Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase (Articolo in rivista)

Type
Label
  • Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase (Articolo in rivista) (literal)
Anno
  • 2008-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1021/jp0774692 (literal)
Alternative label
  • C. Zazza (1,2); A. Amadei (3); A. Palma (4); N. Sanna (1);, S. Tatoli (1,5); M. Aschi (2); (2008)
    Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase
    in The journal of physical chemistry. B; American Chemical Society, Washington (Stati Uniti d'America)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • C. Zazza (1,2); A. Amadei (3); A. Palma (4); N. Sanna (1);, S. Tatoli (1,5); M. Aschi (2); (literal)
Pagina inizio
  • 3184 (literal)
Pagina fine
  • 3192 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 112 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali
  • 9 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 10 (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • 1) CASPUR, Via deiTizii 6b, 00185 Roma. 2) Ingegneria Chimica e Materiali Universita` di L'Aquila. 3) Universita` di Roma Tor Vergata. 4) Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN. 5) Universita` di Roma \"La Sapienza\". (literal)
Titolo
  • Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase (literal)
Abstract
  • In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: a first step mechanically constrained, strongly exothermic proton transfer from the heme-H2O2 complex to the conserved His42, followed by a solvent-protein relaxation involving a large entropy increase. Critical evaluation of PMM/MD data also reveals the crucial role played by specific residues in the reaction pocket and, more in general, by the conformational fluctuations of the overall environment in physiological conditions. (literal)
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