The role of induced fit and conformational changes of enzymes in specificity and catalysis

Abstract

The induced fit mechanism and conformational changes of some enzymes are reviewed. Although it is maintained in the literature that induced fit provides specificity, one simple model for induced fit does not provide specificity, according to the usual definition of specificity: the discrimination by an enzyme between the reactions of two competing substrates. Discrimination is measured by the ratio of the values of $\text{k}{}_{\mathrm{<mtext>cat</mtext>}}\text{K}{}_{\mathrm{m}}$ for the two substrates under both $\text{k}{}_{\mathrm{<mtext>cat</mtext>}}\text{K}{}_{\mathrm{m}}$ and k_cat conditions, and induced fit decreases $\text{k}{}_{\mathrm{<mtext>cat</mtext>}}\text{K}{}_{\mathrm{m}}$ by the same factor for both a good substrate and a poor substrate when a chemical or other central step is rate limiting. For a good substrate, this decrease in $\text{k}{}_{\mathrm{<mtext>cat</mtext>}}\text{K}{}_{\mathrm{m}}$ can result from an increase in K_m without a change in k_cat, while for a poor substrate the decrease can result from a decrease in k_cat without a change in K_m. It is reasonable that specificity results primarily from specific interactions of an enzyme with its substrate, which can be described in terms of “intrinsic binding energy.” There are, however, exceptions that can give specificity from induced fit relative to a hypothetical non-induced fit enzyme. When a conformational change results in the substrate being surrounded on all sides by the enzyme there is additional intrinsic binding energy that can enhance catalysis of the reaction of a specific substrate. A second exception can occur when a binding step is rate limiting for the good substrate while a chemical step is rate limiting for an alternative poor substrate. In this case induced fit can enhance specificity between the good and the poor substrate by slowing the reaction of the poor substrate and not the rate-limiting binding of the good substrate. Another exception in which induced fit can enhance specificity occurs when product release is the rate-limiting step for the good substrate and a chemical step is rate limiting for the alternative poor substrate. In this case the rate of reaction of the poor substrate is slowed, while the rate for the good substrate is not slowed due to the introduction of an alternate pathway for product dissociation. In addition, it is shown that an induced fit enzyme can provide specificity under three types of conditions that are conceivable in vivo. Specificity can occur (i) when the concentration of the substrate oscillates or changes with time; (ii) when the substrate for the induced fit enzyme is provided at a constant rate from a preceding metabolic step; or (iii) when enzyme is in excess of substrate. Induced fit can provide substrate synergism in binding and reactivity. However, it is shown that this provides no advantage in specificity relative to a non-induced fit mechanism, in general. An advantage in specificity can occur when the active site surrounds the substrate, or when the steady-state concentration of a reactive enzyme/substrate binary complex is lowered during turnover relative to its equilibrium concentration. All of these analyses pertain to competition with hydrolysis in a two-substrate reaction as well as to competition with an alternate substrate, despite the fact that water is always present at the active site in the absence of bound substrate.