Theoretical insights in enzyme catalysis.
Towards a rational design of catalytic antibodies.
V.MOLINER, Université Jaume I, Castellon, Espagne
Jeudi 6 mai 2004, 11h30
Recent computational developments have allowed realistic modelling of
chemical processes in biological environments and in particular of enzyme
catalysis. From the original Pauling's proposal about the fit between the
transition state (TS) and the protein environment, different explanations
on the origin of enzymes ability to enhance reaction rates have been
given. Thus, while some scientists have focused in the TS stabilization,
enzyme catalysis has been also explained by focusing on the reactants
structure in the Michaelis complex. All in all, the only real evidence for
Pauling's proposal was the fact that stable compounds that resembled the
TS, transition state analogs (TSAs), were competitive inhibitors of the
enzyme. These stable molecules, TSAs, were pioneering used by Lerner,
Schultz, Benkovik and Tramontano as haptens in immunization processes to
synthesise new catalysts: the catalytic antibody (CA). The study of the
processes associated to the CA activity provides an opportunity to examine
and understand enzyme catalysis and vice versa; the in depth knowledge of
enzyme activity can be used to improve the specificity, selectivity and
efficiency of these new catalysts.
In this talk, we will present an application of flexible hybrid QM/MM
methodology to the study reactions in solution and in enzyme environment.
Our results confirm the promises for realistic modelling of both condensed
phase reactions and suggest that the modelling of molecular systems
containing a huge number of atoms requires an exhaustive exploration of
many structures of similar energy which differ in regard to conformations
of solvent molecules or aminoacid sidechain. Thus, we present a
combination of two techniques - QM/MM statistical simulation methods and
QM/MM internal energy minimizations - to get a deeper insight into the
reaction catalysed by the enzymes. Structures, internal energies and free
energies, taken from the paths of the reaction in solution and in the
enzyme have been analyzed in order to estimate the relative importance of
the reorganization and preorganization effects on enzyme reactions. Id
est; is the enzyme preferentially binding the active conformer of the
substrate, or enzymes provides an environment which stabilizes the
transition state of the reaction to be catalyzed?
Finally, from a molecular mechanism point of view, kinetic isotope effects
(KIE) can be computed using this hybrid methodology in order to compare
our theoretical results with experimental data. We will discuss the
application of our results to the rational design of catalytic antibodies
or the improvement of existing inhibitors.