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Vidossich P.,Laboratori Of Simulacio Computacional I Modelitzacio Cosmolab | Vidossich P.,Institute Of Quimica Terica I Computacional Iqtcub | Vidossich P.,Autonomous University of Barcelona | Fiorin G.,University of Pennsylvania | And 7 more authors.
Journal of Physical Chemistry B | Year: 2010

We have investigated the dynamics of water molecules in the distal pocket of horseradish peroxidase to elucidate the role that they may play in the formation of the principal active species of the enzymatic cycle (compound I, Por°+-FeIV - O) upon reaction of the resting Fe III state with hydrogen peroxide. The equilibrium molecular dynamics simulations show that, in accord with experimental evidence, the active site access channel is hydrated with an average of two to three water molecules within 5 Å from the bound hydrogen peroxide. Although the channel is always hydrated, the specific conformations in which a water molecule bridges H2O2 and the distal histidine, which were found (Derat; et al. J. Am. Chem. Soc. 2007, 129, 6346.) to display a low-energy barrier for the initial acid-base step of the reaction, occur with low probability but are relevant within the time scale of catalysis. Metadynamics simulations, which were used to reconstruct the free-energy landscape of water motion in the access channel, revealed that preferred interaction sites within the channel are separated by small energy barriers (<1.5 kcal/mol). Most importantly, water-bridged conformations lie on a shoulder just 1 kcal/mol above one local minimum and thus are easily accessible. Such an energy landscape appears as a requisite for the effectiveness of compound I formation, whereby the H-bonding pattern involving reactants and catalytic residues (including the intervening water molecule) has to rearrange to deliver the proton to the distal OH moiety of the hydrogen peroxide and thereby lead to heterolytic O-O cleavage. Our study provides an example of a system for which the "reactive configurations" (i.e., structures characterized by a low barrier for the chemical transformation) correspond to a minor population of the system and show how equilibrium molecular dynamics and free-energy calculations may conveniently be used to ascertain that such reactive conformations are indeed accessible to the system. Once again, the MD and QM/MM combination shows that a single water molecule acts as a biocatalyst in the cycle of HRP. © 2010 American Chemical Society.

Vidossich P.,Laboratori Of Simulacio Computacional I Modelitzacio Cosmolab | Vidossich P.,Institute Of Quimica Teorica I Computacional Iqtcub | Alfonso-Prieto M.,Laboratori Of Simulacio Computacional I Modelitzacio Cosmolab | Alfonso-Prieto M.,Institute Of Quimica Teorica I Computacional Iqtcub | And 6 more authors.
Archives of Biochemistry and Biophysics | Year: 2010

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined. © 2010 Elsevier Inc.

Vidossich P.,Autonomous University of Barcelona | Alfonso-Prieto M.,Temple University | Rovira C.,Laboratori Of Simulacio Computacional I Modelitzacio Cosmolab | Rovira C.,Institute Of Quimica Teorica I Computacional Iqtcub | Rovira C.,Catalan Institution for Research and Advanced Studies
Journal of Inorganic Biochemistry | Year: 2012

Catalases and peroxidases are ubiquitous heme enzymes that catalyze the removal of hydrogen peroxide (H2O2). Both enzymes use one molecule of hydrogen peroxide to form a high valent iron intermediate named Compound I (Cpd I). However, whereas catalase Cpd I oxidizes a second H 2O2 molecule to oxygen, peroxidases use this intermediate to oxidize other substrates rather than H2O2. The origin of the different reactivity of peroxidases and catalases is not known, but it is likely to be related to structural differences between the two heme active sites. Recent modeling studies suggest that the oxidation of H2O 2 by catalase Cpd I may take place by two hydrogen atom transfer steps. In this work, we investigate how catalases and peroxidases compare along the same hydrogen transfer steps to give hints into the question why peroxidases cannot efficiently oxidize H2O2. The use of simplified models allows us to probe the direct effect of the proximal ligand (tyrosinate in catalases and histidine in peroxidases) without masking from the protein environment. We show that the nature of the fifth ligand (His in peroxidase and Tyr in catalase) has little effect on the energy barriers of the hydrogen transfer steps. On the contrary, the Cpd I-hydrogen peroxide (O Fe-Operoxide) distance affects significantly the reaction barriers. We propose that the distal side architecture of peroxidases do not allow to attain short OCpd I-Operoxide distances, thus resulting in a lower efficiency towards H2O2 oxidation. © 2012 Elsevier Inc. All rights reserved.

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