Modeling liquid-liquid phase separation and its impact on proteasomal substrate degradation.

Area of Science:

• Biochemistry
• Cell Biology
• Biophysics

Background:

• The proteasome is crucial for protein degradation via the ubiquitin-proteasome system.
• Proteasome-associated liquid-liquid phase separation (LLPS) occurs during substrate processing, but its mechanisms and functional roles are unclear.
• Radiation-sensitive 23 homolog B (RAD23B) is a substrate-shuttling factor involved in proteasomal degradation.

Purpose of the Study:

• To quantitatively characterize proteasome-associated LLPS mediated by RAD23B.
• To elucidate the regulatory mechanisms and functional roles of LLPS in proteasome-mediated degradation.
• To develop a predictive model for proteasomal LLPS dynamics.

Main Methods:

• Development of a reaction-diffusion model with thermodynamic constraints.
• Quantitative characterization of proteasome-associated LLPS dynamics.
• Analysis of LLPS effects on proteasome-mediated degradation efficiency.

Main Results:

• The model successfully captured experimental LLPS dynamics.
• A concentration-dependent phase transition boundary was identified, influenced by proteasome activity and molecular interactions.
• LLPS demonstrated bidirectional, context-dependent effects on degradation efficiency, enhancing or suppressing it.

Conclusions:

• LLPS is a key regulatory mechanism in proteasome-mediated protein degradation.
• The study provides a quantitative model for proteasomal LLPS, offering testable hypotheses.
• Understanding LLPS in proteasomal function is critical for elucidating cellular protein homeostasis.