The model shows spatial aspects of Rab5-domain formation on membranes. Since reaction and cluster formation on the membrane can control vesicle processing, it is of interest to simulate this process using our mprDPD methodology, as a preliminary step towards endocytosis. The reaction mechanisms were taken from the work of our project partners Brusch et.al. [1], and extended to include specific membrane self-organization by mprDPD.
Time course of RAB patch formation.
Species:
cytosol: GAP, GEF
membrane: L Lipid, R active RAB5:GTP, r inactive RAB5:GDP
Reaction scheme:
L --> r
r --> L
R --> r
r + GEF --> r:GEF
r:GEF --> R + GEF
r:GEF --> r + GEF
R + GAP --> R:GAP
R:GAP --> R + GAP
R:GAP --> r + GAP
Interaction-matrix (dpd-repulsion):
L R r GEF GAP r:GEF R:GAP
L 50 50 50 5 5 50 50
R 45 50 15 15 50 50
r 50 5 15 50 50
GEF 15 15 15 15
GAP 15 15 15
r:GEF 50 50
R:GAP 50