The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach
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Altres documents de l'autoria: Reis, Mauro; Nahum Alves, Cláudio; Lameira, Jerônimo; Tuñón, Iñaki; Martí Forés, Sergio; Moliner, Vicent
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The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approachAutoria
Data de publicació
2013Editor
Royal Society of ChemistryTipus de document
info:eu-repo/semantics/articleVersió de l'editorial
http://pubs.rsc.org/en/content/articlepdf/2013/cp/c3cp43968bVersió
info:eu-repo/semantics/publishedVersionParaules clau / Matèries
Resum
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in
glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the
oxidative ... [+]
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in
glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the
oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate
(Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has
been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps)
sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study,
we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular
mechanical (QM/MM) potentials to obtain the Potential of Mean Force of the catalytic oxidative
phosphorylation mechanism of the G3P substrate used by GAPDH. According to our results, the first
stage of the reaction (oxidoreduction) takes place in the Pi site (energetically more favourable), with
the formation of oxyanion thiohemiacetal and thioacylenzyme intermediates without acid–base
assistance of His194. Analysis of the interaction energy by residues shows that Arg249 has an important
role in the ability of the enzyme to bind the G3P substrate, which interacts with NAD+ and other
important residues, such as Cys166, Glu109, Thr167, Ser247 and Thr226, in the GAPDH active site.
Finally, the inhibition mechanism of the GAPDH enzyme by the 3-(p-nitrophenoxycarboxyl)-3-ethylene
propyl dihydroxyphosphonate inhibitor was investigated in order to contribute to the design of new
inhibitors of GAPDH from Trypanosoma cruzi. [-]
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Phys. Chem. Chem. Phys., 2013, Volume 15, Issue 11Drets d'accés
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