Different Intermolecular Interactions Drive Nonpathogenic Liquid–Liquid Phase Separation and Potentially Pathogenic Fibril Formation by TDP-43

Abstract

The liquid–liquid phase separation (LLPS) of proteins has been found ubiquitously in eukaryotic cells, and is critical in the control of many biological processes by forming a temporary condensed phase with different bimolecular components. TDP-43 is recruited to stress granules in cells and is the main component of TDP-43 granules and proteinaceous amyloid inclusions in patients with amyotrophic lateral sclerosis (ALS). TDP-43 low complexity domain (LCD) is able to de-mix in solution, forming the protein condensed droplets, and amyloid aggregates would form from the droplets after incubation. The molecular interactions regulating TDP-43 LCD LLPS were investigated at the protein fusion equilibrium stage, when the droplets stopped growing after incubation. We found the molecules in the droplet were still liquid-like, but with enhanced intermolecular helix–helix interactions. The protein would only start to aggregate after a lag time and aggregate slower than at the condition when the protein does not phase separately into the droplets, or the molecules have a reduced intermolecular helix–helix interaction. In the protein condensed droplets, a structural transition intermediate toward protein aggregation was discovered involving a decrease in the intermolecular helix–helix interaction and a reduction in the helicity. Our results therefore indicate that different intermolecular interactions drive LLPS and fibril formation. The discovery that TDP-43 LCD aggregation was faster through the pathway without the first protein phase separation supports that LLPS and the intermolecular helical interaction could help maintain the stability of TDP-43 LCD.

Disrupting pathologic phase transitions in neurodegeneration

“…Segments of the TDP-43 LCD can form both steric zippers and LARKS. Interestingly, the NTD appears to resist self-assemblies regulated by pathologic (LCD) self-interactions ( 72 ). Similarly, tau protein can be divided into distinct motifs: the negatively charged NTD and CTD and the positively charged proline-rich domain (PRD) and microtubule-binding domain (MTBD) ( Figure 1B ).…”

Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: anIn-SilicoStrategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders

“…Previous investigations have pinpointed interresidue interactions, particularly interactions involving S332 and W334, that contribute to structural conformational changes of TDP-43's amyloidogenic core and subsequent fibril formation. 49,56 It has been suggested by Zhuo et al that the lack of intramolecular interactions between S332 and neighboring residues has a potential impact on fibril initiation. 49 SSNMR with proton detection also revealed a close interaction between the indole Nε1-Hε1 of W334 and the side-chain carbonyl of Q343.…”

Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders

“…Our data (Figures 3 and 4) agree with previous investigations pinpointing inter-residue interactions, particularly interactions involving S332 and W334, that contribute to structural conformational changes of TDP-43's amyloidogenic core and subsequent fibril formation. 49,59 It has been suggested by Zhuo et al that the lack of intramolecular interactions between S332 and neighboring residues has a potential impact on fibril initiation. 49 SSNMR with proton detection also revealed a close interaction between the indole Nε1−Hε1 of W334 and the side-chain carbonyl of Q343.…”