A computational study of the phosphoryl transfer reaction between ATP and Dha in Aqueous Solution
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Other documents of the author: Bordes, Isabel; Ruiz-Pernía, José Javier; Castillo, Raquel; Moliner, Vicent
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comunitat-uji-handle2:10234/7013
comunitat-uji-handle3:10234/8638
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Title
A computational study of the phosphoryl transfer reaction between ATP and Dha in Aqueous SolutionDate
2015Publisher
Royal Society of ChemistryISSN
1477-0520; 1477-0539Bibliographic citation
Organic & Biomolecular Chemistry, 2015, 13, 10179Type
info:eu-repo/semantics/articlePublisher version
http://pubs.rsc.org/En/content/articlepdf/2015/ob/c5ob01079aVersion
info:eu-repo/semantics/acceptedVersionSubject
Abstract
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy
and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an
intermediate ... [+]
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy
and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an
intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated
by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone kinase enzyme. In
this paper the reference uncatalyzed reaction in solution has been studied in order to define the foundations
of the chemical reaction and to determine the most adequate computational method to describe
this electronically complex reaction. In particular, the phosphorylation reaction mechanism between
adenosine triphosphate (ATP) and Dha in aqueous solution has been studied by means of quantum mechanics/molecular
mechanics (QM/MM) Molecular Dynamics (MD) simulations with the QM subset of atoms
described with semi-empirical and DFT methods. The results appear to be strongly dependent on the
level of calculation, which will have to be taken into account for future studies of the reaction catalyzed
by enzymes. In particular, PM3/MM renders lower free energy barriers and a less endergonic process than
AM1d/MM and PM6/MM methods. Nevertheless, the concerted pathway was not located with the former
combination of potentials. [-]
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