Should plasma membrane be its own compartment?

Hello,

I am new to simbiology and would appreciate guidance on this issue! I am modeling several reactions inside a cell, which are affecteed by extracellular ligands & membrane bound receptors. Should the plasma membrane be its own compartment in my model? How should I deal with ligand gated receptors in the plasma membrane (I don't have 'concentrations' of those reeceptors in the PM, but do have intracellular mRNA values).

Thanks in advance for everyone's time & help on this.

Answer 1

[Arthur Goldsipe]

Yes, I think the simplest approach would be to create separate compartments for each location where you need to consider that species reside. In this case, it sounds like you'll want an extracellular compartment, an intracellular compartment, and a membrane compartment. In the case of membrane-bound species, you can still use concentration units, but they will be amount per area instead of amount per volume. Or you can always use extensive units (like moles or molecules) for any of your species. However, you must use extensive units for reaction rates where reactants from different compartments react. You can find more details about reactions involving multiple compartments on this page under "Reactions Spanning Multiple Compartments."

If you expliclty add units to all your components in SimBiology and enable unit conversion, SimBiology will check that the equations are dimensionally consistent.

-Arthur (he/him)