System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system

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Enoch Yeung, Shaobin Guo, Richard M. Murray
Submitted, 2014 Winter q-bio Conference (5 Nov 2013)

An outstanding challenge in the design of synthetic biocircuits is the development of a robust and efficient strategy for interconnecting functional modules. Recent theoretical work demonstrated that a phosphorylation based insulator implementing a dual strategy of high gain and strong negative feedback could potentially serve as a device to attenuate retroactivity. This research investigates the structural identifiability of the phoshorylation based insulator when implemented in an {\it in vitro} transcription-translation cell free expression system. We consider a complex model that provides an intricate description of all chemical reactions and leveraging specific physiologically plausible assumptions, we derive a rigorous simplified model that captures the output dynamics of the phosphorylation based insulator. We perform standard system identification analysis and determine that the model is globally identifiable with respect to three critical parameters. Our findings show the utility of the transcription-translation cell free expression system as a platform for system identification, as it provides extra control inputs for parameter estimation that typically are unavailable in vivo. The parameters estimated are then used as a basis for a simulation study in a parallel experimental work (also submitted to qBio-2014).