Hybrid dynamic/static method for large-scale simulation of metabolism and its implementation to the E-cell system

Abstract

6. Conclusion: There are bright prospects for the modeling of metabolic systems. However, in most cells except cells in which no genetic expression at all occurs, such as human erythrocytes, metabolism is controlled by genes. That is, the maximum activity of each enzyme is regulated by the gene expression, and changes dynamically according to the circumstance. Moreover, because one group of enzyme genes is not expressed under normal conditions, some cases in each pathway are expunged. In such cases and only under specific conditions, the enzyme group associated with that pathway is expressed and operated. It is therefore unlikely the metabolic pathway map created with the aid of data mining from genome sequencing using pathway databases and the GEM system could be applied in its present form. That is, it is not likely that detailed cell simulation could be obtained through metabolic modeling only; rather, the cell simulation would likely be a combination of a gene expression model and signal transmission model controlling it. Although the principles differ from this hybrid method for metabolic systems, we are currently developing a new method to enable modeling of gene expression systems and signal transduction pathways.