Whole-cell computer simulation

April 1, 2011
Sugar Protein

Production of a sugar transporter protein (yellow dots) in the bacterium E. coli in response to sugar in the environment (credit: Luthey-Schulten Group)

Researchers at the Max Planck Institute of Biology in Germany and theoretical scientists at the University of Illinois have built a computer model of a bacterial cell that responds to sugar in its environment and accurately simulates the behavior of living cells.

Running simulations on models of two E. coli strains, the researchers were able to see that bacterial cell architecture affects the reactions that occur within the cells. When sugar was present in its environment, a longer, narrower E. coli strain was able to ramp up production of a sugar-transporter protein much more quickly than a bigger strain.

The computer simulation also showed how molecular crowding influences the behavior of a molecule that, when it binds to DNA, shuts down production of the sugar-transporter protein. Even when it wasn’t bound to DNA, this repressor remained close to the binding site because other molecules in the cell blocked its escape. These intracellular obstacles reduced its ability to diffuse away.

The new model is a first step toward an accurate simulation of a whole working cell, says says Illinois postdoctoral researcher Elijah Roberts and chemistry professor Zaida Luthey-Schulten.

Ref.: Elijah Roberts et al., Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study, PLoS Computational Biology, March 10, 2011.