Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies

Biology Direct

Table 2 List of molecules included in the simulation and their affinities for Rab domains

The molecules that are necessary to model a specific process are enumerated and their affinity for membrane domains specified. For example, to model the hydrolysis of a ganglioside, we included the relevant enzyme, the receptor that transports the enzyme, and cholesterol and protons that modulate the enzyme activity. Other cargo molecules whose transport kinetics are well known, such as Tf, MHC-I, and dextran were added. Soluble and membrane markers are special cargos that are useful to assess the characteristics of the organelles that a selected molecule visit during the simulation. Soluble molecules are easily identified. For a membrane-associated molecule, the affinity for the different domains is inferred from its a priori known destination in a cell. For example, M6PRs are retrieved back to the TGN, so the receptor and the enzyme-bound receptor are given affinity for the TGN domain. Tf and MHC-I are given affinity for RabB and RabC to be sorted out from RabA compartments that eventually mature to late endosomes. Cholesterol is enriched in early endosomal structures and GM2 is sequestered in intraluminal vesicles that accumulate in late endosomes/lysosomes

ISSN: 1745-6150