I am involved in a synthetic biology project where I have to do modelling with ODEs. The biological process I want to model is the chelation of Cd2+ with phytochelatins, to know how much can be chelated. I know the basics of ODEs and I already did other modelling tasks, but I never studied anything related to chelation (I am a computer scientist) so any hint about how these kind of biochemical reactions are modelled would be helpful to get started.

  • $\begingroup$ If you know the stoichiometry and dissociation constant of the binding interaction this should a straightforward task. If the aim is to discover the stoichiometry via modelling, it's unclear to me how that could work. I'm probably missing something - maybe you could expand your question, and/or make it more specific? $\endgroup$
    – Alan Boyd
    Aug 26 '14 at 15:39
  • $\begingroup$ would this be more suited for the chemistry stack exchange? Chelation is a wide field, and there may be existing models based on EDTA, siderophores, and others that could serve as decent starting points. $\endgroup$
    – user137
    Aug 26 '14 at 16:38

One of the best ways that I have found for modeling reaction pathways is to set up a boolean network for that specific pathway. The boolean will give you an idea of the possible different states in that pathway (dependencies) and while not really necessary I find it helps orient you to the system.

The next step once you have yourself oriented is to set up Michaelis-Menten equations which you can then use to run you ODEs. Here is a great primer on how to set up these equations: http://depts.washington.edu/wmatkins/kinetics/michaelis-menten.html

The subsequent modules provided in that link are also helpful in explaining how to set-up quadratic velocity equations and do different sequential models.

Also, I'm sure you know this but, it bears saying: these are all steady-state kinetics. If you are looking for a more accurate model of what is occurring in that reaction you are going to have to set-up stochastic models of your system.

Hopefully, that answers you question. Good luck!


I have found a paper that seems to relavent to the process you are trying to model. It goes into a bit more detail than I think you are looking for but the basics seems sound. Mendoza-Cozatl and Moreno-Sanchez, 2006

  • $\begingroup$ would michailis-menton really apply here? phytochelatin is a polymer that chelates metal ions and gets transported to the vacoule. I guess you could treat it like 2 enzymatic reactions, with chelation as step 1, and transport to vacoule as step 2. But you might get complex cooperativity as more metal ions bind to the phytochelatin. $\endgroup$
    – user137
    Aug 27 '14 at 4:41
  • $\begingroup$ Michaelis-Menton is only relevant to a simplified system that only has explicitly two variables. It seems from the original posting that this is the case. The original poster appears to be only trying to observe chelation and not transport to vacoule which makes this method a valid option. You are correct that you can treat the pathway as individual reactions but those reactions you mention must be considered independently for the Michaelis-Menton approximation to work. Additionally, cooperativity can be identified by a sigmoidal curve as in the classic case of hemoglobin. $\endgroup$ Aug 28 '14 at 1:02

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