Difference between revisions of "Team:Aalto-Helsinki/Modeling synergy"
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− | <h1>Synergy | + | <h1>Synergy model</h1> |
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<p>As such, this problem is quite difficult and would undoubtedly need a lot of research. Instead, we decided to simplify the situation: Could we simulate enzymes and substrates as particles in a cell and model enzyme reactions by simulating their interactions with each other?</p> | <p>As such, this problem is quite difficult and would undoubtedly need a lot of research. Instead, we decided to simplify the situation: Could we simulate enzymes and substrates as particles in a cell and model enzyme reactions by simulating their interactions with each other?</p> | ||
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+ | <p>It just so happens that we can do that. So we did. Our modeling team created a model using Python called the synergy model, as it models the effect of having different enzymes working together.</p> | ||
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<p>To compare between enzymes being close together and not being close together, the model simulates enzyme reactions inside a cell. The model behaves stochastically, and needs to be ran multiple times to ensure reliable results, as its results will vary according to pseudorandom variables.</p> | <p>To compare between enzymes being close together and not being close together, the model simulates enzyme reactions inside a cell. The model behaves stochastically, and needs to be ran multiple times to ensure reliable results, as its results will vary according to pseudorandom variables.</p> | ||
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<p>Settings with both joined enzymes and no joined enzymes were used to get the results presented. In addition to this, the model was tested with settings with competing enzymes to better represent the real-world scenario inside <i>E. coli</i>, where there are multiple competing enzymes consuming butyraldehyde.</p> | <p>Settings with both joined enzymes and no joined enzymes were used to get the results presented. In addition to this, the model was tested with settings with competing enzymes to better represent the real-world scenario inside <i>E. coli</i>, where there are multiple competing enzymes consuming butyraldehyde.</p> | ||
− | <p>The simulation space was set to represent a cross section of an <i>E. coli</i> bacteria. Time resolution of the simulations was set to 1 µs. The simulations considered the initial substrate’s concentration to be constant. The reaction probabilities for different enzymes were set at 15%. Total elapsed simulation time was 0.1 s. The amount of competing enzymes varied from 0% to 1500% of the other enzymes’ amounts between simulations. The other enzymes’ amounts were not varied between simulations. The simulation setting files are available <a href="https://static.igem.org/mediawiki/2015/7/72/Aalto-Helsinki_synergy_model_simulation_data.zip">here</a>.</p> | + | <p>The simulation space was set to represent a cross section of an <i>E. coli</i> bacteria. Time resolution of the simulations was set to 1 µs. The simulations considered the initial substrate’s concentration to be constant. The reaction probabilities for different enzymes were set at 15%. Total elapsed simulation time was 0.1 s. The amount of competing enzymes varied from 0% to 1500% of the other enzymes’ amounts between simulations. The other enzymes’ amounts were not varied between simulations. The simulation setting files are available <a href="https://static.igem.org/mediawiki/2015/6/66/Aalto-Helsinki_synergy_model_setting_files.zip">here</a>. The data files that were gotten from the simulations are available <a href="https://static.igem.org/mediawiki/2015/7/72/Aalto-Helsinki_synergy_model_simulation_data.zip">here</a>. The simulation itself can be downloaded <a href="https://static.igem.org/mediawiki/2015/f/f2/Aalto-Helsinki_synergy_model.zip">here</a>.</p> |
<p>The simulation results indicate that simulations with joined enzymes as opposed to unjoined enzymes achieved higher product creation rates. When more competing enzymes were present in the simulation, the difference between joined and unjoined enzymes became more apparent. In some simulations, joined enzymes got up to 400% reaction rate as opposed to non-joined enzymes. In most simulations, joined enzyme reaction rate changed between 150% and 400% of unjoined enzyme reaction rate, depending on how much competing enzymes there were. In all of the simulations joined enzymes performed as well or better than unjoined enzymes.</p> | <p>The simulation results indicate that simulations with joined enzymes as opposed to unjoined enzymes achieved higher product creation rates. When more competing enzymes were present in the simulation, the difference between joined and unjoined enzymes became more apparent. In some simulations, joined enzymes got up to 400% reaction rate as opposed to non-joined enzymes. In most simulations, joined enzyme reaction rate changed between 150% and 400% of unjoined enzyme reaction rate, depending on how much competing enzymes there were. In all of the simulations joined enzymes performed as well or better than unjoined enzymes.</p> | ||
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<figure style="margin-bottom:2%;"> | <figure style="margin-bottom:2%;"> | ||
<img src="https://static.igem.org/mediawiki/2015/e/e9/Aalto-Helsinki_Synergy_model_timecourse_0_80_300.png" style="max-width:100%;" /> | <img src="https://static.igem.org/mediawiki/2015/e/e9/Aalto-Helsinki_Synergy_model_timecourse_0_80_300.png" style="max-width:100%;" /> | ||
− | <figcaption><b>Figure 3:</b>Time course of | + | <figcaption><b>Figure 3:</b>Time course of end product amounts with both joined and unjoined enzymes and different amounts of competition.</figcaption> |
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<p>The model has some virtues. One of these is that the model is quite lightweight, and can simulate thousands of particles with the resources of a single machine in a reasonable time. The model is also quite flexible, and can be easily configured through the use of its settings file, in which the user can choose both the general settings concerning the simulation space and timescale as well as set the enzymes and substrates that are relevant to the reactions using a human readable file.</p> | <p>The model has some virtues. One of these is that the model is quite lightweight, and can simulate thousands of particles with the resources of a single machine in a reasonable time. The model is also quite flexible, and can be easily configured through the use of its settings file, in which the user can choose both the general settings concerning the simulation space and timescale as well as set the enzymes and substrates that are relevant to the reactions using a human readable file.</p> | ||
− | <p>All in all, the model can be useful if it's remembered that its predictions should be viewed as guidelines only, and if one remembers the simplifications made in the enzymes’ function. </p> | + | <p style="margin-bottom:0;padding-bottom:10%;">All in all, the model can be useful if it's remembered that its predictions should be viewed as guidelines only, and if one remembers the simplifications made in the enzymes’ function. </p> |
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Latest revision as of 06:41, 17 September 2015