Practical 3: Kinetics of the Calvin Cycle.

So far we have investigated simple models with a variety of techniques. Now it is time to bring these together and apply them to a model of realistic complexity.

When you have completed the exercises below, treat the model below as if you are in a virtual lab. Identify experiments that you would like to perform (first identify what you want to know about our in silico chloroplast). Now identify how to accomplish this on the computer. For example, in addition to external phosphate and the Vmax of the light reactions there are two other parameters that have a particularly strong impact on the model behaviour: The rate constant for the fast mass-action reactions "EQMult" and a factor that modulates the sensitivity of TPT to PGA - "PGA_xp_Mult" changing these influences the bi-stable behaviour, can this behaviour be abolished ?

1. Download the model

2. Note: for kinetics modelling you will need to tell ScrumPy to "work harder", by setting m.Tincr = 1.

3. Identify the enzyme subsets - what can you predict about relationships between assimilation flux and other fluxes in the system.
4. Identify the moiety conservation relationships and the associated parameters.
5. Determine flux responses to changing external phosphate (the parameter is "x_Pi_cyt").
6. Determine flux responses to changing light reaction activity (the parameter is "LR_vm").
7. Determine flux control coeeficients over assimilation, export, and storage fluxes. What relationships can you identify - can you explain them ?
8. Can you shift control away from SBPase to (for example) Rubisco. Hint: consider the result from exercise 3 in combination with the ratio of Vmax values.