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Team:University of Sheffield /Modelling
From 2008.igem.org
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Hammad's Model
Click here for Probabilistic approach.
Sam's Model
A mathematical model for the BarA/ UvrY and fluorescence of GFP two-component system is presented and it's dynamic behaviour is analysed. The BarA / UvrY regulates the expression of the GFP in E-coil. The model is validated in a two steps:
- The signal transduction
- The gene expression.
To survive, bacteria monitors their environment constantly and adapt to changing conditions immediately and bacteria have an established signal transduction systems to execute adaptive response to changing environmental conditions. The signal transduction system contains of two protein components: a sensor kinase anchored in the cytoplasmic membrane, and a cytoplasmic response regulator that mediates an adaptive response, that is the gene expression. Sensory Kinase
Sensory kinases typically contain an N-terminal input domain which is connected via a linker to a C-terminal transmitter domain.
Response regulator
Response regulators typically consist of a N-terminal receiver domain coupled to C-terminal output domains.
Upon perception of a stimulus, the input domain of the sensor kinase modulates the signalling activity of its transmitter domain, resulting in autophosphorylation with -phosphoryl group of ATP. Then, the phosphoryl group is transferred to the response regulator receiver domain, resulting in activation of the output domain(s) to trigger gene expression.
The mathematical description of a reaction mechanism representing a two component systems is presented here. The signal transduction of BarA/ Uvry expresses some reactions for auto-phosphorylation of BarA, transference of phosphoryl group of ATP between histine kinase and response regulator, and de-phosphorylation of UvrY, which is a transcription activator that initiates a response by modulating gene transcription, resulting in changes in cell physiological and metabolism to cope with the external environment.
The gene expression of CsrB and GFP are lumped together and represented by binding of the response regulator to free DNA fragments.
