The flow of proteins through the mammalian secretory pathway described by a phenomenological-based semi-physical model

In the present study, we developed a model for the transport of proteins across the secretory pathway using the Phenomenological Based Semi-Physical Model (PBSM) methodology. The model represents the bulk flow of proteins along the organelles of the mammalian secretory pathway and works considering the role played by the Ras GTPase family cycles in the control of the vesicle coat assembly, the recycle of v-SNARE between the organelles of the pathway, and the dynamical equilibrium between the endoplasmic reticulum and the Golgi complex volumes due to the constant flow of vesicle between organelles. We integrate literature kinetic data from human, hamster, and monkey cells for model validation. The model describes the bulk flow of luminal and membrane proteins, following the well-mixing assumption at the intra-organelle level and the mass action law principle, revealing information on the secretory pathway at a quantitative level.