Computer programs like those used in animated movies such as Shrek could soon be helping more cell biologists explain hypotheses — or even to make new discoveries, according to scientists presenting work in San Diego this month at the meeting for the American Society of Cell Biology.
“We want to be able to make predictions,” says Adrian Elcock of the University of Iowa in Iowa City. “At the very least we want our models to reproduce known behaviours.” Elcock is simulating the movement of proteins and other big molecules inside virtual bacterial cells. He built models from known data — including the atomic structures of proteins and concentrations of the 50 most abundant macromolecules in Escherichia coli — and then factored in how the molecular structure of each might cause proteins to stick to each other. His model nicely reproduces established data showing that green fluorescent protein diffuses approximately 10 times more slowly in the crowded environment of a bacterial cell than in a test tube.