RAB 5 membrane kinetics

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.

seq4_brusch_033
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

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