Protein Engineering vol. 16 no. 5 pp. 341-350, 2003
© 2003 Oxford University Press
Insight into the mechanism of the IMP-1 metallo-ß-lactamase by molecular dynamics simulations
1Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany 2Present address: Mayo Group, Division of Biology, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA
3 To whom correspondence should be addressed. e-mail: itbjpl{at}po.uni-stuttgart.de
Two models, a purely nonbonded model and a cationic dummy atom approach, were examined for the modeling of the binuclear zinc-containing IMP-1 metallo-ß-lactamase in complex with a mercaptocarboxylate inhibitor. The cationic dummy atom approach had substantial advantages as it maintained the initial, experimentally determined geometry of the metal-containing active site during molecular dynamics simulations in water. The method was extended to the modeling of the free enzyme and the enzyme in complex with a cephalosporin substrate docked in an intermediate structure. For all three systems, the modeled complexes and the tetrahedral coordination of the zinc ions were stable. The average zinc–zinc distance increased by 
1 Å in the substrate complex compared with the inhibitor complex and the free enzyme in which a hydroxide ion acts as a bridging ligand. Thus, the zinc ions are predicted to undergo a back and forth movement upon the cycle of hydrolysis. In contrast to previous assumptions, no interaction of the Asn167 side chain with the bound cephalosporin substrate was observed. Our observations are in agreement with quantum-mechanical calculations and experimental data and indicate that the cationic dummy atom approach is useful to model zinc-containing metallo-ß-lactamases as free proteins, in complex with inhibitors and in complex with substrates.
Received October 21, 2002; revised March 7, 2003; accepted March 23, 2003.
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