Diversity of mechanisms in Ras–GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modelingстатья
Статья опубликована в высокорейтинговом журнале
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Дата последнего поиска статьи во внешних источниках: 26 июня 2019 г.
Аннотация:The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed
by the cellular protein Ras in complex with the activating protein GAP is an important issue because of
the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis
in the Ras–GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending
on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM)
level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts
leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type
mechanisms. The glutamine-assisted mechanism in the wild-type Ras–GAP, in which the conserved
Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with
the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the
role of the Ras residue Gln61 in Ras–GAP catalysis and explain the retained catalytic activity of the Ras–
GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.