%0 Generic %1 Vazquez2009 %A Vazquez, Alexei %D 2009 %K molecular_crowding arxiv,flux_model,metabolism,combined_model %T Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects %U http://arxiv.org/abs/0910.2043 %X Macromolecules occupy between 34 and 44% of the cell cytoplasm, about halfthe maximum pack- ing density of spheres in three dimension. Yet, there is noclear understanding of what is special about this value. To address thisfundamental question we investigate the effect of macromolecular crowding oncell metabolism. We develop a cell scale flux balance model capturing the mainfeatures of cell metabolism at different nutrient uptakes and macromoleculardensities. Using this model we show there are two metabolic regimes at low andhigh nutrient uptakes. The latter regime is charac- terized by an optimalcytoplasmatic density where the increase of reaction rates by confinement andthe decrease by diffusion slow-down balance. More important, the predictedoptimal density is in the range of the experimentally determined density of E.coli. We conclude that cells have evolved to a cytoplasmatic density resultingin the maximum metabolic rate given the nutrient availability andmacromolecular crowding effects and report a flux balance model accounting forits effect.

@misc{Vazquez2009, abstract = { Macromolecules occupy between 34 and 44% of the cell cytoplasm, about halfthe maximum pack- ing density of spheres in three dimension. Yet, there is noclear understanding of what is special about this value. To address thisfundamental question we investigate the effect of macromolecular crowding oncell metabolism. We develop a cell scale flux balance model capturing the mainfeatures of cell metabolism at different nutrient uptakes and macromoleculardensities. Using this model we show there are two metabolic regimes at low andhigh nutrient uptakes. The latter regime is charac- terized by an optimalcytoplasmatic density where the increase of reaction rates by confinement andthe decrease by diffusion slow-down balance. More important, the predictedoptimal density is in the range of the experimentally determined density of E.coli. We conclude that cells have evolved to a cytoplasmatic density resultingin the maximum metabolic rate given the nutrient availability andmacromolecular crowding effects and report a flux balance model accounting forits effect.}, added-at = {2009-10-21T07:58:09.000+0200}, author = {Vazquez, Alexei}, biburl = {https://www.bibsonomy.org/bibtex/2982e2b5d2d42c063c77108153de0c4e7/penkib}, description = {[0910.2043] Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects}, file = {:/home/yuri/Dropbox/PDF/Vazquez2009_arxiv.pdf:PDF}, interhash = {06c26b902ce90955767cb696518fd0d7}, intrahash = {982e2b5d2d42c063c77108153de0c4e7}, keywords = {molecular_crowding arxiv,flux_model,metabolism,combined_model}, note = {cite arxiv:0910.2043Comment: 4 pages, 3 figures}, timestamp = {2009-10-21T07:58:10.000+0200}, title = {Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects}, url = {http://arxiv.org/abs/0910.2043}, year = 2009 }