Essentials of Computational Chemistry

13.5 CASE STUDY: CATALYTIC MECHANISM OF YEAST ENOLASE 483
Mg
Mg
O
O
enolase + water cap
O
O
H
O
P
rbreaking
H
O
H/D
O H
r making
H
N
H
H
H
H
H
H H
C GHO
Figure 13.8 A 25-atom quantum subsystem embedded in an 8863-atom classical system to
model the catalytic step in the conversion of D-2-phosphoglycerate to phosphoenolpyruvate by
enolase. What factors influence the choice of where to set the boundary between the QM and
MM regions? Alhambra and co-workers found, using variational transition-state theory with
a frozen MM region that was selected from a classical trajectory so as to make the reaction
barrier and thermochemistry reasonable, that the breaking and making bond lengths were 1.75
and 1.12 ˚A, respectively, for H, but 1.57 and 1.26 ˚A, respectively, for D
portion of the trajectory should be representative of the protein structure in the region of
the TS for the reaction.
From this 10 ps region, random structures were selected, and QM/MM calculations were
carried out at the AM1/CHARMM22 level, with the boundary carbon atom of the lysine
side-chain modeled using the GHO approach. In these calculations, the geometry of the
MM region was held frozen, but the QM region was optimized to find reactant, product,
and transition-state structures. When the computed free energies of activation and of the
overall reaction from these structures matched sufficiently closely to experiment, it was
assumed that the MM structure was representative of a typical protein configuration in the
vicinity of the TS, and a more detailed analysis of the kinetics was undertaken to better
understand the experimentally observed isotope effects.