Template:Groningen/Model
The IGEM team Groningen has invested a lot of effort into developing sophisticated models that simulates all parts of our project. In our quest for producing styrene from the polysaccharide cellulose, the first step is to get our enzymes to the place they need to go; cellulose. As the cellulose binding domain of our mini-cellulosome is responsible for this task, we characterized its cellulose binding properties by creating a cutting edge coarse grained molecular dynamics simulation and running it on our 6652 core supercomputer cluster peregrine. The simulation shows the cellulose binding domain as an affinity for cellulose several orders of magnitude higher than the enzymes alone and draw novel insights from this. However by restraining the enzymes together in a scaffold protein, the added rigidity might prove detrimental to enzyme activity. We used an advanced mathematical model to work out the complex system of differential equations that describe this restrained situation, and compared the results to the solubilized enzymes. Luckily, the model shows that restraining the enzymes only impacts their performance negligibly. Finally, we once more harnessed the supercomputing power at our disposal to simulate our synthetic styrene production pathway in the metabolism of S. cerevisiae using a flux based model. We confirmed that yeast is indeed capable of simultaneous growth and high theoretical styrene production. Most strikingly however, we discovered several important metabolic engineering targets, some of which are corroborated by empirical evidence, while others are entirely novel discoveries. Overall all our models have provided us with key insights to aid us in reaching our goal: a sustainable future.
References
[1] Levine, S. E., Fox, J. M., Blanch, H. W., & Clark, D. S. (2010). A mechanistic model of the enzymatic hydrolysis of cellulose. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.22789
[2] Tormo, J., Lamed, R., Chirino, A. J., Morag, E., Bayer, E. A., Shoham, Y., & Steitz, T. A. (1996). Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. The EMBO Journal, 15(21), 5739–5751. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8918451
[3] Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & Vries, A. H. de. (2007). The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. J. Phys. Chem. https://doi.org/10.1021/JP071097F
[4] Sánchez, B. J., Zhang, C., Nilsson, A., Lahtvee, P., Kerkhoven, E. J., & Nielsen, J. (2017). Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints. Molecular Systems Biology. https://doi.org/10.15252/msb.20167411
[5] Ranganathan, S., Suthers, P. F., & Maranas, C. D. (2010). OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1000744
[6] Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., … Fleming, R. M. T. (2017). Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. ArXiv. https://doi.org/10.1038/protex.2011.234