Total concentration in reversible reaction

[Jordi Solà]

Hi folks, 

I have a system in which an enzimatic reaction is tuned by the use of a host that can reversibly bind the substrate 

I have defined the reactions as

S -> P

S + host = [Host·S]

I can follow the total concentration of substrate by HPLC, however this is going to be the sum of free S and substrate in [host·S]. Is there a way to tell copasi this fact?

In this simple scenario I can modulate the system just by ignoring [S] and feeding Copasi [P] and the kinetic constant for S -> P but i have a quite more complex system where telling that this is not a concentration but a 'total concentration' would be nice

Any thoughts? 

Sorry if it is a bit confusing I am quite a begginer

Cheers

J

[Pedro Mendes]

Hi there, welcome

yes, you can create a new variable in COPASI that is the sum of the two
species S and Host-S. You do that in the "Global Quantities" part of the
model. Create a new global quantitiy, give it a name (eg TotalS) and
then set simulation type to be "assignment". Then you have to create a
formula for what it is in the box labeled as Expression: push the little
button that has the COPASI logo on the right and select "Species", then
"Transient Concentrations" and then "[S](t)" and press OK. Now add a "+"
directly on the Expression box, and press the little button again, now
select "Species", "Transient Concentrations" and finally "[S-Hub](t)".
Press OK, then press "Commit" on the bottom of the COPASI window.

This created a new variable:

TotalS = [S](t) + [S-Hub](t)

you can use this new variable for various purposes, for example you can
use it as a target for parameter estimation (ie make the model TotalS be
close to your experimental measures of total S.

(Pressing the little COPASI button above to create the expression is a
way to make sure that you are entering the correct components of the
expression, as expressions can be made up of a lot of different model
components)

Hope this helps
Pedro

> --
> You received this message because you are subscribed to the Google
> Groups "COPASI User Forum" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to copasi-user-fo...@googlegroups.com
> <mailto:copasi-user-fo...@googlegroups.com>.
> To view this discussion visit https://groups.google.com/d/msgid/copasi-
> user-forum/f6309b2c-ec9a-4a37-9012-769b77991455n%40googlegroups.com
> <https://groups.google.com/d/msgid/copasi-user-forum/f6309b2c-
> ec9a-4a37-9012-769b77991455n%40googlegroups.com?
> utm_medium=email&utm_source=footer>.

--
Pedro Mendes, PhD
Professor and Director
Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
group website: http://www.comp-sys-bio.org