Research
Interests
The Substrate Mechanism of Pyruvate
Formate-Lyase (PFL)
In collaboration with Prof. Dr. Hendrik Zipse
(Department of Chemistry, Ludwig-Maximilians-University,
D-81377
Pyruvate
formate-lyase (PFL) holds a central role in the anaerobic glucose metabolism of
E. coli and other bacteria, and uses
a radical mechanism to effect the reversible transformation of pyruvate and
Coenzyme A (CoA) to acetyl-CoA and formate in two half reactions [1]:
As
the first example of a radical enzyme for which the spin was found to be
located on the polypeptide backbone Ca atom
of a glycyl residue, PFL has received significant experimental [2] and
theoretical [3] attention.
The
theoretical studies on this enzyme, apart from playing an important role in the
formation of a generally accepted mechanism of the reaction, are interesting
from a methodological point of view. That is, in a somewhat typical situation
in this field of study, the different models used in the different studies
produced different results.
I am
currently applying QM-MM models to the PFL mechanism in order to clarify
several points. In particular, the dependence of the results on the chosen
model is being thoroughly investigated with a view to making some general
recommendations. In addition, the influence of the surrounding protein on the
reaction is analyzed. Contrary to the commonly held belief that the importance
of the environment on radical reactions is minor, the investigations indicate
that significant catalytic effects are present.
[1] Frey, P. A., Ann. Rev. Biochem., 2001, 70, 121.
[2] Becker, A., Kabsch, W., J.
Biol. Chem. 2002, 272,
40036.
[3] (a) Lucas, M. F., Fernandes, P. A., Eriksson, L. A., Ramos, M. J., J.
Phys. Chem. B 2003, 107,
5751. (b) Himo, F., Eriksson, L. A., J. Am. Chem. Soc. 1998, 120, 11449.