If I understand what you are saying, I think it is too.
You imply that asymmetry in the enzyme results in two isomerase
pathways. This may be true, but it has no consequence on the
prospects for irreversibility. To avoid confusion, let's call these
pathways "D" and "S". Both the "D" and "S" pathways would have their
own kf and kr kinetic constants such that kf_D/kr_D = kr_S/kf_S =
Keq, which reflects the dG of the reaction. When the dG is close to
zero for the
isomerase reaction (which I assume here), then you can't make it
irreversible.
＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
This is not the case, at least in part. Such kind of enzymes, if no
cofactor-needed, use the identical intermediate for the mirror
symmetric reaction. For the D <--> Intermediate <--> S reaction, the
enzyme uses the same pathway. Enzymes, for example, glutamate
racemase and aspartate racemase, use a kind of psudo-mirror symmetric
alignment at the active site to adapt the binding of D or S isomer in
the half A.S., respectively. Other 3 atoms associated to the chiral
center keeps fixed relative conformation during the inversion.
Standard dG(0) of such a reaction is 0. However, at the time when
enzyme works (for example, cell needs D-ASP in an almost pure L-ASP
environment), the racemase moves L-Asp to D-Asp, in this regard, the
dG of the reaction (not standard) is not 0.
Your last sentence means: for a reaction (assuming dG(0) = 0 like
racemic reaction) almost reaches EQ (dG ~ 0), you cannot make it
irreversible----this is true. Just please do not forget: such kind
of enzymes work when the D <--> S EQ is highly broken by nature (dG <<
0) [not dG(0)].
Hopefully I explained clearly!
Lijun
James
All natural epimerases, isomerase and racemases use a mechanism
based on L-amino acids to deal with a mirror-symmetric (quasi-,
sometimes) reaction. In another word, these enzymes use a non-
mirror symmetric structure to deal with a mirror-symmetric
reaction, which itself causes the asymmetric kinetics for different
direction, though the dG is 0. The Arrhenius Law k = A*exp(-dE/RT)
should be understood like this: a mutation's effect to dE will be
symmetric as Dale pointed out. However, the effects on A are
asymmetric. A is related to intramolecular diffusion, substrate-
and product-binding affinity, etc. That is why with mutation these
enzymes changed their kinetics on two directions differently.
Please check glutamate racemase, alanine racemase, aspartate
racemase, DAPE epimerase, if you are interested. Never a 1000 to
1000 relation!
Thus, mutation is possible to make one direction more favored---the
point is you need the correct hit. Of course, such an experiment
is never a Maxwell's demon.
Lijun
On May 19, 2010, at 8:51 AM, Maia Cherney wrote:
You absolutely right, I thought about it.
Maia
Marius Schmidt wrote:
Interestingly, Maxwell's demon pops up here, whoooo... ,
don't do it.
If you change the reaction rate in one direction 1000 times
slower
than
in the other direction, then the reaction becomes practically
irreversible. And the system might not be at equilibrium.
Maia
R. M. Garavito wrote:
Vinson,
As Dale and Randy pointed out, you cannot change the ΔG of
a reaction
by mutation: enzyme, which is a catalyst, affects only the
activation
barrier (ΔE "double-dagger"). You can just make it a
better (or
worse) catalyst which would allow the reaction to flow faster (or
slower) towards equilibrium. Nature solves this problem very
elegantly by taking a readily reversible enzyme, like an
epimerase or
isomerase, and coupling it to a much less reversible reaction
which
removes product quickly. Hence, the mass action is only in one
direction. An example of such an arrangement is the triose
phosphate
isomerase (TIM)-glyceraldehyde 3-phosphate dehydrogenase (GAPDH)
reaction pair. TIM is readily reversible (DHA <=> G3P), but
G3P is
rapidly converted to 1,3-diphosphoglycerate by GAPDH. The
oxidation
and phosphorylation reactions of GAPDH now make TIM "work" in one
direction.
Since many epimerases are very optimized enzymes, why not
consider
making a fusion with a second enzyme (like a reductase) to make
the
system flow in one direction. Of course, this depends on what
you
want to do with the product.
Cheers,
Michael
/
****************************************************************/
/R. Michael Garavito, Ph.D./
/Professor of Biochemistry & Molecular Biology/
/513 Biochemistry Bldg. /
/Michigan State University /
/East Lansing, MI 48824-1319/
/Office:// //(517) 355-9724 Lab: (517) 353-9125/
/FAX: (517) 353-9334 Email: rmgarav...@gmail.com
<mailto:garav...@gmail.com>/
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On May 18, 2010, at 11:54 AM, Dale Tronrud wrote:
Hi,
I'm more of a Fourier coefficient kind of guy, but I thought
that a
ΔG of zero simply corresponded to an equilibrium constant
of one. You
can certainly have reversible reactions with other equilibrium
constants.
In fact I think "irreversible" reactions are simply ones where
the
equilibrium constant is so far to one side that, in practice,
the
reaction
always goes all the way to product.
As Randy pointed out the enzyme cannot change the ΔG (or
the
equilibrium
constant). You could drive a reaction out of equilibrium by
coupling it
to some other reaction which itself is way out of equilibrium
(such as
ATP hydrolysis in the cell) but I don't think that's a simple
mutation of
your enzyme. ;-)
Dale Tronrud
On 05/18/10 00:31, Vinson LIANG wrote:
Dear all,
Sorry for this silly biochemistory question. Thing is that I
have a
reversible epimerase and I want to mutate it into an
inreversible one.
However, I have been told that the ΔG of a reversible
reaction is zero.
Which direction the reaction goes depends only on the
concentration of
the substrate. So the conclusion is,
A: I can mutate the epimerase into an inreversible one. But
it has no
influence on the reaction direction, and hence it has little
mean.
B: There is no way to change a reversible epimerase into an
inversible one.
Could somebody please give me some comment on the two
conclution?
Thank you all for your time.
Best,
Vinson
Dr.habil. Marius Schmidt
Asst. Professor
University of Wisconsin-Milwaukee
Department of Physics Room 454
1900 E. Kenwood Blvd.
Milwaukee, WI 53211
phone: +1-414-229-4338
email: m-schm...@uwm.edu
http://users.physik.tu-muenchen.de/marius/
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
Lijun Liu
Cardiovascular Research Institute
University of California, San Francisco
1700 4th Street, Box 2532
San Francisco, CA 94158
Phone: (415)514-2836
