Athel Cornish-Bowden wrote:
> I should be interested to know the opinions of subscribers to this group
> about whether the points I make about rate-limiting steps on the page cited
> are valid, and, of course, if anyone has views on the others I'll be glad
> to hear about them also.
Great page, I enjoyed reading it. [As for page design and style: nice
to see Cascading Style Sheets.]
I just want to add a small comment, focusing on the traditional
enzymology involving a single enzyme, not even venturing into MCA.
Discussions about the mythical "Rate Limiting Step" in traditional
(single-enzyme) enzymology seem to take place repeatedly, I suppose ever
since Haldane published his "steady-state approximation" of enzyme
catalysis in 1926. The issue is whether a particular step in a
catalytic mechanism for the given enzyme (as opposed to a particular
enzyme reaction in a multienzyme regulation cascade) can be declared as
somehow "rate limiting". A great deal of confusion is seen on this
issue, similar to the RLS in MCA.
When I had an office next to Dexter Northrop at the University of
Wisconsin, the RLS for certain enzyme mechanisms provided the topic for
(too many??) hours of conversation. The issue often was the
interpretation of the Michaelis constant by people interested in
designing inhibitor drugs as substrate analogs (or as transition state
analogs, which is another soap-box issue in an of itself). Of course,
if and only if the chemical step is perfectly "rate limiting" (Rapid
Equilibrium Approximation), then I suppose the Michaelis constant could
be interpreted as a thermodynamic equilibrium constant. Some people
were then looking at small peptide substrates for proteases, trying to
select those with low Km and chemically modify them into successful
inhibitor drugs. And failing, of course.
In the meantime, these issues became mute in the drug design circles,
because things moved from "Rational Drug Design" into "Combinatorial
Chemistry". Anyway, I attached an abstract of a related paper
suggesting a whole new nomenclature for "V/K" and "Km" as a response
(indirect, at least) to the RLS fallacy in enzymology.
-- Petr
_____________________________________________________________________
Petr Kuzmic, Ph.D. * BioKin, Ltd. * Consulting & Software Development
http://www.biokin.com * (608) 256-4790 * (608) 256-1269 FAX
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Dexter B. Northrop
On the Meaning of Km and V/K in Enzyme Kinetics
J. Chem. Educ. 1998 75 1153.
Keywords: enzymes, catalysis, diffusion, biochem, mechanisms, kinetics
Most biochemistry textbooks describe V/K, or kcat/Km, as one of the
fundamental kinetic constants for catalysis in enzymatic reactions and
associate it with some measure of the rate of the chemical
transformation of substrate into product. However, in the reactions of
all enzymes except isomerases and mutases, V/K fails to encompass a
complete turnover. Instead, it can be shown that V/K actually provides a
measure of the rate of capture of substrate by free enzyme into a
productive complex or complexes destined to form products and complete a
turnover at some later time. Similarly, V or kcat provides a measure of
the rate of release of product from the productive enzyme complexes that
constitute capture. It is here suggested that the symbols V/K and kcat
be replaced by kcap and krel, respectively, at least in the teaching of
enzyme kinetics. Capture and release are equally necessary to generate a
complete catalytic turnover, but they are determined by different
things, and the proposed symbolism is less abstract than older
alternatives. Used together, they provide a more accurate definition of
the Michaelis constant, as Km = krel/kcap, which is the kinetic
equivalent of the thermodynamic dissociation constant, Kd = koff /kon.
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