Generic Cell Cycle Model

Equations

The molecular mechanism on our wiring diagram is representation of the suggested biochemical reactions between the regulatory proteins of a general cell cycle engine. The chemical reactions of the interacting molecules can be translated to differential equations by using the principles of biochemical kinetics.

A reaction of the wiring diagram can be described by mass action, Michaelis-Menten and more sophisticated kinetic functions which of these we used at different regulations we chose from our earlier models of cell cycle regulation of individual organisms Chen et al., 2004 , Tyson et al., 2002 , Novak & Tyson, 1997 , Sveiczer et al., 2000 , Novak & Tyson, 1993 , Novak & Tyson, 2004 , Ciliberto et al., 2003 . When a step appears in more than one organism then we used the more complicated function in this model and with parameter changes we compensated this in the case of other organisms. We use the Goldbeter-Koshland function Goldbeter & Koshland, 1981 to model sharp switches for protein activities which quickly changes between active and inactive forms.

We use arbitrary units (au) for concentration units in all equations while we do not know the actual concentrations of most of the regulatory proteins in the cell.

Cdk/cyclin complexes:

Other regulators:

where:

GK is the Goldbeter-Koshland function:

for simulations of periodic cell cycles:

mass = mass/2, when actCycB crosses 0.1 (fission yeast), 0.2 (budding yeast), 0.3 (Mammalian cells) from above.