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Kinetic modelling

FRAP experiments contain information about the diffusional properties of the studied molecule, but also about it’s binding characteristics. Using kinetic modeling and computer simulation, this information can be extracted and hypotheses can be evaluated in comparison with experimental data (Phair 2001).

The lifetime of different molecular states (e.g. freely diffusing or bound) can be simulated by calculating their rates of formation and decay (e.g. k_on and k_off). Two kinds of kinetic models are used by cell biologists for this purpose:

• Compartmental model:
  Biological processes are described by a finite number of compartments that contain a chemical species at a cellular location. Each compartment is defined as “well mixed” (the dynamics are not diffusion limited). The crossover of molecules between compartments represents exchange processes between different places (e.g. cytoplasm and ER), chemical states (e.g. phosphorylation) or chemical interactions (e.g. binding to receptormolecules).
  The transfer rates can be determined by fitting to best match the experimental data. Time is the only variable in a compartmental model.
• Spatial model:
  The cell is divided into a number of spatial elements. In each element the investigated molecule can transfer between different molecular states. Additionally these different molecular states can exchange with neighboring elements by diffusion.

Programs for kinetic modelling Program Link Comment SAAM II www.saam.com Easy compartmental model setup Berkeley Madonna www.berkeleymadonna.com compartmental model Mathlab www.mathworks.com Good graphic output possibilities Gepasi www.gepasi.org Spatial model Freeware Virtual Cell www.nrcam.uchc.edu Easy way to write spatial models freeware (academical use) WinSAAM www.winsaam.com freeware

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contact: Stefan Terjung           last update: 02/06/04