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
These pages describe the model, provide files to load into Gepasi and
execute all the simulations, and present the results of the simulations.
This page is simultaneously
(1) a tutorial on the usage of Gepasi
(2) an example of the power of computer simulation to study pathway
kinetics
(3) a demonstration of some of the properties of enzyme cascades
In a previous thread in this newsgroup, I made the point that enzyme
cascades can slow down the response to a signal. This is very well
illustrated in the results section of this web-article. Figure 12 shows
that the further down in the the cascade an enzyme is located the slower
it responds to the change in concentration of the signal molecule.
REFERENCE
[1] Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical
pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
--
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.
Author of GEPASI, a biochemical kinetics simulator
http://gepasi.dbs.aber.ac.uk/softw/Gepasi.html
