structural disruption potentially leading to aberrant aggregation. In the present study, we have employed long, unbiased all-atom molecular dynamics (MD) simulations to study the conformational stability of the NTD monomer and two of its mutants (L27A and L28A). Since the choice of force field can significantly impact simulation outcomes, we used two different force fields (CHARMM36m and CHARMM36mW). In agreement with experimental data, our simulations using both force fields conclusively demonstrate that the wild-type NTD and the L27A mutant remain structurally stable, while the L28A mutation significantly disrupts tertiary contacts, exposing buried hydrophobic residues and thereby destabilizing the folded structure. Furthermore, across all systems, CHARMM36m simulations exhibited greater overall stability than CHARMM36mW, consistent with our previous study on Aβ fibrils. Importantly, our simulations provide mechanistic insights at the atomic level with significant implications for understanding the NTD’s role in both normal cellular function and pathological aggregation.