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Curly'on - IGEM 2014 INSA-LYON

As functional amyloid fibers biosynthesis is still not totally understood, there aren't many models other than descriptive sketches that represent the curli formation. From these observations we decided to gather the information we could and build models from them as incomplete as they may be, in order to provide future teams working on engineered CsgA with a basis to start from.
We therefore were able to build up two models:

  1. the CurLy'on Simulator, a computed simulation of CsgA secretion and polymerization that, provided with the right parameters, could make for a good alternative to a mathematical model for a protein kinetics study;
  2. the implementation of the only two mathematical models we could find in the literature that seemed relevant (with biological justification) in describing in vitro CsgA polymerisation in C language in a fashion that can be given to a numerical solver, as these models require a heavy calculation power.

  • CurLy'on Simulator

  • Mathematical model

What is left to do

Unfortunately, as we lacked both time and the means to measure several parameters, both the CurLy'On Simulator and the mathematical models are not perfect yet.
Indeed, for the simulator, it is regrettable that we couldn't find anywhere the values of parameters such as the diffusion speed of soluble CsgA in the medium or its secretion rate through the CsgG channels. We also wished we had more time to add some features that we thought might bring even more modeling possibilities, like the implementation of an easy way to (cleanly) include differential equations in the speed calculation of specific particles to lead their movements and thus may represent phenomena such as attraction or protein targeting. Still, we believe our simulator to be a great tool for modeling, although it might prove a bit hard to get used to at first, and we would like to thank DUCHEMIN Louis and BERTHELIER Anthony who developed this program with us despite not being on the team.
As for the differential equations model, as mentioned earlier, what makes us most sorry is that we couldn't actually test the models since we didn't have computers powerful enough to take on the tremendous calculations required. However, once the verification is done, the next step for anyone willing to use it as base for their work would be to use it in a system involving CsgA production (with parameters specific to the used promoter) and secretion (delayed differential equations for the boldest ones, yay!), and maybe also involving the actions of CsgB.