Simone Tatoli a,
b,
Costantino Zazza a,
Nico Sanna a,
Amedeo Palma c,
, Massimiliano
Aschi d,
a
CASPUR, Via dei Tizii, 00185, Rome, Italy
b
Dipartimento di Chimica Universita’ di Roma ‘La Sapienza’, P.le
A. Moro 5, 00185, Rome, Italy
c
Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via
Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy
d
Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita’
di L’Aquila, via Vetoio 67100, L’Aquila, Italy
Received 29 2008; revised 29 2008; accepted 30 2008
Molecular dynamics simulations on hydrogen peroxide complex with wild-type (WT) and Arg38Leu mutated (R38L) Horseradish Peroxidase (HRP) were carried out over nanoseconds timescale in water solution at 300 K. Comparison of the results provides interesting insights about the role of highly conserved Arg38 and His42 residues in the chemical features of HRP, underlying its biological activity which initiates with Compound0 (Cpd0). In the WT-HRP enzyme current molecular dynamics simulations show, for the first time, that Arg38 residue: i) prevents the entrance of water inside the reaction cavity, hence providing a hydrophobic reactive scenario, ii) it maintains the distance between His42 and heme–H2 O2 complex suitable for the occurrence of proton transfer reaction leading, thereafter, to heme–H2 O2 disruption according to Poulos-Kraut mechanism. On the other hand, R38L mutant can be considered as a “wet enzyme” where the presence of water solvent molecules in the heme reaction pocket, unfavoring the initial heme–H2 O2 complex formation, decreases the catalytic efficiency in agreement with experimental kinetics measurements. Furthermore, we note that Arg38Leu mutation pushes the His42 residue far from the heme–H2 O2 complex, making unlikely a direct proton transfer and suggesting that, in the mutant, a solvent water molecule could be involved in the first step of the Poulos-Kraut mechanism.
Keywords: Horseradish Peroxidase enzyme; R38L
mutant; Classical molecular dynamics simulations.