Role of induced fit in enzyme specificity: a molecular forward/reverse switch

Abstract

Enzyme structures solved with and without bound substrate often show that substrate-induced conformational changes bring catalytic residues into alignment, alter the local environment, and position the substrate for catalysis. Although the structural data are compelling, the role of conformational changes in enzyme specificity has been controversial in that specificity is a kinetic property that is not easy to predict based upon structure alone. Recent studies on DNA polymerization have illuminated the role of substrate-induced conformational changes in enzyme specificity by showing that the rate at which the enzyme opens to release the bound substrate is a key kinetic parameter. The slow release of a correct substrate commits it to the forward reaction so that specificity is determined solely by the rate of substrate binding, including the isomerization step, and not by the slower rate of the chemical reaction. In contrast, fast dissociation of an incorrect substrate favors release rather than reaction. Thus, the conformational change acts as a molecular switch to select the right substrate and to recognize and disfavor the reaction of an incorrect substrate. A conformational switch may also favor release rather than reverse reaction of the product.

FIGURE 1.

Free energy profiles for the T7 DNA polymerase. A, conventional free energy diagram for correct (green; dCTP) and mismatched (red; dGTP) nucleotide incorporation reactions. The free energy was calculated as ΔG^‡ = RT(ln(κT/h) – ln(k_obs)) kcal/mol using rate constants from Scheme 1. κ is the Boltzmann constant, T is 293 K, h is Planck's constant, and k_obs is the first-order rate constant. The nucleotide concentration was set equal to 100 μm. B, proposed three-dimensional free energy diagram taking conclusions from our fluorescence studies into account. The diagram includes the alignment of active-site residues as a third axis. This figure was reproduced from Ref. with permission.