Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase

Costantino Zazza, Andrea Amadei,* Amedeo Palma,* Nico Sanna, Simone Tatoli, and Massimiliano Aschi

Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM), Italy, and Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Roma, Italy

Received: September 17, 2007
In Final Form: December 21, 2007

FULL TEXT

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.