Repulsive vs Attractive Crowding Distinctly Regulate TDP-43 Condensates through Region-specific Structural Dynamics

Area of Science:

• Biophysics
• Neuroscience
• Molecular Biology

Background:

• TAR DNA-binding protein 43 (TDP-43) aggregation is a hallmark of neurodegenerative diseases.
• The C-terminal domain (CTD) of TDP-43 drives liquid-liquid phase separation (LLPS) and is intrinsically disordered.
• Understanding TDP-43 condensation is crucial for elucidating disease mechanisms.

Purpose of the Study:

• To investigate how different macromolecular crowding environments affect TDP-43 CTD phase behavior and internal organization.
• To elucidate the distinct mechanisms by which repulsive and attractive crowders modulate TDP-43 condensation.
• To define crowding as a regulatory factor influencing condensate structure and dynamics.

Main Methods:

• Residue-level coarse-grained simulations of TDP-43 CTD condensates.
• Systematic examination of repulsive (steric) and attractive (interaction-based) crowding conditions.
• Region-specific spatial and orientation analyses of condensate architecture and dynamics.

Main Results:

• Both repulsive and attractive crowders maintain correlations between compaction, dimerization, and phase separation.
• Repulsive crowders promote condensation via entropic stabilization; attractive crowders use competitive enthalpic interactions.
• Crowding actively reshapes condensate organization, with distinct effects on helical and intrinsically disordered regions (IDRs).
• Repulsive crowders centralize helices into a dense core, while attractive crowders redistribute them toward the interface.

Conclusions:

• Macromolecular crowding acts as a tunable knob to control region-specific redistribution and dynamics within TDP-43 condensates.
• Distinct entropic and enthalpic contributions of crowding modulate TDP-43 condensation, offering mechanistic insights into disease.
• Findings provide links to physiological modulators and suggest testable readouts for TDP-43 dysregulation.