Modeling Photorespiration Pathway through E-Cell

Photorespiration is a process wherein a plant takes up air and water in order to conduct photosynthesis. In order to understand and manipulate photorespiration, it is important not only to translate photorespiration into mathematical equations but also pipe these equations into a reliable simulation environment. E-Cell is a modeling and simulation environment for biochemical and genetic processes [3]. It allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-Cell simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Our objective is to integrate enzyme rate equations and stoichometry of photorespiration pathway that leading to a reliable simulation environment using E-Cell system.