|
Size: 2666
Comment: Copied from W3 Prac 4
|
Size: 2209
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Practical 4 = == Part 1 - Introduction to elementary modes analysis == '''(a)''' Load the toy model from previous exercises and repeat the examples from the [[ScrumPy/Doc/Tutorial/ScrumPyIntro|tutorial]]. What are the reactions involved in each mode? What are the net stoichiometries of each mode? |
= 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 [[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: |
| Line 5: | Line 5: |
| '''(b)''' Now introduce new reactions into your toy model in order to: ''(i)'' Generate new modes with the same net stoichiometries as previously; ''(ii)'' Generate modes with new net stoichiometries. | 1. The degradation of starch can contribute to the overall export of triose phosphate. 1. Many reaction fluxes appear to be strongly correlated in the face of changes to the local environment (e.g.) varying demand for TP 1. Likewise, many steady-state concentrations also appeared correlated. |
| Line 7: | Line 9: |
| == Part 2 - Elementary modes analysis of the Calvin cycle == In this exercise you will apply elementary modes analysis to a real metabolic system, namely the Calvin cycle of photosynthesis. In brief, plants have some enzymes that are turned on or off in light or dark conditions. The paper referred to in this exercise examines the significance of this, and the potential impact of deregulating one of the enzymes. |
The questions we therefore want to answer are: |
| Line 10: | Line 11: |
| 1. What are the routes from starch to TP? 1. Would these be feasible in the dark? 1. Are the correlations observed between fluxes the resulted of finely tuned enzyme activation/inhibition mechanisms, or something else? 1. 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 == |
|
| Line 12: | Line 19: |
| '''(b)''' Download and familiarise yourself with the following [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/CalvinModes.pdf|paper]]. For the purposes of the practical, ensure that you can relate the network diagrams to the reactions in the model file, and identify which are light activated and which are dark activated. | '''(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. |
| Line 14: | Line 21: |
| '''(c)''' Identify the ''light only'' and ''dark only'' reactions in Table 1 (in the paper) in your model, note that starch synthesis reaction (''!StSynth'') should be available under both conditions, whereas the light reaction should only be available under light conditions. You can add comments to your model like this: | '''(c) '''Calculate the elementary modes of the model. Which are the modes involving starch degradtion? Would you expect them to operate in the dark? |
| Line 16: | Line 23: |
| {{{ #this is a comment }}} '''(d)''' Make two new models - one for light conditions (i.e. comment out ''dark only'' reactions) and one for dark conditions. |
'''(d)''' Calculate the enzyme subsets. Which reactions will exhibit perfectly correlated fluxes at steady state. |
| Line 21: | Line 25: |
| '''(e)''' Load the new models and analyse the elementary modes. How many modes do they each have? What is their overall stoichiometries? | '''(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? |
| Line 23: | Line 27: |
| '''(f)''' If you compare the net stoichiometries of the elementary modes of the dark model with those listed in Table 3 in Poolman ''et al'' (2003), you may note that some modes are missing in your model. To reproduce the stoichiometries in Table 3 you need to define three new transporters of suitable metabolites. Remember to define the transporters as antiporters. | '''(f) MORE''' |
| Line 25: | Line 29: |
| '''(g)''' Identify the ''sedoheptulose-1,7-bisphosphatase'' reaction and include it in the dark model. What is the impact of this change in network topology on the elementary modes of the model? What is the biological significance? | '''(g) MORE <<BR>>''' |
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 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.
- 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 degradtion? Would you expect them to operate in the dark?
(d) Calculate the enzyme subsets. Which reactions will exhibit perfectly correlated fluxes at steady state.
(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?
(f) MORE
(g) MORE