"Guy C. Brown" wrote:
>> Petr Kuzmic wrote:
> >I suppose everybody remembers Knowles' et al. 1980s work on the
> >energetics of the "perfect enzyme".
> >Maybe the horrendous formalism that Knowles at al. invented for their
> >"perfect enzyme" work could be subjected to yet another kind of torture,
> >and cast in terms of MCA??
[...]
> It is interesting to note that "perfect" enzymes in this sense are
> meant to be entirely limited by the substrate binding step,
> whereas the equilibrium binding assumption used in much enzymology/
> transition state theory assumes the opposite - that the catalytic
> step is entirely rate limiting.
A "philosophical" comment:
I think that people always try to make sense of things by /simplifying/
them, that is, by focusing on one extreme behavior or another ("Rapid
Equilibrium Approximation", "perfect enzyme", etc.). Why can't we
somehow hold in the mind a /multitude/ of complementary ways in which
the same phenomenon (in this case enzyme catalysis) presents itself. It
could be the old Aristotelian or binary logic working against us here:
everything has be be /either/ this /or/ that.
Sadly, in the last 20 years of biochemical research, it did not help
that TV Biochemistry (as I call it) become widely accepted. By "TV
Biochemistry" I mean too many people sitting in front of colorful
20-inch displays entranced by beautiful pictures of biomolecules and
twirling them around using a tree-button mouse. Too many people I know
are trying to deduce from these essentially /static/ images (e.g., X-ray
structures) how an essentially /dynamic/ system might function.
There might be a connection between the recent extreme emphasis on
structural information ("TV Biochemistry") and the overly simplistic
approach to enzyme kinetics that is seen in certain textbooks. In both
cases, we have a failure to somehow consider a /dynamic/ system with
mutually inter-dependent components (structural or functional), none of
which are entirely defining or "limiting" the system as a whole.
-- Petr
_____________________________________________________________________
Petr Kuzmic, Ph.D. * BioKin, Ltd. * Consulting & Software Development
http://www.biokin.com * (608) 256-4790 * (608) 256-1269 FAX
