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I. V. Uporov, V. G. Grigorenko, M. Yu. Rubtsova*, A. M. Egorov
Study of the
interaction of tem type beta-lactamases with substrates and inhibitors by
molecular dynamics simulation
Abstract
Molecular
dynamics simulation approach was applied to study complexes of beta-lactamase
TEM-1 and its mutants TEM-32, TEM-37, TEM-39 with substrates (CENTA,
cephalothin) and serine beta-lactamase inhibitors (sulbactam, tazobactam, and
clavulanic acid). For all the complexes examined, the main binding mode was
identified as the electrostatic attraction between the deprotonated carboxyl
group of the beta-lactam ring of the substrate (inhibitor) and the positively
charged NH3+ groups of active site lysines 73 and 234. For some
complexes, a hydrogen bond is also observed between this substrate group or its
carbonyl oxygen with hydroxyl group of catalytic serine 70. Negatively charged
groups of lengthy substrates (CENTA and cephalothin) interact with the
positively charge region formed by the guanidine group of arginine 244 and amino
group of asparagine 276. These electrostatic interactions are the main driving
force leading to substrate binding in the active site of beta-lactamases. It is
shown that the binding energy of substrate CENTA with TEM-1 beta-lactamase is
lower than that for cephalothin with the same protein. This difference in mean
energies results in a significantly lower Michaelis constant for CENTA than for
cephalothin, which has been experimentally confirmed. Our data indicate also
that inhibitors bind to beta-lactamases with inhibitor resistance phenotype
(TEM-32, TEM-37, TEM-39), with greater affinity than with beta-lactamase TEM-1.
Key words:
molecular dynamics, TEM type beta-lactamases, CENTA, cephalothin, sulbactam,
tazobactam, clavulanic acid, antibiotic resistance.
Copyright (C) Chemistry Dept., Moscow State University, 2002
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