THE RTK-MAPK PATHWAY – A BIOPSI MODEL

The RTK-MAPK pathway transduces a signal from receptor tyrosine kinases (RTKs), through the MAP kinase (MAPK) cascade, leading to a change in gene expression patterns. The pathway is composed of 13 kinds of proteins. These bind and form complexes, modify certain residues on their counterparts (mostly by phosphorylation and dephosphorylation of tyrosine, threonine and serine residues), change their conformation and activity, and translocate between different cellular compartments (cytosol, nucleus and membrane).

The BioSPI model is composed of 15 molecular processes (including ATP and GTP), with 24 different domains and 15

sub-domains. Four compartments (extracellular, membrane, cytoplasm and nucleus) were defined. A major portion of current knowledge has been incorporated into a concise (250 lines) formal representation. The local nature of the $\pi$-calculus allowed us to build this large model incrementally.

Full code for the pathway is available here

The code can also be accessed through a clickable map

More details on the pathway can be found through the links here.