S. Vijayakumar et al., MOLECULAR-DYNAMICS SIMULATION OF A CLASS-A BETA-LACTAMASE - STRUCTURAL AND MECHANISTIC IMPLICATIONS, Journal of the American Chemical Society, 117(6), 1995, pp. 1722-1730
A molecular dynamics (MD) simulation of the class A beta-lactamase fro
m S. aureus PC1 has been carried out based on the GROMOS force field.
The simulation treats the enzyme solvated by 7295 molecules of water i
n a hexagonal prism cell using periodic boundary conditions. The overa
ll structural integrity of the molecule is well preserved. Calculated
temperature factors show no dramatic increase in the flexibility of th
e Omega loop, a loosely packed 17-residue segment (residues 163-179) a
djacent to the active site. The salt bridge between Arg164 and Asp179,
believed to be the main stabilizing interaction for the Omega loop, w
as observed to be destabilized in the theoretical model but is compens
ated in part by a new interaction between Arg164 and Glu168. Early in
the simulation, however, a rigid flap-like motion was observed for the
Omega loop which results in a repositioning of the carboxylate group
of Glu166 within hydrogen-bonding distance of the primary nucleophile,
the Ser70 hydroxyl group, coupled with displacement of the ''hydrolyt
ic'' water molecule. The significant repositioning of Glu166 suggests
that its position in the crystal structures of class A beta-lactamases
cannot be taken as conclusive evidence that an acylation mechanism in
volving direct general base catalysis by the Glu166 carboxylate is inc
orrect. Analysis of the mobility of active site water molecules sugges
ts that most of them, including the ''hydrolytic'' and ''oxyanion hole
'' water molecules, exchange with bulk solvent much faster than the ca
talytic time scale.