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Team:Dundee/Project/NetlogoDoc
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Mop Simulation
Software by the Dundee iGEM team is distributed under the terms of the GNU General Public License. GNU General Public License
NetLogo is a multi-agent programmable modelling environment. Dundee iGEM Team used NetLogo as a tool to allow the visualisation of intracellular interactions within our bacterial mops and so to bring the dynamics to life. The aim was to create a simulation in which variables and characteristics can be altered, depending on the cells state, allowing us to observe the effect of such changes on the operation of the mop.
The wet team were utilising two pathways within the cell to transport Protein-Phosphatase 1 to the desired location. The sec system was used in both E. coli and B. Subtilis while the tat system was implemented in E. coli. A full explanation of how these pathways work can be found here.
Within this model, a scenario of our E. coli bacterial mop which utilised the sec protein-translocation pathway was analysed. The investigated section included the cytoplasm, inner & outer membranes, and the periplasm. Fig 1 shows how the world is set up and what the different agents represent.
NetLogo is a multi-agent programmable modelling environment. Dundee iGEM Team used NetLogo as a tool to allow the visualisation of intracellular interactions within our bacterial mops and so to bring the dynamics to life. The aim was to create a simulation in which variables and characteristics can be altered, depending on the cells state, allowing us to observe the effect of such changes on the operation of the mop.
The wet team were utilising two pathways within the cell to transport Protein-Phosphatase 1 to the desired location. The sec system was used in both E. coli and B. Subtilis while the tat system was implemented in E. coli. A full explanation of how these pathways work can be found here.
Model 1 – Sec System in E. Coli
Within this model, a scenario of our E. coli bacterial mop which utilised the sec protein-translocation pathway was analysed. The investigated section included the cytoplasm, inner & outer membranes, and the periplasm. Fig 1 shows how the world is set up and what the different agents represent.
We have several mechanisms in place in order to accurately simulate the operation of our bacterial mop. These come in the form of:
i. PP1 production
PP1 can be produced at a user-chosen rate from the right-side of the world (PP1-production slider). This is in simulation of PP1 from the rest of the cell entering our specific segment. Continuing this simulation, PP1 which encounters the right wall of the world is lost to the rest of the cell and so is removed in the simulation.
Although a similar system could be implemented for PP1 which encounters the upper and lower walls, we can simply assume that an equal number of molecules are lost to an equivalent segment above/below as enter the current segment. Thus, if a molecule of any kind encounters the top/bottom wall it will re-appear at the opposite wall (bottom/top respectively).
ii. Initial-PP1
The number of PP1 setup initially in the cytoplasm is controlled by the initial-PP1 slider, these are then placed at a set of random co-ordinates inside the cytoplasm. iii. Initial-SecB
The initial number of secB proteins (shown as green keys) can be controlled by the initial-SecB slider. PP1 must bind to these proteins before they are allowed to enter the sec gate and become transported at the membrane.The secB proteins cannot enter the periplasm.
iv. gate-size & gate-number
The sec gates have various alteration which can be made to them. The gate-size slider decides how wide each gate is and is measured in number of patches. The gate-number slider allows us to change how many gates are present in this segment of the cell. These gates are spaced an equal distance apart. Both of these properties allows us to predict how the cell could potentially work if the gates have different surface areas or if more gates were present in this area.
Once the PP1-secB complex reaches a gate, the PP1 passes into the periplasm and the secB protein is re-created in the cytoplasm and can be reused.
v. mc-production
Once in the periplasm, PP1 can then bind to microcystin. Microcystin is represented by small purple turtles which are produced (controlled by mc-production slider) at the left side (the cells outer membrane) and, like PP1, can leave the cell at the left but roll over to the top or bottom if they encounter those walls. Microcystin cannot enter the cytoplasm.
vi. mc-number There is also a slider to control the initial number of microcystin (mc-number) upon setup. These initial microcystin are, similarly to initial PP1, produced with a random position in the periplasm.
vii. degP-number
The black square agents represent degradation mechanisms. These degrade both PP1 and complexes which they encounter in the periplasm. An initial number of degradation mechanisms can be set up using the degP-number slider.
These cannot cross the inner or outer membranes but can roll over from top to bottom and vice versa.
Upon the binding of microcystin to PP1, the red circles representing PP1 become purple crosses called complexes. These represent the used PP1 molecules which has bound to a microcystin molecule. These cannot leave the cell or enter the cytoplasm but roll over from top to bottom and vice versa.
- Sliders
- Switches
- Input Controls
- Counters
- Graphs
1.Sliders
i. PP1 production
PP1 can be produced at a user-chosen rate from the right-side of the world (PP1-production slider). This is in simulation of PP1 from the rest of the cell entering our specific segment. Continuing this simulation, PP1 which encounters the right wall of the world is lost to the rest of the cell and so is removed in the simulation.
Although a similar system could be implemented for PP1 which encounters the upper and lower walls, we can simply assume that an equal number of molecules are lost to an equivalent segment above/below as enter the current segment. Thus, if a molecule of any kind encounters the top/bottom wall it will re-appear at the opposite wall (bottom/top respectively).
ii. Initial-PP1
The number of PP1 setup initially in the cytoplasm is controlled by the initial-PP1 slider, these are then placed at a set of random co-ordinates inside the cytoplasm. iii. Initial-SecB
The initial number of secB proteins (shown as green keys) can be controlled by the initial-SecB slider. PP1 must bind to these proteins before they are allowed to enter the sec gate and become transported at the membrane.The secB proteins cannot enter the periplasm.
iv. gate-size & gate-number
The sec gates have various alteration which can be made to them. The gate-size slider decides how wide each gate is and is measured in number of patches. The gate-number slider allows us to change how many gates are present in this segment of the cell. These gates are spaced an equal distance apart. Both of these properties allows us to predict how the cell could potentially work if the gates have different surface areas or if more gates were present in this area.
Once the PP1-secB complex reaches a gate, the PP1 passes into the periplasm and the secB protein is re-created in the cytoplasm and can be reused.
v. mc-production
Once in the periplasm, PP1 can then bind to microcystin. Microcystin is represented by small purple turtles which are produced (controlled by mc-production slider) at the left side (the cells outer membrane) and, like PP1, can leave the cell at the left but roll over to the top or bottom if they encounter those walls. Microcystin cannot enter the cytoplasm.
vi. mc-number There is also a slider to control the initial number of microcystin (mc-number) upon setup. These initial microcystin are, similarly to initial PP1, produced with a random position in the periplasm.
vii. degP-number
The black square agents represent degradation mechanisms. These degrade both PP1 and complexes which they encounter in the periplasm. An initial number of degradation mechanisms can be set up using the degP-number slider.
These cannot cross the inner or outer membranes but can roll over from top to bottom and vice versa.
Upon the binding of microcystin to PP1, the red circles representing PP1 become purple crosses called complexes. These represent the used PP1 molecules which has bound to a microcystin molecule. These cannot leave the cell or enter the cytoplasm but roll over from top to bottom and vice versa.
