Team:UNSW Australia/Model
MODEL
To develop an understanding of the engineered Symbiodinium’s heat shock and ROS response, dry lab modelling was done to supplement the enzyme and oligomerisation assays from the wet lab. In the absence of informative literature about heat shock proteins and response in algae, we conducted our own original research. On the atomic level, to understand the mechanisms behind the HSP enzyme complex’s holdase function we constructed protein structure models. On the macroscopic level, to understand how the new heat shock and ROS response, we constructed a mathematical model to predict how substrates in the system change. This culminated in a more comprehensive understanding of how our engineered symbiodinium could potentially be heat resistant in the Great Barrier Reef.
Mathematical
Heat shock and ROS responses are ubiquitous in living organisms as all environments have temperature fluctuations and a need to mitigate oxidative stress. Mathematical models of the new engineered system were compared to a model of the wild type system to predict the biochemical changes on the level of the cell. Both stochastic and deterministic versions of these models were implemented using the PySB library.
Structural
The central dogma of proteins is that with the understanding of the structure of a protein, comes the understanding of its function. We utilised fold recognition template modelling with the i-TASSER server to impose a reasonable 3D structure onto a sequence of peptides. After the refinement of these monomer models with molecular dynamics simulations, dimers and a larger 12mer complex was constructed to lead to an atomic understanding of how heat shock proteins function.
