Team:UT Dallas/immunobot modeling
Revision as of 03:25, 29 September 2011 by Ssant
Model and simulationThe 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:
Module 2: Transcription/translation of CheZ
In this module, the dimerized complex C2 activates the transcription of the cheZ mRNA. The reactions are the standard transcription and translation reactions illustrated as:
In this module, the CheY protein is dephosphorylated by the CheZ protein and the reaction can be illustrated as:
In this module, the tumbling activity of E coli is characterized by the so-called “bias”, which is defined as the ratio of the time of directed movement and the total time. It is experimentally measured that the bias is a Hill function dependent on the concentration of phosphorylated CheY (Cluzel, Surette et al. 2000).
Using the steady-state value of Yp in the previous two figures, that is 4.08 µM or 14.25µM, the final bias is 6.6% or .01%.
Cluzel, P., M. Surette, et al. (2000). "An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells." Science 287(5458): 1652-5.
Forsten-Williams, K., C. C. Chua, et al. (2005). "The kinetics of FGF-2 binding to heparan sulfate proteoglycans and MAP kinase signaling." J Theor Biol 233(4): 483-99.
Spiro, P. A., J. S. Parkinson, et al. (1997). "A model of excitation and adaptation in bacterial chemotaxis." Proc Natl Acad Sci U S A 94(14): 7263-8.