Section: Overall Objectives

Highlight on modeling GPCR signaling, publication in Molecular Systems Biology with Robert Lefkowitz, recipient of the Nobel prize in Chemistry

In collaboration with Eric Reiter (UMR CNRS-INRA 6175) and Frédérique Clément (EPI SISYPHE) in the framework of the Initiative Action REGATE (2008-2012), and with Robert Lefkowitz (Duke University), recipient of the Nobel prize in Chemistry 2012 for his work on G-Protein Coupled Receptors (GPCR), we have combined experimental approaches with computational modeling to decipher the molecular mechanisms as well as the unexplained complex dynamics governing GPCR signaling, and more precisely the ERK activation by the angiotensin II type 1A receptor (AT1AR) in human embryonic kidney (HEK293) cells.

In [4] , the molecular mechanisms and hidden dynamics governing ERK activation by the angiotensin II type 1A receptor are studied and deciphered, revealing a signal balancing mechanism that is found to be relevant to a wide range of important drug targets composed of other seven-transmembrane receptors. More precisely,

• An ODE-based dynamical model of ERK activation by the prototypical angiotensin II type-1A seven transmembrane receptor has been built and validated using BIOCHAM

• In order to deal with a limited number of experimental read-outs, unknown parameters have been inferred by simultaneously fitting control and perturbed conditions expressed in temporal logic LTL($R_{\text{lin}}$) in BIOCHAM using the covariance method adaptive evolution strategy (CMAES) for continuous optimization (EPI TAO)

• In addition to its well-established function in G-protein uncoupling, G protein-coupled receptor kinase 2 has been shown to exert a strong negative effect on $\beta$-arrestin-dependent signaling and by doing so, to balance G-protein and $\beta$-arrestin signaling. The failure to fit some temporal constraints was the key to infer the existence of these interactions from the computational model.

• This novel function of G protein-coupled receptor kinase 2 has also been evidenced in primary vascular smooth muscle cells naturally expressing the AT1AR and in HEK293 cells expressing other 7TMRs.

These results are the outcome of a long-term collaboration initiated with Eric Reiter in 2004, during which we designed our formal methods for systems biology, and developed Biocham for supporting a tight integration between modeling and biological experiments.