Investigation of physical principles of protein phase transitions

Protein phase transitions, including liquid-to-solid aggregation and liquid-liquid phase separation, are fundamental processes underlying neurodegenerative disorders such as Alzheimer’s (the Aβ peptide and the tau protein), Parkinson’s (the α-synuclein protein), and Huntington’s diseases (the Htt protein). While the molecular mechanisms of aggregation have been extensively studied in vitro, applying these findings to living systems remains challenging due to the dynamic nature of protein synthesis and degradation. To address this, I develop a theoretical model incorporating monomer production, derive integrated rate laws, and analyze the aggregation kinetics of the Huntington’s disease-associated peptide HttQ45 and the tumor suppressor protein P53. This work highlights the impact of continuous monomer production on aggregation. I extend this theoretical framework to protein aggregation involving misfolding to assess whether misfolding or aggregation is the rate-limiting step for a dozen proteins. Beyond the interplay between protein aggregation and production, the interplay between protein aggregation and liquid-liquid phase separation is increasingly recognized as a key driver of pathological aggregation in vivo. For Aβ42 on lipid membranes, I quantify the free energy landscape of liquid-liquid phase separation (LLPS) and fibrillation, demonstrating that LLPS serves as a crucial intermediate step in facilitating aggregation. In the P301L variant of tau, I track individual tau molecules and monitor nucleation and elongation events inside condensates using total internal reflection fluorescence microscopy and spinning disk super resolution by optical pixel reassignment microscope. This reveals that the time-dependent changes in the physical and biochemical properties of biomolecular condensates are characterized by the coexistence of a growing solid phase of tau within a dense liquid phase. The liquid phase becomes increasingly confined to the pores of the growing fibril gel network, yet it retains its initial viscosity and surface tension, showing no signs of ageing. This underscores the critical role of spatial heterogeneity in condensate ageing. By integrating theoretical modeling and statistical analysis with kinetic and microscopy measurements, this thesis establishes a comprehensive framework for understanding protein aggregation in complex biological environments and proposes new strategies for modulating aggregation in neurodegenerative diseases.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2025

Author dc:creator

• Wei, Jiapeng

Advisor dc:contributor.advisor

• Knowles, Tuomas

• amyloid
• biophysics
• LLPS
• protein

Licence

• https://www.repository.cam.ac.uk/bitstreams/66294c26-6f64-4c00-8433-8aab79882aa5/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

Author Identifier

0000-0003-4146-0604

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/391840