Pedro Mendes wrote:
>> In the sequence of my recent article in TiBS [1] where I describe Gepasi
> version 3, I have now released a series of web pages that describe how one
> would use Gepasi to simulate a signalling enzyme cascade:
>>http://gepasi.dbs.aber.ac.uk/metab/signal/signal.html
First of all, congratulations on the publication of the TiBS article.
"Biochemistry by the Numbers" is a much needed contribution. Maybe one
day most people in graduate programs on enzyme kinetics will be taught
that the computing machine is a very powerful research tool indeed.
A quesion arose upon my reading of Pedro's web page. The first reaction
in his mechanism is the phosporylation "Kinase1 -> Kinase1-P", following
the rate equation
v = V ([S]/Km)/(1+Ka/[A]+[S]/Km(1+Ka/[A])),
where A is a signal molecule (activator). The conversion of "Kinase1"
to "Kinase1-P" is catalyzed by a kinase which "is not represented
explicitly in the model but its concentration is part of the V parameter
(limiting rate)". Let us denote this other enzyme as "KinaseX".
The above rate equation assumes that the concentrations of both A
(signal molecule) and S (Kinase1) are infinitely (or at least very much)
larger than the concentration of KinaseX. This assumption ([Kinase1] >>
[KinaseX], [A] >> [KinaseX]) may be perfectly valid in certain
particular cases.
My question is: How could one use the Gepasi software system in the more
general case, where all concentrations (A, Kinase1, KinaseX) are of the
same order of magnitude?
--Petr
_____________________________________________________________
Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA
pkuzmic at biokin.com * http://www.biokin.com * 608.256.1269 fax
