Atomistic Insights\ninto the Stabilization of TDP-43\nProtofibrils by ATP

The aberrant accumulation of the transactive response\ndeoxyribonucleic\nacid (DNA)-binding protein of 43 kDa (TDP-43) aggregates in the cytoplasm\nof motor neurons is the main pathological hallmark of amyotrophic\nlateral sclerosis (ALS). Previous experiments reported that adenosine\ntriphosphate (ATP), the universal energy currency for all living cells,\ncould induce aggregation and enhance the folding of TDP-43 fibrillar\naggregates. However, the significance of ATP on TDP-43 fibrillation\nand the mechanism behind it remain elusive. In this work, we conducted\nmultiple atomistic molecular dynamics (MD) simulations totaling 20\nμs to search the critical nucleus size of TDP-43<sub>282–360</sub> and investigate the impact of ATP molecules on preformed protofibrils.\nThe results reveal that the trimer is the critical nucleus for TDP-43<sub>282–360</sub> fibril formation and the tetramer is the minimal\nstable nucleus. When ATP molecules bind to the TDP-43<sub>282–360</sub> trimer and tetramer, they can consolidate the TDP-43<sub>282–360</sub> protofibrils by increasing the content of the β-sheet structure\nand promoting the formation of hydrogen bonds (H-bonds). Binding site\nanalyses show that the N-terminus of TDP-43<sub>282–360</sub> protofibrils is the main binding site of ATP, and R293 dominates\nthe direct binding of ATP. Further analyses reveal that the π–π,\ncation−π, salt bridge, and H-bonding interactions together\ncontribute to the binding of ATP to TDP-43<sub>282–360</sub> protofibrils. This study decoded the detailed stabilization mechanism\nof protofibrillar TDP-43<sub>282–360</sub> oligomers by ATP,\nand may provide new avenues for the development of drug design against\nALS.