modeling a multiple ligands - fudge factor?

Dominic-Luc Webb molmed domweb at mbox.ki.se
Fri Apr 27 15:41:45 EST 2001


This is a biochemistry enzyme kinetics numerical integration problem.
I know there are some sharp people in here, and I am hoping the
right person would be so kind to step forward.

I am piecing together a math model of enzyme kinetics for an
enzyme which has multiple affector sites. I have ok idea how the
momentary rate of this enzyme is affected by various combinations
of affectors and want to assign a rate for the enzyme for each
binding combination, the sum of all of these being the total
rate of the enzyme for that moment. I do not have experimental
numbers for the forward or reverse rates of binding to each of the
ligands (i.e., I only have ratio of forward/reverse rate, ka). I
am told it would be very difficult to get all these numbers. I have
therefore implemented two fudge factor equations (one for forward and
one for reverse) in which the ratio of the fudged forward and
reverse rates yields the correct ka for the enzyme. I did this to
solve the numerical integration for a multiple ligand binding site
problem of general form...

          kx
Lx + R <=====> LxR
         k-x

D(LxR)/dt = kx[Lx][R] - k-x[LxR]

I need to enter a value for kx and k-x in each iteration and
this is why the fudge factor equations were used.

I have scanned a (neatly, I'd like to think) written one page
description of what I have done, and would like to send this to
right person for comments. I am not sure this is most intelligent
way to model an enzyme. I would really like to hear from
someone who knows about enzyme kinetics.


Dominic-Luc Webb
dominic at enk.ks.se




More information about the Comp-bio mailing list