Help Resources/Modeling Discussion

Ligand depletion in models

Cellucidate Support Dec 07, 2009

Interactions between a ligand and a cell surface receptor represents a type of reaction that is very different from other reactions in a cellular model - these reactions happen outside the cell, not inside the cell.  Because these interaction occurs outside the cell, they generally must be treated differently from other reactions in the model.  The main difference is that while the receptor and other model components exist within the volume of the cell (or on the periphery of the cell in the case of membrane proteins such as receptors), ligands exist in the extracellular space, which in cell culture conditions is generally more than 100-fold larger than the volume of all the cells together (assuming cells are 20 um diameter spheres growing at densities of at most 1e6 cells/mL). 

Because ligands exist in a volume that is at least 100-fold larger than the total cellular volume, on a per cell basis binding of a ligand molecule to a receptor will have a much smaller effect on the amount of remaining ligand than on the amount of remaining free receptor.  We can make an assumption that the concentration of ligand in the media is essentially unchanged by binding of ligand to the receptor.  Based on this assumption, we can reformulate the reactions governing the interactions between ligand and the receptor in order to prevent inaccurate depletion of ligand.  Essentially, we can alter the association and dissociation reactions to prevent changes to the amount of free ligand in the model.

Association:
receptor + ligand -> receptor-ligand-complex + ligand
Dissociation:
receptor-ligand-complex -> receptor