posted on 2016-01-14, 00:00authored byCarles Acosta-Silva, Joan Bertran, Vicenç Branchadell, Antoni Oliva
The purpose of this work is to have
a better understanding of the
mechanism of GTP hydrolysis catalyzed by the elongation factor Tu.
Two main aspects are being discussed in the literature: the associative
or dissociative character of the process and the nature of nucleophile
activation. The calculations of the QM subsystem have been done by
means of the M06-2X density functional and the split valence triple-ζ
6-311+G(d,p) basis set. The environmental effect has been introduced
through the continuum SMD method. We have studied three models of
increasing complexity in order to analyze the different factors that
intervene in the catalytic action. The results obtained in this paper
confirm that the protonated His84 plays a fundamental role in the
catalytic mechanism, but we have also found that the crystallographic
sodium ion has a notable effect in the catalysis. So, our work has
permitted a new insight, complementary to those obtained with QM/MM
calculations, into this very complex process.