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M. S. Shadrina, B. L. Grigorenko, A. V. Nemukhin
Enzyme-substrate structure for the guanosine triphosphate hydrolysis by
the elongation factor EF-Tu: comparison of the results of quantum
and molecular mechanics and molecular dynamics
Abstract
The results of two theoretical
approaches for calculations of equilibrium geometry configurations of the
enzyme-substrate complex for the guanosine triphosphate hydrolysis by the
elongation factor EF-Tu are presented. The results of the combined quantum
mechanics – molecular mechanics (QM/MM) and molecular dynamics simulations are
compared. It is shown that the geometry structure of the reaction center
obtained by the QM/MM method is consistent with the accepted reaction
mechanism, while in the enzyme-substrate structure obtained by the molecular
dynamics simulations with the CHARMM force field, the relative position of the
nucleophilic water and histidine as a base does not correspond to the optimal
arrangement of the reagents.
Copyright (C) Chemistry Dept., Moscow State University, 2002
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