Multiscale simulations of TDP-43 full-length uncover molecular determinants of its phase separation beyond N/C-terminal oligomerization.

Abstract

TAR DNA-binding protein 43 (TDP-43) is a multidomain protein involved in the regulation of RNA processing, and its aggregates have been observed in neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43 is composed of a well-folded N-terminal domain (NTD), two RNA recognition motifs (RRM1/2), an intrinsically disordered C-terminal domain (CTD), and short flexible linkers between folded domains. Recently, TDP-43 has been shown to undergo liquid-liquid phase separation (LLPS) to form membraneless compartments referred to as biomolecular condensates. While NTD oligomerization was shown to promote the phase separation of full-length TDP-43 strongly, CTD can also undergo LLPS on its own. However, the complete picture of domain-level intermolecular interactions of full-length TDP-43 within the biological condensates has remained unclear due to the challenges associated with its purification. Here, we utilize a multiscale simulation approach to get molecular-level insights into the role of interdomain interactions in TDP-43 phase separation. Atomistic, single-chain simulations show that interdomain contacts are mediated by electrostatic interactions. Our coarse-grained, condensed phase simulations also reveal that electrostatic interactions involving RRM/NTD-linker modulate the phase separation of TDP-43, in addition to the NTD/CTD-oligomerization. These findings should pave the way for a greater understanding of molecular determinants of TDP-43 phase separation.