Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications
Fig 6
A. Transphosphorylation of EGFR at the Y1068 site of the EGFR receptor. This reaction has two key requirements: (1) The receptor must be dimerized, specifically through an explicit bond at the “r” site, which corresponds to the transmembrane domain. This bond ensures that the two EGFR molecules are part of the same dimeric complex, enabling one receptor to phosphorylate the Y1068 site of its partner. (2) The Y1068 site on the target receptor must be unbound, allowing it to undergo phosphorylation without interference from existing interactions. B. Dephosphorylation reaction catalyzed by PTP not bound to receptor complex. In this case PTP molecule is not necessary binding to any other molecule, so it may lack any sites. C. Phosphorylation reaction of EGFR dimer catalyzed by Src kinase that is a part of the receptor complex. Note that to be part of a complex, at least one site of Src is required.