Re: [SOSlib-devel] Request for help with a multicompartment problem

[Rainer M. <ra...@tb...>]

Hi Michael,

Michael Hucka wrote:


>... and goes on to give an example of extracellular
>signal molecule binding to membrane receptors where you have
>to deal with separate volumes.
>
>(His solution to the problem was change the rate constant.
>I'll ask if I can forward his reply around.)
>

I haven't read through all the messages yet, but we ran across this
problem  when trying to translate the Schoeberl et al. 2001 model to
SBML. Tell me if this initial comment already helps you, otherwise I
will try to respond in more detail later.

d[A]/dt = -k * [A] * [B]

If A and B are ligand and receptor, and thus A is soluble and 
extracellular
while B is in a membrane compartment, the reaction itself still happens in
A's compartment!! B's reacting domain is also in this compartment! If
in the rest of the model B is described in concentrations in membrane or
cytosol, the modeller will have to convert B's concentration to 
extracellular by a volume ratio Vb/Va and the equation would read


d[A]/dt = -k * [A] * Vb/Va * [B]

... and I think it's the modeller's job to write the kinetic law this way.

I agree with Andrew that in general a reaction between species in 
different compartments makes no physical sense and therefor there can also 
not be correct rate law for such a situation.

Sorry, if this misses the topic our your question and is not really 
helpful or if the above example is also wrong and already covered in your 
previous messages. I'll go through the messages later. But let me know if 
it helps.

Rainer