Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP

The aberrant accumulation of the transactive response deoxyribonucleic acid (DNA)-binding protein of 43 kDa (TDP-43) aggregates in the cytoplasm of motor neurons is the main pathological hallmark of amyotrophic lateral sclerosis (ALS). Previous experiments reported that adenosine triphosphate (ATP), the universal energy currency for all living cells, could induce aggregation and enhance the folding of TDP-43 fibrillar aggregates. However, the significance of ATP on TDP-43 fibrillation and the mechanism behind it remain elusive. In this work, we conducted multiple atomistic molecular dynamics (MD) simulations totaling 20 μs to search the critical nucleus size of TDP-43_282–360 and investigate the impact of ATP molecules on preformed protofibrils. The results reveal that the trimer is the critical nucleus for TDP-43_282–360 fibril formation and the tetramer is the minimal stable nucleus. When ATP molecules bind to the TDP-43_282–360 trimer and tetramer, they can consolidate the TDP-43_282–360 protofibrils by increasing the content of the β-sheet structure and promoting the formation of hydrogen bonds (H-bonds). Binding site analyses show that the N-terminus of TDP-43_282–360 protofibrils is the main binding site of ATP, and R293 dominates the direct binding of ATP. Further analyses reveal that the π–π, cation−π, salt bridge, and H-bonding interactions together contribute to the binding of ATP to TDP-43_282–360 protofibrils. This study decoded the detailed stabilization mechanism of protofibrillar TDP-43_282–360 oligomers by ATP, and may provide new avenues for the development of drug design against ALS.