“There's been a lot of hype about computational biology, but it's actually only useful to address certain types of questions,” says Macara. “This was a compartmental problem, so it was relatively easy to set up the model.” Macara did so with the help of Virtual Cell, a program developed by Leslie Loew and colleagues at the University of Connecticut Health Center, Farmington, CT. Macara plugged in a lot of rate constants, binding constants, and protein concentrations, many of which had been determined in earlier biochemical experiments. The resulting model matched the response of live cells when injected with labeled Ran, even when the levels of certain binding proteins and exchange factors were altered before injection.
There was little effect on the steady-state transport kinetics after changing the levels or behaviors of a number of import factors. And yet the transport rate in vivo falls far short of the maximal rate seen in vitro, suggesting a control point. That control point may be Rcc1. This guanine nucleotide exchange factor converts recently imported RanGDP into RanGTP, thus triggering the discharge of Ran from its import carrier. The model showed that altering the levels of Rcc1 had the most profound effect on the rate of Ran transport. According to Macara, this kind of result “is something that's very hard to determine in a system where everything is coupled to everything else.” Now that he has the working model, however, Macara can determine how accessory factors might alter import, and ask why the cell uses adapters as well as carriers during import. ▪