A computational rule-based model of MAPK/ERK system regulation

The MAPK/ERK pathway coordinates multiple cellular functions, including proliferation, apoptosis, and motility, yet it is frequently modeled as a one-purpose cascade. Pathway complexity stems from the existence of isoforms that are regulated differently and have specific interacting partners. Here, we overcome combinatorial complexity by constructing a rule-based model of the MAPK/ERK pathway that accounts for differential regulation of MEK and RAF isoforms and RAF interactions with 14-3-3 proteins. The model addresses signaling based on the enzymatic cascade as well as regulatory protein-protein interactions. We propose that at low concentrations of growth factors, RAS is activated only in a portion of the membrane. This allows the model to reconcile the observed graded and switch-like responses observed at the upper (RAS and RAF) and the lowest (ERK) tiers of the pathway, respectively. We demonstrate that functional differences between BRAF and CRAF, or ARAF, can arise from their distinct interactions with 14-3-3. The 14-3-3 dimers inhibit all RAF monomers in the closed form and preferentially stabilize BRAF-CRAF or BRAF-ARAF dimers and may not stabilize RAF dimers without BRAF. The constructed model is used to explore qualitative differences in MAPK/ERK pathway signaling across different cell lines. The exploration starts from the nominal model parameters chosen to reflect a generic cell.