Kern has been looking at enzymes for many years, but in Eastern Europe her work was constrained. “We didn't have big enough NMR machines to look at the protein, so we were looking at the substrate during catalysis,” she says. But now money and NMR technologies have caught up with Kern's ambitions. With new NMR methods, different protein conformations can be quantitated, thus yielding the kinetics of protein motion.
The Brandeis group applied these methods to the prolyl cis-trans isomerase cyclophilin A (CypA). They first mapped movements during catalysis, and then found that very similar movements happened with the free enzyme, with frequencies reflecting the turnover number of the enzyme. “All the motions are already there, and constantly going on, even with no substrate around,” says Kern. “Nature has selected proteins so they are sampling defined conformations. They are optimized for catalysis.”A single rate constant for these movements was consistent with the existence of an extensive, connected network of moving residues. Chemical shift changes caused by a collection of individual mutations could be cross-correlated, again suggesting the concerted movement of a network of residues.