Integrating fluorescent biosensor data using computational models.
This book chapter provides a tutorial on how to construct computational models of signaling networks for the integration and interpretation of FRET-based biosensor data. A model of cAMP production and PKA activation is presented to provide an example of the model building process. The computational model is defined using hypothesized signaling network structure and measured kinetic parameters and then simulated in Virtual Cell software. Experimental acquisition and processing of FRET biosensor data is discussed in the context of model validation. This data is then used to fit parameters of the computational model such that the model can more accurately predict experimental data. Finally, this model is used to show how computational experiments can interrogate signaling networks and provide testable hypotheses. This simple, yet detailed, tutorial on how to use computational models provides biologists that use biosensors a powerful tool to further probe and evaluate the underpinnings of a biological response.
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Eric C
EC
Greenwald
Renata K
RK
Polanowska-Grabowska
Jeffrey J
JJ
Saucerman
D015374:Biosensing Techniques / Q000379:methods*; D003198:Computer Simulation; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D057054:Molecular Imaging