Fix thermodynamic association constant while iterating kon and koff

[gemma aragay]

We are using COPASI to try to derive kinetic parametres of a chemical reaction mediated by a synthetic molecular container.

Before we were using the kinetic module of SPECFIT software. In SPECFIT we were able to fix a Ka experimentally measured (relation of kon/koff) letting the software to change kon and koff values (always maintaining the ratio constant). We could not find this option in COPASI. Do you know if this is possible?

[Hoops, Stefan (sh9cq)]

Hello Gemma,

You can create 3 global quantities: Ka, kon, and koff. Here you choose
Ka and kon to be fixed. koff will have an initial expression:
kon/Ka.

You use the global quantities Kon and Koff in the reaction instead of
local values. Now whenever you vary kon the ratio kon/koff will be Ka.

I hope that helps!
Stefan

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

[Pedro Mendes]

Hi,

(I had sent this reply before but it seems it did not go out, apologies if this is a duplicate)

yes, in COPASI you can vary one of the two constants and have the other automatically changed to keep the ratio constant.

You will need to create a "global quantity" for one of the constants,. let's say koff, of type "assignemnt", then set the expression to be:

kon/1000

here I use 1000 as the value of Ka, but you can substitute by whatever value it is. "kon" you should use the button with the copasi logo to pick that parameter (ie you can't just write kon, but rather you pick it from the list of parameters)

I've made a small model (attached) that shows how to do this.

In fact I added all three constants, kon, Ka and koff as global quantities, defined koff in terms of kon and Ka and then set kon and koff to be the rate constants of the reaction.

I hope this helps
Pedro

[gemma aragay]

Thanks a lot for the response!

Missatge de Pedro Mendes <men...@copasi.org> del dia dj., 1 de febr. 2024 a les 13:54:

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Gemma Aragay Esteve
Postdoctoral Researcher
Institute of Chemical Research of Catalonia (ICIQ)
Av. Països Catalans 16 – 43007 Tarragona (Spain)
gar...@iciq.es - www.iciq.es