Team:UT Dallas/immunobot modeling

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Model and simulation

The signaling network from the input of external ligand signal to the output of the tumbling state of a E coli cell can be quantitatively described by a modular model. The model is formulated based on the law of mass action and Michaelis-Menten mechanism and contains four relatively independent modules that are explained in detail below.

Module 1: Activation of ToxR receptor
In this module, the ligand signal activates the ToxR receptor into a dimerized complex formed with the ligand, which is the active state of the receptor. The biochemical reaction can be illustrated as:

where L, R, C and C2 represent the concentration of external ligand, free receptor, recptor-ligand complex, and the dimerized receptor-ligand complex. The first reaction represents the binding/unbinding between the free receptor and the ligand. The second reaction represents the dimerization /undimerization conversions between C and C2. The conservation of the total concentration of the receptor can be written as:

where R^T is the total receptor concentration. The governing differential equations of this module are:



The equations contain binding rate k_f L(R^T-C-2C_2 ), unbinding rate k_r C, dimerization rate k_dim C^2 and undimerization rate 2k_undim C_2, where k_f, k_r, k_dim and k_undim represent the rate constants for binding, unbinding, dimerization and undimerization reactions. The values of the parameters are obtained from (Forsten-Williams, Chua et al. 2005). Typical simulation results in response to L=1 µM are: where the dissociation constant for receptor-ligand binding used in the right figure is 100 times than that in the left figure.
Module 2. Transcription/translation of CheZ
In this module, the dimerized complex C_2 activates the transcription of the cheZ mRNA. The reactions are the standard transcription and translation reactions illustrated as:

Where Zm and Zp represent the concentration of the mRNA and the protein product of CheZ. The formulation of the reactions follow the standard equations for transcription and translation.