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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.
Moscow University Chemistry Bulletin.
2008, Vol. 49, No. 6, P. 389
   

Copyright (C) Chemistry Dept., Moscow State University, 2002
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