E-CELL Project: Towards Whole Cell Simulation

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  • E-CELL Project：細胞のコンピューターシミュレーション

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E-CELL Project (http://www.e-cell.org) was launched in 1996 at Keio University in order to model and simulate various cellular processes with the ultimate goal of simulating the cell as a whole. E-CELL System, a generic software package we have developed, enables us to model not only metabolic pathways but also other higher-order cellular processes such as protein synthesis and signal transduction. Using the system, we have successfully constructed a virtual cell with 127 genes sufficient for "self-support". The gene set was selected from the genome of Mycoplasma genitalium, and the metabolisms include transcription, translation, membrane transport, the glycolysis pathway for energy production, and the phospholipid biosynthesis pathway for membrane structure. Since all its proteins and membrane structure are modeled to degrade spontaneously over time, the virtual cell must keep synthesizing proteins and phospholipid bilayer to sustain its life. It thus uptakes glucose as its energy source, and emptying glucose in the environment would result in "cell death from hunger". During the starvation simulation, we found an interesting and rather counter-intuitive phenomenon: The number of intracellular ATP molecules momentarily increases despite empty glucose. We predict that this phenomenon could actually take place in real cells.

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