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| The goal of this practical is to use what we have learned so far about structural analysis to answer the questions posed at the end of lecture 3, that were part of the motivation for this [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/CalvinModes.pdf|paper]](Poolman 2003). We had previously found, from the analysis of a kinetic model of the same system (which allows us to claculate steady-state values for individual fluxes and concentrations) that: | The goal of this practical is to use what we have learned so far about structural analysis to answer the questions posed at the end of lecture 3, that were part of the motivation for this [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/CalvinModes.pdf|paper]] (Poolman ''et al'' 2003). We had previously found, from the analysis of a kinetic model of the same system (which allows us to claculate steady-state values for individual fluxes and concentrations) that: |
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| 1. The degradation of starch can contribute to the overall export of triose phosphate. | 1. The degradation of starch can contribute to the overall export of triose phosphate (TP, the compounds PGA_ch, GAP_ch and DHAP_ch in the model). |
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| '''(c) '''Calculate the elementary modes of the model. Which are the modes involving starch degradtion? Would you expect them to operate in the dark? | '''(c) '''Calculate the elementary modes of the model. Which are the modes involving starch degradation? Would you expect them to operate in the dark? |
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| '''(d)''' Calculate the enzyme subsets. Which reactions will exhibit perfectly correlated fluxes at steady state. | '''(d)''' Calculate the enzyme subsets. Which reactions will exhibit directly proportional fluxes at steady state. Which are essential for the generation of triose phosphate? |
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| '''(e)''' Calculate the conserved moieties m.ConsMioeties(). This is actually the left null-space described in lecture 3. Each column defines a conservation relationship - what are they? | '''(e)''' Calculate the left null-space of the stoichiometry matrix (m.sm.!LNullSpace()). What does this tell you? Why is this result somewhat inconvenient? |
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| '''(f) MORE''' '''(g) MORE <<BR>>''' |
'''(f) '''The same information can be gained using m.!ConsMoieities(). This also returns a matrix. Identify 3 important differences. |
Practical 4 Structural Analysis of the Calvin Cycle
Introduction
The goal of this practical is to use what we have learned so far about structural analysis to answer the questions posed at the end of lecture 3, that were part of the motivation for this paper (Poolman et al 2003). We had previously found, from the analysis of a kinetic model of the same system (which allows us to claculate steady-state values for individual fluxes and concentrations) that:
- The degradation of starch can contribute to the overall export of triose phosphate (TP, the compounds PGA_ch, GAP_ch and DHAP_ch in the model).
- Many reaction fluxes appear to be strongly correlated in the face of changes to the local environment (e.g.) varying demand for TP
- Likewise, many steady-state concentrations also appeared correlated.
The questions we therefore want to answer are:
- What are the routes from starch to TP?
- Would these be feasible in the dark?
- Are the correlations observed between fluxes the resulted of finely tuned enzyme activation/inhibition mechanisms, or something else?
- Similarly, can we explain the correlations between concentrations - does this tell us anything about the need for the TP-Pi antiporter? Could it be replaced with something else?
Instructions
(a) Create and load the Calvin model as you learned in the previous practical.
(b) Make sure that you can relate the reactions and metabolites in the model to those in the diagrams in lecture 3 and the 2003 paper. The two reactions that have been commented out are only active in the dark and can be ignored for now.
(c) Calculate the elementary modes of the model. Which are the modes involving starch degradation? Would you expect them to operate in the dark?
(d) Calculate the enzyme subsets. Which reactions will exhibit directly proportional fluxes at steady state. Which are essential for the generation of triose phosphate?
(e) Calculate the left null-space of the stoichiometry matrix (m.sm.!LNullSpace()). What does this tell you? Why is this result somewhat inconvenient?
(f) The same information can be gained using m.ConsMoieities(). This also returns a matrix. Identify 3 important differences.