Theoretical Computer Science, vol. 410(33), pp. 3166–3185
GTP-binding proteins, Stochastic -calculus, Process modeling
- Luca Cardelli
- Emmanuelle Caron
- Philippa Gardner
- Ozan Kahramanoğulları
- Andrew Phillips
Abstract Rho GTP-binding proteins play a key role as molecular switches in many cellular activities. In response to extracellular stimuli and with the help of regulators (GEF, GAP, Effector, GDI), these proteins serve as switches that interact with their environment in a complex manner. Based on the structure of a published ordinary differential equations (ODE) model, we first present a generic process model for the Rho GTP-binding proteins, and compare it with the ODE model. We then extend the basic model to include the behaviour of the GDI regulators and explore the parameter space for the extended model with respect to biological data from the literature. We discuss the challenges this extension brings and the directions of further research. In particular, we present techniques for modular representation and refinement of process models, where, for example, different Rho proteins with different rates for regulator interactions can be given as instances of the same parametric model.