Modeling of Human Red Blood Cell
Using the E-CELL Simulation System

Riou Matsushima 12
ryo@sfc.keio.ac.jp

Hisako Nakano

13s96649hn@sfc.keio.ac.jp

Akiko Kawase 14

t96292ak@sfc.keio.ac.jp

Kanako Saito

14

t95401ks@sfc.keio.ac.jp

Naoko Watanabe 14

t96008nw@sfc.keio.ac.jp

Masaru Tomita 14
mt@sfc.keio.ac.jp

1 Laboratory for Bioinformatics
2 Graduate School of Media and Governance

3 Department of Policy Management
4 Department of Environmental Information,Keio University, 5322 Endo, Fujisawa 252-8520, Japan

In this work, we try to model and simulate human red blood cell using E-CELL system, a genericsoftware for simulation of cellular processes [1]. Human red blood cell has been well-studied in last
three decades, and extensive biochemical data on its enzymes and metabolites have been accumulated[2].
The cell uptakes glucose from the environment and processes it through the glycolysis pathway,
generating ATP molecules for other cellular metabolism. The ATP molecules are consumed mostly
for cations transport in order to keep the cell's electroneutrality and osmotic balance. The cell alsohas several other pathways such as nucleotide metabolism and pentose phosphate pathway (Fig. 1).
The model we have constructed using E-CELL contains 44 reactions and 43 intermediates. Kinetics of the most enzymatic reactions are modeled using various types of Michealis-Menten equations(Phosphoglucoisomerase, Triose phosphate isomerase, Adenine phosphoribosyl transferase, etc.).
Kinetics of other enzymatic reactions such as 6-Phosphogluconate dehydrogenase Glutathione reductase and Transaldolase is modeled as Ordered Bi-Ter system and Ping-Pong Bi-Bi system, respectively.
Other reactions use kinetic equations speci c to the reaction (ex, Hexokinase, Pyruvate kinase,etc.), nine of which are membrane transportation.
Kinetic parameters of all the reactions are based on experimental data in the literature [2, 4]. We
then compare behavior of the simulated model cell with that of the real red blood cell observed inlaboratory experiments. We also compare our model with other computer models [3, 4, 5, 6, 7].

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas `GenomeScience' from The Ministry of Education, Science, Sports and Culture in Japan.

References[1] Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K.,Tanida, S., Yugi, K., Venter, J.C., and Hutchison, C., E-CELL: Software environment for wholecell simulation Bioinformatics, (to appear).

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Figure 1: Metabolim in Human Red Blood Cell.
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