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Molecular dynamics simulations of the dinuclear zinc‐β‐lactamase from Bacteroides fragilis complexed with imipenem
Author(s) -
Suárez Dimas,
Díaz Natalia,
Merz Kenneth M.
Publication year - 2002
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10157
Subject(s) - hydroxide , nucleophile , chemistry , zinc hydroxide , zinc , active site , molecular dynamics , substrate (aquarium) , catalysis , computational chemistry , stereochemistry , combinatorial chemistry , inorganic chemistry , organic chemistry , oceanography , geology
Abstract Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc β‐lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc‐bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme‐substrate complex combined with Poisson‐Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the β‐lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the β‐lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1587–1600, 2002