3 Enzyme-Substrate Interactions
3.5 Summary
Molecular dynamics simulations were used to investigate the uncatalyzed and catalyzed cis–
trans interconversion and the role of intramolecular polarizability of the substrate in the catalytic mech-
anism of CypA. As previously observed, preferential binding of the transition state of the substrate by
CypA is the dominant contribution to catalysis. We show that the conformational space of the substrate
is more restricted in the active site of the enzyme than when it is free in solution. The results suggest
that the relative change in conformational entropy of binding the transition state by CypA is positive,
contributing favorably to the relative free energy of binding. Therefore, the overall effect will lead to a
reduction in free energy barrier of the cis–trans isomerization in the active site of the enzyme, as com-
pared to the free substrate in solution.
In addition, our results suggest that intramolecular polarizability due to the loss of the pseudo
double bond character of the C–N bond contributes only about −1.0 kcal/mol to the binding free energy
of the transition state. This surprisingly small contribution from intramolecular polarizability to the free
energy of binding amounts to a fraction of the overall expected barrier reduction. The results, therefore,
validate the use of molecular mechanics force fields with fixed partial charges to reliably describe these
types of systems in which the active site of the enzyme is essentially hydrophobic.
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