Mori grant report (Academic year 2003):
Simulation of Min protein localization in E.coli using the E-Cell3 simulation software

The Graduate School of Media and Governance (Master's course), Bioinformatics Program
Yohei Yamada (yoyo@sfc.keio.ac.jp)

Abstract:
A particle-conserving reaction-diffusion model published by Howard et al., describing the diffusion of Min proteins inside E.coli and their transfer between the cytoplasmic membrane and cytoplasm, has been implemented and analyzed using E-Cell 3, a generic multi-algorithm and multi-timescale software for simulation of cellular processes. Simulation results of this work were compared with numerical and experimental results from literature, and results of analysis suggest the range of MinD density, MinE density, and cell length that is necessary for oscillation of the Min proteins to occur.
(a) (b) (c)
Figure1: Space-time plots of total MinD and MinE
Figure1 illustrates the spatial and temporal oscillations of the Min proteins inside the cell. (b) are the results of Howard et al. (a) and (c) are the results produced using E-Cell3. It is apparent that compared with MinD, MinE is enhanced at midcell.
(a) (b) (c)
Figure2: Time-average distribution plots of total MinD and MinE
Figure2 displays the end result, or the essence of the oscillations. (b) are the results of Howard et al. (a) and (c) are the results produced using E-Cell3. It is clear that the amount of the cell division inhibiting protein MinD is lowest at midcell, which is crucial for proper division site placement.
(a) (b) (c)
Figure3: Bifurcation diagrams of membrane-bound MinD in left pole
Figure3 shows diagrams as a function of (a) total MinD concentration (b) total MinE concentration (c) cell length. The results suggest the range of total MinD (950 to 3600 molecules), total MinE (68 to 184 molecules), and cell length (1.9 to 3.3 micrometers) required to produce oscillation.