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Table 1 Parameters used to characterize the organelles simulated in the model

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

 

Fusion and tethering probability

Recycling probability

Tubulation tendency

Migration on MT

Rab switch

RabA

RabB

RabC

RabD

RabE

RabA

1

0.5

0.0001

0.001

0.001

0.1

0.8

1

→ RabD

RabB

0.5

1

0.3

0.03

0.01

0

1

1

–

RabC

0.0001

0.3

1

0.0001

0.0001

0.3

1

0.5

–

RabD

0.001

0.03

0.0001

0.1

0.001

0

0

− 1

–

RabE

0.001

0.01

0.0001

0.001

1

0

1

−1

–

  1. To model a particular intracellular transport process, the membrane domains surrounding the organelles must be enumerated and characterized. For a standard endocytic route, we have incorporated early (RabA), sorting (RabB), recycling (RabC), and late (RabD) endosomal domains. A TGN domain was also included (RabE). The fusion probabilities were selected according to what is generally accepted in the intracellular transport field (e.g., early and sorting endosomes mix frequently, whereas early and late endosomes seldom fuse). Recycling probabilities were assigned with the same criteria. Tubulation tendency was low for domains surrounding large round organelles (such as late endosomes/lysosomes). Migration on MT was assigned according to the reported position of the organelles in the cell (late endosomes, TGN, and recycling endosomes proximal to the nucleus, and early and sorting endosomes near the plasma membrane). In the pathway simulated, the only switch included was RabA → RabD. Rab cascades like this must be programmed in COPASI, by changing the set of enhancers and inhibitors for the corresponding reactions in the rabs_convertion COPASI file (Additional file 5)