Enzymatic Reactions

It has been argued that a substrate-induced conformational change involving the orientation of catalytic groups cannot affect the specificity for two substrates in an enzymatic system where the chemical step is rate limiting, because such an induced fit would alter the catalytic efficiency for both to an equal extent. To the contrary, the generalized induced-fit treatment described here shows that when critical substrate-specific conformational changes in the enzyme persist in the transition state, specificity is linked to conformational differences between the reactive complex for a good substrate and the related complex for a poor one. Conformational differences are a determinant of specificity when the reaction proceeds via an “induced-fit” transition state. Our treatment also shows that such conformational changes can enhance the specificity of an enzyme with suboptimal catalytic efficiency. If substrate-dependent conformational differences in a primative enzyme can enhance specificity, evolutionary pressure to increase specificity could inseparably link enzymatic specificity to induced conformational changes. In a provocative 1958 paper, Koshland suggested that conformational changes induced by substrate binding could orient functional groups on an enzyme so as to enhance the efficiency of the subsequent chemical process and that such conformational changes could serve as a basis for substrate specificity when the ability of a good substrate to properly align enzymatic groups exceeds that of a poor one with similar chemical reactivity. The suggestion that “induced fit” could serve as a basis for specificity was challenged by Fersht (1974, 1985), who concluded that substrate-induced conformational changes would affect equally the relative catalytic efficiency toward two substrates when the chemical step is rate limiting. However, Fersht’s conclusion rests on the assumption that the reactive conformation of the enzyme * To whom correspondence should be addressed. @ Abstract published in Advance ACS Abstracts, November 15, 1995. is unique, i.e., that an identical alignment of catalytic groups must be achieved in the transition state for any substrate to react. This critical assumption is not widely recognized. The more general formulation of the reaction pathway for an induced-fit enzyme described here allows different substrates to induce nonidentical forms of the activated enzyme such that substrate-dependent conformational differences persist in the transition state and leads to a conclusion more consistent with Koshland’s earlier suggestion about inducedfit specificity (Koshland, 1958; Wolfenden, 1974; Wolfenden & Kati, 1991). In this formulation, differences in the catalytic efficiency toward two substrates can originate, in part, from specific, substrate-induced conformational changes, even when the chemical step is rate limiting. Our analysis also shows how conformational activation can either enhance substrate specificity or mediate against it, depending on one’s reference. That an induced conformational change can affect 0006-2960/95/043415881$09.00/0