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 bymprDPD.

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):

LRr   GEF GAP r:GEFR:GAP

L505050 55 50   50

R4550 1515 50   50

r50  515 50   50

GEF    1515 15   15

GAP15 15   15

r:GEF50   50

R:GAP   50

Copyright 2007. All rights reserved. Web managers:J. S. McCaskill, P. Wagler