Molecular and systems level models of the effects of protein aggregation on the cell cycle

Student thesis: Doctoral ThesisDoctor of Philosophy


One of the greatest successes of the 20th century was the vast improvement in life expectancy. With this improvement came an increasing probability of being diagnosed with an age-related disease. The challenge for the 21th century is to improve the quality of life in old age. To manage or cure age-related diseases, we must first understand what ageing is, and how it causes death. In this project I take the model organism S. cerevisiae (budding yeast) and propose a mechanism for how replicative ageing causes cell death. The hypothesis is centred on proteins called chaperones, which aid in protein folding. As cells age, proteins misfold and bind together to form protein aggregates, causing chaperones to become increasingly busy disassembling and refolding. The increased workload on chaperones may cause cell death as chaperones are also involved in regulating the G1/S cell cycle transition. One chaperone, Ydj1, releases the G1 cyclin, Cln3 from the endoplasmic reticulum (ER), triggering the G1/S transition. Therefore, I propose that cell death is caused by cell cycle arrest, through insufficient chaperone availability to release Cln3 from the ER, caused by protein aggregation. To test this hypothesis, I created multiple mathematical models. First, I built a deterministic model of the G1/S cell cycle transition focusing upon the role of chaperones in cell size regulation. I built on previous work highlighting chaperones as growth rate sensors and expanded their model to include known positive feedback loops, creating switch-like dynamics. My model confirmed that chaperones are growth rate sensors and demonstrated how the transition is affected by mutations. Surprisingly, it found that bistability may not be present in the early G1/S transition, due in part to cell size sensors. Next, I created a stochastic model which coupled the cell cycle to the protein aggregation pathway, to investigate the effect of age upon the cell cycle. This confirmed that upon protein aggregation, the cell cycle progression becomes increasingly difficult, until cell cycle arrest occurs. I was able to qualitatively replicate multiple experiments and show how both mutations within the cell cycle, and changes in growth rate, can affect cellular lifespan. Finally, I wanted to investigate ageing in human neurons and the processes involved in neurodegenerative diseases. I identified 16 yeast proteins whose human homologues may be of interest to Parkinson’s disease, through combining multiple datasets conducted on budding yeast and known literature. I chose the human homologue of INP53, synaptojanin-1, to model structurally, as it is implicated in both Parkinson’s and Alzheimer’s diseases. Furthermore, synaptojanin-1 is similar to chaperones in its multi-functionality, being involved in both removing aggregates through autophagy and other pathways through PIP signalling, meaning it may also become increasingly busy during aggregation. I studied the structure of the 5-phosphatase domain, and its interaction with the signalling molecule phosphatidylinositol 4,5-bisphosphate (PIP2), using molecular dynamics. Simulations showed that it had a stable catalytic site. However, the current structure with one coordinating magnesium ion, may be incorrect, as potassium ions repeatedly approached the catalytic site, suggesting that this system may require two metal ions.
Date of Award1 Jun 2019
Original languageEnglish
Awarding Institution
  • King's College London
SupervisorAttila Csikasz-Nagy (Supervisor) & Edina Rosta (Supervisor)

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