Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift

The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is associated with amyotrophic lateral sclerosis (ALS). The 311–360 fragment of TDP-43 (TDP-43311–360), the amyloidogenic core region, can spontaneously aggregate into fibrils, and the ALS-associated mutation G335D has an enhanced effect on TDP-43311–360 fibrillization. However, the molecular mechanism underlying G335D-enhanced aggregation at atomic level remains largely unknown. By utilizing all-atom molecular dynamics (MD) and replica exchange with solute tempering 2 (REST2) simulations, we investigated influences of G335D on the dimerization (the first step of aggregation) and conformational ensemble of the TDP-43311–360 peptide. Our simulations show that G335D mutation increases inter-peptide interactions, especially inter-peptide hydrogen-bonding interactions in which the mutant site has a relatively large contribution, and enhances the dimerization of TDP-43311–360 peptides. The α-helix regions in the NMR-resolved conformation of the TDP-43311–360 monomer (321–330 and 335–343) play an essential role in the formation of the dimer. G335D mutation induces helix unfolding and promotes α-to-β conversion. G335D mutation alters the conformational distribution of TDP-43311–360 dimers and causes population shift from helix-rich to β-sheet-rich conformations, which facilitates the fibrillization of the TDP-43311–360 peptide. Our MD and REST2 simulation results suggest that the 321–330 region is of paramount importance to α-to-β transition and could be the initiation site for TDP-43311–360 fibrillization. Our work reveals the mechanism underlying the enhanced aggregation propensity of the G335D TDP-43311–360 peptide, which provides atomistic insights into the G335D mutation-caused pathogenicity of TDP-43 protein.