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More Realistic Model for Simulating Min Protein Dynamics: Lattice Boltzmann Method Incorporating the Role of Nucleoids
Abstract:The dynamics of Min proteins plays a center role in accurate cell division. Although the nucleoids may presumably play an important role in prokaryotic cell division, there is a lack of models to account for its participation. In this work, we apply the lattice Boltzmann method to investigate protein oscillation based on a mesoscopic model that takes into account the nucleoid-s role. We found that our numerical results are in reasonably good agreement with the previous experimental results On comparing with the other computational models without the presence of nucleoids, the highlight of our finding is that the local densities of MinD and MinE on the cytoplasmic membrane increases, especially along the cell width, when the size of the obstacle increases, leading to a more distinct cap-like structure at the poles. This feature indicated the realistic pattern and reflected the combination of Min protein dynamics and nucleoid-s role.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1331839Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 909
 P. de Boer, R. Crossley and L. Rothfield, A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli, Cell, 56 (4), 641- 649, 1989.
 P. de Boer, R. Crossley and L. Rothfield, Central role for the Escherichia coli minC gene product in two different cell divisioninhibition systems, Proceedings of the National Academy of Sciences, 87 (3), 1129, 1990.
 P. De Boer, R. Crossley, A. Hand and L. Rothfield, The MinD protein is a membrane ATPase required for the correct placement of the Escherichia coli division site, The EMBO journal, 10 (13), 4371, 1991.
 J. Huang, C. Cao and J. Lutkenhaus, Interaction between FtsZ and inhibitors of cell division, Journal of Bacteriology, 178 (17), 5080-5085, 1996.
 Z. Hu and J. Lutkenhaus, Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE, Molecular Microbiology, 34 (1), 82-90, 1999.
 D. Raskin and P. de Boer, MinDE-dependent pole-to-pole oscillation of division inhibitor MinC in Escherichia coli, Journal of Bacteriology, 181 (20), 6419, 1999.
 X. Fu, Y. Shih, Y. Zhang and L. Rothfield, The MinE ring required for proper placement of the division site is a mobile structure that changes its cellular location during the Escherichia coli division cycle, Proceedings of the National Academy of Sciences of the United States of America, 98 (3), 980-985, 2001.
 D. Raskin and P. de Boer, Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli, Proceedings of the National Academy of Sciences of the United States of America, 96 (9), 4971, 1999.
 S. Rowland, X. Fu, M. Sayed, Y. Zhang, W. Cook and L. Rothfield, Membrane redistribution of the Escherichia coli MinD protein induced by MinE, Journal of Bacteriology, 182 (3), 613-619, 2000.
 C. Hale, H. Meinhardt and P. de Boer, Dynamic localization cycle of the cell division regulator MinE in Escherichia coli, The EMBO journal, 20 (7), 1563-1572, 2001.
 D. Drew, M. Osborn and L. Rothfield, A polymerizationdepolymerization model that accurately generates the self-sustained oscillatory system involved in bacterial division site placement, Proceedings of the National Academy of Sciences of the United States of America, 102 (17), 6114, 2005.
 M. Howard and A. Rutenberg, Pattern formation inside bacteria: fluctuations due to the low copy number of proteins, Physical Review Letters, 90 (12), 128102, 2003.
 M. Howard, A. Rutenberg and S. de Vet, Dynamic compartmentalization of bacteria: accurate division in E. coli, Physical Review Letters, 87 (27), 278102, 2001.
 K. Huang and N. Wingreen, Min-protein oscillations in round bacteria, Physical Biology, 1 229-235, 2004.
 K. Kruse, A dynamic model for determining the middle of Escherichia coli, Biophysical Journal, 82 (2), 618-627, 2002.
 H. Meinhardt and P. de Boer, Pattern formation in Escherichia coli: a model for the pole-to-pole oscillations of Min proteins and the localization of the division site, Proceedings of the National Academy of Sciences of the United States of America, 98 (25), 14202, 2001.
 C. Modchang, P. Kanthang, W. Triampo, W. Ngamsaad, N. Nuttawut, I. Tang and Y. Lenbury, Modeling of the dynamic pole-to-pole oscillations of the min proteins in bacterial cell division: The effect of an external field, Journal of Korean Physical Society, 46 1031-1036, 2005.
 W. Ngamsaad, W. Triampo, P. Kanthang, I. Tang, N. Nuttawut, C. Modjung and Y. Lenbury, A lattice Boltzmann method for modeling the dynamic pole-to-pole oscillations of Min proteins for determining the position of the midcell division plane, Journal of Korean Physical Society, 46 (4), 1025-1030, 2005.
 C. Woldringh, E. Mulder, J. Valkenburg, F. Wientjes, A. Zaritsky and N. Nanninga, Role of the nucleoid in the toporegulation of division, Research in Microbiology, 141 (1), 39, 1990.
 C. Woldringh, The role of co-transcriptional translation and protein translocation(transertion) in bacterial chromosome segregation, Molecular Microbiology, 45 (1), 17-29, 2002.
 S. Dawson, S. Chen and G. Doolen, Lattice Boltzmann computations for reaction diffusion equations, The Journal of Chemical Physics, 98 1514, 1993.
 S. Chen, H. Chen, D. Martnez and W. Matthaeus, Lattice Boltzmann model for simulation of magnetohydrodynamics, Physical Review Letters, 67 (27), 3776-3779, 1991.
 P. Lallemand and L. Luo, Theory of the lattice Boltzmann method: Dispersion, dissipation, isotropy, Galilean invariance, and stability, Physical Review E, 61 (6), 6546-6562, 2000.
 X. Zhang, J. Crawford, A. Glyn Bengough and I. Young, On boundary conditions in the lattice Boltzmann model for advection and anisotropic dispersion equation, Advances in Water Resources, 25 (6), 601-609, 2002.
 J. A. Valkenburg and C. L. Woldringh, Phase separation between nucleoid and cytoplasm in Escherichia coli as defined by immersive refractometry, Journal of Bacteriology, December; 160(3), 1151- 1157, 1984.
 U. Junthorn, S. Unai, P. Kanthang, W. Ngamsaad, C. Modchang, W. Triampo, C. Krittanai, D. Wtriampo and Y. Lenbury, Single-Particle Tracking Method for Quantitative Tracking and Biophysical Studies of the MinE Protein, Journal of the Korean Physical Society, 52 (3), 639- 648, 2008.
 S. Unai, P. Kanthang, U. Junthon, W. Ngamsaad, W. Triampo, C. Modchang and C. Krittanai, Quantitative analysis of time-series fluorescence microscopy using a spot tracking method: application to Min protein dynamics, Biologia, 64 (1), 27-42, 2009.
 Z. Hu, A. Mukherjee, S. Pichoff and J. Lutkenhaus, The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization, Proceedings of the National Academy of Sciences, 96 (26), 14819-14824, 1999.