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Theoretical modeling of enzyme reactions: the thermodynamics of formation of compound 0 in horseradish peroxidase.

Zazza C, Amadei A, Palma A, Sanna N, Tatoli S, Aschi M

Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, Rome, Italy.

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.

Published 7 March 2008 in J Phys Chem B, 112(10): 3184-92.
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