On 16 Sep 97 at 9:11, Petr Kuzmic wrote:
> [...]
> 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,
in that circumstance, i.e. when the concentration of the enzyme is of the
same order of magnitude of the ligands, you have two options
(1) you have a better rate equation that is valid for those conditions
(2) you write the mechanism in terms of its elementary reactions
If (1) is applicable (congratulations!) then all you need is to define a
new kinetic type and enter the equation (in the "Model definition" page,
pressing the button "Kinetic types"). Then select that kinetic type where
appropriate.
Otherwise, you will need to follow (2) and instead of writing
Kinase1 -> Kinase1-P
you would write (using your terminology):
Kinase1 + KinaseX = Kinase1-KinaseX
Kinase1-KinaseX + A = Kinase1-KinaseX-A
Kinase1 + KinaseX-A = Kinase1-KinaseX-A
Kinase1-KinaseX-A -> Kinase1-P + KinaseX-A
(beware that this mechanism might not be correct... I do think that this
one would generate a kinetic function like the one in my example if
Kinase1>>KinaseX and A>>KinaseX as you pointed out - but I am not sure.
Other's might know the correct mechanism)
Of course, this means that you have now a few more constants to find values
for... but maybe you can do a few experiments and use your own DynaFit
program to determine them :) :)
So, high enzyme concentrations are not a problem for Gepasi, at least not
a larger one than for any other purposes.
Best wishes
Pedro.
Pedro Mendes Inst. Biological Sciences
prm at aber.ac.uk (home: pedro at enzyme.demon.co.uk) Univ. Wales, Aberystwyth,
http://gepasi.dbs.aber.ac.uk/pedro/prmhome.htm Ceredigion SY23 3DA, U.K.
http://gepasi.dbs.aber.ac.uk/softw/gepasi.html FAX: +44 (0)1970 622350
