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Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations

Murillo-López, Juliana ; Zinovjev, Kirill ; Pereira, Humberto ; Caniuguir, Andres ; Garratt, Richard ; Babul, Jorge ; Recabarren, Rodrigo ; Alzate-Morales, Jans ; Caballero, Julio ; Tuñón, Iñaki ; Cabrera, Ricardo

Chemical science (Cambridge), 2019-03, Vol.10 (10), p.2882-2892 [Periódico revisado por pares]

England: Royal Society of Chemistry

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  • Título:
    Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations
  • Autor: Murillo-López, Juliana ; Zinovjev, Kirill ; Pereira, Humberto ; Caniuguir, Andres ; Garratt, Richard ; Babul, Jorge ; Recabarren, Rodrigo ; Alzate-Morales, Jans ; Caballero, Julio ; Tuñón, Iñaki ; Cabrera, Ricardo
  • Assuntos: Catalysis ; Crystal structure ; E coli ; Free energy ; Fructose ; Kinases ; Molecular dynamics ; Molecular structure ; Phosphorylation ; Quantum mechanics ; Quantum physics ; Reaction kinetics ; Reaction mechanisms ; Simulation ; Structural analysis
  • É parte de: Chemical science (Cambridge), 2019-03, Vol.10 (10), p.2882-2892
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
  • Descrição: Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the knowledge about the mechanism of the phosphoryl transfer reaction and the transition state lags behind. In this work, we describe the X-ray crystal structure of the homodimeric Pfk-2 from , which contains products in one site and reactants in the other, as well as an additional ATP molecule in the inhibitory allosteric site adjacent to the reactants. This complex was previously predicted when studying the kinetic mechanism of ATP inhibition. After removing the allosteric ATP, molecular dynamic (MD) simulations revealed conformational changes related to domain packing, as well as stable interactions of Lys27 and Asp256 with donor (ATP) and acceptor (fructose-6-) groups, and of Asp166 with Mg . The phosphoryl transfer reaction mechanism catalyzed by Pfk-2 was investigated through Quantum Mechanics/Molecular Mechanics (QM/MM) simulations using a combination of the string method and a path-collective variable for the exploration of its free energy surface. The calculated activation free energies showed that a dissociative mechanism, occurring with a metaphosphate intermediate formation followed by a proton transfer to Asp256, is more favorable than an associative one. The structural analysis reveals the role of Asp256 acting as a catalytic base and Lys27 stabilizing the transition state of the dissociative mechanism.
  • Editor: England: Royal Society of Chemistry
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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