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<h1>Simulation for Potsdam</h1> | <h1>Simulation for Potsdam</h1> | ||
− | <h6>The team from Potsdam has a project with some similarities with our own project. This leaded to collaboration on different fields of the iGEM competition, including modelling. As there was not much known about their system, a model would help with getting more insights and a better understanding. The main problem was that they didn’t know much about the aggregation principle, so we had to make some assumptions and test different approximations, and see how well they fit with the wet-lab results. | + | <h6>The team from Potsdam has a project with some similarities with our own project. This leaded to collaboration on different fields of the iGEM competition, including modelling. As there was not much known about their system, a model would help with getting more insights and a better understanding. The main problem was that they didn’t know much about the aggregation principle, so we had to make some assumptions and test different approximations, and see how well they fit with the wet-lab results.</h6> |
</br></br> | </br></br> | ||
<h2>Approximations</h2> | <h2>Approximations</h2> | ||
− | The first approximation was the concentration of their protein in the yeast cells. They found a rough estimation of a range, which was 0.1 - 1.4 uM. We therefore set the initial concentration to be 0.5 uM, which lies somewhere in between. For the association rate, we took the same as we used for our own simulation, namely 10e5 as found in the paper of Schlosshauer <sup>[1]</sup>. </br></br> | + | <h6>The first approximation was the concentration of their protein in the yeast cells. They found a rough estimation of a range, which was 0.1 - 1.4 uM. We therefore set the initial concentration to be 0.5 uM, which lies somewhere in between. For the association rate, we took the same as we used for our own simulation, namely 10e5 as found in the paper of Schlosshauer <sup>[1]</sup>. </br></br> |
The known information of the system includes the molecular weight of the protein, being 60.4 kDa and the droplet size, with an average diameter of 1.19 um. The weight of a single molecule can be used to approximate the volume of a single molecule with Protein Volume = 1.21 Molecular Weight <sup>[2]</sup>. This leads us to a volume of 73.084 A<sup>3</sup> per molecule. As 10 A=1 nm this means that 73.084 A<sup>3</sup> = 73,1 * 10<sup>-3</sup> nm<sup>3</sup> per molecule. | The known information of the system includes the molecular weight of the protein, being 60.4 kDa and the droplet size, with an average diameter of 1.19 um. The weight of a single molecule can be used to approximate the volume of a single molecule with Protein Volume = 1.21 Molecular Weight <sup>[2]</sup>. This leads us to a volume of 73.084 A<sup>3</sup> per molecule. As 10 A=1 nm this means that 73.084 A<sup>3</sup> = 73,1 * 10<sup>-3</sup> nm<sup>3</sup> per molecule. | ||
</br></br> | </br></br> | ||
− | Like the formula for the volume of the protein, there is a formula for the volume of spheres, which is more generally known, and defined as Volume Sphere = 4/3 &Pi r<sup>3</sup> . Using this formula, we got a volume of 0.88 um<sup>3</sup> = 0.88 * 10<sup>9</sup> nm<sup>3</sup>. When dividing the volumes, you would think that this means that there are about 1,2 * 10<sup>10</sup> proteins in one droplet. However, this is not quite the case, as you have to take into account that sphere packing has a lower density and that there are different ways of packing, and we don’t know which is applicable yet. If we assume there is a surrounding of 4 molecules, as in a tetrahedral lattice, there are only 4,1 * 10<sup>9</sup> molecules that should fit in the droplets. | + | Like the formula for the volume of the protein, there is a formula for the volume of spheres, which is more generally known, and defined as Volume Sphere = 4/3 &Pi r<sup>3</sup> . Using this formula, we got a volume of 0.88 um<sup>3</sup> = 0.88 * 10<sup>9</sup> nm<sup>3</sup>. When dividing the volumes, you would think that this means that there are about 1,2 * 10<sup>10</sup> proteins in one droplet. However, this is not quite the case, as you have to take into account that sphere packing has a lower density and that there are different ways of packing, and we don’t know which is applicable yet. If we assume there is a surrounding of 4 molecules, as in a tetrahedral lattice, there are only 4,1 * 10<sup>9</sup> molecules that should fit in the droplets. </h6> |
</br></br> | </br></br> | ||
<h2>Analysis of Results</h2> | <h2>Analysis of Results</h2> | ||
− | Because simulating that many molecules takes a lot of computer memory, which we didn’t have, we rescaled the system. A yeast cell has a volume of 42 um<sup>3</sup> <sup>[3]</sup> and we used a simulation box with the size of 10 um<sup>3</sup>. If we rescale the measured droplet size, which is 2% of the yeast volume, we expect to have cluster that also have a size of 2% of the initial amount of molecules. This would indicate that the simulated complexed would have an average size of somewhere around 60 molecules, as the initial amount of molecules was 3010. In the table below you can see what the results of the simulation for different valencies are, and that the average complex size of 60 lies between a valency of 3 and of 4. | + | <h6>Because simulating that many molecules takes a lot of computer memory, which we didn’t have, we rescaled the system. A yeast cell has a volume of 42 um<sup>3</sup> <sup>[3]</sup> and we used a simulation box with the size of 10 um<sup>3</sup>. If we rescale the measured droplet size, which is 2% of the yeast volume, we expect to have cluster that also have a size of 2% of the initial amount of molecules. This would indicate that the simulated complexed would have an average size of somewhere around 60 molecules, as the initial amount of molecules was 3010. In the table below you can see what the results of the simulation for different valencies are, and that the average complex size of 60 lies between a valency of 3 and of 4. |
</br></br> | </br></br> | ||
The team of Potsdam used disordered regions that can interact with itself, the valency is not specified and indeed can differ for each protein. | The team of Potsdam used disordered regions that can interact with itself, the valency is not specified and indeed can differ for each protein. | ||
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<div class="sources"> | <div class="sources"> | ||
<sup>[1] </sup>Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science (2004) 13:1660-1669 </br> | <sup>[1] </sup>Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science (2004) 13:1660-1669 </br> | ||
+ | <sup>[2] </sup> Harpaz, Gerstein and Chothia (1994) Structure 2, 641-649 (issue of July 15), | ||
+ | <sup>[3] </sup> R. Milo and R. Phillips, Cell Biology by the Numbers, ISBN: 9780815345374 (2015) | ||
</div> | </div> | ||
</html> | </html> | ||
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Revision as of 09:34, 1 November 2017