AMANDA YARNELL, C&EN WASHINGTON
Nature may prefer to use "promiscuous" enzymes--those capable of catalyzing not just their "primary" reaction but an alternative reaction, too--to kick off the evolution of enzymes with new functions. Most examples of promiscuous enzymes identified thus far are thought to make use of the same active-site configuration to catalyze both primary and promiscuous functions, notes Dan S. Tawfik, a senior scientist at Israel's Weizmann Institute. But he thinks that enzymes' ability to shift shapes could open up further opportunities.
"If an enzyme can adopt multiple conformations, each could theoretically provide a different active site that can accept a different substrate," Tawfik suggests. "And therefore, each conformation may be able to catalyze a different reaction."
He points to several examples in which small structural fluctuations in the active site of an enzyme allow it to catalyze multiple reactions [Trends Biochem. Sci., 28, 261 (2003)]. For example, the movement of a loop of amino acids in the active site of an aminoglycoside kinase enzyme creates two different active sites capable of catalyzing the addition of a phosphoryl group to different sites on 4,6-disubstituted aminoglycosides. And in the active site of a trans-sialidase enzyme, isomerization of a tyrosine side chain gives rise to two different active sites, one catalyzing the cleavage of sialic acid from sugar chains and the other catalyzing the attachment of sialic acid to another substrate.
But Tawfik thinks that enzymes may also take advantage of more substantial conformational changes. He and former postdoc Leo James, now a postdoc at the Medical Research Council's Laboratory of Molecular Biology at the University of Cambridge, have shown that an antibody protein created to bind dinitrophenol exists in two radically different conformations, each of which is capable of binding different antigens [Science, 299, 1362 (2003)]. In one conformation, the antibody sports a deep and narrow cleft in which dinitrophenol binds. In the other, it takes on a flat surface that's capable of promiscuously binding a protein antigen.
"Such conformational diversity can provide alternative active sites capable of promoting promiscuous reactions that are entirely unrelated to the protein or enzyme's primary function," Tawfik says.
Simulations of RNA evolution have suggested that such structural plasticity is required for the evolution of new RNA molecules, Tawfik points out. He predicts that may hold true for enzymes, too. "I think enzymes have maintained some degree of structural plasticity so that they can further evolve when necessary," he tells C&EN.
CHAMELEON The antibody SPE7 (teal) exists in two structurally distinct conformations. One conformation (left) has a deep and narrow binding site that binds the small molecule dinitrophenol that SPE7 was bred to bind (pink). The other conformation (right) has a flat binding surface that promiscuously binds a protein (pink).
IMAGES COURTESY OF LEO JAMES
